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[
International Worm Meeting,
2019]
WormBase (www.wormbase.org) has been serving the scientific community for 19 years as a central repository of genomic and genetic information for C. elegans and other nematodes. We continually enlarge and enrich the included data, develop tools and displays for exploring those data on the website, and improve the back-end database and infrastructure to allow us to capture more data and serve it faster. For example, we are now up-to-date on protein-protein interactions and are developing new displays for these data, and ParaSite now has over 100 nematode genomes! We are fully engaged in the Alliance of Genome Resources (www.alliancegenome.org), which uses the combined expertise of seven information resources to deliver better services to all our communities: advances at WormBase such as our AI-generated descriptions of gene function are now used across the Alliance while advances at the Alliance such as Gene Ontology (GO) ribbons that concisely summarize annotations or enrichment of human disease model annotations are now visible on www.wormbase.org. We are using AI to make the best use of your time: after publication, we have been emailing authors to help us extract information. We are now using AI on a revised Author First Pass form for authors to confirm rather than enter data in their papers, thereby saving keystrokes. Our experiment in making the publication process knowledge-base compatible, www.microPublication.org has taken on a life of its own. Our curators have started to visit various universities and regional meetings to give on-site tutorials and get direct feedback; please contact us if you are interested.
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Marc Vidal, Denis Dupuy, Rock Pulak, Kavitha Venkatesan, Donald Moerman, John Reece-Hoyes, Frederick Roth, Nenad Svrzikapa, Ian Hope, Ryan Viveiros, Domena Tu, Cesar Hidalgo, Murat Tasan, William Mohler, David Baillie, Albert-Laszlo Barabasi, David Lee, Nicolas Bertin, Rebecca Hunt-Newbury, Anne-Ruxandra Carvunis
[
International Worm Meeting,
2007]
*The first 3 authors contributed equally. Correspondence should be addressed to any of the last 3 authors. Much of the complexity of metazoan organisms comes from differential expression of genes to drive cell differentiation. Characterizing the transcriptional activity of gene promoters, in time and in space, is therefore a critical step towards understanding complex biological systems. We developed a new application that enables high-throughput fluorescence expression pattern acquisition, using the nematode profiler (COPAS, Union Biometrica). Individual profiles collected from a mixed stage population are arranged by size into post-embryonic expression chronograms. A chronogram provides a reconstituted time-lapse image of gene expression during development from larva to adult across the length of the worm body. This data format allows unsupervised comparison and clustering of expression patterns, while also providing a clear temporal overview of gene expression. We present an analysis of the spatiotemporal activity of ~5% of the predicted C. elegans promoters driving the expression of green fluorescent protein (GFP) in vivo. Automated comparison and clustering of the obtained ~900 chronograms show that genes co-expressed in space and time tend to belong to common functional categories. Moreover, integration of this localizome dataset with C. elegans protein interactome datasets enables prediction of interaction territories between protein partners.
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[
Japanese Worm Meeting,
2002]
The synaptic connectivity of C. elegans is well known from observations of the somatic system by White et al. and those of the pharyngeal system by Albertson et al. So far, three databases were constructed for computational usage by Achacoso et al. and Durbin, and recently in WormBase. However, they lack some data such as those in tables of White's paper and those in figures of Albertson's book. Our database (K. Oshio, S. Morita, Y. Osana and K. Oka: Technical Report of CCEP, Keio Future No.1, 1998) includes all data described in White's paper and Albertson's book. Unfortunately, some mistakes were found in the database through private communications with John White who is the author of White's paper and with the users of the database. Thus we have been proceeding with the revision to make it perfect one. We are planning to complete the revision in September 2002. The database should be worthwhile not only for neurophysiological studies, but also for post-genomic interests mediating genomes and behavior.
