Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
BACKGROUND: This study examines gene-environment interaction between the MTHFR C667T polymorphism and folic acid in the etiology of orofacial clefts (OFC). We used a pooled-analytical approach on four studies that used similar methods. METHODS: We used logistic regression to analyze the pooled sample of 1149 isolated cases and 1161 controls. Fetal and maternal MTHFR C677T genotypes, and maternal periconceptional exposure to smoking, alcohol, vitamin containing folic acid and folic acid supplements were contrasted between the cleft types [non-syndromic clefts lip or without cleft palate (CL(P)) and non-syndromic cleft palate (CP)] and control groups. RESULTS: There was a reduced risk of CL(P) with maternal folic acid use (p = 0.008; OR = 0.70, 95% CI: 0.65-0.94) and with supplements containing folic acid (p = 0.028, OR = 0.80, 95% CI: 0.65-0.94). Maternal smoking increased the risk of both CL(P) (p < 10 e-3; OR = 1.62, 95% CI: 1.35-1.95) and CP (p = 0.028; OR = 1.38, 95% CI: 1.04-1.83). No significant risk was observed with either maternal or fetal MTHFR C677T genotypes. CONCLUSION: This individual participant data (IPD) meta-analysis affords greater statistical power and can help alleviate the problems associated with aggregate-level data-sharing. The result of this IPD meta-analysis is consistent with previous reports suggesting that folic acid and smoking influence OFC outcomes.
ISSN: 1542-0752

hal-00875899
https://hal.archives-ouvertes.fr/hal-00875899
DOI : 10.1002/bdra.23133
PUBMED : 23670871

Éditeur(s) : HAL CCSD Lippincott, Williams & Wilkins
Résumé : International audience
The aim of the study was to investigate the impact of first-line combined antiretroviral therapy (cART) regimen on the course of CD8 + T-cell counts in human immunodeficiency virus (HIV)-infected patients. A retrospective observational study conducted on the French DAT'AIDS Cohort of HIV-infected patients. We selected 605 patients initiating a first-line cART between 2002 and 2009, and which achieved a sustained undetectable HIV plasma viral load (pVL) for at least 12 months without cART modification. The evolution of CD8 + T-cell counts according to cART regimen was assessed. CD8 + T-cell counts were assessed in 572 patients treated with 2NRTIs+1PI/r (n= 297), 2NRTIs+1NNRTI (n= 207) and 3NRTIs (n= 68). In multivariate analysis, after 12 months of follow-up, the 3NRTIs regimen was associated with a significantly smaller decrease of CD8 + T-cell count compared with NNRTI-containing regimens (–10.2 cells/mL in 3NRTIs vs –105.1 cells/mL; P=0.02) but not compared with PI-containing regimens (10.2 vs –60.9 cells/mL; P=0.21). After 24 months, the 3NRTIs regimen was associated with a smaller decrease of CD8 + T-cell count and % compared with PI/r-and NNRTI-containing regimens (0.2 in 3NRTIs vs –9.9 with PI/r-regimens, P=0.001, and vs –11.1 with NNRTI-regimens, p < 0.0001). A focus analysis on 11 patients treated with an INSTI-containing cART regimen during the study period showed after 12 months of follow-up, a median decrease of CD8 + T-cell count of –155 [inter quartile range: –302; –22] cells/mL. Our data highlight the fact that cART regimens have differential effects on CD8 pool down regulation. Abbreviations: cART = combined antiretroviral therapy, HIV = human immunodeficiency virus, INSTI = integrase strand transfer inhibitor, NNRTI = non-nucleotide reverse transcriptase inhibitor, NRTI = nucleotide reverse transcriptase inhibitor, PI/r = Ritonavir-boosted protease inhibitor, pVL = plasma viral load.
ISSN: 0025-7974

inserm-01408002
http://www.hal.inserm.fr/inserm-01408002
http://www.hal.inserm.fr/inserm-01408002/document
http://www.hal.inserm.fr/inserm-01408002/file/2016%2C%20Poizot-Martin%20-%20First-line%20cART%20regimen%20impacts%20the%20course%20of%20CD8%2B%20T-cell%20counts%20in%20HIV-infected%20patients.pdf
DOI : 10.1097/MD.0000000000005087

Éditeur(s) : HAL CCSD
Résumé : International audience
Fish is a rich source of essential nutrients for fetal development, but in contrast, it is also a well-known route of exposure to environmental pollutants. We assessed whether fish intake during pregnancy is associated with fetal growth and the length of gestation in a panel of European birth cohort studies. The study sample of 151,880 mother-child pairs was derived from 19 population-based European birth cohort studies. Individual data from cohorts were pooled and harmonized. Adjusted cohort-specific effect estimates were combined by using a random- and fixed-effects meta-analysis. Women who ate fish >1 time/wk during pregnancy had lower risk of preterm birth than did women who rarely ate fish (≤ 1 time/wk); the adjusted RR of fish intake >1 but <3 times/wk was 0.87 (95% CI: 0.82, 0.92), and for intake ≥ 3 times/wk, the adjusted RR was 0.89 (95% CI: 0.84, 0.96). Women with a higher intake of fish during pregnancy gave birth to neonates with a higher birth weight by 8.9 g (95% CI: 3.3, 14.6 g) for >1 but <3 times/wk and 15.2 g (95% CI: 8.9, 21.5 g) for ≥ 3 times/wk independent of gestational age. The association was greater in smokers and in overweight or obese women. Findings were consistent across cohorts. This large, international study indicates that moderate fish intake during pregnancy is associated with lower risk of preterm birth and a small but significant increase in birth weight.
The American Journal of Clinical Nutrition

hal-01118513
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118513
PUBMED : 24335057
DOI : 10.3945/ajcn.113.067421

