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[
International Worm Meeting,
2013]
The term 'interaction' in biology can mean one of many different types of relationships (physical, genetic, cellular, chemical) within and between any class of biological entity: gene, RNA, protein, cell, small molecule from the environment, etc. Molecular genetics has successfully sought to identify these entities and show how they interact with others. WormBase is adopting and adapting ways in which these relationships can be displayed in a useful biological context. Many interaction visualization tools, such as Cytoscape, are adept at showing one-to-one relationships and are good at incorporating increasing numbers of entities and their relationships. The WormBase website includes a dynamic Cytoscape window in the interaction widget of gene pages, so users can explore curated relationships captured from the literature and large-scale datasets. User friendly tools now allow these displays to be specified, to show only certain relationships - physical, genetic, regulatory, etc., which cuts down enormously on the 'Hairball Effect' where entities and relationships are indistinguishable. Cytoscape views however, are only one-dimensional in that they are centered on the single entity, and therefore do not present these interactions into the larger biological context. To better visualize these intersecting details, we are using WikiPathways to diagram genetic and physical relationships within cellular, anatomic, life stage, and environmental contexts. WikiPathways is a powerful community-driven pathways database with online and desktop editing tools. We invite the community to take part in creating pathways in WikiPathways, which will be incorporated into widgets on WormBase Process Pages. These Process Pages integrate genetic with anatomical, developmental, and temporal information to focus on the larger biological picture of the nematode rather than on the discrete biological entity, such as the gene. At this poster, we will walk people through our interaction pages and show how to customize your views of Cytoscape interactions. We will introduce WikiPathways, and demonstrate how to use the tools to build your own pathways, and how to submit them to WormBase.
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[
International C. elegans Meeting,
1995]
Two-cell embryos were irradiated with germicidal (254nm) radiation and subsequent cell divisions were determined using Nomarski DIC microscopy. A dose of 30 Jm-2 (which gave ca. 10% survival) delayed P1 and P2 divisions by 27%, versus only 8% for the equivalent AB divisions. Similarly, although exposure to 150 Jm-2 abolished cytokinesis in some AB descendants (resulting in occasional binucleated cells), the next two cell cycles were only 22% longer than in unirradiated controls. Conversely, the P1 and P2 cell cycles averaged 95% longer. The delays in the EMSt, E, and MSt cell cycles were similar to those in the AB lineage, suggesting the longer delays were limited to the P4 progenitors. "Cell-cycle checkpoints" have been documented in other organisms. These afford additional time for restitution of DNA damage. Such checkpoints are apparently largely inoperative in the AB lineage (which generates soma exclusively) but at least partially functional in the cells which give rise to the germ line.
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[
C.elegans Neuronal Development Meeting,
2008]
The pages of WormAtlas are getting a fresh look and organization. These changes will start from the front page and then be implemented throughout the Handbook and many other portions of the website. Here we will explain the principles of the new organization, and show you how to find your favorite features. This is the first major revamping of WormAtlas since its launch in 2002. We hope you will find the site simpler to navigate and we expect it will be more intuitive for beginners. As much as possible, these changes should not disrupt any previous weblinks you have established to your favorite pages. Inside the WormAtlas website, there will be several major changes. First will be an improved adult hermaphrodite handbook; it will include several completely revised chapters and a new one covering the nervous system. Second will be the launch of a handbook for anatomy of the worm embryo. Third will be the addition of more data to Slidable Worm. Lastly, we will be adding many new Neuron pages for the male nervous system in order to highlight new synaptic patterns emerging from the Wired Worm project conducted together with Scott Emmons. The WormImage website is expanding steadily. It now presents much more mutant data, particularly for genes affecting the nervous system. As before, we are relying heavily on MRC datasets, but we will continue to add more from the Riddle and Hall lab files. We encourage more laboratories to share your own best archival TEM and SEM images for this purpose. We are very grateful to many labs that have already contributed ideas, advice and experimental results that are featured on these websites. This work is supported by NIH RR12596.
