Base de données

Research at BF2I is focused on the comprehension of the functions managing the interaction of specific insect pests (aphids and weevils) with their direct biological partners (host plants and symbiotic microorganisms). Research approaches are multi-disciplinary thanks to the different expertise of the staff members.

The central theme of our research is to understand the relationships established between insects and their symbionts elucidating the molecular mechanisms that allow the establishment, maintenance and persistence of these complex interactions in multiple insect generations.

The final goal of research on these complex biological interactions, often involving multiple partners in interaction with the environment, is to identify tools and define new concepts for an integrated approach for plant protection against insect pests. Our research results are to be central for the development of agricultural practices that are sustainable, and respect both the environment and human health.

URGI - Unité de Recherche Génomique Info - is a research unit in genomics and bioinformatics at Institut National de la Recherche Agronomique (INRA), dedicated to plants and crop parasites. The URGI research activity covers data integration as well as genome structure and dynamics. URGI hosts a bioinformatics platform which belongs to the Institut Français de Bioinformatique, the French node of Elixir, the European network of bioinformatics platforms.

Bioinformatics within "Iron and Liver" Group bases its activity on iron metablism as a use-case study. We seek however to propose computationnal approaches that can be applied to other life science domains. Our bioinformatics concerns are data integration in life science, with data continuously evolving in :

• diversity, representation (raw data, textual data, structured XML data, ontologies, graphical data), quality,  quantity and last but not least in density.

More recently we focus on text annotations and large scale extraction of bio-events associating recognized bio-entities of different sorts (genes, diseases, drugs, species, cells and organs) within PubMed publications. Massive computations and mining of the extracted events is challenging : Big data that need to be turned in patterns of pertinent information easily interpretable by biologists and big data that require important computationnal infrastructures.

IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org, is the global reference in immunogenetics and immunoinformatics, created in 1989 by Marie-Paule Lefranc (Université Montpellier 2 and CNRS). IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates. IMGT® provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT® works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT® consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools.

Systematic sequencing genome projects generate large amounts of data that must be annotated for their biological exploitation. If the first annotation step may allow the identification of single genes/gene products, a complementary level of annotation consists in taking into account interactions of the proteins involved in the same supra-molecular system and/or biological process. These interactions can be stable, or transient, and either physical or functional. The cellular functions that emerge from these complex systems are not only an addition of the individual protein properties but result also from the interactions between the proteins. Biological systems result also from a complex evolutionary history, in a sense that partners and/or relationships between them can have been added, removed or replaced along the evolutionary history, with two extreme consequences, the loss or the duplication of systems in a phylogenetic clade. In general, duplicated systems do not conserve the same cellular function. Such a complex evolutionary scenario occurs when partners are encoded by multigenic families. In this framework, our group has focused its activity on two main research axes: i) development of strategies in order to identify, reconstruct and classify, from the genomic sequences, functional supra-molecular assemblies whose members belong to multigenic families and ii) phylogenomics analyses involving also the development of approaches to identify orthologous genes/proteins. ABC systems were initially chosen as a model because they form one of the largest ubiquitous families of paralogous systems that have arisen early in evolution and are involved in many essential physiological processes. The developed strategies lead to the creation and maintenance of a public database dedicated to ABC systems (ABCdb). Since then, we have extended our expertise in phylogenomics analyses on different gene families and systems through collaborations. To address the dynamics of the interaction between biological entities, we started to implement systems biology approaches focused on the modeling of the regulatory pathway of natural genetic transformation in streptococcal species.

With the launch of Bioversity International, the International Network for the Improvement of Banana and Plantain (INIBAP) ceases to exist as an organization (except as a legal entity in France, its host country) but becomes instead the network of collections, curators and information scientists whose responsibility it is to take care of the world’s genetic resources of banana.

The foundation of this network is thus provided by the genebank of the INIBAP Transit Centre in Leuven, Belgium, where the greater part of the banana genepool is held, in trust for humanity, in a tissue culture collection that serves as a ‘safety back-up’ for all the diversity of banana plants growing in field collections, farms and forests around the world. A further safety back-up is provided by a steadily increasing collection of accessions that is held for the long term, without deterioration, by ‘cryopreservation’ in liquid nitrogen.

Regional and national collections around the world serve as field genebanks, holding banana varieties as growing plants, which can be used by banana breeders to make new crosses or multiplied and distributed to farmers in support of banana production. A unified information system is provided by the Musa Germplasm Information System that brings together a wealth of information on the bananas held in collections worldwide, helping users to identify and source the exact kinds of banana they need for their particular purposes. A Taxonomic Advisory Group, bringing together banana taxonomists, molecular scientists, curators and breeders, provides guidance and technical support for clarifying issues of nomenclature and developing strategies for rationalising conservation efforts.

The activities of the network are guided by the Global Conservation Strategy for Musa, which has been developed within the framework of the CGIAR/FAO Global Crop Diversity Trust, and continues to evolve in consultation with partners and in response to the needs of the banana research-and-development community.