Éditeur(s) : HAL CCSD
Résumé : Background. Chlorine is the most widely used disinfectant for drinking water treatment. During treatment process, the natural organic matter present in water reacts with chlorine to form disinfection by-products (DBPs), such as trihalomethanes (THMs) and haloacetic acids (HAAs), the most occurring ones. Several identified DBPs were recognized carcinogens or fetotoxic in animals. We conducted two epidemiological studies to assess the health effects of human exposure to DBPs regarding cancer and reproduction. Association between THM exposure and the risk of bladder cancer: a pooled analysis of 3 European case-control studies. The study included 2381 cases and 3086 controls from 3 case-control studies (France, Finland, Spain). Environmental exposure to SPCs was measured by THM concentrations in water distribution systems, retrospectively estimated through the 40-year exposure window. Information about water uses (tap water ingestion, showers and baths, swimming-pool attendance) was available. An increased risk of bladder cancer was observed, in men only, with increasing THM concentrations in water systems and duration of exposure to chlorinated surface water. No association was observed with exposure through tap water ingestion. Exposure through showers, baths and swimming in pools (available in Spanish study only) was associated with an increased risk of bladder cancer. Three North-American case-control studies were joined to the three European ones into a meta-regression. No specific dose-response relationship was identified for European studies. A global dose-response relationship was consequently estimated, including 4351 cases and 7055 controls. Association between DBP exposure and the risk of preterm birth and Intra-Uterine Growth Retardation (IUGR). This study was conducted within the PELAGIE cohort (3400 pregnant women included in early pregnancy, in Brittany, France, between 2002 and 2006). Exposure during pregnancy was measured by 2 indicators: THM concentrations in water distribution systems and a biomarker of HAA ingestion, the level of trichloroacetic acid in maternal urine at inclusion (in a nested case-control study). The regulatory database SISE-Eaux was used to estimate THMs concentrations in the water distribution systems. Water uses during pregnancy (ingested tap water, swimming-pool attendance, showers and bath frequencies and duration) were collected with questionnaires. Our results suggest an association between prenatal exposure to DBPs (THMs and HAAs) and the risk of IUGR. No association was found with the risk of preterm birth.
Contexte. La chloration est le traitement le plus utilisé pour désinfecter l’eau distribuée à la population. Lors du traitement, des sous-produits de chloration (SPCs) se forment par réaction de la matière organique naturelle présente dans l’eau avec le chlore. Les produits les plus présents sont les trihalométhanes (THMs), les acides haloacétiques (HAAs). Des études toxicologiques (animales et in vitro) ont montré la génotoxicité et/ou carcinogénicité et la reprotoxicité de certains SPCs. Nous avons mené deux études évaluant les effets sur la santé humaine de l’exposition aux SPCs, dans le domaine du cancer et de la reproduction. Association entre exposition aux THMs et risque de cancer de la vessie : une analyse poolée de 3 études cas-témoins européennes. Cette analyse a inclus 2381 cas et 3086 témoins issus de 3 études cas-témoins (France, Espagne, Finlande). L’exposition environnementale aux SPCs a été mesurée par la concentration en THMs estimée rétrospectivement dans les réseaux de distribution d’eau au cours des 40 années de la fenêtre d’exposition. Les usages de l’eau connus sont l’ingestion, les douches et les bains, la fréquentation de piscine (étude espagnole seulement). Une relation croissante a été observée entre le niveau environnemental de THMs, la durée d’exposition à une eau de surface chlorée et le risque de cancer de la vessie, chez les hommes uniquement. Aucune association n’a été observée avec l’exposition via l’ingestion d’eau du robinet. L’exposition via les douches, les bains et la piscine est apparue liée au risque de cancer de la vessie. Trois études cas-témoins nord-américaines ont été intégrées dans une méta-régression. Aucune spécificité européenne de la relation dose-réponse n’a été mise en évidence. Une relation dose-réponse globale incluant 4351 cas et 7055 témoins a été estimée. Association entre exposition aux SPCs et risque de prématurité et de retard de croissance intra-utérin (RCIU). Cette étude est issue de la cohorte bretonne Pélagie (3400 femmes enceintes recrutées en début de grossesse entre 2002 et 2006). L’exposition pendant la grossesse a été mesurée à l’aide de 2 indicateurs : la concentration en THMs de l’eau distribuée dans les réseaux et le dosage d’un biomarqueur urinaire (acide trichloroacétique) pour un sous-échantillon de femmes (étude cas-témoins nichée). Les niveaux dans les réseaux proviennent de la base de données réglementaire SISE-Eaux. Les usages de l’eau du robinet par les femmes pendant la grossesse ont été collectés par questionnaire (quantité d’eau du robinet bue, fréquentation de la piscine, fréquence et durée des douches et des bains). Notre étude suggère une association entre l’exposition prénatale aux SPCs et le risque de RCIU. Aucune association n’est observée avec le risque de prématurité.
https://tel.archives-ouvertes.fr/tel-00927735

Droits : info:eu-repo/semantics/OpenAccess
NNT : 2013REN1B008
tel-00927735
https://tel.archives-ouvertes.fr/tel-00927735
https://tel.archives-ouvertes.fr/tel-00927735/document
https://tel.archives-ouvertes.fr/tel-00927735/file/COSTET_DEIBER_Nathalie4.pdf

