Peter Nagele et al. (2002) Mid-west Worm Meeting "General anesthetic binding sites in C. elegans: Presynaptic SNARE proteins"

C Michael Crowder, Will Placzek, Peter Nagele

[Mid-west Worm Meeting, 2002]

The formation of a ternary complex (SNARE complex) by three presynaptic SNARE proteins - syntaxin, SNAP-25 and VAMP - is a fundamental requirement for neurotransmitter release. Its formation is thought to overcome the repulsive forces between the membranes of the presynaptic nerve terminal and the synaptic vesicle, thereby facilitating membrane fusion. Based on our previous genetic work in C. elegans, which found that a neomorphic mutation unc-64(md130) (unc-64 codes for the C. elegans neuronal syntaxin) caused high-level resistance to volatile anesthetics (PNAS 96: 2479,'99), we hypothesized that a single SNARE protein or the ternary SNARE complex are molecular targets for volatile anesthetics. To test this hypothesis, we produced recombinant SNARE proteins and the SNARE complex and measured their abilities to bind volatile anesthetics by 19 F-NMR. The NMR technique makes use of the fact that when small molecules (the volatile anesthetic) bind to bigger ones (the protein) the movement of the smaller molecule is restricted and can be measured by a drop in what is called the transverse relaxation rate (T2) of the smaller molecule. As measured by a marked drop in T2, the SNARE complex bound volatile anesthetics saturably at clinical concentrations as did SNAP-25 multimers. Syntaxin appears to bind volatile anesthetics in a non-dose-dependent manner over a wide concentration range (0.06 - 6.0 mM). VAMP and monomeric SNAP-25 did not bind volatile anesthetics. To examine if two different volatile anesthetics compete for similar binding sites on syntaxin, we incubated syntaxin at different concentrations of halothane and isoflurane. Addition of isoflurane markedly increased the T2 time of halothane and vice versa, indicating competition between the two anesthetics. Our results show that volatile anesthetics bind to two presynaptic SNARE proteins (syntaxin and SNAP-25 multimers) and the SNARE complex. These proteins share the common structural feature of a 4-alpha-helical bundle, a synthetic form of which has been shown to bind volatile anesthetics. Based on our genetic and biochemical results, SNARE proteins and ternary SNARE complex are plausible presynaptic targets for volatile anesthetic action.

Spieth J et al. (2000) Midwest Worm Meeting "WormBase; a Model Organism Database"

Consortium Wormbase, Spieth J

[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.

Li Y et al. (1997) International C. elegans Meeting "CONTINUING IMPROVEMENTS IN TECHNIQUES FOR PREPARATION OF C. ELEGANS FOR TRANSMISSION ELECTRON MICROSCOPY"

Li Y, Kimble JE

[International C. elegans Meeting, 1997]

We have been continuing to work on protocols for fixation, staining and embedding and want to share our results with the nematode community. Representative micrographs will be shown and protocols will be available for anyone interested.

Spieth J et al. (2000) East Coast Worm Meeting "WormBase; a Model Organism Database"

Consortium Wormbase, Spieth J

[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.

David Hall et al. (2008) Development & Evolution Meeting "What's New on WormAtlas and WormImage?"

Tylon Stephney, Chris Crocker, Zeynep Altun, David Hall, Carolyn Norris, Laura Herndon

[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.

David Hall et al. (2008) C.elegans Neuronal Development Meeting "What's New on WormAtlas and WormImage?"

Laura Herndon, David Hall, Carolyn Norris, Zeynep Altun, Chris Crocker, Tylon Stephney

[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.

