Pascal Fabre

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• Type de publi. : Rapport
• Date de publi. : 01/01/2011
• Auteurs : Pascal NeveuNicole KoenderinkJuliette FabreVirginie Rossard
• Organismes : Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie Écophysiologie des Plantes sous Stress environnementaux Laboratoire de Biotechnologie de l'Environnement [Narbonne]

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• Type de publi. : Article dans une revue
• Date de publi. : 01/01/2011
• Auteurs : Aurore A. PhilibertMarie Laure M. L. Desprez LoustauBénédicte FabrePascal FreyFabien HalkettClaude C. HussonBrigitte Lung Lung-EscarmantBenoit MarçaisCecile RobinCorinne VacherDavid Makowski
• Organismes : Agronomie Mathématiques et Informatique Appliquées Biodiversité, Gènes & Communautés Interactions Arbres-Microorganismes Interactions Arbres-Microorganismes Interactions Arbres-Microorganismes Interactions Arbres-Microorganismes Biodiversité, Gènes & Communautés Interactions Arbres-Microorganismes Biodiversité, Gènes & Communautés Biodiversité, Gènes & Communautés Agronomie Mathématiques et Informatique Appliquées
• Publié dans Journal of Applied Ecology le 02/11/2020

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Résumé : 1. Biological invasions are a major consequence of globalization and pose a significant threat to biodiversity. Because only a small fraction of introduced species become invasive, identification of those species most likely to become invasive after introduction is highly desirable to focus management efforts. The predictive potential of species-specific traits has been much investigated in plants and animals. However, despite the importance of fungi as a biological group and the potentially severe effects of pathogenic fungi on agrosystems and natural ecosystems, the specific identification of traits correlated with the invasion success of fungi has not been attempted previously. 2. We addressed this question by constructing an ad hoc data set including invasive and non-invasive species of forest pathogenic fungi introduced into Europe. Data were analysed with a machine learning method based on classification trees (Random Forest). The performance of the classification rule based on species traits was compared with that of several random decision rules, and the principal trait predictors associated with invasive species were identified. 3. Invasion success was more accurately predicted by the classification rule including biological traits than by random decision rules. The effect of species traits was maintained when confounding variables linked to residence time and habitat availability were included. The selected traits were unlikely to be affected by a phylogenetic bias as invasive and non-invasive species were evenly distributed in fungal clades. 4. The species-level predictors identified as useful for distinguishing between invasive and non-invasive species were traits related to long-distance dispersal, sexual reproduction (in addition to asexual reproduction), spore shape and size, number of cells in spores, optimal temperature for growth and parasitic specialization (host range and infected organs). 5. Synthesis and applications. This study demonstrates that some species-level traits are predictors of invasion success for forest pathogenic fungi in Europe. These traits could be used to refine current pest risk assessment (PRA) schemes. Our results suggest that current schemes, which are mostly based on sequential questionnaires, could be improved by taking into account trait interactions or combinations. More generally, our results confirm the interest of machine learning methods, such as Random Forest, for species classification in ecology.

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• Type de publi. : Article dans une revue
• Date de publi. : 01/01/2011
• Auteurs : Juliette FabreMyriam DauzatVincent NègreNathalie WuytsAnne TireauEmilie GennariPascal NeveuSebastien TisneCatherine MassonnetIrène HummelChristine Granier
• Organismes : Écophysiologie des Plantes sous Stress environnementaux Écophysiologie des Plantes sous Stress environnementaux Écophysiologie des Plantes sous Stress environnementaux Écophysiologie des Plantes sous Stress environnementaux Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie Institut Jean-Pierre Bourgin Écophysiologie des Plantes sous Stress environnementaux Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] Écophysiologie des Plantes sous Stress environnementaux
• Publié dans BMC Plant Biology le 22/10/2020

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Résumé : Renewed interest in plant × environment interactions has risen in the post-genomic era. In this context, high-throughput phenotyping platforms have been developed to create reproducible environmental scenarios in which the phenotypic responses of multiple genotypes can be analysed in a reproducible way. These platforms benefit hugely from the development of suitable databases for storage, sharing and analysis of the large amount of data collected. In the model plant Arabidopsis thaliana, most databases available to the scientific community contain data related to genetic and molecular biology and are characterised by an inadequacy in the description of plant developmental stages and experimental metadata such as environmental conditions. Our goal was to develop a comprehensive information system for sharing of the data collected in PHENOPSIS, an automated platform for Arabidopsis thaliana phenotyping, with the scientific community

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Fichiers liés : 46001_20110929090345774_1.pdf

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• Type de publi. : Rapport
• Date de publi. : 01/01/2011
• Auteurs : J. SoaresM. WilliamsI. JarvisW. BingfangO. LeoP. FabreF. HuynhPascal KosuthDamien LepoutreJ.S. PariharGiuseppe Scarascia-MugnozzaC. JusticeA.J. Weinstein
• Organismes : GEO GENEVA CHE GEO GENEVA CHE Agriculture and Agri-Food CHINESE ACADEMY OF SCIENCES CHN European Commission - Joint Research Centre [Ispra] Centre de Coopération Internationale en Recherche Agronomique pour le Développement Institut de Recherche pour le Développement Territoires, Environnement, Télédétection et Information Spatiale GEOSYS RAMONVILLE FRA ISRO IND CRA ITA UNIVERSITY OF MARYLAND USA USDA FOREST SERVICE USA

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Résumé : The objective of this initiative is to reinforce the international community’s capacity to produce and disseminate relevant, timely and accurate forecasts of agricultural production at national, regional and global scales. This will be achieved by: - enhancing national agricultural reporting systems, including through a global geo-spatial education curriculum to ensure training of participants worldwide; - establishing a sustained international network of agricultural monitoring and research organisations and practitioners; and - creating an operational global agricultural monitoring system of systems based on both satellite and in situ observations.

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• Type de publi. : Article dans une revue
• Date de publi. : 01/01/2011
• Auteurs : Constance XhaardBénédicte FabreAxelle AndrieuxPierre P. GladieuxBenoit BarrèsPascal FreyFabien Halkett
• Organismes : Interactions Arbres-Microorganismes Interactions Arbres-Microorganismes Interactions Arbres-Microorganismes Ecologie Systématique et Evolution Biodiversité, Gènes & Communautés Interactions Arbres-Microorganismes Interactions Arbres-Microorganismes
• Publié dans Molecular Ecology le 29/10/2020

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Résumé : Wild and cultivated plants represent very different habitats for pathogens, especially when cultivated plants bear qualitative resistance genes. Here, we investigated to what extent the population genetic structure of a plant pathogenic fungus collected on its wild host can be impacted by the deployment of resistant cultivars. We studied one of the main poplar diseases, poplar rust, caused by the fungus Melampsora larici-populina. A thousand and fifty individuals sampled from several locations in France were pheno-typed for their virulence profile (ability to infect or not the most deployed resistant cultivar 'Beaupre'), and a subset of these was genotyped using 25 microsatellite markers. Bayesian assignment tests on genetic data clustered the 476 genotyped individuals into three genetic groups. Group 1 gathered most virulent individuals and displayed evidence for selection and drastic demographic changes resulting from breakdown of the poplar cultivar 'Beaupre'. Group 2 comprised individuals corresponding to ancestral populations of M. larici-populina naturally occurring in the native range. Group 3 displayed the hallmarks of strict asexual reproduction, which has never previously been demonstrated in this species. We discuss how poplar cultivation has influenced the spatial and genetic structure of this plant pathogenic fungus, and has led to the spread of virulence alleles (gene swamping) in M. larici-populina populations evolving on the wild host.

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Fichiers liés : Xhaard et al 2011 Mol Ecol_{2230C224-12FA-4AE1-BFBC-851E51B1B0C7}.pdf

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• Type de publi. : Communication dans un congrès
• Date de publi. : 08/11/2010
• Auteurs : Emilie GennariPascal NeveuCaroline DomergJuliette FabreVincent NègreAnne TireauOlivier CorbyCatherine FaronIsabelle Mirbel
• Organismes : Écophysiologie des Plantes sous Stress environnementaux Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie Écophysiologie des Plantes sous Stress environnementaux Écophysiologie des Plantes sous Stress environnementaux Écophysiologie des Plantes sous Stress environnementaux Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie Exchanges, Documents, Extraction, Languages, Web, Ergonomics, Interactions, Semantics, Servers Université de Nice Sophia-Antipolis Université de Nice Sophia-Antipolis

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Résumé : In a scientific context, making available scientific resources like computer programs is a real challenge for multidisciplinary research teams. In this paper, we propose an ontology-based approach to manage, share, reuse and promote software programs in a research community. Specifically, we were interested in the capitalization of R functions, R being a language for statistics and graphics. We designed an ontology to annotate R functions. We adopted the Semantic Web models: annotations are represented into the Resource Description Framework and the ontology in the Ontology Web Language. In the so-built semantic repository, R functions can be retrieved by expressing semantic queries in the SPARQL language. As a result, we have developed a new kind of software repository with semantic inferences. It is based upon the Corese semantic search engine and accessible through a Web Service. It has been adopted by a multidisciplinary team in life sciences.

