Éditeur(s) : Université de Pau et des Pays de l'Adour
Résumé : In a context of decline of European eel (Anguilla anguilla L.) and search for biological markers of habitat use and quality, a multidisciplinary approach was engaged on the Adour estuary and its associated wetlands. Two axes were developed. The first axe aimed at highlighting the successive presence of the species in different ecosystems based on the otolith elemental composition. The second aimed at the evaluation of the chemical pressure underwent by eels based on the contaminant bioconcentration in soft tissues and the early molecular response to the chemical stress. With a view to the analyses of otolith elemental composition taking into account the 3D structure, the low elemental concentration in the matrix and keeping the finest spatial resolution, four micro sampling strategies and multi elemental analyses using femtosecond laser ablation ICP-MS were tested (crater, 1D scan, 2D scan, flash ablation). The strategy showing the best compromise according to the objectives (continuous recording, multi elemental approach) was applied on otolith of yellow eels from the Adour. The simultaneous use of Sr and Ba profiles, after validation, represents a new tool, easy, fast and reliable for the reconstruction of freshwater and brackish ecosystems use by eel avoiding misinterpretation due to vaterite inclusions. Three major behaviors were highlighted on the Adour: a residency in brackish water, a residency in freshwater and nomad behavior. The last one is illustrated by a shift to brackish water after three to four years spent in freshwater. Simultaneously, the study of inorganic and organic contamination of eel soft tissues showed that sampled wetlands are moderately contaminated. These results were confirmed by the first estimation, in wild conditions, of the early response to the chemical stress using the hepatic expression of CYP1A1 gene measured by real time RT-PCR. Conversely, in the downstream part of the Adour estuary, Hg loads in eels, especially methyl mercury, and PCBs analyses indicate values that need further investigations considering the European norms of consumption. The comparison of the different markers used (heavy metal and organochlorinated compounds contamination of soft tissues, condition index) support a lower quality of the estuary despite higher eel growth rate on this site. This study supports the use of numerous markers in integrated studies in order to understand and specify the relationships between eels and their continental growth zones.
Dans un contexte de déclin de l'anguille européenne (Anguilla anguilla L.) et de recherche de marqueurs biologiques retraçant la fréquentation des divers habitats et renseignant sur la qualité de ceux-ci, une approche pluridisciplinaire a été mise en place sur l'estuaire de l'Adour et ses zones humides. Deux axes ont été privilégiés. Le premier cherchait à visualiser la présence successive de l'espèce dans différents écosystèmes en se basant sur la composition élémentaire des otolithes. Le deuxième avait pour but d'évaluer la pression chimique inorganique et organique subie par l'anguille dans les zones d'études en s'appuyant sur la bioconcentration des contaminants dans les tissus mous et la réponse moléculaire précoce au stress chimique. En vue des analyses de la composition élémentaire des otolithes et pour répondre au mieux à la structure en trois dimensions, à la faible concentration des éléments dans la matrice tout en conservant une résolution spatiale la plus fine possible, quatre stratégies de micro-échantillonnage et d'analyses multiélémentaires par ablation laser femtoseconde ICP-MS ont été testées (cratère, scan 1D, scan 2D, ablation flash). La méthodologie présentant le meilleur compromis par rapport aux objectifs fixés (enregistrement continu, approche multiélémentaire) a ensuite été appliquée sur les otolithes d'anguilles jaunes du Bas-Adour. L'utilisation simultanée des profils continus de Sr et de Ba, après validation, constitue un outil facile d'utilisation, rapide et fiable pour reconstruire les historiques de fréquentation des différents écosystèmes estuariens et dulçaquicoles par l'anguille tout en s'affranchissant des problèmes potentiels liés aux inclusions de vatérite, un polymorphe du carbonate de calcium. Trois grands types de comportement ont pu être mis en évidence sur l'Adour : résidence en eau saumâtre, résidence en eau douce et nomadisme. Ce dernier est plus particulièrement illustré par un mouvement marqué vers l'eau saumâtre pour des individus ayant passé de trois à quatre ans dans l'eau douce. Parallèlement, l'étude de la contamination organique et inorganique des tissus mous de l'anguille a permis de déduire à la faible contamination des zones humides échantillonnées. La première estimation en condition naturelle de la réponse précoce au stress chimique par évaluation de l'expression hépatique du gène CYP1A1 par RT-PCR en temps réel confirme ces résultats. En revanche, dans la partie estuarienne aval de l'Adour, les niveaux en Hg, présent en majorité sous sa forme méthylée dans les anguilles, et l'analyse des PCBs indiquent des valeurs qui suscitent un examen plus approfondi au regard des normes européennes en vigueur. La confrontation des différents descripteurs (contamination des tissus mous par les métaux lourds et organochlorés, indice de condition) utilisés conforte la qualité moindre de la zone estuarienne malgré des performances de croissance de l'anguille favorisées sur ces sites. Ainsi, cette étude supporte l'intérêt de la mise en oeuvre de descripteurs multiples utilisés (niveaux de métaux lourds et organochlorés dans les tissus mous, réponse moléculaire au stress chimique, microchimie de l'otolithe, indice de condition, taux de croissance) dans des approches intégrées pour comprendre et préciser les relations existantes entre l'anguille et ses zones de croissance continentales.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2009/these-7381.pdf
http://archimer.ifremer.fr/doc/00000/7381/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This work deals with the problem of finding for a given industrial target the molecule conformation leading to the most efficient crystal polymorph and/or designing unknown crystal packing of new molecules. The originality of the method relies first on constraining the domain of the most probable crystals, before converging towards the predicted packing by a double genetic-refining optimization algorithm. Validation of this approach is discussed on the case study of 46 energetic crystal compounds, using the semi Ab Initio and Molecular Mechanics code GenMol™. This validation shows that all observed structures are retrieved in any circumstances with a relatively high number of good rankings.
ISSN: 0022-0248

