Transformations in higher education in Agricultural and Food Sciences in Central and Eastern Europe

Diffusion du document : INRA Station d'Economie et Sociologie rurales 65 rue de Saint-Brieuc 35042 Rennes Cedex (FRA)Current transformations in higher education in agricultural and food sciences in Central and Eastern Europe render it interesting for the analysis of repercussions of post communist economic and social transition, particularly in the adaptation and restructuration of scientific and technical education.Using an institutional approach and referring to their experience of these educational systems, the authors provide a western view of current transformations and areas of development of higher education in agricultural and food sciences in the countries concerned. The emergence of a new social demand and of new systems of access to employment implies re-evaluation and adaptation of former training models

RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes

RASTA-Bacteria is an automated method that allows quick and reliable identification of toxin/antitoxin loci in sequenced prokaryotic genomes, whether they are annotated Open Reading Frames or not

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

International audienceBACKGROUND: The functions of proteins are strongly related to their localization in cell compartments (for example the cytoplasm or membranes) but the experimental determination of the sub-cellular localization of proteomes is laborious and expensive. A fast and low-cost alternative approach is in silico prediction, based on features of the protein primary sequences. However, biologists are confronted with a very large number of computational tools that use different methods that address various localization features with diverse specificities and sensitivities. As a result, exploiting these computer resources to predict protein localization accurately involves querying all tools and comparing every prediction output; this is a painstaking task. Therefore, we developed a comprehensive database, called CoBaltDB, that gathers all prediction outputs concerning complete prokaryotic proteomes. DESCRIPTION: The current version of CoBaltDB integrates the results of 43 localization predictors for 784 complete bacterial and archaeal proteomes (2.548.292 proteins in total). CoBaltDB supplies a simple user-friendly interface for retrieving and exploring relevant information about predicted features (such as signal peptide cleavage sites and transmembrane segments). Data are organized into three work-sets ("specialized tools", "meta-tools" and "additional tools"). The database can be queried using the organism name, a locus tag or a list of locus tags and may be browsed using numerous graphical and text displays. CONCLUSIONS: With its new functionalities, CoBaltDB is a novel powerful platform that provides easy access to the results of multiple localization tools and support for predicting prokaryotic protein localizations with higher confidence than previously possible. CoBaltDB is available at http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software/cobalten

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021

<p>Abstract</p> <p>Background</p> <p>Small untranslated RNAs (sRNAs) seem to be far more abundant than previously believed. The number of sRNAs confirmed in <it>E. coli </it>through various approaches is above 70, with several hundred more sRNA candidate genes under biological validation. Although the total number of sRNAs in any one species is still unclear, their importance in cellular processes has been established. However, unlike protein genes, no simple feature enables the prediction of the location of the corresponding sequences in genomes. Several approaches, of variable usefulness, to identify genomic sequences encoding sRNA have been described in recent years.</p> <p>Results</p> <p>We used a combination of <it>in silico </it>comparative genomics and microarray-based transcriptional profiling. This approach to screening identified ~60 intergenic regions conserved between <it>Sinorhizobium meliloti </it>and related members of the alpha-proteobacteria sub-group 2. Of these, 14 appear to correspond to novel non-coding sRNAs and three are putative peptide-coding or 5' UTR RNAs (ORF smaller than 100 aa). The expression of each of these new small RNA genes was confirmed by Northern blot hybridization.</p> <p>Conclusion</p> <p>Small non coding RNA (<it>sra</it>) genes can be found in the intergenic regions of alpha-proteobacteria genomes. Some of these <it>sra </it>genes are only present in <it>S. meliloti</it>, sometimes in genomic islands; homologues of others are present in related genomes including those of the pathogens <it>Brucella </it>and <it>Agrobacterium</it>.</p

Analyzing stochastic transcription to elucidate the nucleoid's organization.

International audienceABSTRACT: BACKGROUND: The processes of gene transcription, translation, as well as the reactions taking place between gene products, are subject to stochastic fluctuations. These stochastic events are being increasingly examined as it emerges that they can be crucial in the cell's survival. In a previous study we had examined the transcription patterns of two bacterial species (Escherichia coli and Bacillus subtilis) to elucidate the nucleoid's organization. The basic idea is that genes that share transcription patterns, must share some sort of spatial relationship, even if they are not close to each other on the chromosome. We had found that picking any gene at random, its transcription will be correlated with genes at well-defined short- as well as long-range distances, leaving the explanation of the latter an open question. In this paper we study the transcription correlations when the only transcription taking place is stochastic, in other words, no active or "deterministic" transcription takes place. To this purpose we use transcription data of Sinorhizobium meliloti. RESULTS: Even when only stochastic transcription takes place, the co-expression of genes varies as a function of the distance between genes: we observe again the short-range as well as the regular, long-range correlation patterns. CONCLUSION: We explain these latter with a model based on the physical constraints acting on the DNA, forcing it into a conformation of groups of a few successive large and transcribed loops, which are evenly spaced along the chromosome and separated by small, non-transcribed loops. We discuss the question about the link between shared transcription patterns and physiological relationship and come to the conclusion that when genes are distantly placed along the chromosome, the transcription correlation does not imply a physiological relationship

SORGOdb: Superoxide Reductase Gene Ontology curated DataBase

<p>Abstract</p> <p>Background</p> <p>Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms. Genes encoding SOR were discovered recently and suffer from annotation problems. These genes, named <it>sor</it>, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous. Consequently, many <it>sor </it>remain anonymous or mis-annotated.</p> <p>Description</p> <p>SORGOdb is an exhaustive database of SOR that proposes a new classification based on domain architecture. SORGOdb supplies a simple user-friendly web-based database for retrieving and exploring relevant information about the proposed SOR families. The database can be queried using an organism name, a locus tag or phylogenetic criteria, and also offers sequence similarity searches using BlastP. Genes encoding SOR have been re-annotated in all available genome sequences (prokaryotic and eukaryotic (complete and in draft) genomes, updated in May 2010).</p> <p>Conclusions</p> <p>SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms. It proposes a new classification of SOR into seven different classes and allows biologists to explore and analyze <it>sor </it>in order to establish correlations between the class of SOR and organism phenotypes. SORGOdb is freely available at <url>http://sorgo.genouest.org/index.php</url>.</p

Les mutations de l'enseignement supérieur agronomique et agro-alimentaire en Pologne et en Hongrie : réflexions pour une coopération interuniversitaire européenne

Diffusion du document : INRA Station d'Economie et Sociologie rurales 65 rue de Saint-Brieuc 35042 Rennes Cedex (FRA)Cette étude de l'Enseignement Supérieur Agronomique et Agro-alimentaire de type long, en Pologne et en Hongrie, vise deux objectifs : analyser les conditions d'évolution de l'appareil d'enseignement pour s'adapter aux mutations en cours, proposer les axes d'une politique de coopération inter-universitaire avec les paysd'Europe Occidentale

Stackless Processing of Streamed Trees

International audienceProcessing tree-structured data in the streaming model is a challenge: capturing regular properties of streamed trees by means of a stack is costly in memory, but falling back to finite-state automata drastically limits the computational power. We propose an intermediate stackless model based on register automata equipped with a single counter, used to maintain the current depth in the tree. We explore the power of this model to validate and query streamed trees. Our main result is an effective characterization of regular path queries (RPQs) that can be evaluated stacklessly-with and without registers. In particular, we confirm the conjectured characterization of tree languages defined by DTDs that are recognizable without registers, by Segoufin and Vianu (2002), in the special case of tree languages defined by means of an RPQ