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[
International Worm Meeting,
2003]
WormBase (www.wormbase.org) is an ever-expanding repository of genetic, genomic, and biological information for C. elegans (and other closely related nematodes). The last year has seen many changes to both the database behind WormBase and to the website by which most people access the data. The database is constantly evolving through the refinement of existing data (e.g. ongoing curation of gene models) and the inclusion of new datasets (large and small). Also, because it is a goal to make WormBase easier to use, we have made many improvements to the website, including the addition of new tools for data extraction and many advances to existing pages (particularly the new 'Gene summary' pages). These and other recent improvements will be discussed alongside an overview of some of the new data that have been added to WormBase over the last year (such as the inclusion of the C. briggsae genome assembly). WormBase exists to serve the C. elegans and broader biomedical community, and the WormBase Consortium thanks our many data contributors and collaborators, especially those providing their large-scale datasets, and those providing feedback. Comments, questions and suggestions are always welcome and can be made by emailing wormbase-help@wormbase.org
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[
Neuronal Development, Synaptic Function and Behavior, Madison, WI,
2010]
Regulated exocytosis of secretory vesicles is critically dependent on the assembly of SNARE complexes between the plasma membrane SNAREs, synatxin and SNAP-25 and vesicle-associated synaptobrevin, which render vesicles fusion competent. Tomosyn, a syntaxin-binding protein, forms a complex with syntaxin and SNAP-25 in competition with synaptobrevin predicted to limit fusogenic SNARE complex formation (Fujita et al, 1998). Consistent with these data, the highly conserved C. elegans tomosyn homolog, TOM-1, has been shown to negatively regulate both synaptic and dense-core vesicle release (Gracheva et al., 2006; Gracheva et al.,2007). TOM-1 appears to be associated with both synaptic vesicles (Takamori et al., 2006) and dense core vesicles (Gracheva et al., 2007) via an unknown mechanism. Consequently, the synaptic localization of TOM-1 is dependent on the anterograde vesicle kinesin motor (UNC-104) (McEwen et al., 2006). Given the importance of TOM-1 in the regulation of synaptic strength, we are interested in identifying the mechanism responsible for the synaptic localization of this protein. Neither syntaxin nor SNAP-25, the two established tomosyn-interacting proteins appear to be involved in TOM-1 transport to synapses (McEwen et al., 2006). In order to screen for TOM-1 trafficking defective mutants, we have generated an integrated transgene expressing TOM-1::GFP. We have verified that this protein is expressed at synapses and localizes in an UNC-104-dependent manner. We are currently screening known vesicle-associated candidate proteins by RNAi or by crossing the TOM-1::GFP transgene into reference alleles to examine their potential role in the regulation of tomosyn trafficking. Fujita Y, Shirataki H, Sakisaka T, Asakura T, Ohya T, Kotani H, YokoyamaS, Nishioka H, Matsuura Y, Mizoguchi A, Scheller RH, Takai Y (1998) Tomosyn: asyntaxin-1-binding protein that forms a novel complex in the neurotransmitterrelease process. Neuron 20:905-915. Gracheva EO, Burdina AO, Touroutine D, Berthelot-Grosjean M, Parekh H,Richmond JE (2007) Tomosyn negatively regulates CAPS-dependent peptide releaseat Caenorhabditis elegans synapses. J Neurosci 27:10176-10184. Gracheva EO, Burdina AO, Holgado AM, Berthelot-Grosjean M, Ackley BD,Hadwiger G, Nonet ML, Weimer RM, Richmond JE (2006) Tomosyn inhibits synapticvesicle priming in Caenorhabditis elegans. PLoS Biol 4:
e261.McEwen JM, Madison JM, Dybbs M, Kaplan JM (2006) Antagonistic regulationof synaptic vesicle priming by Tomosyn and UNC-13. Neuron 51:303-315. Takamori S et al. (2006) Molecular anatomy of a trafficking organelle.Cell 127:831-846.