Glass S et al. (1991) International C. elegans Meeting "FUNCTIONAL ANALYSIS OF lin-26, A PUTATIVE TRANSCRIPTION FACTOR"

Labouesse M, Horvitz HR, Glass S

[International C. elegans Meeting, 1991]

The gene l in -2 6 probably functions to specify hypodermal cell fates (see abstract by Labouesse and Horvitz) and encodes a protein with cysteinehistidine repeats similar to those of certain transcription factors. We are using two approaches to determine whether lin-26 acts as a transcription factor. First, we will test the ability of I i n - 2 6 protein to activate transcription of a reporter construct in yeast. We are fusing l in-2 6 cDNA to the GAL4 DNA- binding domain and will test the ability of this fusion protein to transcriptionally activate a UASGAL4-1acZ fusion in yeast. Second, we will test the ability of lin-26 protein to bind DNA and determine the sequences to which it binds. Oligonucleotides with known sequences at each end and degenerate sequences in the middle will be synthesized and mixed with epitope-tagged lin-26 protein made in vitro. The fragments to which the protein binds will then be recovered by using antibodies to precipitate the protein-DNA complex. These fragments will be amplified using PCR and their sequences will be determined; the known sequences at the end of the DNA fragments will be used to prime the PCR reactions. Both wild-type and mutant proteins will be tested in this assay. In the future we would like to continue these studies with the goal of understanding how l in -2 6 protein acts to determine cell fate.

Paul Davis et al. (2008) European Worm Meeting "WormBase - The future of nematode annotation."

Paul Davis, The WormBase Consortium

[European Worm Meeting, 2008]

WormBase, The repository for C. elegans biology is set to continue. supporting the C. elegans scientific community and wider nematode. researchers by increasing the complement of nematodes for which we provide. data. A three tier system will be adopted where C. elegans remains the. main focus (tier 1), but we will strive to offer similar tools to those. provided for elegans for all tier 2 species (C. briggsae, C. remanei, C.. brenneri, C, japonica, Pristionchus pacificus, and Heterorhabditis. bacteriophora). The final tier will contain distantly related nematode. species of medical and agricultural significance. This poster highlights. how we will identify and flag potentially incorrect gene structures or the. location of un-annotated genes in all species. A new infrastructure will be. needed to allow annotation of these genomes as it will have both in-house. and community based elements. It also describes some of the future ideas. and infrastructure initiatives we hope to develop to allow the respective. communities to drive the improvement of the gene sets.

Laura Herndon et al. (2008) C.elegans Aging, Stress, Pathogenesis, and Heterochrony Meeting "What's New on WormAtlas and WormImage?"

Zeynep Altun, Tylon Stephney, Carolyn Norris, Laura Herndon, David Hall, Chris Crocker

[C.elegans Aging, Stress, Pathogenesis, and Heterochrony Meeting, 2008]

We are updating the WormAtlas website to give it a fresh look. This is the first major revamping of WormAtlas since its launch in 2002. 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. We hope you will find the site simpler to navigate and we expect it will be more intuitive for beginners. 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 our slice-by-slice worm viewer, 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, which houses thousands of unpublished electron micrographs and related data, is expanding steadily. It now presents much more data from mutant animals, particularly for genes affecting the nervous system. We continue to rely heavily on MRC datasets, but we are also adding more from the Riddle and Hall lab files, among others. We encourage more laboratories to share their own best archival TEM and SEM images so that this resource can continue to grow and serve the C. elegans community. 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.

Melissa J Kirven-Brooks et al. (2003) International Worm Meeting "A C. elegans Experiment on the International Space Station"

Kristina Lagel, Jeanne Hale, Kevin Sato, Melissa J Kirven-Brooks, Delia Santiago, June Sunga, Debra Reiss Bubenheim

[International Worm Meeting, 2003]

An Incubator will be available on the International Space Station with capabilities that are well suited to examine the effects of microgravity and cosmic radiation on C. elegans. The Space Station Biological Research Project (SSBRP) Incubator provides temperature control between 4 and 45 degrees C, and has commandable data, power and video ports to support life science experiments. For the first Incubator flight (slated for launch in 2005) an experiment is planned with C. elegans, to examine growth, development, reproduction and behavior, as compared to ground-based controls. The C. elegans will be incubated in liquid axenic medium 1 in OptiCell (trademark) containers. During the 90 day increment, cultures will be subcultured and videotaped regularly, and live, chemically preserved and frozen samples will be collected. These samples will be analyzed for changes at the genetic and protein level. Ground studies will be presented on baseline growth and behavior of C. elegans in this hardware. Reference: 1 Lu, NC; Goetsch, KM. Carbohydrate requirement of Caenorhabditis elegans and the final development of a chemically defined medium. Nematologica 39(3):303-311, 1993