Todd W Harris et al. (2005) International Worm Meeting "WormBase v2.0: A new face for WormBase"

Payan Canaran, Lincoln D Stein, Todd W Harris

[International Worm Meeting, 2005]

Over the past few years, development of the WormBase user interface has focused on building a consistent interface comprised of informationally rich displays and user friendly tools for data visualization. This development has been driven by a flood of data culled from literature and large scale analyses by the relentless team of curators at WormBase. User interface development has now shifted to a fundamental rearchitecture of the software that drives WormBase. What should users expect from this redesign? At first glance, nothing new. The rearchitecture is designed to replicate the current WormBase look-and-feel. Under the surface, however, will be a highly configurable and responsive user interface. A My WormBase section of the website will allow users to build a page that contains a browsing history and often-accessed information. Perhaps you would rather have WormBase look more like Ensembl, NCBI or Flybase? Maybe you would like to hide the display of references on the gene page? Such options will be configurable across the site enabling users to build displays that best suit their needs. Pages will also be more flexible. They will respond to range-based queries and display results in a contextually-sensitive manner consistent with the type of query and number of items retrieved. The new site will be directly accessible to data mining. Each human readable section label on individual pages can become a target. Such targets can be accessed by a simple programming interface, enabling users to write efffective data mining scripts quickly and easily. For example, a script could be written to fetch all of the brief identifications listed on the Gene Summary page. Many elements of the rearchitecture will be invisible to end users. Major under-the-hood features include a consistent programming interface for WormBase developers; the ability to generically support additional genomes and species; the ability to be driven from multiple data sources; and maintenance of a persistent browsing state for users. As always, WormBase welcomes your feedback. Please send questions, comments, or suggestions to help@wormbase.org.

van den Ecker, Daniela et al. (2010) C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany "Blue native electrophoresis to study mitochondrial complex I in C. elegans."

van den Brand, Mariel A M, Bossinger, Olaf, Distelmaier, Felix, Mayatepek, Ertan, van den Ecker, Daniela, Nijtmans, Leo G J

[C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany, 2010]

Isolation of mitochondrial proteins and subsequent analysis with blue native / SDS gel electrophoresis (BN-PAGE) is an essential tool to investigate defects of the mitochondrial respiratory chain. During the last years, Caenor habditis elegans ( C. elegans ) has become an important model system to study human disease associated with mitochondrial dysfunction. However, with current BN-PAGE protocols for C. elegans , high quantities of mitochondrial protein are required to yield clear results. To obtain these protein amounts, liquid culture was used so far. However, growth in axenic medium alters metabolism and might have adverse effects on oxidative phosphorylation, which is potentially disadvantageous in view of studies about mitochondrial function . On the other hand, mitochondrial dysfunction in C. elegans is often associated with slow growth and larval arrest. Therefore, it might be difficult to culture sufficient worm quantities on agar plates. Here, we present an optimized approach to isolate mitochondria and respiratory chain complex I from C. elegans grown on solid NGM culture plates. We demonstrate that considerably lower amounts of mitochondrial protein are sufficient to isolate complex I and to display clear in-gel activity results. Moreover, we present the first complex I assembly profiles for C. elegans , obtained by two dimensional BN-PAGE.

Huang X-Y et al. (1991) International C. elegans Meeting "BIOCHEMICAL CHARACTERIZATION OF TWO PROTEINS SPECIFICALLY ASSOCIATED WITH THE TRANS-SPLICED LEADER"

Hirsh DI, Huang X-Y

[International C. elegans Meeting, 1991]

