5 Papers found (0.018 seconds)

Robert Barstead et al. (2005) International Worm Meeting "The C. elegans Gene Knockout Consortium"

Anna Rankin, Candice Navaroli, Owen Dadivas, Joanne Lau, Angela Fisher, Nadereh Rezania, Lucy Liu, Mark Edgley, Robert Barstead, Allison Hay

[

International Worm Meeting,

2005]

The C. elegans Gene Knockout Consortium (http://www.celeganskoconsortium.omrf.org/) pursues systematic targeted gene disruption in the nematode, both upon request for the research community and in the larger context of the whole set of genes for which human orthologs exist (about 7,000 genes). This work is currently based on a reverse-genetics PCR method, generating single-gene deletions. All deletions are stabilized as homozygous or balanced heterozygous strains, the deletion breakpoints are sequenced, and the strains and data are placed immediately into the public domain through our collaborators at the Caenorhabditis Genetics Center (CGC: http://biosci.umn.edu/CGC/CGChomepage.htm) and WormBase (http://www.wormbase.org/). To date the Consortium has generated deletions in more than 1800 genes, and more than 1300 of these have been stabilized and archived at the CGC. Distribution of Consortium strains accounts for an increasing proportion of distributions from the CGC every year, and stood at 20% for the calendar year 2004.The reverse genetics PCR method using UV/TMP as the mutagen has evolved in our hands into a robust system for efficient generation of deletion mutations. However, some target genes have been refractory to this method, and we therefore continue to evaluate other isolation/detection methods (for example, see abstracts on array CGH and resequencing at this meeting). We will report on our latest progress using all methods.Additional authors for whom inadequate space was allowed by abstract submission system: Peter Huang (UBC and BC Genome Sciences Centre), Jason Maydan (UBC), Sheldon McKay (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY).

James P McCarter et al. (2001) International C. elegans Meeting "Genes from Other"

James P McCarter, Todd N Wylie, Robert H Waterston, Brandi Chiapelli, Deana Pape, Michael Dante, Sandra W Clifton, John C Martin

[

International C. elegans Meeting,

2001]

To build upon knowledge gained from the genome of C. elegans , we have begun generating Expressed Sequence Tags (ESTs) from parasitic (and free-living) nematodes. This project will generate >225,000 5' ESTs from 14 species by 2003. Additionally, the Sanger Centre and Edinburgh Univ. will complete 80,000 ESTs from 7 species. Through these combined efforts, we anticipate the identification of >80,000 new nematode genes. At the GSC, approximately 35,000 ESTs have been generated to date including sequences from Ancylostoma caninum, Heterodera glycines, Meloidogyne incognita and javanica, Parastrongyloides trichosuri, Pristionchus pacificus, Strongyloides stercoralis and ratti, Trichinella spiralis, and Zeldia punctata . We will report on our progress in sequence analysis, including the creation of the NemaGene gene index for each species by EST clustering and consensus sequence generation, identification of common and rare transcripts, and identification of genes with orthologues in C. elegans and other nematodes. All sequences are publicly available at www.ncbi.nlm.nih.gov/dbEST. NemaGene sequences and project details are available at WWW.NEMATODE.NET. We would like to thank collaborators who have provided materials and ideas for this project including Prema Arasu, David Bird, Rick Davis, Warwick Grant, John Hawdon, Doug Jasmer, Andrew Kloek, Thomas Nutman, Charlie Opperman, Alan Scott, Ralf Sommer, and Mark Viney. This work is funded by NIH-AI-46593, NSF-0077503, and a Merck / Helen Hay Whitney Foundation fellowship.

