Gijs van Haaften et al. (2006) European Worm Meeting "Identification of Evolutionarily Conserved DNA Damage Response and Radiation Protection Pathways by Genome-Wide RNAi"

Gijs van Haaften, Marcel Tijsterman, Albert Pastink, Ronald H.A. Plasterk, Joris Pothof, Ron Romeijn, Leon H.F. Mullenders, Wouter Koole

[European Worm Meeting, 2006]

Gijs van Haaften, Ron Romeijn1, Joris Pothof, Wouter Koole, Leon H.F. Mullenders1, Albert Pastink1, Ronald H.A. Plasterk and Marcel Tijsterman. Cancer treatment often involves exposure to ionizing radiation or radiomimetic chemotherapeutics. The current challenge in radiation oncology is to identify the most important targets that increase cytotoxicity towards tumor cells but spare normal tissue.. In this study, we present the first comprehensive screen for genes that protect cells against ionizing radiation in an intact animal, the nematode C. elegans. A total of 45 C. elegans genes was identified in a genome wide RNA interference screen for increased sensitivity to ionizing radiation. These include orthologs of well-known human cancer predisposition genes (e.g. ATM) as well as novel genes, including human disease genes not previously linked to defective DNA damage responses. Knockdown phenotypes include defects in DNA damage induced cell cycle arrest and apoptosis, and hypersensitivy to chemotherapeutics. Almost all genes are conserved across animal phylogeny and their relevance for humans was directly demonstrated by showing that their knockdown in human cells results in radiation sensitivity, indicating that this set of genes is important for future cancer profiling and drug development.

Crowell T et al. (1995) International C. elegans Meeting "SYNAPTOTAGMIN-DEFICIENT (SNT-1) MUTANTS OF C. ELEGANS: MOLECULAR AND PHENOTYPIC ANALYSIS"

Crowell T, Rand JB, McManus JR

[International C. elegans Meeting, 1995]

Synaptotagmin is a major synaptic vesicle protein; it contains 2 apparent calcium-binding (PKC-CII) domains and seems to be involved in both exocytosis and endocytosis. The cloning of snt-1 and the isolation of mutants were reported by Nonet et al. (1993). We have now analyzed 17 independent spontaneous snt-1 mutations isolated in our laboratory, as well as alleles isolated by Leon Avery and Erik Jorgensen. Molecular analysis indicates that 12 of the alleles are associated with DNA rearrangements (3 Tc1 insertions, 1 non- Tc1 insertion and 8 deletions), with the remaining alleles due to point mutations. Some of the deletions provide guaranteed molecular null alleles; null mutants are quite uncoordinated, but viable. Phenotypic analysis of snt-1 mutants included quantitative behavioral studies (pharyngeal pumping and head thrashing) and immunoblots. Several of the mutants clearly retain some gene function, and it was possible to establish an alleleic series of phenotypic severity. Partial gene function is retained not only by some of the point mutants, but also by a 66-bp (inframe) deletion which eliminates most of the first CII domain, and by a 9-bp deletion which disrupts the second CII domain. Supported by a grant from MDA

Catarina Morck et al. (2003) International Worm Meeting "Pha-2 encodes a homeobox gene important for pharyngeal muscle development"

Malin Stridh, Marc Pilon, Catarina Morck

[International Worm Meeting, 2003]

pha-2 was iolated in 1993 by Leon Avery in a screen for worms with visible defects in pharyngeal feeding behaviour. Worms in this strain exhibits morphological defects in muscles that form the isthmus and the terminal bulb. Many of the worms arrest as L1 and escapers grow slowly. We have recently cloned the gene and found that pha-2 encodes the homeobox gene M6.3 which is most related to the vertebrate haematopoietic homeobox gene, hex. hex is one of the earliest known marker for anterior visceral endoderm and is involved in anterior-posterior axis formation and in the development of organs such as liver, lungs, thyroid and forebrain. We have sequenced the only existing allele (ad472) and discovered that a point mutation in exon 2 introduces a stop codon such that it should only produce a short truncated protein without a homeodomain. The allele ad472 is thus likely a null allele. To identify pha-2 expressing cells we have made a pPHA-2::GFP reporter *. Our preliminary results indicates that the gene is only expressed in I4, an interneuron, of which the cell body is located in the terminal bulb and which sends out two axons through the isthmus and into the metacorpus. We are currently trying to identify genetic interactors and in particular will investigate if pha-2 regulates or is regulated by pha-4, ceh-22 and myo-2. * in which 2.7 kb of 5UTR from pha-2 was used to drive GFP expression