Éditeur(s) : Springer
Résumé : The great fecundity and very high larval mortality of most marine invertebrates and fish make possible substantial variance in the number of offspring contributed by adults to subsequent generations. The reproductive success of such organisms may thus resemble a sweepstakes lottery, in which a minority of progenitors succeeds in replacing an entire population, while the majority fails to procreate. One specific prediction of this hypothesis, that genetic diversity of newly settled cohorts should be less than that of the adult population, is tested in the present study. Microsatellite DNA markers were examined in naturally spawned juvenile European flat oysters Ostrea edulis (L.), collected over a 12-day period in 1993 from the western Mediterranean Sea, near Sete, France (43 degrees 32'N, 3 degrees 56'E) and grown out for a period of up to 10 months. Variation in these juveniles was compared to that in a pooled sample of adults collected in 1994 from two locations (Thau Lagoon and Port St. Louis) that had statistically homogeneous allelic frequencies. Though nearly twice as large as the pooled adult sample, the juvenile sample had only 60% of the adult allelic diversity. Analyses of linkage disequilibrium and kinship, as well as estimation of the effective number of parents, suggested that 10-20 adults produced this juvenile cohort. This observation supports the hypothesis of sweepstakes reproductive success and suggests that partial inbreeding may occur even in species with large populations and dispersing planktonic larvae.
Marine Biology (0025-3162) (Springer), 2007-03 , Vol. 150 , N. 6 , P. 1173-1182

Droits : 2007 Springer
http://archimer.ifremer.fr/doc/2007/publication-2616.pdf
DOI:10.1007/s00227-006-0441-y
http://archimer.ifremer.fr/doc/00000/2616/

Éditeur(s) : HAL CCSD Elsevier
Résumé : In this study, we assessed past and present influence of ancient mining activity on metal(loid) enrichment in sediments of a former mining watershed (Gardon River, SE France), that is now industrialized and urbanized. A sedimentary archive and current sediments were characterized combining geochemical analyses, zinc isotopic analyses and sequential extractions. The archive was used to establish local geochemical background and recorded (i) increasing enrichment factors (EFs) for Pb, Zn, Cd, Tl, Hg, As and Sb throughout the industrial era, (ii) a contamination peak in 1976 attributed to a tailings dam failure, and (iii) current levels in 2002 and 2011 similar to those of 1969, except for Sb and Hg, reflecting a persisting contamination pattern. Inter-element relationships and spatial distribution of EF values of current sediments throughout the watershed suggested that both ancient and current contamination had a common origin for Pb, Zn, Cd, Tl and As related to the exploitation of Pb/Zn mineralization while old Sb mines and coal extraction area were the main sources for Sb and Hg respectively. This prevailing mining origin was reflected for Zn by a relatively uniform isotopic composition at δ66Zn = 0.23 ± 0.03‰, although slight decrease from 0.23‰ to 0.18‰ was recorded from upstream to downstream sites along the river course in relation with the contribution of the lighter δ66Zn signature (~ 0.08‰) of acid mine drainage impacted tributaries. Results from sequential extractions revealed that the potential mobility of the studied metal(loid)s varied in the order Sb < Tl ≈ As < Zn < Pb < Cd, with an increase of the mobile pool for Cd, Pb, Zn and to a lesser extent for As and Tl associated to increased enrichment. Altogether, these results tend to demonstrate that ancient mining activity still contributes to metal enrichment in the sediments of the Gardon River and that some of these metals may be mobilized toward the water compartment.
ISSN: 0048-9697

hal-01054163
https://hal.archives-ouvertes.fr/hal-01054163
DOI : 10.1016/j.scitotenv.2014.02.078

Éditeur(s) : HAL CCSD Society for Range Management
Résumé : Grasslands and agroecosystems occupy one-third of the terrestrial area, but their contribution to the global carbon cycle remains uncertain. We used a set of 316 site-years of CO(2) exchange measurements to quantify gross primary productivity, respiration, and light-response parameters of grasslands, shrublands/savanna, wetlands, and cropland ecosystems worldwide. We analyzed data from 72 global flux-tower sites partitioned into gross photosynthesis and ecosystem respiration with the use of the light-response method (Gilmanov, T. G., D. A. Johnson, and N. Z. Saliendra. 2003. Growing season CO(2) fluxes in a sagebrushsteppe ecosystem in Idaho: Bowen ratio/energy balance measurements and modeling. Basic and Applied Ecology 4:167-183) from the RANGEFLUX and WORLDGRASSAGRIFLUX data sets supplemented by 46 sites from the FLUXNET La Thuile data set partitioned with the use of the temperature-response method (Reichstein, M., E. Falge, D. Baldocchi, D. Papale, R. Valentini, M. Aubinet, P. Berbigier, C. Bernhofer, N. Buchmann, M. Falk, T. Gilmanov, A. Granier, T. Grunwald, K. Havrankova, D. Janous, A. Knohl, T. Laurela, A. Lohila, D. Loustau, G. Matteucci, T. Meyers, F. Miglietta, J.M. Ourcival, D. Perrin, J. Pumpanen, S. Rambal, E. Rotenberg, M. Sanz, J. Tenhunen, G. Seufert, F. Vaccari, T. Vesala, and D. Yakir. 2005. On the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm. Global Change Biology 11: 1.424-1439). Maximum values of the quantum yield (alpha = 75 mmol.mol(-1)), photosynthetic capacity (A(max) = 3.4 mg CO(2) . m(-2).s-1), gross photosynthesis (P(g,max) = 1.16 g CO(2) . m(-2).d(-1)), and ecological light-use efficiency (epsilon(ecol) = 59 mmol . mol(-1)) of managed grasslands and high-production croplands exceeded those of most forest ecosystems, indicating the potential of nonforest ecosystems for uptake of atmospheric CO(2). Maximum values of gross primary production (8 600 g CO(2) . m(-2).yr(-1)), total ecosystem respiration (7 900 g CO(2) . m(-2).yr(-1)), and net CO(2) exchange (2 400 g CO(2) . m(-2).yr(-1)) were observed for intensively managed grasslands and high-yield crops, and are comparable to or higher than those for forest ecosystems, excluding some tropical forests. On average, 80% of the nonforest sites were apparent sinks for atmospheric CO(2), with mean net uptake of 700 g CO(2) . m(-2).yr(-1) for intensive grasslands and 933 g CO(2) . m(-2).d(-1) for croplands. However, part of these apparent sinks is accumulated in crops and forage, which are carbon pools that are harvested, transported, and decomposed off site. Therefore, although agricultural fields may be predominantly sinks for atmospheric CO(2), this does not imply that they are necessarily increasing their carbon stock.
ISSN: 1550-7424