hal-00857875
https://hal.archives-ouvertes.fr/hal-00857875
DOI : 10.1016/j.jcrysgro.2009.04.002

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background : Trichoderma reesei is the main industrial source of cellulases and hemicellulases required for the hydrolysis of biomass to simple sugars, which can then be used in the production of biofuels and biorefineries. The highly productive strains in use today were generated by classical mutagenesis. As byproducts of this procedure, mutants were generated that turned out to be unable to produce cellulases. In order to identify the mutations responsible for this inability, we sequenced the genome of one of these strains, QM9136, and compared it to that of its progenitor T. reesei QM6a.Results : In QM9136, we detected a surprisingly low number of mutagenic events in the promoter and coding regions of genes, i.e. only eight indels and six single nucleotide variants. One of these indels led to a frame-shift in the Zn2Cys6 transcription factor XYR1, the general regulator of cellulase and xylanase expression, and resulted in its C-terminal truncation by 140 amino acids. Retransformation of strain QM9136 with the wild-type xyr1 allele fully recovered the ability to produce cellulases, and is thus the reason for the cellulase-negative phenotype. Introduction of an engineered xyr1 allele containing the truncating point mutation into the moderate producer T. reesei QM9414 rendered this strain also cellulase-negative. The correspondingly truncated XYR1 protein was still able to enter the nucleus, but failed to be expressed over the basal constitutive level.Conclusion : The missing 140 C-terminal amino acids of XYR1 are therefore responsible for its previously observed auto-regulation which is essential for cellulases to be expressed. Our data present a working example of the use of genome sequencing leading to a functional explanation of the QM9136 cellulase-negative phenotype.
ISSN: 1471-2164

Droits : http://creativecommons.org/licenses/by/
hal-01149671
http://hal.upmc.fr/hal-01149671
http://hal.upmc.fr/hal-01149671/document
http://hal.upmc.fr/hal-01149671/file/Lichius_2015_Genome_sequencing.pdf
DOI : 10.1186/s12864-015-1526-0

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Patterns of connectivity and self-recruitment are recognized as key factors shaping the dynamics of marine populations. Connectivity is also essential for maintaining and restoring natural ecological processes with genetic diversity contributing to the adaptation and persistence of any species in the face of global disturbances. Estimates of connectivity are crucial to inform the design of both marine protected areas (MPAs) and MPA networks. Among several approaches, genetic structure is frequently used as a proxy for patterns of connectivity. Using 8 microsatellite loci, we investigated genetic structure of the two-banded sea bream Diplodus vulgaris, a coastal fish that is both commercially and ecologically important. Adults were sampled in 7 locations (stretches of coastline approximately 8 km long) and juveniles in 14 sites (~100 to 200 m of coastline) along 200 km of the Apulian Adriatic coast (SW Adri-atic Sea), within and outside an MPA (Torre Guaceto MPA, Italy). Our study found similar genetic diversity indices for both the MPA and the surrounding fished areas. An overall lack of genetic structure among samples suggests high gene flow (i.e. connectivity) across a scale of at least 200 km. However, some local genetic divergences found in two locations demonstrate some heterogeneity in processes renewing the population along the Apulian Adriatic coast. Furthermore, two sites appeared genetically divergent, reinforcing our observations within the genetic makeup of adults and confirming heterogeneity in early stage genetics that can come from either different supply populations or from chaotic genetic patchiness occurring under temporal variation in recruitment and in the reproductive success. While the specific role of the MPA is not entirely known in this case, these results confirm the presence of regional processes and the key role of connectivity in maintaining the local population supply.
ISSN: 1932-6203

hal-01442055
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055/file/journal.pone.0167441.pdf
DOI : 10.1371/journal.pone.0167441.s009