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[
International Worm Meeting,
2007]
WormAtlas and WormImage provide users with many resources regarding the functional and structural anatomy of C. elegans. WormAtlas (www.wormatlas.org) is a text-based website that offers a tissue-based Handbook, the Slidable Worm, and online access to key anatomical publications and current EM methods. One can also explore the cell lineages, the neuronal wiring diagram and individual neuron pages that summarize their anatomy, synaptic interactions and receptors. The complete content of WormAtlas is free for nonprofit use. WormAtlas images have been appearing in many publications and some illustrations will be featured in a French TV program about scientists who study C. elegans. We are now completing the Glossary and neuron pages as well as updating the Slidable Worm applet for newer browsers. A completely new edition of the hermaphrodite handbook will appear this year in print format from Cold Spring Harbor Laboratory Press, called C. elegans Atlas. We will continue to update WormAtlas with new information and resources. We plan to add new handbooks for the anatomy of the dauer larva and the embryo, including new findings on nerve ring development. We are planning a new look for the website, with more emphasis on development and aging. WormImage (www.wormimage.org) is an online database developed for remote retrieval of digitized EM data. The archive, now stored at AECOM, includes images from hermaphrodites, males, embryos, adults, dauer, and larval stages that have been generated by several laboratories, including MRC, Missouri and AECOM. Currently the database contains about 20,000 digital images, with more images added weekly. Most images include original hand annotations to mark identified cell types. The user can search this database by animal name, age, sex, or by regional information (head, midbody, tail) or by tissue types to identify potential images of interest. Each image is offered at three different levels of resolution, so that the user can quickly survey many small thumbnails, or concentrate on the details of a few enlarged images. We have recently upgraded the program to make it easy to click through all the thumbnails for one animal in serial order. WormImage will soon include images of key mutant phenotypes and aging animals. We are very grateful to many laboratories that have contributed data to our collections, to peer reviewers who have helped to check our pages for accuracy, and to the Pittsburgh Supercomputing Center for providing mirror sites. This work is funded by NIH RR 12596.
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[
International Worm Meeting,
2017]
Oocytes of many animals form bipolar spindles in the absence of centrosomes, and how these acentrosomal spindles establish bipolarity remains unclear. In C. elegans oocyte meiosis I, spindle microtubules first form a cage-like structure peripheral to the chromosomes, with multiple small and peripheral spindle poles appearing as assembly progresses. These small poles later merge together and ultimately form two mature poles on the opposite sites of the aligned chromosomes (Wolff et al., 2016). Previous studies have documented defects in oocyte meiotic spindle structure in ZYG-9 or TAC-1 depleted oocytes (Matthews LR et al., 1998; Bellanger JM and Gonczy P, 2003; Yang et al., 2003), but when these assembly defects first appear is not known. Using live imaging, we are investigating the temporal requirements for ZYG-9 and TAC-1 during meiotic spindle assembly. Here we show that ZYG-9 and TAC-1 are required very early in spindle formation, with defects that then further interfere with the establishment of spindle bipolarity. Using GFP and mCherry fusions to mark microtubules and chromosomes, respectively, in
zyg-9 (-) oocytes, we have detected defects very early in meiotic spindle assembly. Rather than forming a cage-like structure with all microtubules restricted to the periphery, we instead observed a cage-like structure with some microtubules extending across the interior, projecting through the volume occupied by chromosomes. This abnormal microtubule scaffold subsequently assembled into a multi-polar spindle network, with individual bivalents sometimes surrounded by discrete small bipolar spindles. Ultimately chromosomes often segregated toward more than two poles. Similarly, using GFP fused to ASPM-1 to mark spindle poles, we found that wild-type oocytes had two stable ASPM-1 foci established by metaphase, while
zyg-9 (-) oocytes had multiple ASPM-1 foci that dynamically coalesced and dispersed throughout most of meiosis I. ZYG-9 and TAC-1 form a complex that promotes microtubule assembly (Bellanger JM and Gonczy P, 2003; Le Bot N et al., 2003; Srayko M et al., 2003), and TAC-1 depleted oocytes showed similar phenotypes to the
zyg-9 (-) oocytes. We are currently investigating the localization of the ZYG-9/TAC-1 complex during early meiotic spindle assembly to further advance our understanding of how these proteins contribute to the acentrosomal assembly of bipolar spindles during oocyte meiotic cell division. References: Wolff et al., Mol Biol Cell, 2016; Matthews LR et al., J Cell Biol., 1998; Bellanger JM and Gonczy P, J Cell Biol., 2003; Yang et al., Dev Biol., 2003; Le Bot N et al., Curr Biol., 2003; Srayko M et al., Curr Biol., 2003.
