Hanson, Mariah, Lincoln, Merrick, Goike, Andrew, Aguirre, Cynthia, Schisa, Jennifer, Alker, Ashley
[
International Worm Meeting,
2009]
As C. elegans hermaphrodites age, sperm become depleted, ovulation arrests, and oocytes accumulate in the gonad arm. Large ribonucleoprotein (RNP) granules form in arrested oocytes that include several groups of RNA-binding proteins: P granule proteins, P body-associated proteins, and stress granule-associated proteins. Large RNP granules are also induced in non-arrested oocytes when worms are exposed to environmental stresses such as heat shock and anoxia (1). One hypothesis for the function of RNP granules in arrested or stressed oocytes is they maintain mRNA stability or prevent precocious translation until fertilization or a stress-free environment resumes. Previous work indicated one branch of the major sperm protein (MSP) pathway regulates the subcellular changes of at least some RNA-binding proteins in arrested or stressed oocytes (1). Our current goal is to better define the pathways regulating the assembly of the different classes of proteins that appear to aggregate into large RNP granules in oocytes. We have undertaken a functional RNAi screen to identify genes required for the RNA-binding protein, MEX-3, to assemble into granules when ovulation is arrested. We have identified 11 genes to date, and we are now determining whether these genes also regulate the assembly of P body and stress granule-associated proteins into granules. In parallel, we are asking if the genes that regulate the response to arrested ovulation are also necessary in effecting the oocyte response to environmental stress. In addition to elucidating the pathways that regulate the assembly of RNP granules in oocytes, we are also characterizing the effects on germline development and RNA metabolism when RNP granule assembly is defective to test our hypothesis for RNP granule function. 1) Jud et al., 2008. Dev Biol 318: 38-51.
[
West Coast Worm Meeting,
2000]
We briefly describe the current status and plans for WormBase, initially an extension of the existing ACeDB database with a new user interface. The WormBase consortium includes the team that developed ACeDB (Richard Durbin and colleagues at the Sanger Centre; Jean Thierry-Mieg and colleagues at Montpellier); Lincoln Stein and colleagues at Cold Spring Harbor, who developed the current web interface for WormBase; and John Spieth and colleagues at the Genome Sequencing Center at Washington University, who along with the Sanger Centre team, continue to annotate the genomic sequence. The Caltech group will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level, and gene interactions. Data will be extracted from the literature, as well as by community submission. We look forward to providing the C. elegans and broader research community easy access to vast quantities of high quality data on C. elegans. Also, we welcome your suggestions and criticism at any time. WormBase can be accessed at www.wormbase.org.
[
International Worm Meeting,
2003]
We are Abraham Lincoln High School students using C. elegans in an after-school research class with a sufficiently equipped lab. C. elegans is a good model system for us because there are no ethical issues surrounding its use, it is safe, has a short life span, is easy to grow in a small space, doesn't require special facilities, and is cheap! C. elegans was new to us, so we began the year by learning the basics: mixing media pouring plates, culturing bacteria, seeding plates, identifying males and hermaphrodites, staging worms, comparing N2 and mutants, and setting up crosses. In two months, we became skilled at pipetting, microscopy, sterile technique, chunking, and picking worms. After we had acquired basic skills, we learned how to search the literature. To understand abstracts, we learned new vocabulary. In the process of researching previous work we developed our own questions, and each of us wrote a research proposal. We then merged our ideas and formed two research teams. One team grew C. elegans on Bacillus subtilis, and the other tested the ability of hermaphrodites and males to negotiate a maze. The B. subtilis team first asked whether worms would survive on the thick, malodorous lawn. We then asked if there would be morphological, life cycle, or chemotaxis differences between worms fed B. subtilis and worms fed E. coli. Our data indicated that worms grew on B. subtilis and that, after many generations, they progressed normally through development and continued to show normal morphology. We are continuing to look for sensory disparity using a chemotaxis assay with benzaldehyde or diacetyl as the attractant. The maze team designed a maze using copper to repel worms. We are collecting data comparing the ability of E. coli-fed hermaphrodites versus males to negotiate our maze. We would like to expand the study to include assays with B. subtilis-fed worms. Worm research has gone well at Abraham Lincoln High School. We have asked our own questions, and designed and conducted our own experiments to find answers. We highly recommend that other high schools work with C. elegans. To be successful, the schools need equipment to culture worms, funding for disposable materials, dedicated teachers, and motivated students willing to spend time to do scientific research. The assistance of a scientist with knowledge about C. elegans is also helpful.
[
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.