Éditeur(s) : HAL CCSD E Schweizerbart Science Publishers
Résumé : The occurrence and preservation of aragonite in eclogite-facies rocks of north-eastern Corsica is linked to an uncommon microtexture. Aragonite exclusively occurs as oriented fibres in garnet crystals of a graphitic, more or less siliceous marble that immediately overlies a serpentinite body of the meta-ophiolitic unit. The arrangement of the fibres is grossly radial, but more clearly sectoral in subhedral garnet, the fibres growing perpendicular to the garnet/matrix interface. Raman mapping reveals that the carbonate is calcite in the matrix and in poikiloblastic garnet cores, and that the fibres in the garnet mantle are aragonite alone in the case of a carbonate matrix, and both aragonite and quartz (in distinct fibres) in a quartz–carbonate matrix. These features are interpreted as prograde intergrowths, the result of garnet nucleation and growth in a calcite and then aragonite matrix (±quartz). Upon further heating and/or decompression, the aragonite matrix transformed back to calcite while the carbonates included in garnet retained their original structure, in spite of the relatively high temperature attained (ca. 500 °C). These aragonite relics are one more example of the preservation of a high-pressure polymorph through mechanical shielding of inclusions in a rigid host. The aragonite–garnet intergrowths are similar to quartz–garnet intergrowths described in amphibolite-facies graphitic schists. They are evidence that oriented inclusions in garnet are not necessarily precipitates (‘exsolutions'). Unlike precipitates, their orientation is controlled more by the shape of the garnet growth front than by symmetry constraints.
ISSN: 0935-1221

hal-00411136
https://hal.archives-ouvertes.fr/hal-00411136
DOI : 10.1127/0935-1221/2008/0020-1892

Éditeur(s) : HAL CCSD Wiley
Résumé :  
The chloroplast genome has been widely used to describe genetic diversity in plant species. Its maternal inheritance in numerous angiosperm species and low mutation rate are suitable characters when inferring historical events such as possible recolonization routes. Here we have studied chloroplast DNA variation using PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) with seven pairs of primers and four restriction enzymes in 14 populations of Vouacapoua americana (Caesalpiniaceae) a neotropical tree sampled throughout French Guiana. Population diversity (Hs), total gene diversity (Ht) and differentiation among populations (GST) were estimated using Nei's method as 0.09, 0.87 and 0.89, respectively. This is consistent with the limited gene flow associated with synzoochory in this species. The genetic structure observed in the north of French Guiana suggests that historical events such as contractions and recent recolonizations have had a large impact on the distribution of genetic diversity in this species.
ISSN: 0962-1083

hal-01032176
https://hal.archives-ouvertes.fr/hal-01032176
DOI : 10.1046/j.1365-294x.2000.01027.x

Éditeur(s) : HAL CCSD
Résumé :  
Improvement of wood quality related traits is currently hampered by costly chemical and technological assays and the necessity to wait until the trees are nearly mature to evaluate wood properties. The availability of a vast quantity of genomic data opens now a new avenue to identify early selection criteria based on molecular information and therefore increase selection efficiency. Association mapping is becoming a method of choice to identify QTN (quantitative trait nucleotide) that contribute to complex trait variation. The implementation of this approach requires on the one hand knowledge of the molecular mechanisms underlying trait variation and polymorphism within candidate genes, and on the other hand the availability of phenotypically well characterized genetic material. We are developing this strategy in the frame of the French maritime pine breeding program, an economically important forest tree species in the South Western Europe. About 500 trees from the breeding population were evaluated for wood physical and chemical properties through the analysis of 2,800 half-sib progenies and 1,500 clones in 8 field tests. These same trees are being genotyped at 185 SNPs obtained from the sequencing of 41 candidate genes, and an additional set of 200 eSNPs detected in 147 EST-contigs (to be used as control). Statistical association between the breeding values of the 500 trees and their respective genotypes will be tested using mixed models accounting for relatedness among individuals of the breeding population.
IUFRO-CTIA joint conference, "Adaptation, Breeding and Conservation in the Era of Forest Tree Genomics and Environmental Change"
Québec City, Canada

