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 Royal Society, The
Résumé : International audience
Nucleation mechanisms occurring during dynamic recrystallization play a crucial role in the evolution of microstructures and textures during high temperature deformation. In polycrystalline ice, the strong viscoplastic anisotropy induces high strain heterogeneities between grains which control the recrystallization mechanisms. Here, we study the nucleation mechanisms occurring during creep tests performed on polycrystalline columnar ice at high temperature and stress (T=−5°C;σ=0.5 MPa) by post-mortem analyses of deformation microstructures using cryogenic electron backscatter diffraction. The columnar geometry of the samples enables discrimination of the nuclei from the initial grains. Various nucleation mechanisms are deduced from the analysis of the nuclei relations with the dislocation sub-structures within grains and at grain boundaries. Tilt sub-grain boundaries and kink bands are the main structures responsible for development of polygonization and mosaic sub-structures. Nucleation by bulging at serrated grain boundaries is also an efficient nucleation mechanism near the grain boundaries where strain incompatibilities are high. Observation of nuclei with orientations not related to the ‘parent’ ones suggests the possibility of ‘spontaneous’ nucleation driven by the relaxation of the dislocation-related internal stress field. The complexity of the nucleation mechanisms observed here emphasizes the impact of stress and strain heterogeneities on dynamic recrystallization mechanisms.This article is part of the themed issue ‘Microdynamics of ice’.
ISSN: 1364-503X

hal-01467152
https://hal.archives-ouvertes.fr/hal-01467152
DOI : 10.1098/rsta.2015.0345

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The nucleation and growth processes of spherulitic alkali feldspar have been investigated in this study through X-ray microtomography and electron backscatter diffraction (EBSD) data. Here we present the first data on Shape Preferred Orientation (SPO) and Crystal Preferred Orientation (CPO) of alkali feldspar within spherulites. The analysis of synchrotron X-ray microtomography and EBSD datasets allowed us to study the morphometric characteristics of spherulites in trachytic melts in quantitative fashion, highlighting the three-dimensional shape, preferred orientation, branching of lamellae and crystal twinning, providing insights about the nucleation mechanism involved in the crystallization of the spherulites. The nucleation starts with a heterogeneous nucleus (pre-existing crystal or bubble) and subsequently it evolves forming “bow tie” morphologies, reaching radially spherulitic shapes in few hours. Since each lamella within spherulite is also twinned, these synthetic spherulites cannot be considered as single nuclei but crystal aggregates originated by heterogeneous nucleation. A twin boundary may have a lower energy than general crystal–crystal boundaries and many of the twinned grains show evidence of strong local bending which, combined with twin plane, creates local sites for heterogeneous nucleation.This study shows that the growth rates of the lamellae (10− 6–10− 7 cm/s) in spherulites are either similar or slightly higher than that for single crystals by up to one order of magnitude. Furthermore, the highest volumetric growth rates (10− 11–10− 12 cm3/s) show that the alkali feldspar within spherulites can grow fast reaching a volumetric size of ~ 10 μm3 in 1 s.
ISSN: 0024-4937

hal-01172356
https://hal.archives-ouvertes.fr/hal-01172356
DOI : 10.1016/j.lithos.2014.12.003

Éditeur(s) : HAL CCSD Royal Society of Chemistry
Résumé : International audience
A full equilibrium treatment of molecular aggregation is presented for prototypes of 1D and 3D aggregates, with and without nucleation. By skipping complex kinetic parameters like aggregate size-dependent diffusion, the equilibrium treatment allows to predict directly time-independent quantities such as critical concentrations. The relationships between the macroscopic equilibrium constants for the different paths are first established by statistical corrections and so as to comply with the detailed balance constraints imposed by nucleation, and the composition of the mixture resulting from homogeneous aggregation is then analyzed using the polylogarithm function. Several critical concentrations are distinguished: the residual monomer concentation in equilibrium (RMC) and the critical nucleation concentration (CNC), that is the threshold concentration of total subunits necessary for initiating aggregation. When increasing the concentration of total subunits, the RMC converges more strongly to its asymptotic value, the equilibrium constant of depolymerization, for 3D aggregates and in case of nucleation. The CNC moderately depends on the number of subunits in the nucleus, but sharply increases with the difference between the equilibrium constants of polymerization and nucleation. As the RMC and CNC can be numerically but not analytically determined, ansatz equations connecting them to thermodynamic parameters are proposed
PCCP : Physical chemistry chemical physics

Droits : info:eu-repo/semantics/OpenAccess
hal-01565995
https://hal.archives-ouvertes.fr/hal-01565995
https://hal.archives-ouvertes.fr/hal-01565995/document
https://hal.archives-ouvertes.fr/hal-01565995/file/Aggregates_in_equilibrium.pdf
DOI : 10.1039/c6cp08369b

Éditeur(s) : Springer
Résumé : Batch culture experiments using viral enrichment were conducted to test the response of a coastal bacterial community to autochthonous (i.e., co-existing) or allochthonous riverine viruses. The effects of viral infections on bacterial dynamics and activity were assessed by epifluorescence microscopy and thymidine incorporation, respectively, whereas the effect of viral infection on bacterial community composition was examined by polymerase chain reaction-single strand conformation polymorphism 16S ribosomal RNA fingerprinting. The percentages of high nucleic acid-containing cells, evaluated by flow cytometry, were significantly correlated (r (2) = 0.91, n = 12, p < 0.0001) to bacterial production, making this value a good predictor of active cell dynamics along the study. While confinement and temperature were the two principal experimental factors affecting bacterial community composition and dynamics, respectively, additions of freshwater viruses had significant effects on coastal bacterial communities. Thus, foreign viruses significantly reduced net bacterial population increase as compared to the enrichment treated with inactivated virus. Moreover, freshwater viruses recurrently and specifically affected bacterial community composition, as compared to addition of autochthonous viruses. In most cases, the combined treatment viruses and freshwater dissolved organic matter helped to maintain or even enhance species richness in coastal bacterial communities in agreement to the 'killing the winner' hypothesis. Thus, riverine virus input could potentially influence bacterial community composition of the coastal bay albeit with modest modification of bulk bacterial growth.
Microbial Ecology (0095-3628) (Springer), 2009-02 , Vol. 57 , N. 2 , P. 295-306

