IMGT®, the international ImMunoGeneTics information system®

IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org), was created in 1989 by Marie-Paule Lefranc, Laboratoire d'ImmunoGénétique Moléculaire LIGM (Université Montpellier 2 and CNRS) at Montpellier, France, in order to standardize and manage the complexity of immunogenetics data. The building of a unique ontology, IMGT-ONTOLOGY, has made IMGT® the global reference in immunogenetics and immunoinformatics. IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins or antibodies, T cell receptors, major histocompatibility complex, of human and other vertebrate species, proteins of the IgSF and MhcSF, and related proteins of the immune systems of any species. IMGT® provides a common access to standardized data from genome, proteome, genetics and 3D structures. IMGT® consists of five databases (IMGT/LIGM-DB, IMGT/GENE-DB, IMGT/3Dstructure-DB, etc.), fifteen interactive online tools for sequence, genome and 3D structure analysis, and more than 10 000 HTML pages of synthesis and knowledge. IMGT® is used in medical research (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas and 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, vaccinology). IMGT is freely available at http://www.imgt.org

Reduction of Electron Beam Induced Radiation Damage of Organic Material by Cooling to 4 K (Cryo Electron Microscopy)

Structure investigations of organic, in particular biological, material are frequently performed with a strong electron beam. If the dose is higher than le/Å2, as required e.g. for high resolution electron microscopy, the results are strongly influenced by radiation damage. There are no means for preventing breaking of chemical bonds and ionizing of atoms and fractures of molecules due to the electron impact. The secondary processes, however, such as diffusion or evaporation of the fragments, can be strongly reduced by cooling the specimen to 4 K (cryoprotection). A suitable instrument for experimenting with cryoprotection is a microscope equipped with a superconducting lens system. Topics relevant for cryomicroscopy are: instrumentation; determination of cryoprotection factors of various materials by electron diffraction; direct imaging in particular for information on the steric structure of the material; preparation conditions for an effective cryoprotection. Though the knowledge of the physics and chemistry causing radiation damage at 4 K is still limited, a useful application of cryoprotection is already possible

Topological signature of deterministic chaos in short nonstationary signals from an optical parametric oscillator

Although deterministic chaos has been predicted to occur in the triply resonant optical parametric oscillator (TROPO) fifteen years ago, experimental evidence of chaotic behavior in this system has been lacking so far, in marked contrast with most nonlinear systems, where chaos has been actively tracked and found. This situation is probably linked to the high sensitivity of the TROPO to perturbations, which adversely affects stationary operation at high power. We report the experimental observation in this system of a burst of irregular behavior of duration 80 microseconds. Although the system is highly nonstationary over this time interval, a topological analysis allows us to extract a clearcut signature of deterministic chaos from a time series segment of only 9 base cycles (3 microseconds). This result suggests that nonstationarity is not necessarily an obstacle to the characterization of chaos

Evolution of the T-cell receptor (TR) Loci in the adaptive immune response: The tale of the TRG locus in mammals

T lymphocytes are the principal actors of vertebrates’ cell-mediated immunity. Like B cells, they can recognize an unlimited number of foreign molecules through their antigen-specific heterodimer receptors (TRs), which consist of αβ or γδ chains. The diversity of the TRs is mainly due to the unique organization of the genes encoding the α, β, γ, and δ chains. For each chain, multi-gene families are arranged in a TR locus, and their expression is guaranteed by the somatic recombination process. A great plasticity of the gene organization within the TR loci exists among species. Marked structural differences affect the TR γ (TRG) locus. The recent sequencing of multiple whole genome provides an opportunity to examine the TR gene repertoire in a systematic and consistent fashion. In this review, we report the most recent findings on the genomic organization of TRG loci in mammalian species in order to show differences and similarities. The comparison revealed remarkable diversification of both the genomic organization and gene repertoire across species, but also unexpected evolutionary conservation, which highlights the important role of the T cells in the immune response

The t cell receptor (Trb) locus in tursiops truncatus: From sequence to structure of the alpha/beta heterodimer in the human/dolphin comparison

The bottlenose dolphin (Tursiops truncatus) belongs to the Cetartiodactyla and, similarly to other cetaceans, represents the most successful mammalian colonization of the aquatic envi-ronment. Here we report a genomic, evolutionary, and expression study of T. truncatus T cell receptor beta (TRB) genes. Although the organization of the dolphin TRB locus is similar to that of the other artiodactyl species, with three in tandem D-J-C clusters located at its 3’ end, its unique-ness is given by the reduction of the total length due essentially to the absence of duplications and to the deletions that have drastically reduced the number of the germline TRBV genes. We have analyzed the relevant mature transcripts from two subjects. The simultaneous availability of rear-ranged T cell receptor α (TRA) and TRB cDNA from the peripheral blood of one of the two speci-mens, and the human/dolphin amino acids multi-sequence alignments, allowed us to calculate the most likely interactions at the protein interface between the alpha/beta heterodimer in complex with major histocompatibility class I (MH1) protein. Interacting amino acids located in the com-plementarity-determining region according to IMGT numbering (CDR-IMGT) of the dolphin variable V-alpha and beta domains were identified. According to comparative modelization, the atom pair contact sites analysis between the human MH1 grove (G) domains and the T cell receptor (TR) V domains confirms conservation of the structure of the dolphin TR/pMH

To what extent do fiscal regimes equalize opportunities for income acquisition among citizens?.

This paper employs the theory of equality of opportunity, described in Roemer’s book (Equality of Opportunity, Harvard University Press, 1998), to compute the extent to which tax-and-transfer regimes in 11 countries equalize opportunities among citizens for income acquisition. Roughly speaking, equality of opportunity for incomes has been achieved in a country when it is the case that the distributions of post-fisc income are the same for different types of citizen, where a citizen’s type is defined by the socio-economic status of his parents. Intuitively, a country will have equalized opportunity if the chances of earning high (or low) income are equal for citizens from all family backgrounds. Of course, pre-fisc income distributions, by type, will not be identical, as long as the educational system does not entirely make up for the disadvantage that children, who come from poor families face, but the tax-and-transfer system can play a role in rectifying that inequality. We include, in our computation, two numbers that summarize the extent to which each country’s current fiscal regime achieves equalization of opportunities for income, and the deadweight loss that would be incurred by moving to the regime that does.Fiscal regimes; Equal opportunities; Income acquisition;

Ambient Air Pollution, Social Inequalities and Asthma Exacerbation in Greater Strasbourg (France) Metropolitan Area: the PAISA Study

International audienceThe socio-economic status (SES) of populations has an influence on the incidence or mortality rates of numerous health outcomes, among which respiratory diseases (Prescott et al., 2003; Ellison-Loschmann et al., 2007). Considering asthma, the possible contribution of SES to overall prevalence –regardless of asthma severity-, remains controversial in industrialized countries. Several studies indicate that allergic asthma is more prevalent in more well-off populations whereas the non-allergic forms of asthma are more common in the deprived ones (Cesaroni et al., 2003; Blanc et al., 2006). On the other hand, severe asthma whatever its etiology appears to be more frequent in the latter populations, as compared to the more affluent (Basagana et al., 2004). Risk factors for exacerbations (e.g., passive smoking (Wright Subramanian, 2007), psychosocial stress (Gold & Wright, 2005), cockroach allergens (Kitch et al., 2000), and suboptimal compliance with anti-inflammatory medication (Gottlieb et al., 1995)) are generally more common among people with asthma and low SES than their better-off counterparts. These observations support the hypothesis that some factors more present in deprived populations contribute to asthma exacerbation (Mielck et al., 1996)