Martinelli SD et al. (1997) International C. elegans Meeting "ACEDB IN 1997"

Thierry-Mieg J, Durbin RM, Martinelli SD

[International C. elegans Meeting, 1997]

The ACEDB worm genome database has been released more frequently since 1995, approaching monthly. It currently uses 500 MB disk space, having doubled since May 1996, and we expect this to double again in the next year as the genomic sequence is finished (more space is required when building from updates). For those not requiring the genomic sequence, we now also make available a smaller database of around 60MB containing all other information. Regular data sources include bibliography, address and strain lists (CGC), genomic sequence and analysis (Consortium), WBG and WM abstracts (Leon Avery), physical map (Alan Coulson), EMBL sequences. Genetic data and gene expression data come to us continuously but irregularly, either from members of the worm community or from a literature search. Data from the current call for genetic data (WBG 14.5) will be included this summer, in conjunction with the new map from the CGC. In 1996, new classes were added for gene expression information: Expr_pattern, Life_stage, Cell_group. Our thanks to Ian Hope for initiating this, and to his lab and Donna Albertson for early data. More extensive use of these classes requires more active input from the community. We are endeavouring to provide connections between Genes/Strains/Clones/Sequences and expression data, as well as to Papers/WBG articles. We plan during this year to provide graphical WWW access to ACEDB. We would value other suggestions for new user interfaces, new types of data, further connections between classes or improved terminology. ACEDB ftp sites are ncbi.nlm.nih.gov/repository/acedb/, ftp.sanger.ac.uk/pub/acedb/, lirmm.lirmm.fr/genome/acedb/.

Theresa Stiernagle et al. (2005) International Worm Meeting "Caenorhabditis Genetics Center"

Amy Daly, Mary Ann Tuli, Jonathan Hodgkin, Leon Avery, Robert Herman, Theresa Stiernagle

[International Worm Meeting, 2005]

The Caenorhabditis Genetics Center (CGC), supported by NIH NCRR, supplies Caenorhabditis strains and information to researchers. The Minnesota team is responsible for acquiring, maintaining and distributing worm stocks, and generating and maintaining a C. elegans bibliography. The English team acts as a clearing house for C. elegans genetic nomenclature and maintains the genetic map. The Texas team maintains the C. elegans web page. The CGC now has over 6670 different strains. We strive to have at least one allele of every published gene and all chromosome rearrangements, duplications and deficiencies. In addition, we have several strains of species closely related to C. elegans. Strains are available upon written request, which should include a brief statement of the intended use of the strains. Email requests (to stier@cbs.umn.edu) are satisfactory. The CGC bibliography currently includes over 6870 research articles and book chapters. Various types of information are available electronically from the CGC. You can get current strain lists, the C. elegans researcher directory, nomenclature guidelines, and the CGC bibliography at biosci.cbs.umn.edu/CGC. The English site contains a series of forms for submission of genetic map data, and this is the preferred method of data collection (www.sanger.ac.uk/Projects/C_elegans/CGC). Tables of data from the biennially produced map book are available for viewing or downloading. The Worm Breeder's Gazette and lots of other useful worm information are made available by Leon Avery at elegans.swmed.edu or at Nektarios Tavernarakis European mirror of this site at elegans.imbb.forth.gr. We like to be acknowledged in papers for providing strains. We also like to receive reprints of worm papers (.pdf files are encouraged).

