Gonzalez de la Rosa, Pablo Manuel et al. (2021) International Worm Meeting "New ends with new technology: chromosome diminution in Oscheius nematodes"

Moll, Robin, Tracey, Alan, Blaxter, Mark, Gonzalez de la Rosa, Pablo Manuel, Kieninger, Manuela

[International Worm Meeting, 2021]

Chromosome diminution involves specific deletion of parts of the germline genome from somatic cells. This phenomenon, first described in ascaridid nematodes, has been found widely (in protists, plants and animals), but occurs sporadically within any given clade. Using long read genome sequencing we identified chromosome diminution in the rhabditine nematode Oscheius tipulae, where this phenomenon had not been reported before. Many kilobases of DNA are removed from each end of every chromosome, including deletion of expressed genes, and new telomeres synthesized (see https://doi.org/10.1093/g3journal/jkaa020). By long-read sequencing of additional species we have identified similar patterns of diminution across the genus Oscheius - deletion of subtelomeric sequence and addition of new telomeres. Using these sequences we have explored the genomic contexts of diminution and begun to test hypotheses of the mechanism and functions of diminution. Long read sequencing has changed our understanding of Oscheius genomes, and we wonder if diminution processes may be more widely distributed.

Nariya, Hardik et al. (2017) International Worm Meeting "An investigation of the effects of artificial light at night on C. elegans offspring production and lifespan."

Buchanan, Bryant, Wise, Sharon, Zhushma, Rosa, Nariya, Hardik, Shinn-Thomas, Jessica

[International Worm Meeting, 2017]

Artificial light at night (ALAN) has many broad-scale and global implications for ecosystems and wildlife that have evolved under a 24-h circadian cycle. With increased urbanization, artificial light at night has directly altered natural photoperiods and nocturnal light intensity. Artificial light at night can disrupt behavioral patterns such as foraging activity and mating in animals. Disturbances in natural light and dark cycles also affect melatonin-regulated circadian and seasonal rhythms in Drosophila. We investigated the impact of ecologically relevant levels of light pollution on an important invertebrate model, Caenorhabditis elegans, as the impact of night lighting at these light levels is currently unknown. In this study, we exposed worms to artificial light at four intensities: 10-4 lx (control, comparable to natural nocturnal darkness), 10-2 lx (comparable to full-moon lighting and a low level of light pollution), 1 lx (comparable to dawn/dusk or intense light pollution), and 100 lx (dim daylight level comparable to extreme light pollution) on a 12L:12D photoperiod (100 lx treatments experienced constant light). We measured the impact of these light treatments on offspring production in hermaphroditic C. elegans. We grew worms for 2 generations in each light treatment, and then recorded the lifespan and counted the number of hatched offspring produced in the F3 generation. Our data show no significant differences among light levels for lifespan or offspring production suggesting that at least for these life history traits, ALAN does not affect these soil nematodes. Future directions include measuring additional life history traits and circadian gene expression for worms exposed to ALAN.

Shownkeen R et al. (1995) International C. elegans Meeting "THE CAENORHABDITIS ELEGANS PHYSICAL MAP"

Chissoe SL, Waterston RH, Fraser A, Sulston JE, Shownkeen R, Coulson AR

[International C. elegans Meeting, 1995]

Twelve contigs of cosmids and yeast artificial chromosomes (YACs) span more than 95Mb of the 100Mb C.elegans genome. 650 markers link the physical and genetic maps.Hybridisation of tag-sequenced cDNA clones to a map-representative set of YACs indicates that the map incorporates in excess of 99.8% of genes. The map is accessible in ACeDB. We (S.C.) are investigating the representation by bacterial artificial chromosomes (BACs) of regions of the genome not represented by cosmids. Two grids of YACs, of 958 clones ('Poly2') and 223 clones ('Suppoly') are available on request. The latter represents regions of the genome that have been characterised or better defined since the selection of clones for the former. Cosmid clones and YAC grids are available from the Sanger Centre (requests to alan@sanger.ac.uk; FAX 01223 494919). YAC clones and 'cm' series cDNA clones are available from the Sanger Centre or Washington University (rw@nematode. wustl.edu; FAX 314 362 2985).

Chan S et al. (1991) International C. elegans Meeting "SEEKING UNC-40."

Culotti JG, Su M-W, Chan S, Hedgecock EM

[International C. elegans Meeting, 1991]

unc-40 is required with unc-6 to guide ventral migrations on the nematode epidermis (Hedgecock et al., Neuron 4, 61-85, 1990). We have positioned unc-40 genetically by 3-factor crosses with dpy-5 and bli-4 as flanking markers and we have isolated 5 new alleles of unc-40 (2 spontaneous, 2 gamma, and 1 EMS) making a total of 12. DNAs from cosmids covering this region (obtained from Alan Coulson and John Sulston) are being used to probe DNA and RNA from the mutants and DNA from strains carrying duplications that break to either side of unc-40 (obtained from Anne Rose's laboratory). We are also injecting cosmid DNAs into gonads to look for rescue by germline transformation. The brood sizes of various unc-40 alleles are very small, so we have resorted to injecting the wild type in order to create a series of transformed lines, each carrying an extrachromosomal array of a different cosmid. Each array will be passed into appropriately marked unc-40 animals to ask if any can rescue the mutant phenotype. Mosaic experiments are also underway to determine whether unc-40 acts in migrating cells.