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[
East Coast Worm Meeting,
2000]
ACeDB, has served the C. elegans community as a genome and genetic database. However, because it was mainly funded as part of the C. elegans sequencing project, its scope of active curation has been essentially limited to genetic maps and to genome sequence annotations. Funding is being sought to extend and expand ACeDB to make a more complete Model Organism Database, called WormBase, with complete coverage of core genomic, genetic, anatomical and functional information about C. elegans. The two top priorities will be data curation and user interface. WormBase will include up-to-date annotation of the genomic sequence, the current genetic and physical maps and experimental data on the function and interactions of cells and genes, as well as development and organismal behavior. Direct links to the sources of biological material, such as the strain collection of the Caenorhabditis Genetics Center, and to data sets maintained by others will be provided. Data will be recovered from the literature and direct contribution of the individual laboratories. While WormBase will act as a central forum through which every laboratory will be able to contribute, WormBase professional curators will ensure detailed attribution of data sources and check consistency and integrity. The standard access to WormBase will be Web based, both for consultation and for data submission. The Web site will center on five pages providing users with entre via Gene, Cell or Process pages, and Sequence and Genetic Map Viewers. Coordination of the project and the main curation site will be at Caltech. Curation and annotation of genomic sequence will take place at the two sequencing centers, the Sanger Centre and Washington University. The Montpellier team will develop interfaces to new large-scale projects and development of new user interfaces will take place at Cold Spring Harbor.
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[
Development & Evolution Meeting,
2008]
The pages of WormAtlas are getting a fresh look and organization.These changes will start from the front page and then be implemented throughout the Handbook and many other portions of the website.Here we will explain the principles of the new organization, and show you how to find your favorite features.This is the first major revamping of WormAtlas since its launch in 2002.We hope you will find the site simpler to navigate and we expect it will be more intuitive for beginners.As much as possible, these changes should not disrupt any previous weblinks you have established to your favorite pages.Inside the WormAtlas website, there will be several major changes. First will be an improved adult hermaphrodite handbook; it will include several completely revised chapters and a new one covering the nervous system. Second will be the launch of a handbook for anatomy of the worm embryo.Third will be the addition of more data to Slidable Worm.Lastly, we will be adding many new Neuron pages for the male nervous system in order to highlight new synaptic patterns emerging from the Wired Worm project conducted together with Scott Emmons. The WormImage website is expanding steadily.It now presents much more mutant data, particularly for genes affecting the nervous system.As before, we are relying heavily on MRC datasets, but we will continue to add more from the Riddle and Hall lab files.We encourage more laboratories to share your own best archival TEM and SEM images for this purpose.We are very grateful to many labs that have already contributed ideas, advice and experimental results that are featured on these websites.This work is supported by NIH RR12596.
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[
Midwest Worm Meeting,
2000]
ACeDB, has served the C. elegans community as a genome and genetic database. However, because it was mainly funded as part of the C. elegans sequencing project, its scope of active curation has been essentially limited to genetic maps and to genome sequence annotations. Funding is being sought to extend and expand ACeDB to make a more complete Model Organism Database, called WormBase, with complete coverage of core genomic, genetic, anatomical and functional information about C. elegans. The two top priorities will be data curation and user interface. WormBase will include up-to-date annotation of the genomic sequence, the current genetic and physical maps and experimental data on the function and interactions of cells and genes, as well as development and organismal behavior. Direct links to the sources of biological material, such as the strain collection of the Caenorhabditis Genetics Center, and to data sets maintained by others will be provided. Data will be recovered from the literature and direct contribution of the individual laboratories. While WormBase will act as a central forum through which every laboratory will be able to contribute, WormBase professional curators will ensure detailed attribution of data sources and check consistency and integrity. The standard access to WormBase will be Web based, both for consultation and for data submission. The Web site will center on five pages providing users with entre via Gene, Cell or Process pages, and Sequence and Genetic Map Viewers. Coordination of the project and the main curation site will be at Caltech. Curation and annotation of genomic sequence will take place at the two sequencing centers, the Sanger Centre and Washington University. The Montpellier team will develop interfaces to new large-scale projects and development of new user interfaces will take place at Cold Spring Harbor.