AVID: An integrative framework for discovering functional relationships among proteins

BACKGROUND: Determining the functions of uncharacterized proteins is one of the most pressing problems in the post-genomic era. Large scale protein-protein interaction assays, global mRNA expression analyses and systematic protein localization studies provide experimental information that can be used for this purpose. The data from such experiments contain many false positives and false negatives, but can be processed using computational methods to provide reliable information about protein-protein relationships and protein function. An outstanding and important goal is to predict detailed functional annotation for all uncharacterized proteins that is reliable enough to effectively guide experiments. RESULTS: We present AVID, a computational method that uses a multi-stage learning framework to integrate experimental results with sequence information, generating networks reflecting functional similarities among proteins. We illustrate use of the networks by making predictions of detailed Gene Ontology (GO) annotations in three categories: molecular function, biological process, and cellular component. Applied to the yeast Saccharomyces cerevisiae, AVID provides 37,451 pair-wise functional linkages between 4,191 proteins. These relationships are ~65–78% accurate, as assessed by cross-validation testing. Assignments of highly detailed functional descriptors to proteins, based on the networks, are estimated to be ~67% accurate for GO categories describing molecular function and cellular component and ~52% accurate for terms describing biological process. The predictions cover 1,490 proteins with no previous annotation in GO and also assign more detailed functions to many proteins annotated only with less descriptive terms. Predictions made by AVID are largely distinct from those made by other methods. Out of 37,451 predicted pair-wise relationships, the greatest number shared in common with another method is 3,413. CONCLUSION: AVID provides three networks reflecting functional associations among proteins. We use these networks to generate new, highly detailed functional predictions for roughly half of the yeast proteome that are reliable enough to drive targeted experimental investigations. The predictions suggest many specific, testable hypotheses. All of the data are available as downloadable files as well as through an interactive website at . Thus, AVID will be a valuable resource for experimental biologists

Caenorhabditis elegans: a model to monitor bacterial air quality

<p>Abstract</p> <p>Background</p> <p>Low environmental air quality is a significant cause of mortality and morbidity and this question is now emerging as a main concern of governmental authorities. Airborne pollution results from the combination of chemicals, fine particles, and micro-organisms quantitatively or qualitatively dangerous for health or for the environment. Increasing regulations and limitations for outdoor air quality have been decreed in regards to chemicals and particles contrary to micro-organisms. Indeed, pertinent and reliable tests to evaluate this biohazard are scarce. In this work, our purpose was to evaluate the <it>Caenorhaditis elegans </it>killing test, a model considered as an equivalent to the mouse acute toxicity test in pharmaceutical industry, in order to monitor air bacterial quality.</p> <p>Findings</p> <p>The present study investigates the bacterial population in dust clouds generated during crop ship loading in harbor installations (Rouen harbor, Normandy, France). With a biocollector, airborne bacteria were impacted onto the surface of agar medium. After incubation, a replicate of the colonies on a fresh agar medium was done using a velvet. All the replicated colonies were pooled creating the "Total Air Sample". Meanwhile, all the colonies on the original plate were isolated. Among which, five representative bacterial strains were chosen. The virulence of these representatives was compared to that of the "Total Air Sample" using the <it>Caenorhaditis elegans </it>killing test. The survival kinetic of nematodes fed with the "Total Air Sample" is consistent with the kinetics obtained using the five different representatives strains.</p> <p>Conclusions</p> <p>Bacterial air quality can now be monitored in a one shot test using the <it>Caenorhaditis elegans </it>killing test.</p

Magnetic films of metal-graphene-polymer nanocomposites

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Thin film of magnetic nanocomposites with zero effective conductivity for RF applications

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Thin film of magnetic nanocomposites with zero effective conductivity for RF applications

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Microenvironment impact on acneic and non-acneic strains of Cutibacterium acnes.

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Microenvironment impact on Cutibacterium acnes: growth, virulence and biofilm formation of acneic and non-acneic strains

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Microenvironment impact on Cutibacterium acnes: growth, virulence and biofilm formation of acneic and non-acneic strains

International audienc

Microenvironment impact on acneic and non-acneic strains of Cutibacterium acnes.

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DESEQUESTRATION DE POLLUANTS DE TYPE HYDROCARBURES AROMATIQUES POLYCYCLIQUES A L'INTERFACE EAU/SEDIMENTS A L'AIDE DE TENSIOACTIFS D'ORIGINE SYNTHETIQUE OU BIOLOGIQUE

International audienceDans le cadre du projet RESSOLV (REstauration des Sédiments et SOLs Vulnérables), projet émergeant du réseau de recherche Haut-Normand SCALE, les travaux présentés montrent les premiers résultats concernant le comportement de micropolluants organiques présents à l'interface eau/sédiments et leur déséquestration par des agents tensioactifs. Le but du projet est en fait d'atténuer la pollution des sédiments de dragage des ports, entre autre en Hydrocarbures Aromatiques Polycycliques (HAP), afin de diminuer leur teneur en dessous du niveau N 2 , voire N 1 de la réglementation GEODE 2000, et de pouvoir ainsi autoriser une immersion en mer ou une valorisation des sédiments dragués. Un procédé d'électromigration étant envisagé pour atténuer les teneurs en polluants cibles, il s'avère indispensable de solubiliser des espèces neutres et hydrophobes, telles les HAP, dans des systèmes chargés ayant la capacité de les transporter, grâce à un champ électrique, à travers le fluide interstitiel aqueux. Par conséquent, dans un premier temps, nous avons d'abord tenté de comprendre le comportement d'adsorption d'un mélange de 16 HAP à l'interface avec des surfaces modèles, telles le sable et le kaolin. Ces 16 HAP, présents à l'état de traces, ont été analysés après un enrichissement par SPE (Solid Phase Extraction), suivi d'une séparation et d'un dosage par chromatographie liquide alliée à une détection fluorimétrique. L'obtention d'isothermes d'adsorption, pour chaque HAP, a permis de comparer l'adsorption des HAP lourds par rapport aux HAP légers, ainsi que leur comportement sur les deux surfaces modèles. Dans un deuxième temps, un tensioactif anionique synthétique, le dodécyl sulfate de sodium (SDS) a été incorporé dans le milieu afin de désorber les HAP et de les re-solubiliser en phase aqueuse, afin de pouvoir mettre en oeuvre le procédé d'électromigration. Le SDS, utilisé à 10 fois sa concentration micellaire critique, a effectivement permis de re-solubiliser en partie les HAP, son effet étant moindre sur les HAP très lourds. Par la suite, des essais ont été effectués à partir d'un biosurfactant anionique original, de type cyclolipopeptide, produit par une souche bactérienne apparentée à Pseudomonas fluorescens, l'avantage du biosurfactant par rapport au SDS étant sa biodégradabilité et sa capacité à être produit in situ, en continu dans le réacteur