hal-01190754
https://hal.archives-ouvertes.fr/hal-01190754
DOI : 10.2111/rem-d-09-00072.1
PRODINRA : 214043

Résumé : Nous avons étudié les phénomènes de polyploïdisation chez l'igname Dioscorea alata qui comprend trois cytotypes diploïde (2n=40), triploïde (2n=60) et tétraploïde (2n=80) en vue d'optimiser les stratégies de production d'hybrides polyploïdes. Chez ce complexe polyploïde l'augmentation de la ploïdie est corrélée avec une augmentation de la vigueur et des rendements plus élevés et plus stables. Dans un premier temps nous avons démontré l'autotétraploïdie des variétés tétraploïdes à l'aide de trois approches différentes: des analyses d'hérédité de marqueurs microsatellites, l'observation de phénomènes de double réduction et l'étude des méioses des cellules mères de pollen. Nous avons ensuite déterminé quels sont les mécanismes les plus probables à l'origine des polyploïdes naturels via l'étude de la transmission de l'hétérozygotie parentale à l'aide de microsatellites et par l'étude des incompatibilités au niveau de l'albumen lors de différents croisements intracytotypes et intercytotypes en utilisant la cytométrie en flux. Les résultats obtenus montrent que les polyploïdes de D. alata seraient apparus via la formation de gamètes non réduits de clones diploïdes. Le pool triploïde se serait édifié et diversifié uniquement par voie femelle, du fait de la non viabilité des croisements intercytotypes et de la stérilité des femelles et mâles triploïdes. Le pool tétraploïde serait apparu par union de deux gamètes non réduits de clones diploïdes (polyploidisation sexuelle bilatérale). Par la suite ce pool aurait été diversifié via des croisements intercy
We studied polyploidisation phenomena in the yam Dioscorea alata that includes three cytotypes -diploid (2n=40), triploid (2n=60) and tetraploid (2n=80) -in order to optimise polyploid hybrid production strategies. In this complex polyploid, the increase in ploidy is correlated with an increase in vigour and higher and more stable yields. We first showed the autotetraploidy of tetraploid varieties using three different approaches: heredity analyses of microsatellite markers, the observation of double reduction phenomena, and the study of meiosis of pollen mother cells. We then determined the mechanisms most likely to be at the origin of natural polyploids through the study of the transmission of parental heterozygoty using microsatellites and the study of incompatibilities at the endosperm level at the time of different intracytotypic and intercytotypic crosses using flow cytometry. The results obtained reveal that the polyploids of D. alata probably appeared through the formation of non-reduced gametes of diploid clones. The triploid pool would then have been constituted and diversified through the female pathway as a result of the non-viability of intercytotypic crosses and the sterility of female and male triploids. The tetraploid pool would have appeared as a result of the union of two non-reduced gametes of diploid clones (bilateral sexual polyploidisation). This pool would then have diversified through intercytotypic crosses with the formation of 2n gamètes through both the female and the male pathway, as well as by intracytotypic crosses within the 4X pool.