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Fichiers liés : 2010_Neveu_RED, Resource Discovery.pdf

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• Type de publi. : Communication dans un congrès
• Date de publi. : 20/09/2010
• Auteurs : Catherine BastienArnaud DowkiwVéronique JorgeElodie VoisinVanina GuerinMarc VillarPatrick PoursatSébastien DuplessisPascal FreyBénédicte FabreAnnegret KohlerChristophe PlomionCéline C. LalanneAlois BressonF. BittonPatricia Faivre Rampant
• Organismes : Unité de recherche Amélioration, Génétique et Physiologie Forestières Unité de recherche Amélioration, Génétique et Physiologie Forestières Unité de recherche Amélioration, Génétique et Physiologie Forestières Unité de recherche Amélioration, Génétique et Physiologie Forestières Unité de recherche Amélioration, Génétique et Physiologie Forestières Unité de recherche Amélioration, Génétique et Physiologie Forestières Génétique et Biomasse Forestières Orléans Interactions Arbres-Microorganismes Interactions Arbres-Microorganismes Unité Expérimentale Forestière Lorraine Interactions Arbres-Microorganismes Biodiversité, Gènes & Communautés Biodiversité, Gènes & Communautés Unité de recherche en génomique végétale Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) Unité de recherche en génomique végétale

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Résumé : Broad-spectrum resistance to Melampsora larici-populina (Mlp) leaf rust is a major challenge for poplar breeding in Northern Europe. When no rust epidemic was evident in the natural Populus nigra populations, cultivation of inter-specific clones carrying qualitative resistances have strongly modified both qualitative and quantitative pathogenicity components of Mlp populations in cultivated areas. In monoclonal poplar plantations, durability of rust resistance will depend strongly on (1) resistance mechanisms pyramided in a given genotype, (2) genetic diversity present in Mlp populations submitted to these high selection pressures and (3) possibility of recombination rate associated with sexual reproduction on larch. Recent results on genetic and molecular bases of Mlp-poplar interaction and multidisciplinary research projects in development will be presented. Although quantitative resistance (QR) is often considered more durable, a multidisciplinary approach is being conducted at INRA not only to identify optimal genetic constructions for broad spectrum resistance but also to predict potential adaptation of the pathogen. Starting with a single Populus deltoides x P. trichocarpa F1 pedigree, much attention is being paid to two major loci, R1 and RUS, that both map on LG XIX. Dominant allele R1 is inherited from P. deltoides. It controls a qualitative resistance to M. larici-populina, and it was found to be statistically associated with QR levels in several P. deltoides x P. trichocarpa F1 progenies. Dominant allele RUS is inherited from P. trichocarpa. It has major effect of uredinia size and other QR components in both intraspecific and interspecific F1 progenies. Fine mapping of RUS is being conducted using a 1410 genotype F1 host progeny, and a BAC library was constructed to generate a physical map of 2000 kb around RUS. A promising BAC clone has been identified and sequenced. In parallel, an expressional approach based on the analysis of RUS and rUS infected material generated transcriptional and translational candidates. Opportunities offered by genetic variability available in Populus nigra, the natural host of Mlp, are currently explored in inter-specific crosses and in a new F1 mapping pedigree. Moreover, a collection of more than 1100 P.nigra genotypes collected in different natural European populations has been recently evaluated for rust resistance to initiate an association genetic study. On the pathogen side, several populations of M. larici-populina that underwent contrasted selection pressures by RUS are being characterized for their phenotypes and for their genotypes at several microsatellite loci. The first results demonstrate the existence of preadaptation in “wild” pathogen populations and a clear selective pressure by the host. All these results will be discussed in the framework of poplar breeding strategies and poplar cultivar deployment.

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Fichiers liés : IPS-V Book of Abstracts_1.pdf

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• Type de publi. : Communication dans un congrès
• Date de publi. : 07/09/2010
• Auteurs : Anne TireauCaroline DomergOlilvier CorbyJuliette FabreCatherine FaronEmilie GennariAlexandre GranierIsabelle MirbelVincent NègrePascal Neveu
• Organismes : Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie Écophysiologie des Plantes sous Stress environnementaux Exchanges, Documents, Extraction, Languages, Web, Ergonomics, Interactions, Semantics, Servers Écophysiologie des Plantes sous Stress environnementaux Université de Nice Sophia-Antipolis Écophysiologie des Plantes sous Stress environnementaux Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie Université de Nice Sophia-Antipolis Écophysiologie des Plantes sous Stress environnementaux Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie

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Fichiers liés : 48827_20120321043127304_1.pdf

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• Type de publi. : Communication dans un congrès
• Date de publi. : 21/07/2010
• Auteurs : Olilvier CorbyCaroline DomergJuliette FabreCatherine FaronAlexandre GranierIsabelle MirbelVincent NègrePascal NeveuAnne Tireau
• Organismes : Exchanges, Documents, Extraction, Languages, Web, Ergonomics, Interactions, Semantics, Servers Écophysiologie des Plantes sous Stress environnementaux Écophysiologie des Plantes sous Stress environnementaux Université de Nice Sophia-Antipolis Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie Université de Nice Sophia-Antipolis Écophysiologie des Plantes sous Stress environnementaux Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie

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Résumé : The research work of biologists often requires the development of a lot of scripts or functions to manipulate and analyse experimental data. In the laboratory LEPSE specialized on the analysis and modelling of plant responses and adaptation to variable environmental stresses, dozens of R functions are produced every year, concerning various fields such as genetic analyses, high throughput data phenotyping or environmental interactions and involving several databases. As a result, there is an important turn-over of function authors and users which generates different problems like re-using, sharing or understanding of these functions. In this context, in the framework of the DESIR project1, we have initiated a knowledge management action aiming to capitalize, organize, share and valorize these functions through the development of a knowledgebased repository of these functions. Given the great diversity of the functions produced, their associated documentation is heterogeneous and it is not pertinent to organise them into packages. We decided instead to index them with some formalized knowledge describing them, in order to retrieve them by formal reasoning. For this purpose, we developed an ontology providing a controlled and structured vocabulary that captures the concepts and properties necessary to describe R functions. This ontology comprises concepts and properties to describe functions – like ”Author”, ”Intention”, ”Argument”, ”Value” – as well as the relations between functions – like ”hasForRCoreCall”, ”canBeUsedAfter”, ”isAdaptedFrom”, ”looksLike”. As a result functions can be retrieved according to a wide range of criterii: thier author and/or the graphics produced, their intention(s) (e.g. perform multidimensional exploration), the function(s) they call (e.g. the ”lm” R core function or a specific function of the repository) –more generally, it is relevant to generate the call graph of one function to understand it–, the functions from which they are adapted –this makes easier the maintenance of the repository–, the functions after or before which they should be used –this helps to construct chainings of treatments–, their similarity with other functions, etc. To formalize both the ontology and the annotations of R functions, we adopted the SemanticWeb models : The annotations are represented into the Resource Description Framework2 (RDF) and the ontology in the Ontology Web Language3 (OWL). As a result we are able to semantically retrieve R functions by expressing queries in the SPARQL language4. We developed a semantic web application for the repository and search of annotated R functions. It relies upon the semantic engine Corese (Corby et al. 2004) dedicated to ontological query answering on the Semantic Web: Corese enables to interpret and process SPARQL queries on RDF annotations and OWL ontologies. Our application provides an environment for (1) storage and annotation : a prototype of Web user interface allows authors to upload R functions (one function per file) and to describe them in a few minutes; and (2) powerful search: users can find and get R functions with a global and accurate understanding and receive suggestions to support their search. To conclude, we have built a semantic repository of annotated R functions to centralize and share R functions for biologists. It capitalizes expert know-hows that would otherwise oftenly be lost or become nonusable because of a lack of documentation and description. We are convinced that this kind of repository developed for the LEPSE could benefit a much wider community of R function authors and users and be adapted to handle other programming languages.

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• Type de publi. : Article dans une revue
• Date de publi. : 25/01/2010
• Auteurs : Muriel BoucartChristine MoroniPascal DespretzFlorence PasquierMichèle Fabre-Thorpe
• Organismes : Laboratoire de Neurosciences Fonctionnelles et Pathologies Laboratoire de Neurosciences Fonctionnelles et Pathologies Laboratoire de Neurosciences Fonctionnelles et Pathologies Département de neurologie [Lille] Centre de recherche cerveau et cognition
• Publié dans Neurocase le 01/11/2020

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Résumé : We tested rapid-categorization in a patient who was impaired in face and object recognition. Photographs of natural scenes were displayed for 100 ms. Participants had to press a key when they saw an animal among various objects as distractors or human faces among animal faces as distractors. Though the patient was impaired at figure/ground segregation, recognized very few objects and faces, she categorized animals and faces with a performance ranging between 70 and 86% correct. Displaying pictures in isolation did not improve performance. The results suggest that rapid categorization can be accomplished on the basis of coarse information without overt recognition.

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