Mary Ann Tuli et al. (2005) International Worm Meeting "CGC and WormBase"

Theresa Stiernagle, Robert Herman, Jonathan Hodgkin, Richard Durbin, Mary Ann Tuli

[International Worm Meeting, 2005]

WormBase is an international consortium of biologists and computer scientists from Caltech (USA), Cold Spring Harbour Laboratory (USA), Wellcome Trust Sanger Institute (UK) and the Genome Sequencing Center at Washington University (USA). WormBase is dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C.elegans and some related nematodes. WormBase can be freely accessed at www.wormbase.org and is also available for download at ftp://ftp.wormbase.org/pub/wormbase/. A new database release is produced every three weeks. The UK WormBase group works closely with the Caenorhabditis Genetics Center (CGC) to curate genetic nomenclature and maintain the C.elegans genetic map. Detailed guidelines are accessible via http://www.cbs.umn.edu/CGC/Nomenclature/nomenguid.htm Since WS126 (June 2004) all CDSs, transcripts and pseudogenes have been assigned an identifier of the form WBGene00000001. This identifier is unique and remains stable when the gene object is updated. Release WS140 (March 2005) contains 44107 WBGeneIDs of which 24506 are from C.elegans, and 19587 from C.briggsae. The number of CDS objects which have been assigned a CGC approved gene name is 5707. In release WS140 (March 2005) the Variation class was introduced as a more efficient way to handle most of what was in the Allele and Locus classes. The Variation class incorporates the following: Alleles, SNPs (both confirmed and predicted), RFLPs and transposon insertions. Curation of allele data by WormBase biologists is an ongoing project and recent efforts have seen the number of Allele objects in the database increase from about 9000 in WS110 (October 2003) to about 11200 in WS140 (March 2005). Allele information is either captured from scientific journals or submitted directly by researchers using the WormBase submission forms at http://wormbase.org/db/curate/base WormBase is supported by a grant from the National Human Genomes Reseach Institute at the US National Institute of Health #P41 HG02223 and the British Medical Research Council. CGC is supported by NIH NCRR.

Bell, Taylor et al. (2011) International Worm Meeting "A writing intensive Caenorhabditis elegans laboratory exercise for undergraduates examining oxidative stress and antioxidants."

Ryan, Rabiul, King, Lauren, Slaunwhite, Erin, Murley, Kathleen, March, Amanda, Bell, Taylor, Kohn, Rebecca E., Murphy, Katherine, Betzu, Justine, Pall, Matthew, Hartl, Amy, Frymoyer, Christopher, Brown, Loreal, Fontana, Marissa, Hamilton, Christina, McLarnon, Caitlyn, Meeley, Lauren

[International Worm Meeting, 2011]

An open-ended laboratory exercise was developed for an undergraduate Molecular Neurobiology course. The goal of the exercise was for students to design and carry out an experiment to examine how oxidative stress affects Caenorhabditis elegans strains with mutations affecting nervous system function and whether an antioxidant could protect the worms from damage. A writing intensive component of the laboratory was included for students to submit their findings to a peer-reviewed journal. This exercise would be accessible for a variety of upper level courses, including neuroscience and cell biology. Students successfully designed their experiments based on information in the Materials and Methods sections in related scientific journal articles. Students chose conditions for inducing oxidative stress and for incorporating an antioxidant in the experiment. The professor teaching the course and a student teaching assistant experienced with C. elegans research guided students in experimental design, trouble shooting difficulties, and analyzing findings. Students' results showed that strains with defects in neurotransmitter release had a higher percentage of lethality than a strain with a wild type nervous system. The antioxidant they chose to work with, L-ascorbic acid, decreased the percentage of lethality for some strains. Students worked in groups of four during scheduled laboratory times as well as during additional times to maintain their strains and perform experimental trials. During laboratory meeting times, students spent part of their time discussing effective approaches for writing scientific papers. Drafts of student manuscripts went through student peer-review and review by their instructor to prepare for submission to a journal. Three student groups chose to submit their manuscripts to the journal, IMPULSE, An Undergraduate Journal for Neuroscience, and one group chose to submit to The Journal of Young Investigators. Both journals are designed for undergraduate authors.

