IMGT, the international ImMunoGeneTics information system®

The international ImMunoGeneTics information system® (IMGT) (http://imgt.cines.fr), created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire LIGM (Université Montpellier II and CNRS) at Montpellier, France, is a high-quality integrated knowledge resource specializing in the immunoglobulins (IGs), T cell receptors (TRs), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune systems (RPI) that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT includes several sequence databases (IMGT/LIGM-DB, IMGT/PRIMER-DB, IMGT/PROTEIN-DB and IMGT/MHC-DB), one genome database (IMGT/GENE-DB) and one three-dimensional (3D) structure database (IMGT/3Dstructure-DB), Web resources comprising 8000 HTML pages (IMGT Marie-Paule page), and interactive tools. IMGT data are expertly annotated according to the rules of the IMGT Scientific chart, based on the IMGT-ONTOLOGY concepts. IMGT tools are particularly useful for the analysis of the IG and TR repertoires in normal physiological and pathological situations. IMGT is used in medical research (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, biotechnology related to antibody engineering (phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (clonalities, detection and follow up of residual diseases) and therapeutical approaches (graft, immunotherapy and vaccinology). IMGT is freely available at http://imgt.cines.fr

Recovering probabilities for nucleotide trimming processes for T cell receptor TRA and TRG V-J junctions analyzed with IMGT tools

<p>Abstract</p> <p>Background</p> <p>Nucleotides are trimmed from the ends of variable (V), diversity (D) and joining (J) genes during immunoglobulin (IG) and T cell receptor (TR) rearrangements in B cells and T cells of the immune system. This trimming is followed by addition of nucleotides at random, forming the N regions (N for nucleotides) of the V-J and V-D-J junctions. These processes are crucial for creating diversity in the immune response since the number of trimmed nucleotides and the number of added nucleotides vary in each B or T cell. IMGT^®sequence analysis tools, IMGT/V-QUEST and IMGT/JunctionAnalysis, are able to provide detailed and accurate analysis of the final observed junction nucleotide sequences (tool "output"). However, as trimmed nucleotides can potentially be replaced by identical N region nucleotides during the process, the observed "output" represents a <it>biased </it>estimate of the "true trimming process."</p> <p>Results</p> <p>A probabilistic approach based on an analysis of the standardized tool "output" is proposed to infer the probability distribution of the "true trimmming process" and to provide plausible biological hypotheses explaining this process. We collated a benchmark dataset of TR alpha (TRA) and TR gamma (TRG) V-J rearranged sequences and junctions analysed with IMGT/V-QUEST and IMGT/JunctionAnalysis, the nucleotide sequence analysis tools from IMGT^®, the international ImMunoGeneTics information system^®, <url>http://imgt.cines.fr</url>. The standardized description of the tool output is based on the IMGT-ONTOLOGY axioms and concepts. We propose a simple first-order model that attempts to transform the observed "output" probability distribution into an estimate closer to the "true trimming process" probability distribution. We use this estimate to test the hypothesis that Poisson processes are involved in trimming. This hypothesis was not rejected at standard confidence levels for three of the four trimming processes: TRAV, TRAJ and TRGV.</p> <p>Conclusion</p> <p>By using trimming of rearranged TR genes as a benchmark, we show that a probabilistic approach, applied to IMGT^®standardized tool "outputs" opens the way to plausible hypotheses on the events involved in the "true trimming process" and eventually to an exact quantification of trimming itself. With increasing high-throughput of standardized immunogenetics data, similar probabilistic approaches will improve understanding of processes so far only characterized by the "output" of standardized tools.</p

De las catacumbas a los últimos confines: violencia, sentido y representación en los periplos del martirio