Theresa Stiernagle et al. (2003) International Worm Meeting "Caenorhabditis Genetics Center"

Amy Daly, Robert Herman, Jonathan Hodgkin, Leon Avery, Theresa Stiernagle, Chao-Kung Chen

[International Worm Meeting, 2003]

The Caenorhabditis Genetics Center (CGC), supported by NIH NCRR, supplies Caenorhabditis strains and information to researchers. The Minnesota team is responsible for acquiring, maintaining and distributing worm stocks, generating and maintaining a C. elegans bibliography, and publishing the Worm Breeder's Gazette (WBG). The English team acts as a clearinghouse for C. elegans genetic nomenclature and maintains the genetic map. The Texas team maintains the C. elegans web page. The CGC now has over 5000 different strains. We strive to have at least one allele of every published gene and all chromosome rearrangements, duplications and deficiencies. In addition, we have several strains of species closely related to C. elegans. Strains are available upon written request, which should include a brief statement of the intended use of the strains. Email requests (to stier@biosci.cbs.umn.edu) are satisfactory. The CGC bibliography currently includes over 5500 research articles, reviews and book chapters. The WBG is currently published twice each year. We would like comments about whether or not the WBG should be continued. Various types of information are available electronically from the CGC. You can get current strain lists, the C. elegans researcher directory, nomenclature guidelines, and the CGC bibliography at biosci.cbs.umn.edu/CGC. The English site contains a series of forms for submission of genetic map data, and this is the preferred method of data collection (www.sanger.ac.uk/Projects/C_elegans/CGC). Tables of data from the biennially produced map book are available for viewing or downloading. The Worm Breeder's Gazette and lots of other useful worm information are made available by Leon Avery at elegans.swmed.edu or at Nektarios Tavernarakis' European mirror of this site at elegans.imbb.forth.gr. We like to be acknowledged in papers for providing strains. We also like to receive reprints of worm papers (.pdf files are encouraged).

C Axang et al. (2004) European Worm Meeting "FINE MAPPING AND RESCUING OF THREE PHARYNGEAL MUTANTS IN C. ELEGANS."

M Rauthan, M Pilon, C Axang

[European Worm Meeting, 2004]

We are trying to clone and characterize three pharyngeal mutants, mnm-2, mnm-4 and pha-3. mnm-2 and mnm-4 was first reported in a screen for worms exhibiting abnormal morphology of the M2 neurons (Mrck et al. (2003) Dev.Biol. 260:158). The mnm-2 mutation results in an ipsilateral outgrowth of the M2 neurons in the pharynx and has been mapped to a putative position of -2.82 on LG X by three factor mapping. The mnm-4 mutant, with a preliminary position of -3.62 on LG V, exhibits a twisted pharynx with 100 % penetrance. The mutation is semi-dominant such that the heterozygotes show a much less pronounced twisting of the pharynx. The twisted pharynx of mnm-4 resembles that of dig-1 and mig-4, both of which encode adhesion molecules. The pharyngeal mutant pha-3 shows an abnormally shaped pharynx where the isthmus, instead of being uniform in diameter along its length, is tapered and becomes thinner at the front. The pha-3 mutant was reported in 1993 by Leon Avery and was picked in a screen for worms with visible defects in pharyngeal feeding behavior. It has been mapped to a putative position of -5.51 on LG IV. By using genetic tools like deletion studies, three factor crosses and snip-SNP mapping, we will narrow down the position of mnm-2, mnm-4 and pha-3. This in order to proceed with rescue experiments which ultimately will help us in cloning and characterizing these genes. Studying these genes will hopefully tell us more about the development of the pharynx in C. elegans and how the trajectories of the twenty pharyngeal neurons of C. elegans are established.

M Rauthan et al. (2004) European Worm Meeting "FINE MAPPING AND RESCUING OF THREE PHARYNGEAL MUTANTS IN C. ELEGANS."

M Rauthan, M Pilon, C Axang

[European Worm Meeting, 2004]

We are trying to clone and characterize three pharyngeal mutants, mnm-2, mnm-4 and pha-3. mnm-2 and mnm-4 was first reported in a screen for worms exhibiting abnormal morphology of the M2 neurons (Mrck et al.(2003) Dev.Biol.260:158). The mnm-2 mutation results in an ipsilateral outgrowth of the M2 neurons in the pharynx and has been mapped to a putative position of -2.82 on LG X by three factor mapping. The mnm-4 mutant, with a preliminary position of -3.62 on LG V, exhibits a twisted pharynx with 100 % penetrance. The mutation is semi-dominant such that the heterozygotes show a much less pronounced twisting of the pharynx. The twisted pharynx of mnm-4 resembles that of dig-1 and mig-4, both of which encode adhesion molecules. The pharyngeal mutant pha-3 shows an abnormally shaped pharynx where the isthmus, instead of being uniform in diameter along its length, is tapered and becomes thinner at the front. The pha-3 mutant was reported in 1993 by Leon Avery and was picked in a screen for worms with visible defects in pharyngeal feeding behavior. It has been mapped to a putative position of -5.51 on LG IV. By using genetic tools like deletion studies, three factor crosses and snip-SNP mapping, we will narrow down the position of mnm-2, mnm-4 and pha-3. This in order to proceed with rescue experiments which ultimately will help us in cloning and characterizing these genes. Studying these genes will hopefully tell us more about the development of the pharynx in C. elegans and how the trajectories of the twenty pharyngeal neurons of C. elegans are established.