Hafeez, Zaki et al. (2021) International Worm Meeting "Investigating the Diversity and Distribution of Caenorhabditis elegans in Georgia"

Shaver, Amanda, Hafeez, Zaki, Edison, Arthur, Anderson, Lindsay, Mohamed, Youssef, Spencer, Deontis, Shah, Man, Asif, Muhammad Zaka, Muzio, Cole

[International Worm Meeting, 2021]

The Caenorhabditis elegans Natural Diversity Resource (CeNDR) maintains a library of strains of C. elegans collected from every continent except Antarctica (Caenorhabditis elegans Natural Diversity Resource [CeNDR], 2020). However, currently, there is only one C. elegans strain from the state of Georgia cataloged in CeNDR (CeNDR, 2020). In an attempt to expand upon the diversity of these collected strains and in an effort to study the distribution of C. elegans in Georgia, we set forth to collect a number of wild nematode isolates. Samples of rotting and decaying vegetation were collected from a variety of locations across Georgia. Data such as temperature, location, and sample type were recorded along with images of each collection site using the Nematode Field Sampling app within the data collection app Fulcrum. Nematodes were isolated from these samples and screened by visual inspection for morphological similarity to C. elegans. Potential C. elegans strains were then cultivated. To confirm that an isolate is indeed C. elegans, we will perform PCR and gel electrophoresis. For worms with an appropriately sized PCR band, we intend to submit samples of the PCR product for Sanger sequencing. We will then use NCBI BLAST to compare the sequencing results of the wild isolates with known species. Finally, we will submit frozen isolates of C. elegans to CeNDR for cataloging and whole-genome sequencing. Caenorhabditis elegans Natural Diversity Resource. (2020, August 30). Global Strain Map [Interactive Map]. Retrieved March 24, 2021 from https://www.elegansvariation.org/strain/global-strain-map

Sonnhammer ELL (1995) International C. elegans Meeting "PROTEIN FAMILIES FOUND IN 12 MB OF GENOMIC DNA FROM C. ELEGANS"

Sonnhammer ELL

[International C. elegans Meeting, 1995]

The proteins predicted in the sequence generated by the genome project are released as a protein sequence database called Wormpep, which is incorporated into Swissprot. Release 8 (March 95) of Wormpep contains the translations of 1965 predicted genes in 12 megabases of genomic DNA from a total of 398 cosmids on chromosome II, III and X. About 50% of the predicted proteins can be classified based on sequence homology with other proteins. Examples of the most common domains are: EGF (125), IG superfamily (60, 45 in one protein), protein kinase (54), RNA-binding (32), fibronectin type III (20), homeobox (18) and reverse transcriptase (10). Of the proteins that don't show homology, many are similar to each other, thus forming new families. This often involves neighboring proteins or repeated domains within one protein. We have extracted such families by clustering Wormpep based on sequence similarity with the Domainer algorithm (Sonnhammer and Kahn, Prot. Sci. 3:482). The largest families were analysed in more detail by constructing the multiple alignment and using it to search for homology more sensitively. We also looked for Prosite motifs, transmembrane features and coiled-coil regions. The poster describes 10 new protein families, each comprising 5-15 members. In some cases searching with the whole family revealed previously undetected similarities. Examples of this are: TPR domains and a 7-helix transmembrane family possibly interacting with G-proteins. Two other families are likely transmembrane proteins.

Steven G Kuntz et al. (2005) International Worm Meeting "Comparative sequence analysis using novel nematode sequences for efficient cis-regulatory element identification in a Hox cluster."

Erich M Schwarz, Steven G Kuntz, John DeModena, Paul W Sternberg, Tristan DeBuysscher, Barbara J Wold

[International Worm Meeting, 2005]

Understanding the transcriptional regulation of developmentally important genes can be aided by cross-species genetic comparisons. We hope to learn how to most efficiently infer regulatory regions from comparative sequence analysis. Such comparative analysis was used to dissect a large regulatory region in C. elegans, the non-coding sequence surrounding the Hox cluster genes lin-39 and ceh-13. The region studied includes 19 kb of intergenic sequence as well as 8 kb of intronic sequence; exons were not included. The corresponding region in Caenorhabditis spp. CB5161 and PS1010 was sequenced; comparison to C. elegans and C. briggsae showed that only 2% of it was strongly conserved. Twelve clusters of conserved elements -- each element being 18 to 40 bp long -- could be identified. Near ceh-13, the conserved elements are entirely upstream. However, near lin-39 the sites are evenly distributed upstream and in introns. For in vivo testing of these putative regulatory elements, flanking sequences were included upstream and downstream of each element. One element has been previously identified as an enhancer element, functional during embryogenesis (Streit et al. [2002], Dev. Biol. 242, 96-108). A second computationally identified element corresponds to the microRNA mir-231. As of March 2005, a third element was demonstrated to drive strong reporter expression in the posterior bodywall muscle when used with a basal promoter. Further analysis will be used to determine the regulatory properties of each element, as well as combined effects of these elements.

