Assessing parallel gene histories in viral genomes

Background: The increasing abundance of sequence data has exacerbated a long known problem: gene trees and species trees for the same terminal taxa are often incongruent. Indeed, genes within a genome have not all followed the same evolutionary path due to events such as incomplete lineage sorting, horizontal gene transfer, gene duplication and deletion, or recombination. Considering conflicts between gene trees as an obstacle, numerous methods have been developed to deal with these incongruences and to reconstruct consensus evolutionary histories of species despite the heterogeneity in the history of their genes. However, inconsistencies can also be seen as a source of information about the specific evolutionary processes that have shaped genomes. Results: The goal of the approach here proposed is to exploit this conflicting information: we have compiled eleven variables describing phylogenetic relationships and evolutionary pressures and submitted them to dimensionality reduction techniques to identify genes with similar evolutionary histories. To illustrate the applicability of the method, we have chosen two viral datasets, namely papillomaviruses and Turnip mosaic virus (TuMV) isolates, largely dissimilar in genome, evolutionary distance and biology. Our method pinpoints viral genes with common evolutionary patterns. In the case of papillomaviruses, gene clusters match well our knowledge on viral biology and life cycle, illustrating the potential of our approach. For the less known TuMV, our results trigger new hypotheses about viral evolution and gene interaction. Conclusions: The approach here presented allows turning phylogenetic inconsistencies into evolutionary information, detecting gene assemblies with similar histories, and could be a powerful tool for comparative pathogenomics.IGB was funded by the disappeared Spanish Ministry for Science and Innovation (CGL2010-16713). Work in Valencia was supported by grant BFU2012-30805 from the Spanish Ministry of Economy and Competitiveness (MINECO) to SFE. BMC is the recipient of an IDIBELL PhD fellowship.Mengual-Chuliá, B.; Bedhomme, S.; Lafforgue, G.; Elena Fito, SF.; Bravo, IG. (2016). Assessing parallel gene histories in viral genomes. BMC Evolutionary Biology. 16:1-15. https://doi.org/10.1186/s12862-016-0605-4S11516Hess J, Goldman N. Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: Yeasts revisited. PLoS ONE. 2011;6:e22783.Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. 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Rhesus macaque θ-defensin isoforms: expression, antimicrobial activities, and demonstration of a prominent role in neutrophil granule microbicidal activities

θ-defensins account for a major portion of the antimicrobial activity in macaque neutrophil granules and for the superior activity of macaque preparations compared those from human PMNs

Qualität und Qualitätssicherung in der Berufsbildung

Heute ist der Begriff Qualität in aller Munde. Er bezeichnet die Güte eine Produktes oder einer Dienstleistung. Diese Güte ist nun aber nicht einfach pauschal am Markennamen oder an der anerkannten Tradition — so etwa „Made in Germany“ oder „Schweizer Qualität“ — bisheriger Leistungen erkennbar. Viel mehr wird Qualität vor Ort, situationsbezogen und von Fall zu Fall bestimmt. Das vor uns Sichtbare wird entsprechend unterschiedlichen Ansprüchen bewertet und je nach dem als zweckmäßig und gut befunden. Denn die Bedürfnisse der Einzelnen, als Nachfrager von Produkten und Dienstleistungen sind vielfältiger geworden. Außerdem ist auch der „gute Ruf“ einer Branche, Firma oder eben auch Institution eine viel prekärere und zeitlich unstabilere Größe als in früheren Zeiten