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[
International C. elegans Meeting,
1999]
A database of synaptic connectivity of 302 neurons of the C. elegans has been constructed[1] from the observations of Albertson and Thomson[2] and White et al.[3] by some of the present authors. A network formed by 302 neurons of the C. elegans is represented on a computer by a network which consists of 302 dots combined by (arrowed) bonds. To analyse the structure of the neural network, behavior of a random walker on it is studied. The walker is displaced among dots which represent neurons over bonds which model synaptic connection. In terms of walking distance defined by minimum time steps which is necessary for the random walker to be displaced between neurons, distances among all neurons, whose synaptic connectivity are described by the above authors, have been determined. Almost all neurons are located within the walking distance of three time steps but walking distance among phalingeal neurons and somatic neurons are more than four time steps. The network is extended in a (more than) nine dimensional space around three nanohedra which are mutually combined by manifolds of less dimension. Each nanohedron consists of nine dots representing interneurons mutually connected by synapses and these nanohedra are located near the center of the network. The lattice is biased by the rectification of the chemical synapse in the sence that a random walker prefers to be displaced from sensory neurons to motor neurons. [1] K. Oshio, S. Morita, Y. Osana and K. Oka: C. elegans connectivity data, Technical report of CCEP, Keio Future No.1 (1998) [2] D. G. Albertson and J. N. Thomson: Phil. Trans R. Soc. Lond. B. 275 (1976) 299 [3] J. G. White, E. Southgate, J. N. Thomson and S. Brenner: Phil. Trans. R. Soc. Lond. B 314 (1986) 1.
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[
International Worm Meeting,
2011]
WormBook
(http://www.wormbook.org/) is a comprehensive, open-access collection of original peer-reviewed chapters covering the biology of C. elegans and other nematodes. We have recently initiated a major series of chapter revisions so that WormBook remains comprehensive and current. Additionally, we have commissioned several chapters on nematodes other than C. elegans. These will provide content to support the sequence data contained in WormBase, and will include chapters on individual species and taxonomic groups, as well as transverse chapters devoted to morphological features and physiological functions. In the past two years, WormBook has successfully relaunched the Worm Breeder's Gazette as an on-line informal newsletter. To date, we have published 70 articles by over 200 authors from 16 countries. The Worm Breeder's Gazette has become a widely accessible forum for the distribution of current information about all aspects of nematode research including preliminary results, sequence data, and new methods.
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[
International C. elegans Meeting,
1991]
As announced in the last Gazette, we are writing a computer database system, named acedb, to handle the genetic and molecular information produced by the genome project and the whole community. This is a mouse and windows based program written for Unix workstations. It already runs under the windowing systems Xll and Sunview, and will be available to those interested at the time of the meeting. With some effort, advanced Macs or PC's can be used as X terminals if connected by ethernet to a Unix system running acedb. It is even possible, though a little slow, to connect via internet to a computer running at another site. We are currently looking into a stand alone Mac version, but no promises yet. The basic design is to store data in objects organized in classes. Current classes are: Chromosome, Clone, Author, Laboratory, Gene_Class, Gene, Allele, Rearrangement, Strain, Journal, Paper, Mutagen, 2_Point_Data, 3_Point)data, DNA, Protein, Keyword. So each gene is an object, as is each author, and each strain. You can display information about an object by selecting it from a list created from the main menu, or by using a more complex (and powerful) combinatorial query procedure. Each displayed object pops up in its own window, and several can be seen at once. As well as textual objects and sequences you can display genetic and physical maps. It is possible to move easily between related objects, including between maps of different types. Any displayed information can be laserprinted, and the complete information about any list of objects can be dumped to a plain ascii file for editing or transferring to another program. The second important aspect of acedb is the integration of processing tools. Indeed, a central aim of the project is to allow us to build, maintain and use links between the genetic and physical maps, and between them and the sequence as it becomes available. We are currently working on ways to add genetic map and sequence calculations. At present we have gathered data from the CGC, the mapping project and EMBL. However, we are hoping to add as much related information as possible from the community. Our whole design is very flexible, and we are not limited to any fixed format or set of object features. We are collaborating with Bruce Schatz on a scheme for gathering and redistributing this information based on his Worm Community global communication system. Finally, we encourage suggestions from everyone on useful additions and improvements.
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Raciti, Daniela, Tuli, Mary-Ann, Yook, Karen, Sternberg, Paul, Chan, Juancarlos, Kishore, Ranjana, Wang, Xiaodong
[
International Worm Meeting,
2015]
Comprehensive manual curation of the C. elegans literature is a primary goal of WormBase (www.wormbase.org), and is among the most important activities of the curation staff. Curators extract and annotate over twenty different data types from published research. For some of these data types, such as gene expression patterns, curation is up to date, however, curation of other data types such as capturing the phenotype of mutant alleles and RNAi is sorely lagging. With the increasing number of new publications, a backlog of older papers and growing number of genome sequencing projects, for WormBase to meet our goal of complete literature curation, our dedicated curators need help from the research community.While WormBase has always welcomed data submissions, until now we have only minimally encouraged community participation. In our effort to explore new models for reporting, capturing, and annotating research results, we have been developing tools, which will allow the community to actively participate in the curation process. These tools make up The WormBase Community Curation system.Submissions received via this system will be prioritised for curation and inclusion in WormBase. Authors of newly published papers will be invited to submit their data via user-friendly forms with detailed instructions. Researchers are also invited to review and update existing annotations as well as submit data that is not intended for journal publication. Our strategy will allow different levels of submission and review, and the web forms will enforce standards appropriate to each data type. The aim is that this semi-automated approach to annotation will make it easier for us to capture bursts of curatorial energy from researchers.We currently support the following data types: Expression Patterns, Gene Descriptions, and Variation Data (both molecular and phenotypic), with plans to extend the system to other data types in the future.We hope these tools will evolve into platforms for authors to receive citation credit (in the form of a micro publication) when submitting individual pieces of data that have not been published.The system is available from the www.wormbase.org and will be presented at a Workshop during this meeting. .
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[
West Coast Worm Meeting,
2004]
WormBook is a new, online book currently under development that will be an up-to-date resource for a range of topics relevant to C. elegans biology. Due to the exponential growth of the field, both The Nematode C. elegans and C. elegans II are now out-of-date. The growing complexity and sheer number of topics can no longer be done justice by another print version. Instead, utilizing an online format for WormBook will afford numerous advantages over print. WormBook will serve as a tightly linked component of WormBase, providing a context to elaborate on the facts that WormBase provides and offer a more general treatment of the information. Chapters in WormBook will be extensively cross-referenced among themselves, as well as in and out of Worm Base. WormBook will be replacing and building on the functions of the two previous print books, as well as Worm Breeder's Gazette. The WormBook Editorial Board has already begun soliciting contributions from authors and we plan to have it freely available by June, 2005.
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[
International Worm Meeting,
2009]
Dauer is an alternative form during C. elegans development. C. elegans enters the dauer stage in adverse environment for long-term survival. Dauers have many unusual features which are not shown in other developmental stages. For example, pharyngeal pumping is almost arrested and fat storage is increased. Behavior pattern is also different. Chemotaxis and thermotaxis do not occur in the dauer stage. In plates, they are lethargic but actively respond to mechanical stimulation. Among many characters of dauers, nictation is a very notable behavior. Nictation is the dauer specific behavior that is observed in three-dimensional space. They can climb up onto any projection and wave their body on the top. Although C. elegans is known as the free-living organism in the soil, many Caenorhabditis species associate with other species such as snails and insects. Nictation would be beneficial behavior for their dispersal to other ecological niche. It was also reported that most of naturally isolated C. elegans were dauer larvae. To identify the genes and neural circuits for nictation, we established nictation assay system and used genetic approach. By screening of pre-existing mutants, we found that the function and development of specific neurons are important for nictation. Further characterization of candidate genes will elucidate the mechanism which underlies this specific behavior. Corresponding author: elegans@snu.ac.kr (J. Lee).
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[
International Worm Meeting,
2003]
Several studies have shown a positive correlation between stress-resistance and longevity in the nematode C. elegans. We hypothesized that within an isogenic population variation in expression levels of stress-resistance proteins may be the cause of the non-identical mortality observed for individual worms. In an attempt to isolate long-lived individuals within an isogenic population we integrated a GFP reporter construct under the control of a heat-stress inducible promoter (from the small heat shock protein
hsp-16.2) into N2 Bristol and obtained the (non-roller) line GP73. Using the Union Biometrica COPAS worm sorter we were able to efficiently separate adult sub-populations based on quantitative GFP expression level following a sub-lethal heat-shock. We subsequently found that in these sorted sub-populations, Hsp-16.2 reporter activity positively correlated with thermotolerance to a lethal heat shock and, in addition, could be used as a predictor of remaining longevity. (n.b. First two authors contributed equally)