Labouesse M et al. (2000) European Worm Meeting "Towards a genome-wide collection of transposon insertions"

Segalat LS, Labouesse M, Sookhareea S, Laloux L

[European Worm Meeting, 2000]

With the genome sequence being complete, it is essential to determine the function of each predicted gene. As an alternative to the gene-directed PCR-based search for deletions, we have launched a large-scale project whose long-term objective is to isolate insertions of transposable elements in most C. elegans genes. To do so, we have chosen to use techniques based on the random insertion of natural worm transposons, an approach which has been pioneered in the Plasterk lab. Starting from mutator backgrounds, we generate clones and determine the position of new insertions of Tc1, Tc3 and Tc5 by a modification of the transposon insertion display protocol described in the WBG (Vol 14, n4 page 20), in which DNA flanking transposons can be amplified by anchored PCR, and sequenced. Transposon insertions should potentially provide a wide spectrum of alterations, which will be needed as genetic tools besides the knock-outs. We are currently running small-scale pilot experiments on a few hundred clones to optimize the protocols and validate the approach. In a near future, we also intend to test exogenous transposons such as Mos1 (Bessereau et al, 1999 Worm Meeting). As of March 15th, our collection contains over 500 clones in which a total of 400 different insertions of Tc1, Tc3 and Tc5 have been identified (most clones we generate contain 0 to 2 insertions). The distribution of the insertions on the genetic map does not reveal any major bias. Over 50% of insertions fall in genes. Introns tend to favor insertions because of their high TA content. These strains are available to the C. eleganscommunity upon request. A web server should be in operation soon. In the meantime, requests should be addressed to Laurent Segalat (segalat@maccgmc.univ-lyon1.fr).

H Van Luenen et al. (1999) International C. elegans Meeting "World-wide worm SNPs: Dissecting the molecular evolution of the species using a high density SNP map"

R Plasterk, R Koch, H Van Luenen

[International C. elegans Meeting, 1999]

We would like to reconstruct the history of the C. elegans species at the genome level, therefore we sampled the genomes of four natural isolates (strain CB4857 isolated in Claremont, California, RC301 from Freiburg, Germany, TR403 from Madison, Wisconsin and AB1 from Adelaide, Australia) for single nucleotide polymorphisms (SNPs). Random genomic DNA fragments from the 4 strains were shotgun cloned and sequenced. There was no selection for transcribed or non-transcribed regions of the genome. In total we sequenced 1572 clones resulting in over 1 Mb of sequence information. The sequences are compared to the canonical Bristol N2 sequence to ask the question whether the clone maps to a unique sequence, and -if so- whether it contains polymorphisms. Once a SNP is identified we check other strains for the presence of the same polymorphism by PCR amplification and sequence analysis. In an initial experiment we found approximately one SNP per 3000 bp sequenced. The SNPs are randomly spread over the genome. Based on these observations we expect to find approximately 500 SNPs, one in every 200 kb. In the initial experiment we found, as expected, that several SNPs initially detected in one strain were also present in some but not all other strains. For example: a T in the Australian AB1, is a G at the same position in Bristol N2 in cosmid K10D2 at position 27946, and we found it to be like AB1 in the Californian CB4857 strain and the German RC301 strain, while the TR403 strain from Wisconsin resembles the Bristol N2 strain. Thus different patches of the genome have different ancestors. With our high density SNP map we will generate a genome map for each isolate which will show how each genome is patched together from a limited set of parental strains. The SNP's will be added to ACeDB, and can also be used as markers on the genetic map. They can be recognised by PCR followed by sequencing, but we also found that the SNPs we looked at could be visualised by SSCP analysis. We thank Jane Rogers and Amanda McMurray for their assistance in sequencing the clones.

Mary Ann Tuli et al. (2006) European Worm Meeting "CGC and WormBase"

Richard Durbin, Robert Herman, Theresa Stiernagle, Mary Ann Tuli, Jonathan Hodgkin

[European Worm Meeting, 2006]

WormBase is an international consortium of biologists and computer scientists from Caltech (USA), Cold Spring Harbor Laboratory (USA), Wellcome Trust Sanger Institute (UK) and the Genome Sequencing Center at Washington University (USA).. WormBase is dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C.elegans, and some related nematodes. WormBase can be freely accessed at www.wormbase.org, and is also available for download at ftp://ftp.wormbase.org/pub/wormbase. A new data release is produced every three weeks. The UK WormBase group works closely with the Caenorhabditis Genetics Center (CGC) to curate genetic nomenclature and maintain the C.elegans genetic map. Detailed guidelines are accessible via http://www.cbs.umn.edu/CGC/Nomenclature /nomedguid.htm. All CDSs, transcripts and pseuodgenes are assigned an identifier of the form WBGene00000001. This identifier is unique and remains stable when the gene object is updated. Release WS150 (November 2005) contains 44644 WBGeneIDs of which 25043 are from C.elegans, and 19587 from C.briggsae. The number of CDS objects, which have been assigned a CGC approved gene name is 6638. In release WS140 (March 2005) the Variation class was introduced as a more efficient way to handle most of what was in the Allele and Locus class. The Variation class incorporates the following: Alleles, SNPs (both confirmed and predicted), RFLPs and transposon insertions. Curation of allele data by WormBase biologists is an ongoing project and in response to the WormBase 2005 Users survey (http://www.wormbase.org/announcements/newsletters /pdf/2006-01.pdf) we will curate these more intensely. Allele information is either captured from scientific journals or submitted directly be researchers using the WormBase submission forms at http://wormbase.org/db/curate.base. WormBase is supported by a grant from the National Human Genome Research Institute at the US National Institute of Health #P41 HG02223 and the British Medical Research Council. CGC is supported by NIH NCRR.