hal-01032075
https://hal.archives-ouvertes.fr/hal-01032075

Éditeur(s) : HAL CCSD Elsevier
Résumé : Field isolates of Toxoplasma gondii in Europe and North America have been grouped into three clonal lineages that display different virulence in mice. Whether the genetic structure of the parasite is related to clinical expression in humans has not yet been demonstrated. We developed an enzyme-linked immunosorbent assay which uses lineage-specific, polymorphic polypeptides derived from the dense granule antigens, GRA5 and GRA6. Our goal was to compare serotypical patterns observed in asymptomatic versus symptomatic (ocular disease and severe infection in human immunodeficiency virus (HIV)-positive patients) infections among patients from Europe and South America. Independent of the clinical presentation of the disease, serotypes differed according to geographical origin, with a homogeneous distribution of serotype II in Europe and of serotypes I and III in South America. We conclude that GRA5-GRA6 serotyping is an interesting tool to study serotype prevalence in populations but it is not an accurate marker of pathogenicity of Toxoplasma infection in humans.
ISSN: 1286-4579

hal-00306841
https://hal.archives-ouvertes.fr/hal-00306841
DOI : 10.1016/j.micinf.2008.04.001
PUBMED : 18539501

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.
ISSN: 1755-098X

hal-01094222
https://hal-agroparistech.archives-ouvertes.fr/hal-01094222
DOI : 10.1111/j.1755-0998.2010.02916.x

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Genetic recombination occurs during meiosis, the key developmental programme of gametogenesis. Recombination in mammals has been recently linked to the activity of a histone H3 methyltransferase, PR domain containing 9 (PRDM9), the product of the only known speciation-associated gene in mammals. PRDM9 is thought to determine the preferred recombination sites--recombination hotspots--through sequence-specific binding of its highly polymorphic multi-Zn-finger domain. Nevertheless, Prdm9 knockout mice are proficient at initiating recombination. Here we map and analyse the genome-wide distribution of recombination initiation sites in Prdm9 knockout mice and in two mouse strains with different Prdm9 alleles and their F(1) hybrid. We show that PRDM9 determines the positions of practically all hotspots in the mouse genome, with the exception of the pseudo-autosomal region (PAR)--the only area of the genome that undergoes recombination in 100% of cells. Surprisingly, hotspots are still observed in Prdm9 knockout mice, and as in wild type, these hotspots are found at H3 lysine 4 (H3K4) trimethylation marks. However, in the absence of PRDM9, most recombination is initiated at promoters and at other sites of PRDM9-independent H3K4 trimethylation. Such sites are rarely targeted in wild-type mice, indicating an unexpected role of the PRDM9 protein in sequestering the recombination machinery away from gene-promoter regions and other functional genomic elements.
ISSN: 0028-0836

hal-00877666
https://hal.archives-ouvertes.fr/hal-00877666
DOI : 10.1038/nature11089
PUBMED : 22660327

Résumé : Three species of man.-rove oysters, Crassostrea rhizophorae, C. brasiliana, and C. gasar, have been described along the Atlantic shores of South America and Africa. Because the distribution of these molluscs is of great biological and commercial interest, their taxonomy and distribution deserve further clarification. Therefore, 15 populations were sampled from both continents. Their 16S mitochondrial polymorphism was studied by sequencing and PCR-RFLP analysis. Two haplotypes were identified. Haplotype a was the only one observed in Africa, but it was also observed in South America together with haplotype b. Because C. gasar is the only mangrove oyster identified on the west coast of Africa, haplotype a was attributed to this species, which has thus been shown to occur in South America. Haplotype b is attributed to C. rhizophorae. The karyotypes of specimens of C. gasar, from Africa and from South America, were very similar, and both species were observed at the same location in Brazil. The occurrence of C. gasar in South America adds a third species-in addition to C rhizophorae and C. brasiliana-to the list of species present along these coasts. The predominant surface circulation patterns in this part of the Atlantic Ocean favor the hypothesis that C. gasar was transported from Africa to America. Finally, a phylogenetic tree built with seven 16S sequences from Crassostrea and Saccostrea species showed that C. gasar is intermediate between the American Crassostrea species (C virginica and C. rhizophorae) and the Asian species (C. gigas and C ariakensis).
Biological Bulletin (0006-3185), 2002-06 , Vol. 202 , N. 3 , P. 232-242

Droits : Marine Biological Laboratory.
http://archimer.ifremer.fr/doc/2002/publication-2790.pdf
http://archimer.ifremer.fr/doc/00000/2790/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé :  
Mechanical signals have an impact on plant development. Tropical rainforest trees display large variability for life-history traits related to biomechanics and therefore are a unique study system to better understand biomechanical trait variability from an evolutionary perspective. From sequences and gene expression data available in model species, we developed specific primers for six candidate genes for mechano-sensing in five tropical species. Most of the gene sequences were polymorphic in most species.
ISSN: 1614-2942

hal-01019738
https://hal.archives-ouvertes.fr/hal-01019738
DOI : 10.1007/s11295-010-0363-1

