An alternative strategy for cloning minor permeases in Aspergillus nidulans

The uapC gene was cloned by complementation of the cryosensitive phenotype of uapA mutants following the instant gene bank method. The analysis of the transformants is presented and a strategy to clone other transport related genes is proposed

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment

Identification of Pathogenicity-Related Genes in the Vascular Wilt Fungus Verticillium dahliae by Agrobacterium tumefaciens-Mediated T-DNA Insertional Mutagenesis

Verticillium dahliae is the causal agent of vascular wilt in many economically important crops worldwide. Identification of genes that control pathogenicity or virulence may suggest targets for alternative control methods for this fungus. In this study, Agrobacteriumtumefaciens-mediated transformation (ATMT) was applied for insertional mutagenesis of V. dahliae conidia. Southern blot analysis indicated that T-DNAs were inserted randomly into the V. dahliae genome and that 69% of the transformants were the result of single copy T-DNA insertion. DNA sequences flanking T-DNA insertion were isolated through inverse PCR (iPCR), and these sequences were aligned to the genome sequence to identify the genomic position of insertion. V. dahliae mutants of particular interest selected based on culture phenotypes included those that had lost the ability to form microsclerotia and subsequently used for virulence assay. Based on the virulence assay of 181 transformants, we identified several mutant strains of V. dahliae that did not cause symptoms on lettuce plants. Among these mutants, T-DNA was inserted in genes encoding an endoglucanase 1 (VdEg-1), a hydroxyl-methyl glutaryl-CoA synthase (VdHMGS), a major facilitator superfamily 1 (VdMFS1), and a glycosylphosphatidylinositol (GPI) mannosyltransferase 3 (VdGPIM3). These results suggest that ATMT can effectively be used to identify genes associated with pathogenicity and other functions in V. dahliae

Etude d'une approche de Retour d'Expérience pour la découverte d'enseignements génériques dans le domaine humanitaire

National audienceUn intérêt croissant est exprimé par les organisations pour le développement d'approches visant à valoriser et tirer parti des expériences passées afin d'améliorer leurs processus de décision. Dans ce cadre de Retour d'Expérience, l'étude d'approches semi-automatisées pour la capitalisation et l'exploitation des connaissances revêt un intérêt central. Ce papier présente l'étude d'une approche au carrefour de plusieurs domaines : l'Ingénierie des Connaissances, l'Analyse Multicritère et l'Extraction d'Information. Elle repose sur une forme spécifique de raisonnement à partir de cas qui vise à établir une relation entre l'évaluation a posteriori de la performance de cas similaires et les caractéristiques des cas qui l'impactent. In fine, l'exploitation de ce lien a pour objectif d'identifier des enseignements génériques permettant de guider les processus décisionnels. Cette approche vise un cadre applicatif concret : la réponse logistique déployée par une ONG pour supporter des missions en situation d'urgence humanitaire

Identification de l’information pertinente pour la prise de décision : Application à la logistique humanitaire

International audienc

Coping with imprecision during a semi-automatic conceptual indexing process

International audienceConcept-based information retrieval is known to be a powerful and reliable process. It relies on a semantically annotated corpus, i.e. resources indexed by concepts organized within a domain ontology. The conception and enlargement of such index is a tedious task, which is often a bottleneck due to the lack of (semi-)automated solutions. In this paper, we first introduce a solution to assist experts during the indexing process thanks to semantic annotation propagation. The idea is to let them position the new resource on a semantic map, containing already indexed resources and to propose an indexation of this new resource based on those of its neighbors. To further help users, we then introduce indicators to estimate the robustness of the indexation with respect to the indicated position and to the annotation homogeneity of nearby resources. By computing these values before any interaction, it is possible to visually inform users on their margins of error, therefore reducing the risk of having a non-optimal, thus unsatisfying, annotation