RNA trans-splicing in nematodes involves the transfer of an evolutionarily conserved 22-nucleotide spliced-leader (SL) and a trimethylguanosine (TMG) cap to the 5'-end of the recipient mRNA. The physiological role of trans-splicing, of the SL and the biological effect of TMG cap at the 5' ends of mRNAs are not yet understood. The possibility has been raised that SL itself has a catalytic role in splicing. The TMG cap has recently been shown to be an essential nuclear targeting signal. We hope to learn the functions of SL or transsplicing by identifying proteins specifically bound to SL and elucidating their functions. Electrophoretic mobility shift assays combined with competition analysis showed two proteins SLBP1 and SLPB2, bind specifically to SL1. The binding can be stimulated by a cap structure at the 5' end of SL. Although SLBP2 can bind SL1 RNA, SLBP1 seems unable to bind SL1 RNA. This may be due to the highly structured SL1 RNA interfering SLBP1 binding. We are presently testing the binding of SLBP1 and SLBP2 to SL2. UV cross-linking and SDS-PAGE revealed that SLBP1 has a molecular mass of 57kD and SLBP2 of 30kD. Nitrocellulose filter retention assay showed that the binding between SLBP1 and SL1, SLBP2 and SL1 conforms to a simple biomolecular reaction. SLBP1 has been purified to homogeneity as judged by silver staining on SDS-PAGE. Gel filtration analysis indicates that SLBP1 exists as a monomer and a dimer in solution. However we do not know whether dimerization is required for RNA binding. We intend to isolate their genes and generate antibodies against SLBP1 and SLBP2 to further characterize their biochemical properties and biological functions.

Tuli, Mary-Ann et al. (2013) International Worm Meeting "Genomic variation data in WormBase."

Davis, Paul, Williams, Gary, Tuli, Mary-Ann, Howe, Kevin, Paulini, Michael

[International Worm Meeting, 2013]

We continue to see growth in volume and diversity of nematode genomic variation data, in large part due to increasing research effort in whole-genome sequencing (WGS) of numerous C.elegans mutant and wild-isolate strains. WormBase have responded to the challenges presented by this growth by making changes to the way in which we curate, store and display variation data. One significant change has been to more-clearly distinguish between naturally-occurring polymorphisms and laboratory-induced mutations at the display level. These are now show in two separate tables on Gene Summary pages, with laboratory-induced alleles identified by the allele designation of the laboratory of origin, and naturally-occurring polymorphisms identified by WormBase variation accessions. We have also begun to consolidate redundant data from independent wild-isolate sequencing projects. Previously, if a specific molecular variation had been identified by multiple independent projects, and/or in multiple strains, a separate variation object would have been created for each. Now, a single reference variation is created which cross-references all studies that have characterised that variation and all strains that carry it. A new version of the WormBase website was launched in early 2012, and we continue to refine and improve the display of variation data. Coloured fields in the Strain widget on the Variation Summary Page clearly show which strains carry a variation and whether the strain is available from the CGC. The Gene Summary Page now allows customisation in the the way Variations are viewed; both variation tables can be sorted by various properties, including type of molecular change, effect on the protein, and the number of associated phenotypes. We have also increased the complement of variation tracks on the genome browser, clearly separating classical alleles from those generated by large-scale sequencing projects, and creating additional tracks for single-nucleotide variants that confer a putative change-of-function on a protein. We we continue to refine the presentation of this data, and welcome feedback from the C.elegans research community.

Herndon, L.A. et al. (2011) International Worm Meeting "New and Improved: WormImage 2.0 and WormAtlas Mobile."

Herndon, L.A., Hall, D.H., Altun, Z.F., Xu, M., Stephney, T., Wolkow, C.A., Crocker, C., Fisher, K.

[International Worm Meeting, 2011]

We announce the release of WormImage 2.0. The WormImage database houses over 55,000 unpublished electron micrographs and their related metadata. This new version of WormImage still includes access to this enormous collection of C. elegans micrographs, but now features a new look and a new search interface making the data more easily accessible to users. To streamline the website, users can now search directly from the front page. As before, search criteria allow users to narrow results by sex, genotype, age, body portion and tissue type of the animal, but now this is found all on one page. Additionally, with new expandable menu options, one can now select a single tissue or multiple tissue types with just a few clicks. Search results are presented in a new format that is simpler, making it easier to screen through and navigate among all the images. The dataset offered by WormImage continues to expand and welcomes all laboratories to share their best archival TEM and SEM images so that this resource can continue to grow and serve the C. elegans community. The WormAtlas website is also growing and changing. To adapt to the increased demand for mobile-ready content, WormAtlas is now available in a format optimized for access from mobile devices. This allows for users to quickly navigate through the handbook chapters without worrying about zooming in on small icons and menu bars. We are also pleased to announce that WormAtlas will soon feature a new handbook section on the Dauer Larva. Sections for this new handbook will be posted as they become available. In addition to adding new content, we are also continually updating material on WormAtlas to keep the information available to users current. As such, the Individual Neuron pages are being revised and feature new images and data. Slidable Worm is expanding as well, with the ongoing addition of new slices. This work is supported by NIHRR 12596 to DHH.