http://www.theses.fr/2012AGUY0519/document

Éditeur(s) : Université de la Réunion
Résumé : The green turtle (Chelonia mydas) is an emblematic species of marine life. However, nowadays it is subject to many threats (poaching, by-catch). Even if there is deep growing measures for its protection, the green turtle still is an endangered species and it is listed in Appendix I of Washington Convention (CITES). In order to elaborate efficient conservation and management plans, perfect knowledge of green turtle biology, but also of its population structure and their characteristics, are needed. In this thesis, we have assessed genetic structure of green turtle populations in the South-Western Indian Ocean by using genetic tools. In all, 1551 tissue samples have been collected from our study zone and from our control site French Polynesia (37 samples). All kinds if individuals were sampled (except males in reproductive phase) from 15 sampling sites including nesting, foraging, and immature development site. We used both control region of mitochondrial DNA and 6 microsatellite loci to better infer maternal and paternal lineages. We identified 29 haplotypes in the South-Western Indian Ocean. They are distributed in 3 independent and highly divergent clades, including one composed with haplotypes from Atlantic Ocean. For 7 of these haplotypes, it was the first time they were detected in the study zone. Fifteen haplotypes were previously undescribed, distributed in all the 3 clades. These new haplotypes seem to be specific to the South-Western Indian Ocean, which is then an original zone. Besides, we found a high allelic richness. These results show the South-western Indian Ocean is rich and very diversified. This region plays an important role in the global diversity of the species. The South-Western Indian Ocean is one of the two contact zones presently known between the two metapopulations of green turtles (Atlantic-Mediterranean and Indo-Pacific). This contact induces a genetic cline based on CM8 (Atlantic) and C3 (Indo-Pacific) haplotype frequencies. Analysis of the microsatellite differentiation between individuals provides evidence of genetic exchanges between the two metapopulations in the region. The South-Western Indian Ocean participates to green turtle global genetic mixing. Studying the influence of several intrinsic and extrinsic factors on population structuring provides useful information for management plan elaboration. We found no significant difference between genetic structures of foraging females and males, contrary to immature turtles which seem to be organised in 'regional pools'. This organisation could be due to both immature natal homing and influence of oceanic currents. High mitochondrial differentiation of nesting females and low global microsatellite differentiation of our samples indicate male-mediated gene flow among populations of the study zone. The genetic composition of a sampling site presents no significant variation along the year, even if we could notice some trends. Nevertheless, it can be significantly different from a year to an other one. This may result from alternation of distinct populations on the same site. We noticed different evolution in 10 or 20 years of the genetic composition depending on the sampling site. Geographic distance seems not to have significant influence on population structuring concerning microsatellite markers. Nesting females of Saziley Beach (Mayotte Island, Comoros Archipelago) present genetic divergence from females nesting in the two other sampled beaches of this island. The observed population structure shows no contradiction with the organisation of oceanic currents in the South-Western Indian Ocean. Comparing the results from the two genetic markers used, we identified 8 genetic differentiated clusters of turtles in the study zone and at least 6 distinct populations. These clusters constitute 8 potential management units (MUs) which could serve as basis in the elaboration of conservation and management plans.
La tortue verte (Chelonia mydas) constitue l'un des espèces emblématiques de la vie marine, pourtant de nombreuses menaces pèsent de nos jours encore sur sa survie (braconnage, captures accidentelles). Ainsi, malgré l'essor de mesures de protection menées à travers pour sa sauvegarde, la tortue verte constitue une espèce 'en danger d'extinction' et figure dans l'Annexe I de la Convention de Washington (CITES). Afin d'élaborer des plans de gestion et de conservation qui soient efficaces, il est important d'avoir une parfaite connaissance de la biologie de la tortue verte, mais aussi de la structure de ses populations et de leurs caractéristiques. C'est dans ce cadre que s'inscrit la présente étude. L'objectif de cette étude était d'acquérir des connaissances sur la structure des populations de tortues vertes dans le sud-ouest de l'océan Indien grâce à l'utilisation de l'outil génétique. Au total, 1551 échantillons de tissu ont été collectés dans la zone d'étude et dans notre site témoin la Polynésie française (37 échantillons). Toutes les catégories d'individus ont été échantillonnées (excepté les mâles en phase de reproduction) et les 15 sites d'échantillonnage comprennent à la fois des sites de ponte, d'alimentation et de développement pour les immatures. Deux types de marqueurs ont été utilisés : la région contrôle de l'ADN mitochondrial et 6 loci microsatellites, afin d'appréhender au mieux l'apport des lignées maternelles et paternelles. Nous avons pu mettre en évidence la présence dans le sud-ouest de l'océan Indien de 29 haplotypes distincts, appartenant à trois clades fortement divergents dont l'un constitué d'haplotypes originaires de l'océan Atlantique. Parmi ces haplotypes, 7 ont été détectés pour la première fois dans la zone d'étude, et 15 autres n'ont jamais été précédemment décrits chez cette espèce. Ils sont présents dans chacun des 3 clades d'haplotypes. Ces nouveaux haplotypes semblent spécifiques à la région, et en font une zone originale. On observe par ailleurs une grande richesse allélique dans les effectifs analysés. Ces résultats montrent que le sud-ouest de l'océan Indien est une zone riche et très diversifiée. Cette région joue un rôle important dans la diversité génétique globale de l'espèce. Le sud-ouest de l'océan Indien constitue l'une des deux seules zones connues à l'heure actuelle de contact entre les deux métapopulations de tortues vertes (Atlantique-Méditerranée et Indo-Pacifique). Ce contact a entraîné la formation d'un cline génétique portant principalement sur les fréquences relatives des haplotypes CM8 (Atlantique) et C3 (Indo-Pacifique). Les résultats obtenus lors de l'analyse microsatellite de la différenciation entre les individus originaires des deux métapopulations montrent que le sud-ouest de l'océan Indien constitue une zone d'échanges génétiques entre les deux métapopulations, participant au brasage génétique de l'espèce. L'étude de facteurs, intrinsèques et extrinsèques, pouvant influencer la structuration des populations apportent de nombreuses informations qui pourraient s'avérer utiles lors de l'élaboration de plans de gestion. La structure des femelles et des mâles en alimentation ne diffère pas, contrairement à celle des immatures qui semble s'organiser en 'pools régionaux' qui seraient le fruit de l'interaction d'un comportement de philopatrie et d'une influence des courants océaniques. La forte différenciation mitochondriale des femelles en ponte et la très faible différenciation microsatellite observée à l'échelle de la région, indiquent l'existence de flux de gènes via les mâles. La composition génétique d'un site ne varie pas de manière significative au cours de l'année. Par contre, elle peut varier d'une année à l'autre, signifiant l'alternance dans certains sites de ponte de plusieurs populations distinctes. L'évolution de la composition génétique d'un groupe, au cours de 10 ou 20 ans, diffère selon le site considéré. La distance ne semble pas influencer de manière significative la structuration des populations au niveau microsatellite. Les femelles en ponte sur la plage de Saziley (Mayotte) diffèrent génétiquement de celles pondant sur les deux autres plages de l'île. La structure observée des populations est en accord avec l'organisation des courants océanique dans la région. La confrontation des résultats obtenus à partir des deux marqueurs génétiques utilisés, permet la détermination de 8 ensembles génétiquement différenciés dans la zone d'étude et l'identification d'au moins 6 populations distinctes. Ces ensembles constituent autant d'unités de gestion (MUs) potentielles qui pourront servir de base à l'élaboration de plans de gestion et de conservation.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/these-3532.pdf
http://archimer.ifremer.fr/doc/00000/3532/

