A Gene Ontology Tutorial in Python.

This chapter is a tutorial on using Gene Ontology resources in the Python programming language. This entails querying the Gene Ontology graph, retrieving Gene Ontology annotations, performing gene enrichment analyses, and computing basic semantic similarity between GO terms. An interactive version of the tutorial, including solutions, is available at http://gohandbook.org

A case for hornblende dominated fractionation of arc magmas: the Chelan Complex (Washington Cascades)

Amphibole fractionation in the deep roots of subduction-related magmatic arcs is a fundamental process for the generation of the continental crust. Field relations and geochemical data of exposed lower crustal igneous rocks can be used to better constrain these processes. The Chelan Complex in the western U.S. forms the lowest level of a 40-km thick exposed crustal section of the North Cascades and is composed of olivine websterite, pyroxenite, hornblendite, and dominantly by hornblende gabbro and tonalite. Magmatic breccias, comb layers and intrusive contacts suggest that the Chelan Complex was build by igneous processes. Phase equilibria, textural observations and mineral chemistry yield emplacement pressures of ∼1.0GPa followed by isobaric cooling to 700°C. The widespread occurrence of idiomorphic hornblende and interstitial plagioclase together with the lack of Eu anomalies in bulk rock compositions indicate that the differentiation is largely dominated by amphibole. Major and trace element modeling constrained by field observations and bulk chemistry demonstrate that peraluminous tonalite could be derived by removing successively 3% of olivine websterite, 12% of pyroxene hornblendite, 33% of pyroxene hornblendite, 19% of gabbros, 15% of diorite and 2% tonalite. Peraluminous tonalite with high Sr/Y that are worldwide associated with active margin settings can be derived from a parental basaltic melt by crystal fractionation at high pressure provided that amphibole dominates the fractionation process. Crustal assimilation during fractionation is thus not required to generate peraluminous tonalit

Effets des programmes de prévention à focus neuromusculaire chez l’athlète adolescente: revue de la littérature et méta-analyse

Dans la pratique du sport, les athlètes adolescentes sont particulièrement à risque de blessures en raison du niveau élevé d'exposition à un stade de grands changements physiologiques. La pratique des échauffements à focus neuromusculaire lors des entraînements ainsi qu’en compétition semble représenter une approche optimale afin de diminuer le taux de blessures. L’objectif de notre revue est d’évaluer l’effet des programmes de prévention à focus neuromusculaire sur le risque de blessures du membre inférieur chez l’adolescente sportive.Während des Sporttreibens sind jugendliche Athleten aufgrund der grossen physiognomischen Veränderungen, denen sie ausgesetzt sind, besonders verletzungsgefährdet. Ein Aufwärmen mit Fokus auf die Neuromuskulär während des Trainings sowie des Wettkampfes scheint daher ein optimaler Ansatz zu sein um die Anzahl Verletzungen zu verringern. Ziel dieser Arbeit ist es, den Effekt von präventiven Programmen mit Fokus auf die Neuromuskulär auf das Risiko von Verletzungen der Unteren Extremität der Jugendlichen zu evaluieren

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.

Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree inference or genuine discordance among the loci analyzed). Existing tree visualization tools are however not well suited to these tasks. In particular, side-by-side comparison of trees can prove challenging beyond a few dozen taxa. Here, we introduce Phylo.io, a web application to visualize and compare phylogenetic trees side-by-side. Its distinctive features are: highlighting of similarities and differences between two trees, automatic identification of the best matching rooting and leaf order, scalability to large trees, high usability, multiplatform support via standard HTML5 implementation, and possibility to store and share visualizations. The tool can be freely accessed at http://phylo.io and can easily be embedded in other web servers. The code for the associated JavaScript library is available at https://github.com/DessimozLab/phylo-io under an MIT open source license

Phylogenetic profiling: how much input data is enough?

