ViralORFeome: an integrated database to generate a versatile collection of viral ORFs.

Large collections of protein-encoding open reading frames (ORFs) established in a versatile recombination-based cloning system have been instrumental to study protein functions in high-throughput assays. Such 'ORFeome' resources have been developed for several organisms but in virology, plasmid collections covering a significant fraction of the virosphere are still needed. In this perspective, we present ViralORFeome 1.0 (http://www.viralorfeome.com), an open-access database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. ViralORFeome provides a convenient interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. Most importantly, ViralORFeome has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain. A subset of plasmid constructs generated with ViralORFeome platform has been tested with success for heterologous protein expression in different expression systems at proteome scale. ViralORFeome should provide our community with a framework to establish a large collection of virus ORF clones, an instrumental resource to determine functions, activities and binding partners of viral proteins.

Hepatitis C virus infection protein network.

A proteome-wide mapping of interactions between hepatitis C virus (HCV) and human proteins was performed to provide a comprehensive view of the cellular infection. A total of 314 protein-protein interactions between HCV and human proteins was identified by yeast two-hybrid and 170 by literature mining. Integration of this data set into a reconstructed human interactome showed that cellular proteins interacting with HCV are enriched in highly central and interconnected proteins. A global analysis on the basis of functional annotation highlighted the enrichment of cellular pathways targeted by HCV. A network of proteins associated with frequent clinical disorders of chronically infected patients was constructed by connecting the insulin, Jak/STAT and TGFbeta pathways with cellular proteins targeted by HCV. CORE protein appeared as a major perturbator of this network. Focal adhesion was identified as a new function affected by HCV, mainly by NS3 and NS5A proteins.

Human pentastomiasis in Sub-Saharan Africa.

Pentastomiasis is a rare zoonotic infection but it is frequently observed in Africa and Asia. Most human infections are caused by members of the Armillifer armillatus species. They are responsible for visceral pentastomiasis in Western and Central Africa. Humans may be infected by eating infected undercooked snake meat or by direct contact with an infected reptile. An increasing number of infections are being reported in Congo, Nigeria, and Cameroon. Despite an occasionally high number of nymphs observed in human viscera, most infections are asymptomatic and often diagnosed by accident during surgery or autopsy. The clinical presentation of pentastomiasis is quite varied and depends on infected tissues. The liver, lungs, and pleura are most frequently involved. Abdominal emergencies have been reported. Diagnostic delays always occur and diagnosis focuses on the patient's lifestyle and living environment. It is mainly based on the morphological description of the parasite's calcified cuticle, the site of the lesion, and the parasite's region of origin. Most patients do not require any treatment. Personal measures such as avoidance of contact with snake droppings are recommended to prevent transmission. Imported pentastomiasis has been observed in African migrants.

Measurements of δ13C in CH4 and using particle dispersion modeling to characterize sources of Arctic methane within an air mass.

A stratified air mass enriched in methane (CH4) was sampled at ~600 m to ~2000 m altitude, between the north coast of Norway and Svalbard as part of the Methane in the Arctic: Measurements and Modelling campaign on board the UK's BAe-146-301 Atmospheric Research Aircraft. The approach used here, which combines interpretation of multiple tracers with transport modeling, enables better understanding of the emission sources that contribute to the background mixing ratios of CH4 in the Arctic. Importantly, it allows constraints to be placed on the location and isotopic bulk signature of the emission source(s). Measurements of δ13C in CH4 in whole air samples taken while traversing the air mass identified that the source(s) had a strongly depleted bulk δ13C CH4 isotopic signature of -70 (±2.1)‰. Combined Numerical Atmospheric-dispersion Modeling Environment and inventory analysis indicates that the air mass was recently in the planetary boundary layer over northwest Russia and the Barents Sea, with the likely dominant source of methane being from wetlands in that region.

Sea urchin elongation factor 1delta (EF1delta) and evidence for cell cycle-directed localization changes of a sub-fraction of the protein at M phase.

Eukaryotic elongation factor 1 (eEF1) is a translational multimolecular complex reported in higher eukaryotes to be a target of CDK1/cyclin B, the universal regulator of M phase, but whose role in the cell cycle remains to be determined. A specific polyclonal antibody was produced and used to characterize the delta subunit of sea urchin elongation factor 1 (SgEF1delta) in early embryos, a powerful model for investigating cell cycle regulation. The SgEF1delta protein was present in unfertilized eggs as two isoforms of 35 and 37 kDa, issued from two different mRNAs. The two canonical eEF1delta partners, eEF1gamma and eEF1beta, were shown to co-immunoprecipitate with the SgEF1delta isoforms. Both isoforms were associated in a macromolecular complex, which resolved upon gel filtration chromatography at a molecular weight > 400 kDa, suggesting association with other yet unidentified partners. After fertilization, the amount as well as the ratio of both SgEF1delta isoforms remained constant during the first cell division as judged by Western blotting. Immunofluorescence analysis showed that a pool of the protein concentrated as a ring at the embryo nuclear location around the period of nuclear envelope breakdown and was visualized later as two large spheres around the mitotic spindle poles. Thus, the eEF1delta protein shows cell cycle-specific localization changes in sea urchin embryos.