Éditeur(s) : Public Library Science
Résumé : Biological invasions rank amongst the most deleterious components of global change inducing alterations from genes to ecosystems. The genetic characteristics of introduced pools of individuals greatly influence the capacity of introduced species to establish and expand. The recently demonstrated heritability of microbial communities associated to individual genotypes of primary producers makes them a potentially essential element of the evolution and adaptability of their hosts. Here, we characterized the bacterial communities associated to native and non-native populations of the marine green macroalga Caulerpa racemosa through pyrosequencing, and explored their potential role on the strikingly invasive trajectory of their host in the Mediterranean. The similarity of endophytic bacterial communities from the native Australian range and several Mediterranean locations confirmed the origin of invasion and revealed distinct communities associated to a second Mediterranean variety of C. racemosa long reported in the Mediterranean. Comparative analysis of these two groups demonstrated the stability of the composition of bacterial communities through the successive steps of introduction and invasion and suggested the vertical transmission of some major bacterial OTUs. Indirect inferences on the taxonomic identity and associated metabolism of bacterial lineages showed a striking consistency with sediment upheaval conditions associated to the expansion of their invasive host and to the decline of native species. These results demonstrate that bacterial communities can be an effective tracer of the origin of invasion and support their potential role in their eukaryotic host's adaptation to new environments. They put forward the critical need to consider the 'meta-organism' encompassing both the host and associated micro-organisms, to unravel the origins, causes and mechanisms underlying biological invasions.
Plos One (1932-6203) (Public Library Science), 2013-07 , Vol. 8 , N. 7 , P. -

Droits : 2013 Aires et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
http://archimer.ifremer.fr/doc/00157/26791/24886.pdf
DOI:10.1371/journal.pone.0068429
http://archimer.ifremer.fr/doc/00157/26791/

Éditeur(s) : Elsevier
Résumé : Genetic variation was surveyed at 11 microsatellite loci and at 517 bp of the mitochondrial control region to investigate the presence of genetic stock structure in swordfish (Xiphias gladius) in four proximal localities of the southwest Indian Ocean. One aim of this study was to serve as a preliminary examination for congruency of structure detected by these two genetic markers, prior to conducting a more comprehensive basin-wide survey of the Indian Ocean and nearby surrounding areas. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences both revealed a great homogeneity between samples. Genetic diversity detected at the regional scale was not significantly higher than detected at the local scale. Results suggest that the southwest Indian Ocean globally functions as a unique panmictic population. However, some discrete genetic differences appeared that could possibly indicate influence from a second genetic pool in the northern part of the Indian Ocean. This structure appeared to be sex-dependent with genetic differences higher among female than among male samples. This result may indicate a higher level of spawning area fidelity for females with a subsequent sampling bias tending to homogenise male genotypic distributions. (c) 2009 Elsevier B.V. All rights reserved.
Fisheries Research (0165-7836) (Elsevier), 2009-05 , Vol. 97 , N. 3 , P. 263-269

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6455.pdf
DOI:10.1016/j.fishres.2009.03.004
http://archimer.ifremer.fr/doc/00000/6455/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Background We conducted this systematic review and meta-analysis to address the open question of a possible association between the socioeconomic level of the neighborhoods in which pregnant women live and the risk of Congenital Heart Defects (CHDs), Neural Tube Defects (NTDs) and OroFacial Clefts (OFCs). Methods We searched MEDLINE from its inception to December 20th, 2015 for case-control, cohort and ecological studies assessing the association between neighborhood socioeconomic level and the risk of CHDs, NTDs and the specific phenotypes Cleft Lip with or without Cleft Palate (CLP) and Cleft Palate (CP). Study-specific risk estimates were pooled according to random-effect and fixed-effect models. Results Out of 245 references, a total of seven case-control studies, two cohort studies and two ecological studies were assessed in the systematic review; all studies were enrolled in the meta-analysis with the exception of the two cohort studies. No significant association has been revealed between CHDs or NTDs and neighborhood deprivation index. For CLP phenotype subgroups, we found a significantly higher rate in deprived neighborhoods (Odds Ratios (OR) = 1.22, 95% CI: 1.10, 1.36) whereas this was not significant for CP phenotype subgroups (OR = 1.20, 95%CI: 0.89, 1.61). Conclusion In spite of the small number of epidemiological studies included in the present literature review, our findings suggest that neighborhood socioeconomic level where mothers live is associated only with an increased risk of CLP phenotype subgroups. This finding has methodological limitations that impede the formulation of firm conclusions, and further investigations should confirm this association. © 2016 Deguen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
ISSN: 1932-6203

hal-01406070
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01406070
DOI : 10.1371/journal.pone.0159039
PUBMED : 27783616

Éditeur(s) : HAL CCSD
Résumé : International audience
Women who drink light-to-moderately during pregnancy have been observed to have lower risk of unfavourable pregnancy outcomes than abstainers. This has been suggested to be a result of bias. In a pooled sample, including 193 747 live-born singletons from nine European cohorts, we examined the associations between light-to-moderate drinking and preterm birth, birth weight, and small-for-gestational age in term born children (term SGA). To address potential sources of bias, we compared the associations from the total sample with a sub-sample restricted to first-time pregnant women who conceived within six months of trying, and examined whether the associations varied across calendar time. In the total sample, drinking up to around six drinks per week as compared to abstaining was associated with lower risk of preterm birth, whereas no significant associations were found for birth weight or term SGA. Drinking six or more drinks per week was associated with lower birth weight and higher risk of term SGA, but no increased risk of preterm birth. The analyses restricted to women without reproductive experience revealed similar results. Before 2000 approximately half of pregnant women drank alcohol. This decreased to 39% in 2000–2004, and 14% in 2005–2011. Before 2000, every additional drink was associated with reduced mean birth weight, whereas in 2005–2011, the mean birth weight increased with increasing intake. The period-specific associations between low-to-moderate drinking and birth weight, which also were observed for term SGA, are indicative of bias. It is impossible to distinguish if the bias is attributable to unmeasured confounding, which change over time or cohort heterogeneity. © 2017, Springer Science+Business Media B.V.
ISSN: 03932990

hal-01647159
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01647159
DOI : 10.1007/s10654-017-0323-2
PUBMED : 29027084