Phylogenetic profiling is a well-established approach for predicting gene function based on patterns of gene presence and absence across species. Much of the recent developments have focused on methodological improvements, but relatively little is known about the effect of input data size on the quality of predictions. In this work, we ask: how many genomes and functional annotations need to be considered for phylogenetic profiling to be effective? Phylogenetic profiling generally benefits from an increased amount of input data. However, by decomposing this improvement in predictive accuracy in terms of the contribution of additional genomes and of additional annotations, we observed diminishing returns in adding more than ∼ 100 genomes, whereas increasing the number of annotations remained strongly beneficial throughout. We also observed that maximising phylogenetic diversity within a clade of interest improves predictive accuracy, but the effect is small compared to changes in the number of genomes under comparison. Finally, we show that these findings are supported in light of the Open World Assumption, which posits that functional annotation databases are inherently incomplete. All the tools and data used in this work are available for reuse from http://lab.dessimoz.org/14_phylprof. Scripts used to analyse the data are available on request from the authors

Alignments with non-overlapping moves, inversions and tandem duplications in O ( n 4) time

Sequence alignment is a central problem in bioinformatics. The classical dynamic programming algorithm aligns two sequences by optimizing over possible insertions, deletions and substitutions. However, other evolutionary events can be observed, such as inversions, tandem duplications or moves (transpositions). It has been established that the extension of the problem to move operations is NP-complete. Previous work has shown that an extension restricted to non-overlapping inversions can be solved in O(n 3) with a restricted scoring scheme. In this paper, we show that the alignment problem extended to non-overlapping moves can be solved in O(n 5) for general scoring schemes, O(n 4log n) for concave scoring schemes and O(n 4) for restricted scoring schemes. Furthermore, we show that the alignment problem extended to non-overlapping moves, inversions and tandem duplications can be solved with the same time complexities. Finally, an example of an alignment with non-overlapping moves is provide

Intensification of slow reversible chemical transformation: carboxylation of resorcinol as a case study

Conjugated kinetic and thermodynamic modeling is suggested as a suitable approach to identify a novel process window (NPW) for the intensification of slow reversible reactions. The aqueous Kolbe-Schmitt synthesis of β-resorcylic acid is taken as a model. The potential of operating at high pressure (P) and temperature (T) is evaluated in order to reduce the characteristic reaction time (tr) and increase the specific productivity. For the first time, a reliable kinetic model for this reaction is derived from batch experiments. Based on this model, an NPW of P=10 bars, T=453 K is determined for a continuous reactor operated at a residence time of 28 s. It is predicted that the specific productivity can be increased by a factor of 100 with a 4.2 times less concentrated KHCO3 solution, as compared to a conventional batch process, if the reaction is kinetically controlled. The model prediction is experimentally validated with a continuously operated milli-reactor equipped by SMXS mixer elements (Sulzer Chemtech, Switzerland) ensuring a fast mixing (characteristic mixing time ~4.10-2 s). The milli-reactor renders exclusively β-resorcylic acid (selectivity 100%) and confirms process intensification (PI) of two orders of magnitude as compared to conventional batch operatio

Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life.

Membrane proteins are crucial in transport, signaling, bioenergetics, catalysis, and as drug targets. Here, we show that membrane proteins have dramatically fewer detectable orthologs than water-soluble proteins, less than half in most species analyzed. This sparse distribution could reflect rapid divergence or gene loss. We find that both mechanisms operate. First, membrane proteins evolve faster than water-soluble proteins, particularly in their exterior-facing portions. Second, we demonstrate that predicted ancestral membrane proteins are preferentially lost compared with water-soluble proteins in closely related species of archaea and bacteria. These patterns are consistent across the whole tree of life, and in each of the three domains of archaea, bacteria, and eukaryotes. Our findings point to a fundamental evolutionary principle: membrane proteins evolve faster due to stronger adaptive selection in changing environments, whereas cytosolic proteins are under more stringent purifying selection in the homeostatic interior of the cell. This effect should be strongest in prokaryotes, weaker in unicellular eukaryotes (with intracellular membranes), and weakest in multicellular eukaryotes (with extracellular homeostasis). We demonstrate that this is indeed the case. Similarly, we show that extracellular water-soluble proteins exhibit an even stronger pattern of low homology than membrane proteins. These striking differences in conservation of membrane proteins versus water-soluble proteins have important implications for evolution and medicine