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Nematode news in brief
1Department of Molecular Biology, University of Wyoming, Laramie WY
Correspondence to: Decrepitus W. Picker (davidfay@uwyo.edu)
Names Given to Children of C. elegans Scientists Will Now Require Jonathan Hodgkin’s Approval (Oxford UK). In a move widely viewed as a gross overreach on the part of the C. elegans Genetics Center and WormBase, Jonathan Hodgkin has been authorized to oversee the naming of all human progeny spawned by C. elegans researchers. The apparent last-minute power grab follows in the wake of the announcement that Tim Schedl of Washington University will soon be taking over for Hodgkin. Although initial reports suggested that all children would be categorized by three- or four-letter names, followed by a number, recent statements from Hodgkin suggest at least some degree of flexibility. “We’re not trying to dictate everything,” said a conciliatory Hodgkin, “however, basic standards must be maintained for the sake of the field.” “For example,” he continued, “this practice of christening all of one’s offspring with the same first letter, like ‘Kylee’, ‘Kaleb’ and ‘Kirsten’, simply must stop.” “Also,” added a visibly frustrated Hodgkin, “enough of the weird spellings for common names already. There is no bloody ‘y’ in Alex. The pillars of our field all have boring traditional names like Bob, John, Sydney, Alan, Marty, and Andy. It didn’t stop them from distinguishing themselves, did it?” “It’s what’s on the inside that counts,” went on Hodgkin, forcing a smile and speaking more calmly. “But if you’re thinking of naming your daughter McKayla or Micalya or some such nonsense, think again. Maybe that’s okay for a Drosophila geneticist, but not in my house and not on my watch dammit!”
Hobert Laboratory Experiences “Deeply Concerning” Month-Long Drought in Publications (New York, NY). A failure to publish any articles during the past 26 days has led to speculation of deep-seated problems within the normally productive laboratory of Oliver Hobert. An official statement issued by the laboratory cited “complications with certain experiments, the untimely departure of several key personnel and one particularly unreasonable reviewer at Nature” as causative factors in the lab’s notable decline. Nevertheless, sources close to the lab say that while the Hobert lab may well be down, it is far from out. According to the official statement, the laboratory intends to “re-double our efforts in order to publish 8–10 papers a month for the remainder of the year.” If accomplished, this would put the laboratory on target for publishing 102 papers in 2013, down from 391 in 2012.
Roller Worm Having ‘One of Those Days’ (Petri Dish, 20°C). A left-handed roller is “just having one of those days, I guess,” the mildly aggravated adult hermaphrodite reported at an impromptu press conference. “I feel like I’m expending quite a bit of effort but not getting anywhere,” continued the 7-day-old gravid nematode. “Plus, I’m running out of food in my immediate vicinity and can’t seem to navigate to the thicker part of the lawn.” “Damn that OP50 smells good though,” added the roller, who will likely bag within the next 48 hours in the absence of productive locomotion. “But it’s important to be comfortable in one’s own cuticle,” said the largely resigned but grotesquely twisted round worm. “I am what I am and that’s no one’s fault. It’s not like some evil all-controlling being purposely engineered me to be this way. That would be sick!”
Vulval Monologues Opens to Critical Acclaim (Minneapolis, MN). A performance piece highlighting the critical role of the nematode vulva in egg laying and mating has received largely positive reviews from the nation’s theatre critics. The play, which consists of approximately 80 short monologues, highlights the essential roles of the anchor cell and Delta/Notch signaling in vulval patterning as well as the unique plights of Vul and Muv mutants. Performers include a diverse cast that spans the Caenorhabditis genus (elegans, briggsae, remanei, japonicaand sp. 5) and also incorporates more-divergent roundworm species. In a particularly shattering piece, entitled “7”, the fate of apoptotic VPCs in Pristionchus pacificus is described in great mechanistic detail. Other monologues take a more light-hearted approach, such as the comedic piece entitled “No Ciceptive No Pain”, which describes the experience of UTSE perforation in young adult hermaphrodites. The play is not without controversy, however, as the Mog, Fog and Tra communities have taken issue with the play’s lack of inclusion and relatively narrow focus. In addition, a musical highlighting the male C. elegans experience will be premiering in early 2014 entitled “The Ray Raps”.
Pre-approval of strains donated to the CGC
1Caenorhabditis Genetics Center (CGC), Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis MN
Correspondence to: Aric Daul (cgc@umn.edu)
The worm community continues to be quite generous with their strains, and the CGC collection is growing at a record pace: we’ve added more than 4,500 strains in the past two years and we are proud to note that our collection is currently composed of more than 18,000 strains. The CGC actively seeks alleles of genes not currently represented in the collection and unusual alleles of already represented genes, as well as useful new deficiencies and balancers. Other types of strains are also welcomed into the collection. However, we simply cannot accept every strain labs would like to send us, nor can we accept entire lab collections when a laboratory closes down. Ensuring that we have the infrastructure in place to maintain and store the collection as it rapidly expands is a growing concern. We ask your cooperation as we become more selective about which strains will be added to the CGC collection.
