The Gene Ontology resource: enriching a GOld mine

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations

Non-typhoidal salmonella bacteraemia among HIV-infected Malawian adults: High mortality and frequent recrudescence

Objective: Non-typhoidal salmonella (NTS) bacteraemia is a common, recurrent illness in HIV-infected African adults. We aimed to describe the presentation and outcome of NTS bacteraemia, the pattern of recurrence, and to determine whether recurrence results from re-infection or recrudescence. Design: One hundred consecutive adult inpatients with NTS bacteraemia in Blantyre, Malawi, were treated with chloramphenicol. Survivors were prospectively followed to detect bacteraemic recurrence. Methods: index and recurrent isolates were typed by antibiogram, pulsed-field gel electrophoresis and plasmid analysis to distinguish recrudescence from re-infection. Results: Inpatient mortality was 47%, and 1-year mortality was 77%. A total of 77 out of 78 cases were HIV positive. Anaemia was associated with inpatient death, and several features of AIDS were associated with poor outpatient survival. Among survivors, 43% (19/44) had a first recurrence of NTS bacteraemia at 23-186 days. Among these, 26% (5/19) developed multiple recurrences up to 245 days. No recurrence was seen after 245 days, despite follow-up for up to 609 days (median 214). Suppurative infections were not found at presentation, and were only seen twice at recurrence. Index and recurrent paired isolates were identical by phenotyping and genotyping, consistent with recrudescence, rather than re-infection. Conclusion: NTS bacteraemia has a high mortality (47%) and recurrence (43%) rate in HIV-infected African adults. Recurrence is caused by recrudescence rather than reinfection. As focal infections were rarely found, recrudescence may often be a consequence of intracellular tissue sequestration. There is an urgent need for improved primary treatment and secondary prophylaxis in Africa

Nutrient cycling in Lake Kivu

This chapter summarizes the knowledge on mixing and transport processes in Lake Kivu. Seasonal mixing, which varies in intensity from year to year, influences the top ∼65 m. Below, the lake is permanently stratified, with density increasing stepwise from ∼998 kg m−3 at the surface to ∼1,002 kg m−3 at the maximum depth of 485 m. The permanently stratified deep water is divided into two distinctly different zones by a main gradient layer. This gradient is maintained by a strong inflow of relatively fresh and cool water entering at ∼250 m depth which is the most important of several subaquatic springs affecting the density stratification. The springs drive a slow upwelling of the whole water column with a depth-dependent rate of 0.15–0.9 m year−1. This upwelling is the main driver of internal nutrient recycling and upward transport of dissolved gases. Diffusive transport in the deep water is dominated by double-diffusive convection, which manifests in a spectacular staircase of more than 300 steps and mixed layers. Double diffusion allows heat to be removed from the deep zone faster than dissolved substances, supporting the stable stratification and the accumulation of nutrients and gases over hundreds of years. The stratification in the lake seems to be near steady-state conditions, except for a warming trend of ∼0.01°C year−1.