Rankin CH et al. (1997) International C. elegans Meeting "THE ROLE OF GLUTAMATE TRANSMISSION IN HABITUATION OF THE TAP WITHDRAWAL RESPONSE"

Wicks SR, Rankin CH

[International C. elegans Meeting, 1997]

We have been investigating the effects of mutations in 3 genes on habituation to tap. These mutations, suggested to us by Leon Avery, are eat-4, avr-14 and avr-15; all have been hypothesized to be involved in inhibitory glutamate transmission . In earlier work (Wicks and Rankin, 1997) we showed that the most likely site of habituation was the chemical synapses from the touch cells onto the interneurons, and that these synapses were most likely to be inhibitory (Wicks and Rankin, 1995). The eat-4 gene is thought to encode a transporter required for glutamate neurotransmission (Lee and Avery, pers. comm.). Our results suggest that, although the initial levels of responding are normal in eat-4 animals, habituation of the tap withdrawal reflex is broadly affected suggesting that glutamate transmission may be involved in habituation of the touch receptors. Habituation of eat-4 animals is very rapid compared to wild-type worms. Recovery from habituation in eat-4 animals is also delayed. The avr-15 gene is thought to encode the a glutamate-gated chloride channel subunit. Avery (pers. comm.) has hypothesized that the eat-4 is involved in glutamate transport in the pre-synaptic neurons and that avr-15 affects the post-synaptic inhibitory glutamate receptor. Avr-15 worms respond normally to tap, but show a slightly slower rate of habituation than for wild-type worms. We have also begun testing avr-14 worms (hypothesized to interact with avr-15; C. Johnson, pers. comm.) as well as the avr-14;avr-15 double strain. With the avr-14;avr-15 double we see a slower rate of habituation and a more rapid rate of recovery than for wild-type worms.

Consortium Wormbase (2000) Worm Breeder's Gazette "Update on the C. elegans database WormBase"

Consortium Wormbase

[Worm Breeder's Gazette, 2000]

WormBase (www.wormbase.org) is an international consortium of biologists and computer scientists 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 builds upon the existing ACeDB database of the C. elegans genome by providing curation from the literature, an expanded range of content and a user friendly web interface. The team that developed and maintained ACeDB (Richard Durbin, Jean Thierry-Mieg) remains an important part of WormBase. Lincoln Stein and colleagues at Cold Spring Harbor are leading the effort to develop the user interface, including visualization tools for the genome and genetic map. Teams at Sanger Centre (led by Richard Durbin) and the Genome Sequencing Center at Washington University, St. Louis (led by John Spieth) continue to curate the genomic sequence. Jean and Danielle Thierry-Mieg at NCBI spearhead importation of large-scale data sets from other projects. Paul Sternberg and colleagues at Caltech will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level; and gene interactions. Paul Sternberg assumes overall responsibility for WormBase, and is delighted to hear feedback of any sort. WormBase has recently received major funding from the National Human Genome Research Institute at the US National Institutes of Health, and also receives support from the National Library of Medicine/NCBI and the British Medical Research Council. WormBase is an expansion of existing efforts, and as such continues to need you help and feedback. Even with the increased scope and funding, all past contributors to ACeDB remain involved. The Caenorhabditis Genetics Center (Jonathan Hodgkin and Sylvia Martinelli) collaborate with WormBase to curate the genetic map and related topics. Ian Hope and colleagues continue to supply expression data to WormBase. Leon Avery will continue his superb website and serves as one advisor to WormBase. While the major means of access to WormBase is via the world wide web, downloadable versions of WormBase as well as the acedb software engine will continue to be available.