Beginning August 1, 2013, we require a Strain Review Form to be submitted and approved prior to sending strains to the CGC. This new system will help us streamline our operation and ensure each strain has complete information including a genotype that conforms to the accepted nomenclature rules. A primarily focus is to eliminate/avoid redundancies in the collection; so, for example, please do not submit multiple lines of the same transgene unless there is a compelling reason to do so.
A new CGC website is in development that will include an on-line strain donation form, but in the meantime, we have made a downloadable template available on our website. If you have a strain that you would like to donate to the CGC, please complete a Strain Review Form (available at https://www.cbs.umn.edu/cgc/sending-strains) and email it to CGC@umn.edu for approval BEFORE sending the strains. You will be asked to provide complete genotypic and phenotypic information using proper C.elegans nomenclature (http://www.wormbase.org/about/userguide/nomenclature) and a brief justification for why the strain should be added to the CGC. We will evaluate the requests and reply with our decision as quickly as possible.
Thank you for your cooperation. We look forward to continuing to serve the worm community.
Aric Daul & the CGC Staff
Endogenous locus modification by genome engineering: proposed nomenclature
1Department of Genetics, Washington University School of Medicine, St Louis MO, 1Department of Biochemistry, University of Oxford, Oxford, UK
Correspondence to: Tim Schedl,Jonathan Hodgkin (ts@genetics.wustl.edu)
1Present and 2Past WormBase Gene Name Curators.
New methods for genome engineering (TALENs, CRISPR-Cas9, etc.) are increasingly being applied to C. elegans. These entail some additional recommendations to the standard Genetic Nomenclature Guidelines (http://www.wormbase.org/about/userguide/nomenclature), as described below. The aim is to provide compact and unambiguous ways of describing and referring to engineered changes to endogenous loci, as distinct from transgenic constructs that are inserted elsewhere in the genome.
Each engineered modification to an endogenous locus (point mutations, deletions, insertions or combinations thereof) should receive a unique allele designation, using the standard allele designation of the originating laboratory. For example: bus-50(e5000).
Optional brackets can be employed to provide additional information.
Example: bus-50(e5000[T110E]) (an engineered missense mutation).
An engineered fusion of GFP to the C-terminus of BUS-50 would be:
bus-50(e5001[bus-50::gfp]).
As a shorter and more convenient form, and where unambiguous, this could be referred to as:
bus-50::gfp. Such abbreviations should be clearly defined where first used in a paper.
An engineered insertion of GFP plus the unc-119(+) selectable marker, flanked by loxP sites, would be:
bus-50(e5002[bus-50::gfp + loxP unc-119(+) loxP]).
Each additional engineering of the endogenous locus requires a new allele number. In the example of bus-50(e5002), following Cre-mediated recombinase removal of unc-119(+) so that a single loxP site remains, the new genotype would be bus-50(e5003[bus-50::gfp +loxP]) or bus-50(e5003) for short.
Engineered insertions in apparent intergenic regions are given standard Is insertion names, for example eIs2002. Optional descriptors can include the nature of the insertion, e.g., [unc-119::gfp] and the position in the genome, e.g., [III:2992500], to give eIs2002[unc-119::gfp] or eIs2002[unc-119::gfp, III:2992500].
Engineered changes to existing Is (or Si) insertions should receive new Is numbers using originating lab’s prefix. The original Is insertion can be indicated in brackets with a preceding asterisk (*), in order to allow searches for all derivatives from a given insertion.
For example, an engineered change from GFP to mCherry in eIs2002 might be named as ozIs909, or ozIs909[unc-119::mCherry *eIs2002].
An online OrthoList tool to query worm-human gene homology
1Howard Hughes Medical Institute, 2Department of Chemical Engineering, 3Department of Genetics and Development, 4Department of Biochemistry and Molecular Biophysics, 5Columbia University, New York NY
Correspondence to: Daniel Shaye (ds451@columbia.edu)
There are about 20,000 protein-coding genes in C. elegans (WormBase WS238). We previously generated OrthoList, a compendium of C. elegans genes with human orthologs, by a meta-analysis of the results of four different orthology-prediction programs (Shaye and Greenwald, 2011.). Through compiling OrthoList, we found that 7,663 genes have predicted human orthologs, corresponding to about 38% of the worm genome. We also described how OrthoList addressed various disparities in, and limitations of, prior studies and validated it as a potential tool for streamlining RNAi screens.
We originally provided OrthoList as a spreadsheet with multiple tabs. We have now made a simple online tool that facilitates its use for determining worm-human orthology and generating personalized lists of genes of interest for RNAi screens or other purposes. The tool is available at http://www.greenwaldlab.org/ortholist.
A search window (Figure 1) allows input of worm or human genes, one or many at a time. Worm genes should be introduced as WBgene IDs, common names or locus IDs to retrieve the predicted human ortholog(s). Human genes should be introduced as Ensembl ENSG IDs to retrieve the predicted C. elegans ortholog(s).
Results are returned as a table (Figure 2), in which the search term(s) are highlighted and orthologs are listed, along with which program(s) predicted the relationship. If a feeding RNAi clone is available, its location is also listed. Results can be exported to a CSV document, which can be read by text-editing and spreadsheet programs.
Figures
Figure 1: OrthoList search input.
Figure 2: OrthoList search result output.