Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation

GermOnline is a web-accessible relational database that enables life scientists to make a significant and sustained contribution to the annotation of genes relevant for the fields of mitosis, meiosis, germ line development and gametogenesis across species. This novel approach to genome annotation includes a platform for knowledge submission and curation as well as microarray data storage and visualization hosted by a global network of servers.

AVAILABILITY

The database is accessible at http://www.germonline.org/. For convenient world-wide access we have set up a network of servers in Europe (http://germonline.unibas.ch/; http://germonline.igh.cnrs.fr/), Japan (http://germonline.biochem.s.u-tokyo.ac.jp/) and USA (http://germonline.yeastgenome.org/).

SUPPLEMENTARY INFORMATION

Extended documentation of the database is available through the link 'About GermOnline' at the websites.

GermOnline, a cross-species community knowledgebase on germ cell differentiation

GermOnline provides information and microarray expression data for genes involved in mitosis and meiosis, gamete formation and germ line development across species. The database has been developed, and is being curated and updated, by life scientists in cooperation with bioinformaticists. Information is contributed through an online form using free text, images and the controlled vocabulary developed by the GeneOntology Consortium. Authors provide up to three references in support of their contribution. The database is governed by an international board of scientists to ensure a standardized data format and the highest quality of GermOnline's information content. Release 2.0 provides exclusive access to microarray expression data from Saccharomyces cerevisiae and Rattus norvegicus, as well as curated information on approximately 700 genes from various organisms. The locus report pages include links to external databases that contain relevant annotation, microarray expression and proteome data. Conversely, the Saccharomyces Genome Database (SGD), S.cerevisiae GeneDB and Swiss-Prot link to the budding yeast section of GermOnline from their respective locus pages. GermOnline, a fully operational prototype subject-oriented knowledgebase designed for community annotation and array data visualization, is accessible at http://www.germonline.org. The target audience includes researchers who work on mitotic cell division, meiosis, gametogenesis, germ line development, human reproductive health and comparative genomics.

Beta-thymosin, a modulator of the actin cytoskeleton is increased in regenerating retinal ganglion cells

Beta-thymosins are actin monomer-binding polypeptides that are expressed in a neuronal growth-specific manner during embryonic development. Here, we show that regenerating retinal ganglion cells and non-neuronal cells of the optic nerve transiently activate beta-thymosin transcription after optic nerve lesion in the zebrafish. In retinal cell cultures, beta-thymosin is found at highest concentration in growth cones, branching points and varicosities of neurite-extending retinal ganglion cells. These places often exhibit reduced phalloidin staining, indicating that beta-thymosin promotes the disassembly of actin filaments. Beta-thymosin distribution within neurons in culture is distinct from actin, tubulin and the actin-severing protein gelsolin. Ectopic expression of beta-thymosin in a central nervous system (CNS) catecholaminergic cell line leads to alterations in the shape of the cell bodies and neurites. Beta-thymosin-positive cells spread more fully and exhibit an excessive degree of branching. We partially cloned two other actin-binding proteins, profilin and gelsolin, and analysed their expression patterns. Profilin is constitutively expressed in virtually all cells. Gelsolin, like beta-thymosin, is selectively increased in regenerating retinal ganglion cells. During development, however, gelsolin mRNA is not detected in the nervous system. These findings indicate that distinct mechanisms control the actin cytoskeleton in embryonic and regenerating neurons, and that beta-thymosin may be a major regulator of actin dynamics in the zebrafish CNS.