Etude sur la mise en place d\u27un service de consultation de bases de données externes et de cédéroms au sein de la salle de références de la direction des collections spécialisées (BNF).

Etude sur la mise en place d\u27un service de consultation de bases de données externes et de cédéroms au sein de la salle de références de la direction des collections spécialisées (BNF)

Outils anti-plagiat

Intervention à la 6e journée FORMIST qui s\u27est déroulée le 15 juin 2006 à l\u27ENSSIB. Ce document présente les grandes caractéristiques des outils anti-plagiat, et donne des points de départ bibliographiques et des ressources sur ce sujet

Characterisation of juvenile hormone esterase in Drosophila melanogaster

International audienceThis work is devoted to the study of the influence of inter-component coupling on the performance of EMC filters. A preliminary study on a simple LC filter allowed us to highlight the influence of the components placements on the quality of the filter. A procedure for evaluating inter-component coupling using optimization methods and 3D digital models is proposed. This procedure has been validated in the case of a loop-loop structure. The developed models will be used later to perform optimizations of the components placements to improve the quality of the filter in its design

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

BACKGROUND: Regulatory networks often employ the model that attributes changes in gene expression levels, as observed across different cellular conditions, to changes in the activity of transcription factors (TFs). Although the actual conditions that trigger a change in TF activity should form an integral part of the generated regulatory network, they are usually lacking. This is due to the fact that the large heterogeneity in the employed conditions and the continuous changes in environmental parameters in the often used shake-flask cultures, prevent the unambiguous modeling of the cultivation conditions within the computational framework. RESULTS: We designed an experimental setup that allows us to explicitly model the cultivation conditions and use these to infer the activity of TFs. The yeast Saccharomyces cerevisiae was cultivated under four different nutrient limitations in both aerobic and anaerobic chemostat cultures. In the chemostats, environmental and growth parameters are accurately controlled. Consequently, the measured transcriptional response can be directly correlated with changes in the limited nutrient or oxygen concentration. We devised a tailor-made computational approach that exploits the systematic setup of the cultivation conditions in order to identify the individual and combined effects of nutrient limitations and oxygen availability on expression behavior and TF activity. CONCLUSION: Incorporating the actual growth conditions when inferring regulatory relationships provides detailed insight in the functionality of the TFs that are triggered by changes in the employed cultivation conditions. For example, our results confirm the established role of TF Hap4 in both aerobic regulation and glucose derepression. Among the numerous inferred condition-specific regulatory associations between gene sets and TFs, also many novel putative regulatory mechanisms, such as the possible role of Tye7 in sulfur metabolism, were identified

Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae - A chemostat culture study

FWN – Publicaties zonder aanstelling Universiteit Leide

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data

<p>Abstract</p> <p>Background</p> <p>Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow precise manipulation of individual culture parameters and therefore precludes a quantitative analysis of the (combinatorial) influence of these parameters on transcriptional regulation. Steady-state chemostat cultures, which do enable accurate control, measurement and manipulation of individual cultivation parameters (e.g. specific growth rate, temperature, identity of the growth-limiting nutrient) appear to provide a promising experimental platform for such a combinatorial analysis.</p> <p>Results</p> <p>A microarray compendium of 170 steady-state chemostat cultures of the yeast <it>Saccharomyces cerevisiae </it>is presented and analyzed. The 170 microarrays encompass 55 unique conditions, which can be characterized by the combined settings of 10 different cultivation parameters. By applying a regression model to assess the impact of (combinations of) cultivation parameters on the transcriptome, most <it>S. cerevisiae </it>genes were shown to be influenced by multiple cultivation parameters, and in many cases by combinatorial effects of cultivation parameters. The inclusion of these combinatorial effects in the regression model led to higher explained variance of the gene expression patterns and resulted in higher function enrichment in subsequent analysis. We further demonstrate the usefulness of the compendium and regression analysis for interpretation of shake-flask-based transcriptome studies and for guiding functional analysis of (uncharacterized) genes and pathways.</p> <p>Conclusion</p> <p>Modeling the combinatorial effects of environmental parameters on the transcriptome is crucial for understanding transcriptional regulation. Chemostat cultivation offers a powerful tool for such an approach.</p

Oxygen availability strongly affects chronological lifespan and thermotolerance in batch cultures of Saccharomyces cerevisiae

Stationary-phase (SP) batch cultures of Saccharomyces cerevisiae, in which growth has been arrested by carbon-source depletion, are widely applied to study chronological lifespan, quiescence and SP-associated robustness. Based on this type of experiments, typically performed under aerobic conditions, several roles of oxygen in aging have been proposed. However, SP in anaerobic yeast cultures has not been investigated in detail. Here, we use the unique capability of S. cerevisiae to grow in the complete absence of oxygen to directly compare SP in aerobic and anaerobic bioreactor cultures. This comparison revealed strong positive effects of oxygen availability on adenylate energy charge, longevity and thermotolerance during SP. A low thermotolerance of anaerobic batch cultures was already evident during the exponential growth phase and, in contrast to the situation in aerobic cultures, was not substantially increased during transition into SP. A combination of physiological and transcriptome analysis showed that the slow post-diauxic growth phase on ethanol, which precedes SP in aerobic, but not in anaerobic cultures, endowed cells with the time and resources needed for inducing longevity and thermotolerance. When combined with literature data on acquisition of longevity and thermotolerance in retentostat cultures, the present study indicates that the fast transition from glucose excess to SP in anaerobic cultures precludes acquisition of longevity and thermotolerance. Moreover, this study demonstrates the importance of a preceding, calorie-restricted conditioning phase in the acquisition of longevity and stress tolerance in SP yeast cultures, irrespective of oxygen availability

Contributions of individual cover crop species to rainfed maize production in semi-arid cropping systems

Cover crop (CC) species selection can contribute to reducing soil penetration resistance (brassica species), improved soil nitrogen (N) cycling (legume species), and suppression of weeds (grass species). However, one of the main concerns about including CCs in water-limited environments is soil water use and the consequences to subsequent crops. To determine the effects of individual CC species under water-limited environments, we evaluated fall and spring CC biomass produced, and soil water and N content, penetration resistance, weed density and biomass during the maize growing season, and maize grain yield. The experiment was conducted under a winter wheat-maize-fallow rotation at two locations (North Platte and Grant, NE) during 2016−2017 and 2017−2018 (four site-years). Treatments consisted of seven popular CC species plus a control (fallow), planted after winter wheat harvest. Spring oats, Siberian kale, and purple top turnip produced greater fall biomass, while cereal rye produced the greatest amount of spring biomass. However, cereal rye reduced soil volumetric water content in North Platte 2016−2017 and increased soil penetration resistance from 20–30 cm soil depth across site-years likely due to soil water use. Spring cover crop growth suppressed weeds early in the maize growing season. Due to its aboveground biomass production, cereal rye decreased weed density and biomass by 80 and 88 %, respectively, compared to the fallow treatment. On the other hand, except for brassicas, CCs decreased N levels in the soil during maize growing season, and all CC species reduced maize grain yield up to 30 % compared to fallow (except spring oats). Spring oats can be an alternative to cereal rye as CC species for semi-arid regions. However, since CCs did not promote any maize yield gain, our findings suggest that producers should use caution when incorporating CCs in their cropping systems in water-limited environments. This research provides valuable information on the potential impact of CCs on rainfed maize production, as well as help producers and agronomists develop better CC management programs for cropping systems in semi-arid regions

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN.PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN.PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN.PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN.PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains