GéOnto : Enrichissement d'une taxonomie de concepts topographiques

National audienceIn this paper we present the GéOnto project, aiming in particular to build an ontology of topographic concepts. This ontology is made by enrichment of a first taxonomy developed beforehand, through the analysis of two types of textual documents: technical database specifications and description of journeys. This work relies on natural language processing and ontology alignment techniques, as well as external knowledge resources such as dictionaries and gazetteers

Rapid accumulation and low degradation: Key parameters of Tomato yellow leaf curl virus persistence in its insect vector Bemisia tabaci

Of worldwide economic importance, Tomato yellow leaf curl virus (TYLCV, Begomovirus) is responsible for one of the most devastating plant diseases in warm and temperate regions. The DNA begomoviruses (Geminiviridae) are transmitted by the whitefly species complex Bemisia tabaci. Although geminiviruses have long been described as circulative non-propagative viruses, observations such as long persistence of TYLCV in B. tabaci raised the question of their possible replication in the vector. We monitored two major TYLCV strains, Mild (Mld) and Israel (IL), in the invasive B. tabaci Middle East-Asia Minor 1 cryptic species, during and after the viral acquisition, within two timeframes (0–144 hours or 0–20 days). TYLCV DNA was quantified using real-time PCR, and the complementary DNA strand of TYLCV involved in viral replication was specifically quantified using anchored real-time PCR. The DNA of both TYLCV strains accumulated exponentially during acquisition but remained stable after viral acquisition had stopped. Neither replication nor vertical transmission were observed. In conclusion, our quantification of the viral loads and complementary strands of both Mld and IL strains of TYLCV in B. tabaci point to an efficient accumulation and preservation mechanism, rather than to a dynamic equilibrium between replication and degradation. (Résumé d'auteur

Analyses linguistiques et techniques d'alignement pour créer et enrichir une ontologie topographique

National audienceOne of the goals of the GéOnto project is to build an ontology of topographic concepts. This ontology results from the enrichment of a first taxonomy developed beforehand, through the analysis of two types of textual documents: technical database specifications and description of journeys. This work relies on natural language processing and ontology alignment techniques, as well as external knowledge resources such as dictionaries and gazetteers.Dans cet article, nous présentons le projet GéOnto dont un des buts est de construire une ontologie de concepts topographiques. Cette ontologie est réalisée par enrichissement d'une première taxonomie de termes réalisée précédemment, et ce grâce à l'analyse de deux types de documents textuels : des spécifications techniques de bases de données et des récits de voyage. Cet enrichissement s'appuie sur des techniques automatiques de traitement du langage et d'alignement d'ontologies, ainsi que sur des connaissances externes comme des dictionnaires et des bases de toponymes

Sweet and Sour Ehrlichia: Glycoproteomics and Phosphoproteomics Reveal New Players in Ehrlichia ruminantium Physiology and Pathogenesis

Ehrlichia ruminantium; N-glycoproteins; O-GlcNAcylated proteinsEhrlichia ruminantium; N-glicoproteïnes; Proteïnes O-GlcNAciladesEhrlichia ruminantium; N-glicoproteínas; Proteínas O-GlcNAciladasUnraveling which proteins and post-translational modifications (PTMs) affect bacterial pathogenesis and physiology in diverse environments is a tough challenge. Herein, we used mass spectrometry-based assays to study protein phosphorylation and glycosylation in Ehrlichia ruminantium Gardel virulent (ERGvir) and attenuated (ERGatt) variants and, how they can modulate Ehrlichia biological processes. The characterization of the S/T/Y phosphoproteome revealed that both strains share the same set of phosphoproteins (n = 58), 36% being overexpressed in ERGvir. The percentage of tyrosine phosphorylation is high (23%) and 66% of the identified peptides are multi-phosphorylated. Glycoproteomics revealed a high percentage of glycoproteins (67% in ERGvir) with a subset of glycoproteins being specific to ERGvir (n = 64/371) and ERGatt (n = 36/343). These glycoproteins are involved in key biological processes such as protein, amino-acid and purine biosynthesis, translation, virulence, DNA repair, and replication. Label-free quantitative analysis revealed over-expression in 31 proteins in ERGvir and 8 in ERGatt. While further PNGase digestion confidently localized 2 and 5 N-glycoproteins in ERGvir and ERGatt, respectively, western blotting suggests that many glycoproteins are O-GlcNAcylated. Twenty-three proteins were detected in both the phospho- and glycoproteome, for the two variants. This work represents the first comprehensive assessment of PTMs on Ehrlichia biology, rising interesting questions regarding ER-host interactions. Phosphoproteome characterization demonstrates an increased versatility of ER phosphoproteins to participate in different mechanisms. The high number of glycoproteins and the lack of glycosyltransferases-coding genes highlight ER dependence on the host and/or vector cellular machinery for its own protein glycosylation. Moreover, these glycoproteins could be crucial to interact and respond to changes in ER environment. PTMs crosstalk between of O-GlcNAcylation and phosphorylation could be used as a major cellular signaling mechanism in ER. As little is known about the Ehrlichia proteins/proteome and its signaling biology, the results presented herein provide a useful resource for further hypothesis-driven exploration of Ehrlichia protein regulation by phosphorylation and glycosylation events. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD012589

Apport de l'émission acoustique pour la modélisation de l'endommagement des composites à matrice céramique

La durabilité et la fiabilité sont deux facteurs clés dont la maîtrise est essentielle en vue de l’utilisation des composites à matrice céramique (CMC) pour des applications aéronautiques. Il est nécessaire pour cela de pouvoir estimer la durée de vie des structures en service. Cela requiert de quantifier l’endommagement mais aussi d’identifier les différents mécanismes qui en sont à l’origine et d’établir leur chronologie. L’Emission Acoustique (EA) est une technique qui permet de répondre à cette problématique. En effet, les mécanismes d’endommagement s’accompagnent de libération d’énergie sous forme d’ondes élastiques transitoires. L’objectif de ce travail est d’étudier le comportement lors d’essais de fatigue sous air dans le domaine de température [500°C-1200°C] d’un composite Cf/[Si-B-C] à matrice auto-cicatrisante et de comprendre les mécanismes physiques mis en jeu dans le but de prévoir sa durée de vie. La cinétique de la fissuration matricielle a été identifiée par analyse statistique multi variables des données d’EA. De plus, les effets d’atténuation liés à la croissance de l’endommagement ont été pris en compte dans l’analyse de l’énergie des sources acoustiques. Cela a permis de déterminer un coefficient d’atténuation B sensible à l’ouverture des fissures. Cette méthode constitue en elle-même une nouvelle méthode de suivi. Ainsi, cette nouvelle approche rend possible le suivi de la dynamique de la fissuration matricielle ainsi que de l’ouverture des fissures qui a priori ne génère pas d’émission acoustique. Les informations obtenues permettent d’alimenter ou de valider des modèles d’endommagement