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Reliable molecular typing tools are required for a better understanding of the molecular epidemiology of Plasmodium vivax. The genes msp3a and msp1_block5 are highly polymorphic and have been used as markers in many P. vivax population studies. These markers were used to assess the genetic diversity of P. vivax strains from French Guiana (South America) and to develop a molecular typing protocol. METHODS: A total of 120 blood samples from 109 patients (including 10 patients suffered from more than one malaria episode, samples were collected during each episode) with P. vivax infection were genotyped. All samples were analysed by msp3a PCR-RFLP and msp1_b5 gene sequencing was performed on 57 samples. Genotyping protocol applied to distinguish between new infection or relapse from heterologus hypnozoites and treatment failure or relapse from homologus hypnozoites was based on analysing first msp3a by PCR-RFLP and secondly, only if the genotypes of the two samples are identical, on sequencing the msp1_b5 gene. RESULTS: msp3a alleles of three sizes were amplified by PCR: types A, B and C. Eleven different genotypes were identified among the 109 samples analysed by msp3a PCR-RFLP. In 13.8% of cases, a mixed genotype infection was observed. The sequence of msp1_b5 gene revealed 22 unique genotypes and 12.3% of cases with mixed infection. In the 57 samples analysed by both methods, 45 genotypes were found and 21% were mixed. Among ten patients with two or three malaria episodes, the protocol allowed to identify five new infections or relapses from heterologous hypnozoites and six treatment failures of relapses from homologous hypnozoites. CONCLUSION: The study showed a high diversity of msp3a and msp1_b5 genetic markers among P. vivax strains in French Guiana with a low polyclonal infection rate. These results indicated that the P. vivax genotyping protocol presented has a good discrimination power and can be used in clinical drug trials or epidemiological studies.
ISSN: 1475-2875

pasteur-00590981
https://hal-riip.archives-ouvertes.fr/pasteur-00590981
DOI : 10.1186/1475-2875-8-40
PUBMED : 19284592

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Studies focusing on the effect of invasive species on the genetic diversity of native marine invertebrates remain scant. Here we report diversity among French populations of the intertidal gastropod Ocenebra erinacea (Linnaeus, 1758) sampled in the presence and absence of the invasive Ocenebra inornata (Recluz, 1851). Between 1999 and 2004, a total of 352 individuals of O. erinacea was collected from 15 sites, five of which had the invasive present, and genotyped at the mitochondrial locus cox1. No statistical difference was observed between polymorphism levels recorded within native populations exposed to the invasive, compared with populations sampled in the absence of O. inornata. No sign of native population decline was detected in response to the invader. While significant shifts in native O. erinacea population sizes have previously been reported in the literature, genetic effects may take longer to accumulate, or may be undetectable without a larger panel of genetic markers. By contrast, large genetic distances and significant population differentiation were recorded between Atlantic and Mediterranean O. erinacea samples, suggesting that these populations have distinct evolutionary histories. Comparison of genetic divergence within the closely related genus Nucella suggests that the Atlantic populations of O. erinacea and those from Thau Lagoon in the Mediterranean may belong to different species or subspecies.
ISSN: 0173-9565

hal-01064464
https://hal.archives-ouvertes.fr/hal-01064464
https://hal.archives-ouvertes.fr/hal-01064464/document
https://hal.archives-ouvertes.fr/hal-01064464/file/Ocenebra_revision_submission_to_MarEcol.pdf
DOI : 10.1111/maec.12208

Éditeur(s) : HAL CCSD Hindawi Publishing Corporation
Résumé : International audience
HLA-G is a nonclassical major histocompatibility complex molecule first described at the maternal-fetal interface, on extravillous cytotrophoblasts. Its expression is restricted to some tissues in normal conditions but increases strongly in pathological conditions. The expression of this molecule has been studied in detail in cancers and is now also beginning to be described in infectious diseases. The relevance of studies on HLA-G expression lies in the well known inhibitory effect of this molecule on all cell types involved in innate and adaptive immunity, favoring escape from immune control. In this review, we summarize the features of HLA-G expression by type of infections (i.e, bacterial, viral, or parasitic) detailing the state of knowledge for each pathogenic agent. The polymorphism, the interference of viral proteins with HLA-G intracellular trafficking, and various cytokines have been described to modulate HLA-G expression during infections. We also discuss the cellular source of HLA-G, according to the type of infection and the potential role of HLA-G. New therapeutic approaches based on synthetic HLA-G-derived proteins or antibodies are emerging in mouse models of cancer or transplantation, and these new therapeutic tools may eventually prove useful for the treatment of infectious diseases.
ISSN: 2314-8861

hal-01063925
https://hal.archives-ouvertes.fr/hal-01063925
https://hal.archives-ouvertes.fr/hal-01063925/document
https://hal.archives-ouvertes.fr/hal-01063925/file/Immunomodulatory%20Properties%20of%20HLA-G.pdf
DOI : 10.1155/2014/298569

