FRED 2: an immunoinformatics framework for Python.

UNLABELLED: Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable in immunological research and usually requires comprehensive pipelines including multiple tools and data sources. Non-standard input and output formats of immunoinformatics tools make the development of such applications difficult. Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications. FRED 2 is implemented in Python and designed to be extendable and flexible to allow rapid prototyping of complex applications. AVAILABILITY AND IMPLEMENTATION: FRED 2 is available at http://fred-2.github.io CONTACT: schubert@informatik.uni-tuebingen.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

EpiToolKit--a web-based workbench for vaccine design.

UNLABELLED: EpiToolKit is a virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows combining tools into complex workflows. For inexperienced users it offers simplified interfaces to guide the users through the analysis of complex immunological data sets. AVAILABILITY AND IMPLEMENTATION: http://www.epitoolkit.de CONTACT: schubert@informatik.uni-tuebingen.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Parasitic growth of Pseudomonas aeruginosa in co-culture with the chitinolytic bacterium Aeromonas hydrophila.

Polymer-degrading bacteria face exploitation by opportunistic bacteria that grow with the degradation products without investing energy into production of extracellular hydrolytic enzymes. This scenario was investigated with a co-culture of Aeromonas hydrophila and Pseudomonas aeruginosa with chitin as carbon, nitrogen and energy source. In single cultures, A. hydrophila could grow with chitin, while P. aeruginosa could not. Co-cultures with both strains had a biphasic course. In the first phase, P. aeruginosa grew along with A. hydrophila without affecting it. The second phase was initiated by a rapid inactivation of and a massive acetate release by A. hydrophila. Both processes coincided and were dependent on quorum sensing-regulated production of secondary metabolites by P. aeruginosa. Among these the redox-active phenazine compound pyocyanin caused the release of acetate by A. hydrophila by blocking the citric acid cycle through inhibition of aconitase. Thus, A. hydrophila was forced into an incomplete oxidation of chitin with acetate as end-product, which supported substantial growth of P. aeruginosa in the second phase of the co-culture. In conclusion, P. aeruginosa could profit from a substrate that was originally not bioavailable to it by influencing the metabolism and viability of A. hydrophila in a parasitic way.