Beitel GJ et al. (1991) International C. elegans Meeting "CLONING AND SEQUENCING OF THE SYNTHETIC MULTIVULVAL GENE lin-9"

Beitel GJ, Horvitz HR

[International C. elegans Meeting, 1991]

A synthetic Multivulva phenotype can result from mutations in two separate genes, while each mutation alone results in an apparently wild-type phenotype (Ferguson and Horvitz, Genetics 123:109-121,1989). Mutations that can cause this synthetic Multivulva (syn Muv) phenotype have been grouped into two classes, A and B, such that a double mutant carrying one mutation in each class will have the syn Muv phenotype. Iin-9(nll2) III is a class B mutation that results in an apparently wild-type phenotype by itself. We previously reported that ZK637 and overlapping cosmids can rescue lin-9 (WBG 11(2 ): p 29,1990). We have now identified an 8 kb subclone with rescuing activity. Using this 8 kb fragment to probe Stuart Kim's cDNA library, six positive plaques representing at least three independent clones were isolated. This 8 kb probe also detects a message of approximately 2.5 kb on Northern blots. The message level appears similar in eggs and mixed-stage populations. We are currently sequencing these cDNAs and looking for evidence that these transcripts do in fact represent the lin-9 gene. This work will be greatly aided by the genomic sequence provided by Molly Craxton, John Sulston and Alan Coulson, as ZK637 was fortuitously chosen as one of the first cosmids to be sequenced in the worm genome sequencing project.

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

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

[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.

Pettitt J et al. (1991) International C. elegans Meeting "A PUTATIVE CYSTEINE RICH PROTEIN IN A. SUUM IS ALMOST A COLLAGEN."

Kingston IB, Pettitt J

[International C. elegans Meeting, 1991]

During the course of our studies of the collagen gene family in Ascaris suum, we isolated one bacteriophage clone from an A. suum genomic library which hybrldized to a C. elegans collagen gene probe but did not contain any collagen (Gly-X-Y) coding regions. Instead, this clone contained an open reading frame which encoded many repeats of the amino acid sequence Gly-Pro-Cys-cys. The expression of this putative gene was examlned by Northern blot analysis. No transcripts were detected in any adult tissue but the gene appeared to be highly expressed in a mixed population of L3 and L4 stage larvae. A search of several protein databases identified only one similar protein; a putative Drosophila sperm protein. With a view to conducting genetic analysis of the protein, we searched for a homologue of the A. suum protein in C. elegans. Using an oligonucleotide which would encode part of the Gly-Pro-Cys-Cys repeats sequence, and taking into account the published C. elegans codon preferences, we probed Alan Coulson's YAC filters and obtained signals from three overlapping YAC clones, which mapped to linkage group IV. We then narrowed the region of hybridisation down to two cosmids, EOlF10 and F41Cl, and we are now sub-cloning and sequencing this region to determine if it does contain the homologue of the A. suum gene.

Boom J et al. (1991) International C. elegans Meeting "OPSIN-FAMILY GENES OF CAENORHABDITIS ELEGANS."

Burr AHJ, Boom J, Hayes M

[International C. elegans Meeting, 1991]

Hoping to find a gene for the visual pigment responsible for the light sensitivity of C. elegans (Burr, 1985), we have cloned 5 unique genomic fragments which hybridize with cDNA probes derived from the Drosophila ninaE opsin gene CThis is one of four opsin genes expressed in Drosophila eyes). A 1.6 kb cDNA probe provided by Charles Zuker was used to screen a C. elegans genomic library in Lambda Charon 4 phage ( made by Terry Snutch) at moderate stringency (62 C; 1 x SSPE). Thirteen positive phage were grouped into 5 unique classes (designated s401-s405) based on the restriction patterns produced by combined digestion with EcoRI and HindIII. The digests were labelled by either of the two PstI fragments of the coding region of the probe. The 5 classes mapped to widely separated cosmids of the C. elegans genome ( courtesy of Alan Coulson and John Sulston). Since hybridization occurred at moderate stringency levels, there appears to be a greater sequence homology between the ninaE and C. elegans opsin genes than between ninaE and many visual pigment opsin genes for which lower stringency levels are necessary for cross-hybridization. It is also possible that the genes we have isolated could be genes of other members of the family of opsin-like receptor proteins. These include hormone, neurotransmitter and pheromone sensors. However, in investigations of vertebrates these others do not cross-hybridize with opsin genes. We plan to identify the function of the five genes by obtaining their sequence and studying their expression and hope to have some sequence to report by meeting time.

Ray C et al. (1991) International C. elegans Meeting "ISOLATION AND CHARACTERIZATION OF A CAENORHABDITIS ELEGANS CYSTEINE PROTEASE GENE."

Ray C, McKerrow JH

[International C. elegans Meeting, 1991]

A gene fragment, generated by PCR, of conserved protease gene sequence was used as a probe to isolate cDNA and genomic clones encoding a Caenorhabditis elegans cysteine protease. Alan Coulson and John Sulston have fingerprinted the genomic clone to the middle of linkage group V. The coding sequence of 987 bp was interrupted by two small introns. The predicted amino acid sequence of the mature C. elegans cysteine protease was homologous to those of other eucaryotic cysteine proteases, particularly to that of the nematode parasite Haemonchus contortus (48%) and to that of the trematode parasite Schistosoma mansoni hemoglobinase (52%). The pro region of the C. eleaans protease was homologous only to that of the H. contortus enzyme, implying a similar mechanism of protease activation. Northern blots were used to show that transcription of the C. elegans cysteine protease gene was temporally regulated: 1 kb transcripts were detected in larvae and adults, but not in embryos. In situ hybridization analysis showed that transcription was also spatially regulated, occurring only in the intestine. Protease activity, assayed with fluorecently tagged peptide substrates, was also found to be gut- specific. Studying cysteine protease gene regulation in C. elegans can now provide new insights into the mechanisms of nematode gut development and gut-specific gene regulation. In addition, because of the molecular similarities at both the DNA and protein levels between the cysteine proteases of C. elegans and those of parasitic worms, this work is relevant to understanding gene expression in parasitic worms.

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/.