Todd N Wylie et al. (2001) International C. elegans Meeting "NEMATODE.NET, a Tool for Navigating Sequences from Parasitic and Free-living Nematodes"

James P McCarter, John C Martin, Robert H Waterston, Todd N Wylie, Sandra W Clifton

[

International C. elegans Meeting,

2001]

Two web sites have been established to allow easier access to nematode sequences from species other than C. elegans and C. briggsae ; WWW.NEMATODE.NET is maintained by the Genome Sequencing Center (GSC) at Washington University in collaboration with North Carolina State University, and WWW.NEMATODES.ORG is maintained by Mark Blaxter's lab at the University of Edinburgh. Useful features being built for NEMATODE.NET include the following - 1) Searches: All nematode expressed sequence tags (ESTs) generated at the GSC, currently 32,000 from 10 species, and NemaGene clusters built from these ESTs, are available for BLAST and text searching. Searches can be directed by species, library, or nematode clade in a way that is not possible using the NCBI EST database dbEST. 2) FTP: All EST project data can be downloaded for local analysis including FASTA files and sequence trace image files. 3) Trace Viewer: Fluorescent trace representations for each EST can be viewed. Traces can sometimes provide additional sequence information not included in the EST due to quality value cut-offs. 4) Project Updates: Information is available about libraries in construction and sequencing in progress as the project expands toward 235,000 ESTs. 5) Clone Requests: Details on clone availability and ordering procedure are provided. 6) Links: The site includes an up-to-date set of 300 links to information on human, animal, and plant parasitic nematodes. Further plans for NEMATODE.NET include linking of ESTs to their closest C. elegans homologues by DAS third-party curation of Wormbase. This work is funded by NIH-AI-46593, NSF-0077503, and a Merck / Helen Hay Whitney Foundation fellowship.

Roussell DL et al. (1991) International C. elegans Meeting "A PUTATIVE RNA HELICASE FROM C. ELEGANS THAT SHARES HOMOLOGY WITH THE GERMLINE-SPECIFIC HELICASES, VASA AND PL10."

Bennett KL, Gharib S, Roussell DL

[

International C. elegans Meeting,

1991]

We are interested in those genes (and their protein products) that establish the germline in the developing embryo of nematodes. Potential candidates for germline determinants include the protein component of the P-granules. Mutants that lack or improperly segregate these maternallysupplied granules do not develop a germline, are sterile, and are phenotypically grouped into a class of mutants appropriately called grandchildless (Schupbach and Wieschaus, Dev. Biol. 195:302-317; Martin et al., C. elegans Meeting Report, CSH, pp. 197). The first gene to be cloned that corresponds to a known grandchildless locus is the vasa gene from Drosophila melanogaster ( Lasko and Ashburner, Nature 335:611-617; Hay et al., Cell 55:577-587). We have cloned a potential vasa-equivalent from Caenorhabditis elegans by the polymerase chain reaction (PCR). Degenerate oligonucleotide primers were designed from the predicted vasa amino acid sequence. The PCR-amplified C. elegans DNA was purified, cloned and sequenced. Amino acid sequence comparisons show 48% perfect amino acid homology (and 66% homology with conserved amino acid changes) between the Drosophila vasa and the Caenorhabditis PCR clone that we call NCI. In addition, this clone shares 48% perfect amino acid homology with the mouse gene PL10, a male germ cell- specific helicase (Leroy et al., Cell 57:549-559). The NCI insert DNA hybridizes to a 6.4 Kb and 4.3 Kb DNA fragment on Southerns of EcoRI digested C. elegans genomic DNA. The NCI hybridization probe also identifies two overlapping YACs on the YAC grid (kindly provided by Bob Waterston), which places this putative RNA helicase gene on linkage group I between dpy-5 and unc-15. We do not yet know if this defines one or multiple genes. On Northern analyses of poly A+ RNA from mixed stage C. elegans, NCI hybridizes to a 2.6 Kb RNA and to a larger, relatively less-abundant RNA. The PCR clone, NCI, has also been used as a hybridization probe to isolate several C. elegans genomic clones from a lambda EMBL4 library that was previously constructed in this laboratory. Hybridization to one genomic clone, CEA-I, is confined to an EcoRI fragment of the same approximate size as that detected on genomic Southerns. We are also currently characterizing potential NCI cDNAs from a library provided by Stuart Kim. Sequence analysis of the genomic and cDNA clones should determine if the C. elegans clone is vasa-like, PL10-like, or another putative RNA helicase.