Ion transport chapter added to WormBook

by Leave a Comment

Membrane ion transport in non-excitable tissues, by Keith Nehrke, has just been published in the Cell biology section. This chapter discusses calcium signaling during defecation, fertilization, locomotion, and wound closure, as well as the role of pH, proton signaling, and osmotic balance in C. elegans behavior and physiology.

Please proceed to read this chapter and others on nematode biology at http://www.wormbook.org/. If you have any comments or suggestions, please submit them via the Feedback page on wormbook.org.

Thank you for your interest in WormBook, and happy holidays!

Jane

WormBook: Polarity establishment chapter updated

by Leave a Comment

Polarity establishment, asymmetric division and segregation of fate determinants in early C. elegans embryos, by Lesilee Rose and Pierre Goenczy, has been published in the Developmental control and Cell biology sections of WormBook. This chapter updates their 2005 chapter, Asymmetric cell division and axis formation in the embryo. The updated chapter presents important progress in elucidating the mechanisms that transform an isotropic system into a polarized one in the first cell cycle, and further discusses how cell signaling in subsequent divisions builds upon the initial polarity to further refine cell fates.

Please proceed to read this chapter and others on nematode biology at http://www.wormbook.org/. If you have any comments or suggestions, please submit them via the Feedback page on wormbook.org.

Jane

New in WS246: Curation of Wnt signaling papers

by Leave a Comment

Wnt signaling in C. elegans, both canonical and non-canonical, governs cell polarity and asymmetric cell divisions that ultimately affect endoderm specification, vulva and gonad development, neuroblast migration, neuron branching and outgrowth, formation of the postdeirid sensilla and male tail ray and spicule formation (see WormBook chapters on Wnt signaling for reviews). For the WS246 and WS247 releases of WormBase, WormBase curators have focused on curating papers directly relevant to Wnt signaling in C. elegans. This curation includes Wnt-related genetic and regulatory interactions, anatomy function, mutant phenotypes (by allele and RNAi), expression patterns, Gene Ontology annotations, and cross-species gene orthology and gene models for other nematode species.

New in WS246: Automatically generated gene descriptions

by Leave a Comment

WormBase has been writing concise descriptions of genes that appear in the Overview widget of the gene page. Written in prose, these descriptions provide a quick overview of gene function. Since the process of manually writing gene descriptions is a relatively slow process, many genes lacked such descriptions.

A new experimental tool at WormBase aims to fill these gaps by automatically creating gene descriptions which are visible in the Overview widget of gene pages.  The semi-automated process of generating these descriptions relies on pre-existing orthology and Gene Ontology annotations (biological process, molecular function, and cellular component) in WormBase.  This process offers a broad coverage for genes lacking manually drafted descriptions.

New Features for WS246

by Leave a Comment

Human Disease Data Update

As part of WormBase efforts to curate genes that are potential models for inherited human diseases, 867 genes have been predicted as potential disease genes. In addition curation efforts added publications on experiments using C.elegans genes to investigate human genetic diseases to 181 genes. And 244 genes have been identified from publications as being relevant to research in that field.

WormBase curates human disease relevance data by designating genes as ‘Experimental models’ for a specific human disease based on experimental data published in the literature. In addition to manual curation, an automated data pipeline designates genes as ‘Potential models’ based on orthology with the human gene. Detailed text descriptions called ‘Human disease relevance’ descriptions describe how the elegans gene is a genetic model for the human disease. All human disease relevant data can be found in the ‘Human Diseases’ widget and in the ‘Overview’ section on gene pages.