Glenn White (2007) International Worm Meeting "C. elegans in Undergraduate Education: A Cell Biology Laboratory Research Project and Using unc-54 as a Model Gene for a Bioinformatics Course."

Glenn White

[International Worm Meeting, 2007]

The ease of growing and maintaining C. elegans makes it an ideal organism for teaching undergraduates. I incorporated the worm into 2 upper level courses: Cell Biology and Introduction to Bioinformatics. In cell biology, I used the worm for a demonstration lab on SDS-PAGE and hsp70 gene induction. Based upon previous work in my lab, it is known that exposing worms to 33 oC for 60 minutes will induce hsp70 and can be observed on Coomassie stained Laemmli gels. The lab lecture introduces SDS-PAGE and the topic of stress response as modeled in the worm. This lab eliminates any ethical issues involving obtaining a fresh vertebrate tissue sample and preparation of a whole worm homogenate is very simple. Depending upon the length of the laboratory, worms can be pre-treated at the elevated temperature beforehand or during the session as a recovery period is required. Quantitative densitometry can be performed on digitized gel images using NIH Image and analyzed for levels of hsp70 induction in another lab session. In addition, I involved a cell biology class with longevity studies, and we demonstrated that sodium azide exposure reduces the worm''s lifespan. This lab required considerably more effort as students had to develop competent single worm transfer skills. Working in pairs, students exposed worms to sodium azide, and then transferred control and exposed worms to individual NGM plates. The worms were then monitored daily over the next two weeks (necessitating student responsibility and weekend access to the lab to record age at death). The class obtained a preliminary result that allowed two research students to repeat these experiments in order to obtain publishable data. This study lends itself well to teaching the scientific method through hypothesis development and experimental design, even though it is a remarkably simplistic study. Finally, I am currently using the unc-54 gene (myosin B) as the model gene to study in a newly created Bioinformatics class. Unc-54 is an excellent model gene as it is 1) part of a superfamily, 2) part of a multigene myosin II family, 3) has many homologs, 4) has a conserved intron, 5) has a coiled-coil tail, and 6) molecular phylogenetic trees based upon amino acid sequence give slightly different evolutionary relationships for the four striated muscle myosin IIs when comparing head/motor domain sequences versus rod/tail sequences. Wormbase is particularly useful in helping students understand conserved intron position. Students research the gene of their choosing, but all computer lab work involves analyzing unc-54 exclusively. Student feedback indicates this course has helped them understand evolution in a way they had not appreciated beforehand.

Herndon, Laura A. et al. (2009) International Worm Meeting "New and Improved: WormAtlas 2.0 and WormImage."

Herndon, Laura A., Altun, Zeynep F., Stephney, Tylon, Hall, David H., Crocker, Chris

[International Worm Meeting, 2009]

We announce the release of WormAtlas2.0. This new version of WormAtlas includes all previous information, but features a new look and many new additions. The main page adopts a tighter format by using drop down menus and more image based icons for intuitive navigation throughout the site. The Handbook is reorganized and provides a table of contents in a static frame for each section to allow for easy maneuvering to subsections and figures. The Hermaphrodite Handbook has updated content including an entirely new section covering the nervous system. Each section features new and updated figures and each figure now links to a separate page with the figure and legend and also to a high resolution version showing even greater detail. The Male Handbook also has been converted to the new layout and we are planning to introduce new content in the near future. Similarly, the Individual Neuron pages are being updated to a new format and will contain new figures, including a major expansion of the Male-specific neurons and their wiring patterns (see Emmons et al., this meeting). Slidable Worm is also gaining new pages and we have initiatives underway to streamline and accelerate this process. It is our hope that WormAtlas2.0 will be simpler to navigate and that beginners will find it more accessible. We encourage feedback from members of the C. elegans community on ways to improve the new version of WormAtlas. The WormImage website houses thousands of unpublished electron micrographs and related data, and has been expanding steadily. It now presents 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 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 people who have already contributed ideas, advice and experimental results that are featured on these websites. This work is supported by NIHRR 12596 to DHH.