Résumé : Aux Antilles, la faible fréquence des coronaropathies pourrait être liée à des facteurs génétiques, ethniques et/ou une distribution spécifique des facteurs de risque cardio-vasculaire (FDRCV). Les propriétés l'ANP (Atrial Natriuretic Peptide) et l'influence de certains polymorphismes de son gène, fréquents dans les populations d'ascendance Africaine pourraient également être en cause. L'analyse des dossiers de 638 patients coronariens consécutifs a mis en évidence une forte prévalence de l'hypertension artérielle et du diabète dans cette population et révélé des différences significatives dans la prévalence des FDRCV entre Afro-Caribéens (AC), Caucasiens et descendants de migrants Indiens. L'analyse angiographique de 420 patients AC a révélé que le diabète était le FDRCV le plus fortement lié à la sévérité des lésions coronaires alors l'obésité apparaissait comme un facteur protecteur. La transfection in vitro, de cellules musculaires lisses artérielles par une construction adénovirale porteuse du gène de l'ANP a entrainé une inhibition de la prolifération et de la migration cellulaire de 31 % et 25% respectivement. In vivo, cet effet s'est traduit par une réduction de 25% de la formation néotimale et de 28% du rapport intima/média dans un modèle d'hyperplasie de carotide de rat. Dans étude transversale incluant 210 sujets diabétiques AC nous avons mis en évidence une association entre le polymorphisme rs5065 (22381>C) du gène de l'ANP et l'existence d'une coronaropatbie. Dans cette étude, l'odds ratio de la présence d'une coronaropathie chez les porteurs de l'allèle mineur de cette mutation (TC/CC) était de 0,50 (0,26- 0,96; P = 0,038).
In Guadeloupe and Martinique, the low frequency ofcoronary artery disease (CAD) could be related to genetic or ethniefactors and/or specifie distribution ofcardiovascular risk factors (CRFs). Atrial Natriuretic Peptide (ANP) properties and influence of sorne of ANP gene polymorphism that are frequent in populations of African descent could also be involved in CAD occurrence. We retrospectively studied 638 consecutive patients with documented CAO and found a high prevalence of hypertension and diabetes in this population. This study also demonstrated significant differences in the prevalence of CRFs between Afro-Caribbean (AC), Caucasians and Indians migrants. The angiographie analysis of420 patients revealed that in AC, diabetes emerged as the strongest CFR related to the severity ofcoronary lesions while obesity appeared as a protective factor. After transfection by an adenoviral construct carrying the ANP gene, vascular smooth muscle cell proliferation stimulated by 10% fetal calf serum was reduced by 31% and migration by 25%. In vivo, in rat carotid artery model ofvascular injury, neointima formation and intima/media ratio was reduced by 25% and 28% respectively. In a cross-sectional study inc1uding 210 AC diabetics we found an association between rs5065 (22381> C) polymorpbism and the presence of coronary artery disease suggesting that the minor allele could have a protective effect against CAD. The odds ratio for the presence ofCAD in carriers ofthe minor allele ofthis mutation (TC / CC) was 0.50 (0.26-0.96, P = 0.038).

