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[
Worm Breeder's Gazette,
1994]
C. elegans Molecular Genetics and Long PCR Scott R. Townsend, Cathy Savage, Alyce L. Finelli, Ting Xie, and Richard W. Padgett, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08855
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[
International C. elegans Meeting,
1995]
We hope to provide a demonstration of the current state of the ACeDB worm database on Unix workstations, and if possible Apple Macintosh, throughout the poster sessions. This will be based on the new version 4 release of the acedb software (Jean Thierry-Mieg, Richard Durbin and numerous others), which contains many new features for greater efficiency, more flexible printing, and display of new features.
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Development,
2024]
Asymmetric cell divisions can produce daughter cells of different sizes, but it is unclear whether unequal cell cleavage is important for cell fate decisions. A new paper in Development explores the role of unequal cleavages in Caenorhabditis elegans embryos. To learn more about the story behind the paper, we caught up with first author Thomas Mullan and corresponding author Richard Poole, Associate Professor of Developmental Biology at University College London, UK.
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[
Worm Breeder's Gazette,
1997]
May 31, 1997 will mark the end of our current five-year contract with the NIH National Center for Research Resources, which supports the activities of the CGC. The activities in St. Paul have involved primarily the acquisition, maintenance and distribution of stocks and information about stocks, acquisition and maintenance of the C. elegans bibliography, and publication and distribution of The Worm Breeder's Gazette (WBG) and WBG Subscriber Directory. Genetic nomenclature and the genetic map have been managed for the period 1992-1997 by Jonathan Hodgkin (CGC Map Curator) on a subcontract. Currently, the subcontract provides half of Sylvia Martinelli's salary, plus travel and minor expenses. Additional support from within the MRC Laboratory of Molecular Biology and the Sanger Centre has been used to fund other essential resources such as computer equipment, as well as Jonathan's and Richard Durbin's time. Richard has been involved in mapkeeping through his work on ACeDB. We are pleased that Jonathan, Richard and Sylvia agreed to continue their work for another five years. We have submitted an application for a new five year contract that would include a subcontract for nomenclature and mapkeeping on essentially the same terms as before. A description of the nomenclature and mapkeeping activities is given in the following abstract. We are grateful to Leon Avery for setting up our CGC gopher server and also for arranging for the electronic submission of WBG abstracts (as well as abstracts for various C. elegans meetings). His C. elegans WWW server has become an essential resource for the worm community. We were therefore pleased to include Leon (only 5% effort) in a second subcontract as part of our new CGC application. We welcome comments and suggestions about any of the CGC activities.
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[
International Worm Meeting,
2003]
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[
International Worm Meeting,
2003]
As part of a consortium of laboratories in Canada and Sweden (see McKay, et al, "Gene expression profiles in cells, tissues and development of C. elegans"), we have developed computational and biological approaches to assist in high throughput analysis of gene expression. Biological source material for SAGE libraries was generated using synchronized populations as well as micro-dissected gut tissue. We are also refining GFP-mediated cell sorting techniques to isolate other cell types from disrupted embryos. SAGE data are generated and tracked in an automated pipeline from sequencing of cloned concatamers through to annotation, quality control and mapping of individual tags. Tags are associated with attributes such as cumulative phred scores, source clone, parent ditag and tag-to-gene mapping data to aid in downstream quality filtering and analysis steps. To facilitate tag-to-gene mapping and comparison of SAGE and Affymetrix GeneChip technologies, a virtual C. elegans transcriptome with both confirmed and estimated untranslated regions (UTRs) for all known and predicted transcripts was constructed using the current gene models and expressed sequence tag (EST) data annotated in wormbase. We are also refining tag-to-gene mapping methods in order to detect previously undocumented transcripts and alternative splice variants. Comparison of the Affymetrix C. elegans chip with the current virtual transcriptome showed that about 97% of the confirmed or predicted transcripts are detected by all or part of at least one probe set. At the time of writing, four developmentally staged SAGE libraries to be used in developmental gene expression profiling have been completed. Preliminary SAGE studies and results of a direct comparison of gene expression levels measured from the same biological source material with SAGE, long-SAGE and Affymetrix GeneChip technologies will be presented. This project is funded by Genome British Columbia and Genome Canada.
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Brief Bioinform,
2000]
Acedb is one of the more venerable pieces of Genomics software. Acedb was originally created in 1992 by Richard Durbin and Jean Thierry-Mieg to manage the data from the Caenorhabditis elegans mapping project and subsequently the C. elegans sequencing project. From beginnings as a C. elegans-specific tool, it has been continuously developed into a flexible suite of data management, display and scripting tools providing facilities for managing and annotation mapping information and DNA and peptide sequences.This paper gives a basic overview of the Acedb suite, and step-by-step guidance on how to download and install Acedb. It is intended to take an Acedb novice to stage where they can begin to experiment and explore the facilities that are available.
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Bioessays,
2008]
Homology is the similarity between organisms due to common ancestry. Introduced by Richard Owen in 1843 in a paper entitled "Lectures on comparative anatomy and physiology of the invertebrate animals", the concept of homology predates Darwin's "Origin of Species" and has been very influential throughout the history of evolutionary biology. Although homology is the central concept of all comparative biology and provides a logical basis for it, the definition of the term and the criteria of its application remain controversial. Here, I will discuss homology in the context of the hierarchy of biological organization. I will provide insights gained from an exemplary case study in evolutionary developmental biology that indicates the uncoupling of homology at different levels of biological organization. I argue that continuity and hierarchy are separate but equally important issues of homology.
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[
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.
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[
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.