Perry MD et al. (1997) International C. elegans Meeting "DETECTION OF A HER-1-BINDING PROTEIN IN C. ELEGANS EXTRACTS"

Perry MD, Rajwans N

[International C. elegans Meeting, 1997]

The genetic pathway regulating C. elegans sex determination has a cell-nonautonomous step. We are testing an hypothesis that a small male-specific HER-1 protein is the secreted signalling ligand for this cell interaction. To initiate characterization of this novel cysteine-rich protein we generated a transgenic strain that overproduces HER-1 from an hsp-16 promoter. Following a masculinizing heat-shock, these hermaphrodites synthesize three new proteins, 16, 17, and 18 kDa, that cross-react with affinity-purified rat anti-HER-1 antibodies (processed HER-1 is expected to migrate at 18 kDa). In parallel, we engineered baculovirus vectors to express HER-1 in insect tissue culture cells. These cells secrete relatively high amounts of HER-1 into the culture medium (~ 2 ug/mL). This recombinant protein migrates slightly slower in SDS-PAGE gels, suggesting it may be post-translationally modified (e.g., N-linked glycosylation). We are now using standard fractionation techniques to purify these HER-1 proteins. A variety of arguments suggest that the 170 kDa transmembrane protein encoded by tra-2 is likely to be a receptor for her-1's signal. We used partially purified HER-1 to probe far western blots of N2 XX hermaphrodite protein extracts and detected an interaction with a ~170 kDa protein. We are exploring several approaches to identify this HER-1-binding protein.

Robbie Rae et al. (2007) International Worm Meeting "Susceptibility and immune response of Pristionchus species exposed to pathogenic bacteria."

Ralf J. Sommer, Robbie Rae

[International Worm Meeting, 2007]

Caenorhabditis elegans is susceptible to infection by bacteria associated with insect parasitic nematodes such as Photorhabdus luminescens and Xenorhabdus nematophila (Couillault and Ewbank, 2002). We exposed several species of Pristionchus (Pristionchus pacificus California and Washington strains, Pristionchus entomophagus and Pristionchus maupasi) to P. luminescens, X. nematophila and Moraxella osloensis. Mortality was assessed over a 20-day period and compared with C. elegans. We hypothesized that Pristionchus was not susceptible to bacterial infection as it lacks a grinder and bacteria will pass through the gut alive and intact. In a second experiment we investigated the possible role of glutathione produced by Pristionchus to detoxify and protect the nematode from bacterial pathogens. Glutathione transferase proteins were extracted from nematodes exposed to pathogenic and non-pathogenic bacteria and were analysed using SDS-PAGE, 2D Electrophoresis and identified using MALDI-TOF. Total glutathione produced by the nematodes was also examined and compared with C. elegans. Couillault, C. and Ewbank, J.J. 2002. Diverse bacteria are pathogens of Caenorhabditis elegans. Infection and Immunity, 4705-4707.

Ali MY et al. (1997) International C. elegans Meeting "EXPRESSION STUDIES OF THE OSM-3 KINESIN USING ANTI-OSM-3 ANTIBODIES DURING DEVELOPMENT"

Siddiqui SS, Shakir MA, Ohnishi H, Ali MY, Miwa J, Siddiqui ZK

[International C. elegans Meeting, 1997]

OSM-3 is a kinesin like protein in C. elegans (Shakir et al., 1993) and is an ortholog of the sea urchin spKRP85/KRP95 kinesins (Scholey, 1996). Earlier we have shown that a reporter gene osm-3:: lacZ exclusively expresses in a set of 26 chemosensory neurons that are exposed to the external environment through a hole in the cuticle (Tabish et al., 1995). Here, we have report raising rabbit polyclonal antibodies against OSM-3 specific peptides in the N-terminus region (motor domain); and the C- terminus region (the cargo binding domain). Immunoblotting experiments using the C-terminus specific Anti-OSM-3 antibodies reveal high molecular weight bands (210, 130, and 90 KD) in C. elegans proteins run on SDS/PAGE, and similar bands in He La cells proteins. Indirect immunofluoresence shows that anti-OSM-3 antibodies (both made against N and C terminus specific peptides) stain chemosensory neurons and many other neurons,suggesting a wider expression pattern for the OSM-3 protein than the expression studies based on the reporter gene. We are also using these antibodies to immunoprecipitate the multimeric complexes of the other kinesin like and kinesin associated proteins that may interact with the OSM-3 kinesin. We thank Y. Tabuse, and J. Miwa for their support.