http://www.theses.fr/2012AGUY0553/document

Résumé : Le maintien de ressources génétiques suffisamment larges est nécessaire pour assurer la viabilité et le potentiel évolutif des populations naturelles. Cette thèse a le principal objectif de caractériser la diversité et la variabilité génétique chez le genre Virola (Myristicaceae) pour décrire les processus évolutifs qui en sont à l'origine. Premièrement,une étude de la régénération d'un échantillonnage exhaustif de V. michelii a été menée dans une parcelle du dispositif expérimental de Paracou ayant subi une exploitation forestière de faible intensité et comparée à une parcelle témoin. La diversité génétique mesurée à partir de marqueurs AFLP (Amplified Fragment-Length Polymorphism, N=229) en zones perturbées s'est révélée être plis grande qu'en zone non-perturbées. Puis, l'adaptation locale a été étudiée à travers ces mêmes individus et certains loci (AFLP) montrent une sélection divergente pour des environnements contrastés, indiquant un signe d'adaptation. Enfin, l'étude des niveaux de divergence génétique chez trois espèces de Virola du bouclier guyanais (V. michelii, V. surinamensis et V. kwatae) montrent que deux d'entre elles (V. surinamensis et V. kwatae) montrent de fortes similarités génétiques malgré leur distribution sur des environnements contrastés. des Flux de gènes intersécifiques ont été mis en évidence chez ces deux espèces-soeurs et l'hypothèse d'une spéciation écologique est avancée. Ce travail a permis d'aborder différents processus évolutifs à l'origine de la diversité génétique actuelle chez ces espèces forestières tropicales et peut fournir une contribution pour appréhender le devenir des populations.
Genetic diversity is an essential component of biodiversity. The maintenance of sufficient genetic resources is needed to ensure the adaptive potential and the viability of natural populations. In the current context of global changes, the study of adaptation in living organisms is a key task, particularly for tropical forest trees that are dominant components (in terms of biomass and as ecological drivers) of some of the most diverse ecosystems on Earth. The main objective of this thesis is to characterize genetic diversity and genetic variability to understand the evolutionary processes that act on them. This ecological-genetic study was carried out at the interspecific and intraspecific level in the Virola genus.If overall high levels of genetic diversity are a guarantee of prosperity for the future of the species, it seems essential to perform studies on the impact of environmental disturbance on genetic diversity. In the first section, the genetic consequences of regeneration dynamics were studied in an exhaustive sample of V. michelii in a low-intensity logging plot and in a control plot at the Paracou experimental site. A greater genetic diversity, measured from AFLP markers (Amplified Fragment Length Polymorphism, N = 229), was found in perturbed areas. Because studying genetic diversity within species may be useful for understanding species adaptation to environmental changes, in the second section. I studied local adaptation in a population of V. michelii on the Paracou experimental site. A genome scan approach with AFLPs (N = 229) was conducted on 77 adult individuals and 401 juveniles to identify genetic differences between populations associated to contrasting conditions for an array of environmental variables. Some loci (N = 2) were found to be subject to divergent selection, indicating adaptation to contrasting habitats.In the third section, the study of levels of genetic divergence in three Virola species of the Guiana Shield (V. michelii, V. surinamensis and V. kwatae) was investigated for nuclear and chloroplast molecular markers. V. surinamensis and V. kwatae showed strong genetic similarities despite their contrasting habitats preferences. Coalescent analyses have revealed, on one hand, a recent divergence between these two species suggesting an ecological speciation, and one the other hand that interspecific gene flow occurs between these sister-species.This work focuses on understanding evolutionary processes shaping genetic diversity and provides a useful contribution for biodiversity conservation programs.

http://www.theses.fr/2011AGUY0480/document

Éditeur(s) : HAL CCSD American Society of Clinical Oncology
Résumé : International audience
PURPOSE: Determining whether environmental estrogens are associated with the risk of prostate cancer may have important implications for our general understanding of this disease. The estrogenic insecticide chlordecone was used extensively in the French West Indies, contaminating the population for more than 30 years. We analyzed the relationship between exposure to chlordecone and the risk of prostate cancer. PATIENTS AND METHODS: We investigated 623 men with prostate cancer and 671 controls. Exposure was analyzed according to case-control status, using either current plasma concentration or a cumulative exposure index based on years of exposure. We genotyped two single-nucleotide polymorphisms (rs3829125 and rs17134592) in the gene encoding chlordecone reductase. RESULTS: We found a significant increase in the risk of prostate cancer with increasing plasma chlordecone concentration (odds ratio [OR], 1.77; 95% CI, 1.21 to 2.58 for the highest tertile of values above the limit of detection [LD]; P trend = .002) and for cumulative exposure index (OR, 1.73; 95% CI, 1.04 to 2.88 for the highest quartile; P trend = .004). Stronger associations were observed among those with a positive family history of prostate cancer and among those who had lived in a Western country. The rs3829125 and rs17134592 allele variants were in complete linkage disequilibrium and were found at low frequency (0.04). Among subjects with plasma chlordecone concentrations above the LD, carriers of the allele variants had a higher risk of prostate cancer (OR, 5.23; 95% CI, 0.82 to 33.32). CONCLUSION: These findings support the hypothesis that exposure to environmental estrogens increases the risk of prostate cancer.
ISSN: 0732-183X

inserm-00518099
http://www.hal.inserm.fr/inserm-00518099
DOI : 10.1200/JCO.2009.27.2153
PUBMED : 20566993

Éditeur(s) : HAL CCSD SAGE Publications (UK and US)
Résumé : International audience
Genetic approaches have shown that several genes could modify caries susceptibility; AmelogeninX (AMELX) has been repeatedly designated. Here, we hypothesized that AMELX mutations resulting in discrete changes of enamel microstructure may be found in children with a severe caries phenotype. In parallel, possible AMELX mutations that could explain resistance to caries may be found in caries-free patients. In this study, coding exons of AMELX and exon-intron boundaries were sequenced in 399 individuals with extensive caries (250) or caries-free (149) individuals from nine French hospital groups. No mutation responsible for a direct change of amelogenin function was identified. Seven single-nucleotide polymorphisms (SNPs) were found, 3 presenting a high allele frequency, and 1 being detected for the first time. Three SNPs were located in coding regions, 2 of them being non-synonymous. Both evolutionary and statistical analyses showed that none of these SNPs was associated with caries susceptibility, suggesting that AMELX is not a gene candidate in our studied population.
ISSN: 0022-0345

hal-01545481
https://hal.archives-ouvertes.fr/hal-01545481
DOI : 10.1177/0022034513482941