En este trabajo propongo un análisis transversal de las figuras del mártir y del martirio. Recurriendo a la noción de mediación, en la primera parte analizo el rol protagónico de las representaciones del martirio en las prácticas de la memoria durante la segunda mitad del siglo XVI. Analizo algunas de las condiciones que contribuyeron a la emergencia de una "cultura del martirio" y el rol de las mediaciones en tal surgimiento. En la segunda parte, estudio la forma en que el (re)descubrimiento de las catacumbas romanas, abrió un campo de producción de sentido en torno a la figura del martirio. En la tercera parte, centrándome en la Compañía de Jesús, analizo algunas mediaciones a través de las cuáles las figuras del martirio transgredieron las fronteras de iglesias y conventos para proyectarse a los últimos confines en un mundo en plena expansión.Neste artigo proponho uma análise transversal das figuras do mártir e do martírio. Usando a noção de mediação, na primeira parte eu tento analisar o papel de liderança de representações de martírio em práticas de memória durante a segunda metade do século XVI. Eu analiso algumas das condições que contribuíram para o surgimento de uma "cultura do martírio" e o papel da mediação nesta emergência. Na segunda parte, eu estudo como a (re) descoberta das catacumbas romanas abriu um campo de produção de significados em torno da figura do martírio. Na terceira parte, com foco na Companhia de Jesus, analiso algumas mediações pelas quais as representações do martírio transgrediram as fronteiras de igrejas e conventos para se projetar nas fronteiras de um mundo em plena expansão mundial.This paper proposes a cross-sectional analysis of martyr and martyrdom. Through the notion of mediation, in the first part I analyze the leading role of representations of martyrdom in memory practices during the second half of the sixteenth century. I analyze some of the conditions that contributed to the emergence of a "martyrdom's culture" and the role of mediation in such emergence. The second part studies how the (re)discovery of the Roman catacombs encouraged the production of meanings around the figure of martyrdom. In the third part, focusing on the Society of Jesus, I analyze a few instances of mediation through which the figures of martyrdom transgressed the boundaries of churches and convents to project themselves to the last frontiers of a world in full expansion.Fil: Salamanca Villamizar, Carlos Arturo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Impact d'une perturbation polluante d'origine organique sur les populations et les communautés d'invertébrés benthiques et en dérive d'une rivière méditerranéenne, le Tavignano (Corse)

This paper deals with effects of a perturbation due to organic pollution on macroinvertebrates communities in a mediterranean river of central Corsica. The study was based chiefly on consideration of benthic and drift samples. The effects of an heavy pollution were much the same as described for other streams, but reactions of several taxa seemed to be less marked. In the most polluted area of this speedy well oxygenated river, oligochetae, molluscs, chirono-mid larvae showed a marked increase in density but never occurred in enormous numbers. In this corsican river, the communities of the lentic habitats were more affected by the organic pollution than the lotic ones. Drift samples showed clear reactions to organic pollution : decreasing drift diversity and density of aquatic organisms, increasing drift density of emerging fauna, disappearing oligotrophia species. Drift communities were more closely related to benthic lotic communities than to lentic ones. We suggest that in this river type, the biotic index method applied on benthic samples cannot detect biological consequences of severe organic pollution, although it gives good results with drift samples which will be considered as indicators of river quality.L'impact d’une perturbation d'origine organique sur une rivière méditerranéenne a été étudié principalement à travers les modifications subies par les peuplements d'invertébrés. L'étude est basée sur l'analyse des prélèvements benthiques et des prélèvements de dérive. Les effets de la pollution sur les communautés sont peu différents de ceux observés dans d’autres cours d’eau. Dans le secteur le plus perturbé de ce cours d'eau rapide et bien oxygéné, les taxons saprophiles (Oligochètes , Gastéropodes , larves de Chironomides) ont une densité plus élevée mais ne forment pas de populations très abondantes ; les taxons polluo-sensibles se maintiennent avec de faibles effectifs. Les communautés des habitats lénitiques sont plus affectées par la pollution organique que les communautés des habitats lotiques de la rivière. L’échantillon de dérive traduit bien les modifications du peuplement aquatique de macroinvertébrés dans la zone la plus perturbée : diminution de la diversité et de la densité de dérive, augmentation des densités de dérive des émergents , disparition totale des taxons polluo-sensibles. La méthode des indices biotiques, appliquée à l'échantillon benthique , ne convient pas pour traduire l'impact biologique de la pollution dans ce type de cours d'eau. Par contre, les résultats sont satisfaisants avec l’échantillon de dérive.Giudicelli Jean, Légier Pierre, Musso J. J., Prévôt Gérard. Impact d'une perturbation polluante d'origine organique sur les populations et les communautés d'invertébrés benthiques et en dérive d'une rivière méditerranéenne, le Tavignano (Corse). In: Ecologia mediterranea, tome 12 n°1-2, 1986. pp. 31-61