WormBase: A modern Model Organism Information Resource

WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase\u27s role as a founding member of the nascent Alliance of Genome Resources

Mutations in synaptojanin disrupt synaptic vesicle recycling

Journal ArticleSynaptojanin is a polyphosphoinositide phosphatase that is found at synapses and binds to proteins implicated in endocytosis. For these reasons, it has been proposed that synaptojanin is involved in the recycling of synaptic vesicles. Here, we demonstrate that the unc-26 gene encodes the Caenorhabditis elegans ortholog of synaptojanin. unc-26 mutants exhibit defects in vesicle trafficking in several tissues, but most defects are found at synaptic termini

Micropublication: incentivizing community curation and placing unpublished data into the public domain

Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases. Further, many publicly funded experimental observations remain invisible to curation simply because they are never published: results often do not fit within the scope of a standard publication; trainee-generated data are forgotten when the experimenter (e.g. student, post-doc) leaves the lab; results are omitted from science narratives due to publication bias where certain results are considered irrelevant for the publication. While authors are in the best position to curate their own data, they face a steep learning curve to ensure that appropriate referential tags, metadata, and ontologies are applied correctly to their observations, a task sometimes considered beyond the scope of their research and other numerous responsibilities. Getting researchers to adopt a new system of data reporting and curation requires a fundamental change in behavior among all members of the research community. To solve these challenges, we have created a novel scholarly communication platform that captures data from researchers and directly delivers them to information resources via Micropublication. This platform incentivizes authors to publish their unpublished observations along with associated metadata by providing a deliberately fast and lightweight but still peer-reviewed process that results in a citable publication. Our long-term goal is to develop a data ecosystem that improves reproducibility and accountability of publicly funded research and in turn accelerates both basic and translational discovery

Micropublication: Incentivizing community curation and placing unpublished data into the public domain

UNLABELLED: Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases. Further, many publicly funded experimental observations remain invisible to curation simply because they are never published: results often do not fit within the scope of a standard publication; trainee-generated data are forgotten when the experimenter (e.g. student, post-doc) leaves the lab; results are omitted from science narratives due to publication bias where certain results are considered irrelevant for the publication. While authors are in the best position to curate their own data, they face a steep learning curve to ensure that appropriate referential tags, metadata, and ontologies are applied correctly to their observations, a task sometimes considered beyond the scope of their research and other numerous responsibilities. Getting researchers to adopt a new system of data reporting and curation requires a fundamental change in behavior among all members of the research community. To solve these challenges, we have created a novel scholarly communication platform that captures data from researchers and directly delivers them to information resources via Micropublication. This platform incentivizes authors to publish their unpublished observations along with associated metadata by providing a deliberately fast and lightweight but still peer-reviewed process that results in a citable publication. Our long-term goal is to develop a data ecosystem that improves reproducibility and accountability of publicly funded research and in turn accelerates both basic and translational discovery. DATABASE URL: www.micropublication.org

Mutations in Synaptojanin Disrupt Synaptic Vesicle Recycling

Synaptojanin is a polyphosphoinositide phosphatase that is found at synapses and binds to proteins implicated in endocytosis. For these reasons, it has been proposed that synaptojanin is involved in the recycling of synaptic vesicles. Here, we demonstrate that the unc-26 gene encodes the Caenorhabditis elegans ortholog of synaptojanin. unc-26 mutants exhibit defects in vesicle trafficking in several tissues, but most defects are found at synaptic termini. Specifically, we observed defects in the budding of synaptic vesicles from the plasma membrane, in the uncoating of vesicles after fission, in the recovery of vesicles from endosomes, and in the tethering of vesicles to the cytoskeleton. Thus, these results confirm studies of the mouse synaptojanin 1 mutants, which exhibit defects in the uncoating of synaptic vesicles (Cremona, O., G. Di Paolo, M.R. Wenk, A. Luthi, W.T. Kim, K. Takei, L. Daniell, Y. Nemoto, S.B. Shears, R.A. Flavell, D.A. McCormick, and P. De Camilli. 1999. Cell. 99:179–188), and further demonstrate that synaptojanin facilitates multiple steps of synaptic vesicle recycling

Determination of the Spawning Season of Bigmouth Sleeper in Puerto Rico by Examination of Gonad Maturation and Reproductive Hormone Cycles

Bigmouth sleepers, Gobiomorus dormitor, are diadromous fish that have potential for hatchery production as both food and sport fish and for conservation purposes. Understanding of bigmouth sleeper maturation and seasonal hormone cycling are necessary in order to realize hatchery production. Therefore, seasonal trends in gonadosomatic index (GSI) and plasma vitellogenin, estradiol, progesterone and total testosterone concentrations were examined in wild and captive populations in Puerto Rico during the presumed spawning season. The spawning season for wild river populations of bigmouth sleepers was protracted over several months, but peaks in male testosterone (6.5 ng/mL) and female vitellogenin (11.3 ng/mL), estradiol (3.3 ng/mL), and GSI (9.5—12.0%) demonstrated that the bigmouth sleeper spawning season occurred primarily in July and August in southwestern Puerto Rico. Captive female broodstock held in shallow hatchery ponds demonstrated accelerated maturation, presumably due to warmer water temperatures in the ponds. Therefore, induced and natural spawning attempts using captive female bigmouth sleeper broodstock should be conducted from June through July. However, advanced gonadal maturation and increased testosterone production in captive males was minimal. Hence, induced spawning for captive rearing purposes should use wild broodstock captured during the peak of the natural spawning season in July and August

WormBook: the online review of Caenorhabditis elegans biology

WormBook () is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12 chapters, it has grown to over 100 chapters, covering nearly every aspect of C.elegans research, from Cell Biology and Neurobiology to Evolution and Ecology. WormBook also serves as the text companion to WormBase, the C.elegans model organism database. Objects such as genes, proteins and cells are linked to the relevant pages in WormBase, providing easily accessible background information. Additionally, WormBook chapters contain links to other relevant topics in WormBook, and the in-text citations are linked to their abstracts in PubMed and full-text references, if available. Since WormBook is online, its chapters are able to contain movies and complex images that would not be possible in a print version. WormBook is designed to keep up with the rapid pace of discovery in the field of C.elegans research and continues to grow. WormBook represents a generic publishing infrastructure that is easily adaptable to other research communities to facilitate the dissemination of knowledge in the field

WormBase: a multi-species resource for nematode biology and genomics

WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system

WormBase: a comprehensive resource for nematode research

WormBase (http://www.wormbase.org) is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, WormBase has evolved into a powerful research tool in its own right. In the past 2 years, we expanded WormBase to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base