Résumé : La tuberculose, maladie très ancienne, est plus que jamais présentée sur la scène sanitaire mondiale avec 9 millions de nouveaux cas par an. Cette maladie, qui demeure une cause majeure de mortalité, est un des problèmes les plus difficiles à résoudre en santé publique et à échelle internationale. Les diverses programmes de lutte, lancés par l’Organisation Mondiale de la Santé (OMS), pour prévenir et garantir la guérison des patients tuberculeux, se heurtent à des difficultés qui hypothèquent leur efficacité. En effet, l'expansion du virus de rinimunodéficience humaine (VIII) et son influence néfaste sur la susceptibilité à la tuberculose, l'accroissement rapide de la tuberculose multirésistante, la pauvreté ainsi que la croissance démographique, sont un ensemble de facteurs préjudiciables à l'application des mesures préventives et curatives. Les contextes économiques difficiles conduisant indubitablement au cumul de ces facteurs, ont fait une césure entre les pays riches et les pays pauvres quant à l'incidence et la révolution de la tuberculose à échelle mondiale. Pour atténuer la disparité des résultats des luttes antituberculeuses, les méthodologies employées en épidémiologie de la tuberculose doivent s'inscrire dans une démarche d'efficacité. Les marqueurs moléculaires, indispensables à l'identification et à la classification des souches appartenant au complexe Mycobacterium tuberculosis (MTC) ont chacun des potentialités qui leur sont propres dont il convient de cerner pour une utilisation adéquate dans les études épidémiologiques et phylogénétiques. Le but de cette thèse consiste à extraire des connaissances nouvelles des résultats de génotypage stockées dans les bases de données, connaissances relatives au polymorphisme du support génomique pour estimer la contribution de chaque marqueur dans la classification de MTC. Le recours à différentes méthodes de reconstruction phylogénétique et de modélisation des données fut indispensable. A la lumière des résultats obtenus, cette thèse propose une nouvelle méthodologie de classification, pour rétablissement d'une phylogéographie robuste de MTC en relation avec l'histoire des migrations humaines qui aurait débutée en Afrique subsaharienne. Chaque méthode de génotypage ayant une efficience et un cout propres, qu'il convient de mesurer par rapport aux moyens disponibles et aux résultats escomptes, il est donc intéressant de renforcer la connaissance des marqueurs et de proposer différentes alternatives menant à la classification des mycobactéries. Ainsi, les résultats obtenus dans cette thèse apportent plus de cohérence aux solutions proposées pour la caractérisation des clones de MTC circulant dans le monde.
Tuberculosis, very old disease, is more than ever presented on the global health scene with 9 million new cases per year. This disease, which remains a major cause of mortality is one of the most intractable public health and international issues. The various control programs, launched by the World Health Organization (WHO) to prevent and guarantee the cure of tuberculosis patients face difficulties that undermine their effectiveness. Indeed, the expansion of human virus rinimunodéficience (VIII) and its negative influence on susceptibility to tuberculosis, the rapid growth of multidrug-resistant tuberculosis, poverty and population growth, are a set of factors detrimental to application of preventive and curative measures. The difficult economic circumstances undoubtedly leading to accumulation of these factors have a break between rich and poor countries about the impact and the revolution of tuberculosis worldwide. To address the disparity of the results of tuberculosis struggles, the methodologies used in epidemiology of tuberculosis must be part of a process efficiency. Molecular indispensable to the identification and classification of strains belonging to the Mycobacterium tuberculosis complex (MTC) markers each have their own potentials that need to be identified for proper use in epidemiological and phylogenetic studies. The purpose of this thesis is to extract new knowledge of the results of genotyping data stored in databases, knowledge of the polymorphism of genomic carrier to estimate the contribution of each marker in the classification of TCM. The use of different methods of phylogenetic reconstruction and modeling data was essential. In light of the results obtained, the thesis proposes a new classification methodology for a robust recovery phylogeography of TCM in connection with the history of human migration have started in sub-Saharan Africa. Each genotyping method with cost efficiency and equity, should be measured in relation to the resources available and discounts results, it is interesting to strengthen the knowledge of markers and propose alternatives leading to the classification of mycobacteria. Thus, the results obtained in this thesis bring more coherence to the proposed characterization of clones MTC circulating worldwide solutions.

http://www.theses.fr/2012AGUY0518/document