The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Observation et modélisation de nanostructures magnétiques excitées par microondes en vue d'une application capteur

TOULOUSE3-BU Sciences (315552104) / SudocSudocFranceF

Rayleigh–Bénard convection in a cubic cell under the effects of gas radiation up to Ra=1E9

International audienceThis paper investigates radiative transfer effects on Rayleigh-Bénard convection in a cubic cell over a large range of Rayleigh numbers, from Ra = 1E3 (below the onset of convection) to Ra = 1E9 in the turbulent regime. Coupled direct numerical simulations are carried out for a radiating air/H2O/CO2 mixture at room temperature, using a Chebyshev spectral method for the flow and a ray-tracing method for the radiation field. For the highest Rayleigh numbers, a subgrid model is used to account for the radiation of the smallest, non-optically thin, turbulent scales. Symmetry and time-averaging (for unsteady solutions) are applied to compare coupled and uncoupled results, regardless of the multiple flow configurations that may be obtained. At low Rayleigh number, the potential energy decreases, and the onset of convection is delayed when radiation is taken into account. However, once convection settles, the potential energy increases with radiation, leading to a higher convective flux in the core and a higher kinetic energy. Specific contributions of radiative transfer to the potential energy balance and to the thermal energy balance are highlighted. It is also shown that the ratio of radiative and convective source terms in the energy balance roughly scales as Ra^−1/2 and that radiative transfer effects weaken at high Rayleigh numbers. Finally, radiative transfer effects on turbulence budgets of mechanical and thermal fluctuations are analysed in the range 1E7 ≤ Ra ≤ 1E9. The magnitude of each term of these budgets is stronger when radiation is taken into account. However, radiative dissipation has little influence on the temperature fluctuation budget

Assessment of a spectral vanishing viscosity LES model for 3D Rayleigh-Bénard convection in a cubic cell

International audienceRayleigh-Be ́nard (RB) convection is a challenging topic for both academic research and for several applica- tions in the field of atmospheric physics, industrial applications, and building insulation. The actual applica- tions involve high Rayleigh or Grashoff numbers but the Direct Numerical Simulations (DNS) remain limited to relatively small values of these numbers. Approximate models are required for the prediction of flow fields and heat transfer at higher numbers. The aim of this study is to assess the ability of a Large Eddy Simulation (LES) model to predict accurate mean values and second order moments of temperature and velocity fields. The reference fields are provided by DNS simulations under the Boussinesq approximation in a RB cell filled with air at a Rayleigh number (Ra) up to 109. The employed numerical DNS method is based on a Tchebychev pseudo-spectral method and the most appropriate LES model in this case appears to be the Spectral Vanishing Viscosity (SVV) model where high order modes are exponentially damped to stabilize the numerical scheme. The predicted mean velocity and temperature fields from this LES model, as well as their second order mo- ments, are compared to DNS values. A sensitivity study to the SVV parameters, i.e. the Tchebychev mode cutoff and the damping amplitude, is carried out. The model appears to be a promising approach for accurate predictions at much higher Rayleigh numbers

Cell wall peptidolipids of \u3ci\u3eMycobacterium avium\u3c/i\u3e: from genetic prediction to exact structure of a nonribosomal peptide

Mycobacteria have a complex cell wall structure that includes many lipids; however, even within a single subspecies of Mycobacterium avium these lipids can differ. Total lipids from an M. avium subsp. paratuberculosis (Map) ovine strain (S-type) contained no identifiable glycopeptidolipids or lipopentapeptide (L5P), yet both lipids are present in other M. avium subspecies. We determined the genetic and phenotypic basis for this difference using sequence analysis as well as biochemical and physico-chemical approaches. This strategy showed that a nonribosomal peptide synthase, encoded by mps1, contains three amino acid specifying modules in ovine strains, compared to five modules in bovine strains (C-type). Sequence analysis predicted these modules would produce the tripeptide Phe-N-Methyl-Val-Ala with a lipid moiety, termed lipotri- peptide (L3P). Comprehensive physico-chemical analysis of Map S397 extracts confirmed the structural formula of the native L3P as D-Phe-N-Methyl-L-Val-L- Ala-OMe attached in N-ter to a 20-carbon fatty acid chain. These data demonstrate that S-type strains, which are more adapted in sheep, produce a unique lipid. There is a dose-dependent effect observed for L3P on upregulation of CD251 CD8 T cells from infected cows, while L5P effects were static. In contrast, L5P demonstrated a significantly stronger induction of CD251 B cells from infected animals compared to L3P

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Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

International audienceHumans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. Here, we characterized, using RNA sequencing, the transcriptional response of primary monocytes from Africans and Europeans to bacterial and viral stimuli—ligands activating Toll-like receptor pathways (TLR1/2, TLR4, and TLR7/8) and influenza virus—and mapped expression quantitative trait loci (eQTLs). We identify numerous cis-eQTLs that contribute to the marked differences in immune responses detected within and between populations and a strong trans-eQTL hotspot at TLR1 that decreases expression of pro-inflammatory genes in Europeans only. We find that immune-responsive regulatory variants are enriched in population-specific signals of natural selection and show that admixture with Neandertals introduced regulatory variants into European genomes, affecting preferentially responses to viral challenges. Together, our study uncovers evolutionarily important determinants of differences in host immune responsiveness between human populations

Emotional Speech Comprehension in Deaf Children with Cochlear Implant

International audienceAbstract We examined the understanding of emotional speech by deaf children with cochlear implant (CI). Thirty deaf children with CI and 60 typically developing controls (matched on chronological age or hearing age) performed a computerized task featuring emotional prosody, either embedded in a discrepant context or without any context at all. Across the task conditions, the deaf participants with CI scored lower on the prosody-bases responses than their peers matched on chronological age or hearing age. Additionally, we analyzed the effect of age on determining correct prosody-based responses and we found that hearing age was a predictor of the accuracy of prosody-based responses. We discuss these findings with respect to delay in prosody and intermodal processing. Future research should aim to specify the nature of the cognitive processes that would be required to process prosody

Emotional Speech Comprehension in Deaf Children with Cochlear Implant

We examined the understanding of emotional speech by deaf children with cochlear implant (CI). Thirty deaf children with CI and 60 typically developing controls (matched on chronological age or hearing age) performed a computerized task featuring emotional prosody, either embedded in a discrepant context or without any context at all. Across the task conditions, the deaf participants with CI scored lower on the prosody-bases responses than their peers matched on chronological age or hearing age. Additionally, we analyzed the effect of age on determining correct prosody-based responses and we found that hearing age was a predictor of the accuracy of prosody-based responses. We discuss these findings with respect to delay in prosody and intermodal processing. Future research should aim to specify the nature of the cognitive processes that would be required to process prosody