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
UNLABELLED: ABSTRACT: BACKGROUND: Genomics, transcriptomics and proteomics of glioblastoma multiforme (GBM) have recently emerged as possible tools to discover therapeutic targets and biomarkers for new therapies including immunotherapy. It is well known that macroscopically complete surgical excision, radiotherapy and chemotherapy have therapeutic limitations to improve survival in these patients. In this study, we used a differential proteomic-based technique (2D-Difference Gel Electrophoresis) coupled with matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry to identify proteins that may serve as brain tumor antigens in new therapeutic assays. Five samples of patients presenting a GBM and five samples of microscopically normal brain tissues derived from brain epileptic surgery specimen were labeled and run in 2D-PAGE (Two-Dimensional Polyacrylamide Gel Electrophoresis) with an internal pool sample on each gel. Five gels were matched and compared with DIA (Difference In-gel Analysis) software. Differential spots were picked, in-gel digested and peptide mass fingerprints were obtained. RESULTS: From 51 protein-spots significantly up-regulated in GBM samples, mass spectrometry (MS) identified twenty-two proteins. The differential expression of a selected protein set was first validated by western-blotting, then tested on large cohorts of GBM specimens and non-tumor tissues, using immunohistochemistry and real-time RT-PCR. CONCLUSIONS: Our results confirmed the importance of previously described proteins in glioma pathology and their potential usefulness as biological markers but also revealed some new interesting targets for future therapies.
ISSN: 1477-5956

inserm-00585020
http://www.hal.inserm.fr/inserm-00585020
http://www.hal.inserm.fr/inserm-00585020/document
http://www.hal.inserm.fr/inserm-00585020/file/1477-5956-9-16.pdf
DOI : 10.1186/1477-5956-9-16

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
BACKGROUND: HIV cohort collaborations, which pool data from diverse patient cohorts, have provided key insights into outcomes of antiretroviral therapy (ART). However, the extent of, and reasons for, between-cohort heterogeneity in rates of AIDS and mortality are unclear. METHODS: We obtained data on adult HIV-positive patients who started ART from 1998 without a previous AIDS diagnosis from 17 cohorts in North America and Europe. Patients were followed up from 1 month to 2 years after starting ART. We examined between-cohort heterogeneity in crude and adjusted (age, sex, HIV transmission risk, year, CD4 count and HIV-1 RNA at start of ART) rates of AIDS and mortality using random-effects meta-analysis and meta-regression. RESULTS: During 61 520 person-years, 754/38 706 (1.9%) patients died and 1890 (4.9%) progressed to AIDS. Between-cohort variance in mortality rates was reduced from 0.84 to 0.24 (0.73 to 0.28 for AIDS rates) after adjustment for patient characteristics. Adjusted mortality rates were inversely associated with cohorts' estimated completeness of death ascertainment [excellent: 96-100%, good: 90-95%, average: 75-89%; mortality rate ratio 0.66 (95% confidence interval 0.46-0.94) per category]. Mortality rate ratios comparing Europe with North America were 0.42 (0.31-0.57) before and 0.47 (0.30-0.73) after adjusting for completeness of ascertainment. CONCLUSIONS: Heterogeneity between settings in outcomes of HIV treatment has implications for collaborative analyses, policy and clinical care. Estimated mortality rates may require adjustment for completeness of ascertainment. Higher mortality rate in North American, compared with European, cohorts was not fully explained by completeness of ascertainment and may be because of the inclusion of more socially marginalized patients with higher mortality risk.
ISSN: 0300-5771

hal-00875138
https://hal.archives-ouvertes.fr/hal-00875138
DOI : 10.1093/ije/dys164
PUBMED : 23148105

Éditeur(s) : HAL CCSD
Résumé :  
The spatial genetic differentiation among European beech stands in western Germany was analysed by a new method. The genetic structure at 8 enzyme gene loci of 100 sampled populations was used as data base. The data represent authors' own results and published data from 8 different studies. For 10 geographic distance classes [h] from 0 to 500 km, the average genetic distance between the populations for each single gene locus, a gene-pool distance and the semivariances of genetic diversity gam were computed. Significant deviation from random spatial genetic structure was tested by permutation analysis. In many cases (Lap-B, Mdh-B, Mdh-C and 6Pgdh-C) the mean genetic distance between stands with spatial distance up to 200 km was significantly smaller and the genetic distance between stands with geographic distances of 200 and 400 km was significantly greater than expected for random spatial genetic structure. Similar tendencies were found for the gene-pool distance and the semivariances of diversity. Kriging, as a method for spatial interpolation, was used to draw synthetic maps of the spatial patterns of allelic frequencies and genetic diversity. The influence of postglacial recolonisation and regeneration with foreign seed material on the spatial genetic patterns are discussed
Forest genetics