Daniel Lawson et al. (2005) International Worm Meeting "How many genes in the worm C.elegans?"

Tamberlyn Bieri, Paul Davis, Daniel Lawson, Phil Ozersky

[International Worm Meeting, 2005]

It has been seven years since the C.elegans genome sequence was 'essentially' completed (WS7, December 1998) but the sequencing consortium has been active in completing/improving the sequence since then. Milestones along this path have included the addition of the final telomeric end (WS83, August 2002), complete contiguation of the sequence (WS90, November 2002) and the substitution of the last uncalled 'N' in the consensus sequence (WS127, June 2004). This process has added 3 Mb of sequence giving a genome size estimate of 100.3 Mb (WS140, March 2005). Curation at the sequence level is still an active process although changes are infrequent and tend to be single base insertion or deletion corrections based on comparison with transcript sequences.The WS7 release of the genome contained 19,099 protein-coding sequences (18,891 genes excluding alternate isoforms) and at least 800 RNA genes. With the improvement to the genome sequence, incorporation of several hundred thousand transcript sequences (ESTs,cDNAs and OSTs) and comparison to the C.briggsae genome sequence WormBase has added to and corrected many gene predictions. The WS140 release contained 22,420 protein-coding sequences (19,735 genes excluding alternate isoforms) and at least 910 RNA genes. Hence, the worm is currently predicted to have approximately 20,300 genes (excluding pseudogenes). We are currently working on a number of avenues to identify missing genes (comparison of the gene predictions from Genefinder and Twinscan, analysis of C.briggsae similarity regions and more generally regions with similarity to any known protein or RNA sequence in the public databases). We will discuss the results of these efforts and their implications to the gene count for C.elegans, which we expect to rise by approximately 500 (based on preliminary analysis).WormBase encourages the community to provide feedback regarding gene predictions. WormBase curators can be contacted at wormbase-help@wormbase.org.

Blumenthal, Tom et al. (2009) International Worm Meeting "Of operons and outrons: a genomic and experimental analysis."

Waterston, Bob, Blumenthal, Tom, MacMorris, Peg, Hillier, LaDeana, Allen, Mary Ann, Morton, Jason

[International Worm Meeting, 2009]

An estimated 55% of C. elegans genes are trans-spliced by SL1 (Zorio et al. Nature 372:270, 1994). The vast majority of these genes contain an outron, with a promoter just upstream of the trans-splice site, but how far upstream? We present evidence that outron lengths vary widely, but average ~200-250 bp. An estimated 15% of genes are SL2 trans-spliced and these are mostly or entirely downstream in operons. We have analyzed the C. elegans transcriptome over development by next generation sequencing (Hillier et al., Genom.Res. March 19, 2009), examining the frequency of SL1 and SL2 trans-splicing across the genome. The results provide evidence for 7,074 SL1- and 2,128 SL2-trans-spliced transcripts, consistent with the earlier estimates based on far less data. We demonstrate that SL1 and SL2 trans-splicing are indeed two separate phenomena, with most gene transcripts trans-spliced to either >95% SL1 or >95% SL2. As expected, SL2 trans-splicing occurs almost entirely at downstream genes in operons. We show that length matters: >50% of intercistronic lengths are ~100 bp, and there is a very strong tendency for downstream genes following this apparently optimal gene spacing to be trans-spliced almost entirely to SL2. Some downstream genes in operons have longer spacing, sometimes much longer. These genes generally are trans-spliced to a mixture of SL1 and SL2, and many or all of these operons contain internal promoters as judged by the presence of the histone variant H2A.Z (Whittle et al., PLOSGenet.4:1,2008), and thus represent what has been termed hybrid operons (Huang et al., Genom.Res.17:1478, 2007). The ratio of SL2 to SL1 usage varies with stage, with a greater frequency of SL1 trans-splicing in L2 larvae, trending to greater SL2 trans-splicing in later stages. A small fraction of SL2 trans-spliced genes are not (apparently) downstream in operons. Our results suggest that some of these actually represent operons with long spacing, whereas others may be due to a non-operon mechanism that results in preferential usage of SL2.