hal-01032093
https://hal.archives-ouvertes.fr/hal-01032093

Éditeur(s) : Elsevier
Résumé : The aim of this study was to distinguish between sources of the complex variety of Marennes-Oléron Bay suspended particulate organic matter (SPOM) contributing to the tropho-dynamics of the Marennes-Oléron oyster farming bay. Basic biomarkers (Chl a, C/N and POC/Chl a ratios), carbon and nitrogen stable isotopes from SPOM were analyzed and the microalgae community was characterized. The sampling strategy was bimonthly from March 2002 to December 2003; samples were taken from an intertidal mudflat. Four main sources contributed to the SPOM pool: terrigenous input from rivers, neritic phytoplankton, resuspended microphytobenthos and periodic inputs from intertidal Zostera noltii meadows. Seasonal fluctuations were observed in both years of the study period: (1) SPOM collected in the spring of 2002 (δ13C = −250/00 to −230/00) was mainly composed of fresh estuarine inputs; (2) SPOM from the summer and fall of 2002 and 2003 was predominantly neritic phytoplankton (δ13C = − 220/00 to −190/00); (3) SPOM from the winter of 2002, spring of 2003 and winter of 2003 (δ13C = −21 to −230/00) was composed of a mixture of decayed terrigenous river inputs and pelagic phytoplankton, which was predominantly resuspended microphytobenthos. In the summer of 2003—the warmest summer on record in southern France and Europe—SPOM was particularly enriched for 13C, with δ13C values ranging from −140/00 to −120/00. Pulses in δ13C values, indicative of 13C-enriched decaying materials, extended into the fall. These were attributed to benthic intertidal inputs, including both resuspended microphytobenthos and Z. noltii detritus. Changes in SPOM sources in Marennes-Oléron Bay may lead to differences in the quality of the trophic environment available for reared oysters.
Estuarine, Coastal and Shelf Science (0272-7714) (Elsevier), 2008-07 , Vol. 78 , N. 3 , P. 576-586

Droits : 2008 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/2008/publication-4313.pdf
DOI:10.1016/j.ecss.2007.11.001
http://archimer.ifremer.fr/doc/00000/4313/

Éditeur(s) : Nature Publishing Group
Résumé : Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.
Isme Journal (1751-7362) (Nature Publishing Group), 2013-10 , Vol. 7 , N. 10 , P. 1985-1996

Droits : 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13
http://archimer.ifremer.fr/doc/00160/27117/28369.pdf
DOI:10.1038/ismej.2013.90
http://archimer.ifremer.fr/doc/00160/27117/

Éditeur(s) : Elsevier Science Bv
Résumé : In New Caledonia, shrimp hatcheries are confronted with mass mortality in the larval stages, a phenomenon poorly understood as no specific causative agent has been identified. This has resulted in an excessive use of prophylactic antibiotics, although their adverse effects in aquaculture are notorious. The present work was thus aimed at selecting potential probiotic strains for penaeid hatcheries. From a pool of more than 400 marine bacterial isolates sampled from the local marine environment seven strains exhibited in vitro antagonistic activity towards Vibrio harveyi. These isolates were characterized both phenotypically and genotypically using a biochemical approach and 16S rDNA sequencing. Six out of these seven strains were found to belong to the genus Pseudoalteromonas, the last one belonging to the Vibrionaceae family and related to the Harveyi clade. Selected probiotic candidates were individually tested for antagonistic activities in vitro using a green fluorescent protein (GFP)-labelled transconjugant of V. harveyi and for inherent pathogenicity towards cultured shrimp larvae at two different developmental stages. This approach enabled rapid processing and selection of candidates to be tested in our experimental hatchery. Four different experiments were conducted to test candidate strains either alone or in combination. Repeated trials showed that postlarval survival was significantly improved by adding the strain NC201 individually to the rearing water compared to unchallenged controls. The analysis of immune-related gene expressions showed that the Litsty PEN3 transcript abundance of larvae was significantly increased after being reared in probiotic-containing water; however no significant difference in lysozyme gene expression was recorded in this study. Together, these results open new insights into the use of these strains as potential substitutes to antibiotherapy in shrimp larval rearing in New Caledonia.
Aquaculture (0044-8486) (Elsevier Science Bv), 2014-08 , Vol. 432 , P. 475-482

Droits : 2014 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00190/30129/28591.pdf
DOI:10.1016/j.aquaculture.2014.04.031
http://archimer.ifremer.fr/doc/00190/30129/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Low-level exposure to polychlorinated biphenyl-153 (PCB-153) and dichlorodiphenyldichloroethylene (p-p'-DDE) can impair fetal growth; however, the exposure-response relationship and effect modifiers of such association are not well established. This study is an extension of an earlier European meta-analysis. Our aim was to explore exposure-response relationship between PCB-153 and p-p'-DDE and birth outcomes; to evaluate whether any no exposure-effect level and susceptible subgroups exist; and to assess the role of maternal gestational weight gain (GWG). We used a pooled dataset of 9377 mother-child pairs enrolled in 14 study populations from 11 European birth cohorts. General additive models were used to evaluate the shape of the relationships between organochlorine compounds and birth outcomes. We observed an inverse linear exposure-response relationship between prenatal exposure to PCB-153 and birth weight [decline of 194g (95% CI -314, -74) per 1μg/L increase in PCB-153]. We showed effects on birth weight over the entire exposure range, including at low levels. This reduction seems to be stronger among children of mothers who were non-Caucasian or had smoked during pregnancy. The most susceptible subgroup was girls whose mothers smoked during pregnancy. After adjusting for absolute GWG or estimated fat mass, a reduction in birth weight was still observed. This study suggests that the association between low-level exposure to PCB-153 and birth weight exists and follows an inverse linear exposure-response relationship with effects even at low levels, and that maternal smoking and ethnicity modify this association.
ISSN: 0160-4120

hal-01118572
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118572
PUBMED : 25314142
DOI : 10.1016/j.envint.2014.09.013