Droits : 2009 Springer
http://archimer.ifremer.fr/doc/2009/publication-6636.pdf
DOI:10.1007/s00248-008-9428-1
http://archimer.ifremer.fr/doc/00000/6636/

Éditeur(s) : HAL CCSD Wiley
Résumé : Unveiling the genetic basis of local adaptation to environmental variation is a major goal in molecular ecology. In rugged landscapes characterized by environmental mosaics, living populations and communities can experience steep ecological gradients over very short geographical distances. In lowland tropical forests, interspecific divergence in edaphic specialization (for seasonally flooded bottomlands and seasonally dry terra firme soils) has been proven by ecological studies on adaptive traits. Some species are nevertheless capable of covering the entire span of the gradient; intraspecific variation for adaptation to contrasting conditions may explain the distribution of such ecological generalists. We investigated whether local divergence happens at small spatial scales in two stands of Eperua falcata (Fabaceae), a widespread tree species of the Guiana Shield. We investigated Single Nucleotide Polymorphisms (SNP) and sequence divergence as well as spatial genetic structure (SGS) at four genes putatively involved in stress response and three genes with unknown function. Significant genetic differentiation was observed among sub-populations within stands, and eight SNP loci showed patterns compatible with disruptive selection. SGS analysis showed genetic turnover along the gradients at three loci, and at least one haplotype was found to be in repulsion with one habitat. Taken together, these results suggest genetic differentiation at small spatial scale in spite of gene flow. We hypothesize that heterogeneous environments may cause molecular divergence, possibly associated to local adaptation in E. falcata.
ISSN: 1010-061X

hal-01032412
https://hal.archives-ouvertes.fr/hal-01032412
DOI : 10.1111/jeb.12069

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Meiotic recombination predominantly occurs at discrete genomic loci called recombination hotspots, but the features defining these areas are still largely unknown (reviewed in refs 1-5). To allow a comprehensive analysis of hotspot-associated DNA and chromatin characteristics, we developed a direct molecular approach for mapping meiotic DNA double-strand breaks that initiate recombination. Here we present the genome-wide distribution of recombination initiation sites in the mouse genome. Hotspot centres are mapped with approximately 200-nucleotide precision, which allows analysis of the fine structural details of the preferred recombination sites. We determine that hotspots share a centrally distributed consensus motif, possess a nucleotide skew that changes polarity at the centres of hotspots and have an intrinsic preference to be occupied by a nucleosome. Furthermore, we find that the vast majority of recombination initiation sites in mouse males are associated with testis-specific trimethylation of lysine 4 on histone H3 that is distinct from histone H3 lysine 4 trimethylation marks associated with transcription. The recombination map presented here has been derived from a homogeneous mouse population with a defined genetic background and therefore lends itself to extensive future experimental exploration. We note that the mapping technique developed here does not depend on the availability of genetic markers and hence can be easily adapted to other species with complex genomes. Our findings uncover several fundamental features of mammalian recombination hotspots and underline the power of the new recombination map for future studies of genetic recombination, genome stability and evolution.
ISSN: 0028-0836

hal-00877681
https://hal.archives-ouvertes.fr/hal-00877681
DOI : 10.1038/nature09869
PUBMED : 21460839

Éditeur(s) : HAL CCSD
Résumé : International audience
Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various intermediate forms which can be reshuffled by minor modifications of physico-chemical conditions or amino-acid sequences. To bypass this complexity, the multifaceted phenomenon of fibril formation is reduced here to its most elementary principles defined for a linear prototype of fibril. Selected generic features, including nucleation, elongation, and conformational recruitment, are modeled using minimalist hypotheses and tools, by separating equilibrium from kinetic aspects and in vitro from in vivo conditions. These reductionist approaches allow to bring out known and new rudiments, including the kinetic and equilibrium effects of nucleation, the dual influence of elongation on nucleation, the kinetic limitations on nucleation and fibril numbers, and the accumulation of complexes in vivo by rescue from degradation. Overlooked aspects of these processes are also pointed: the exponential distribution of fibril lengths can be recovered using various models because it is attributable to randomness only. It is also suggested that the same term "critical concentration" is used for different things, involved in either nucleation or elongation
Journal of Chemical Physics

hal-01263103
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01263103
DOI : 10.1063/1.4940149
PUBMED : 26801045

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
TEM Study of Heavitree quartzite deformed at high temperatures and a pressure of 1.5 GPa with three different preparations: water-added, vacuum dried, and sodium doped show a wide range of dislocation microstructure. The vacuum dried sample has a very heterogeneous dislocation distribution varying from almost no dislocations to very high densities. Dislocation nucleation occurs by cross-slip mechanisms, such as Frank-Read sources and Orowan loops around hard inclusions. Shear bands develop in the basal plane composed of two closely spaced shear planes. Dislocations have straight segments and they are aligned along directions of dense packing, suggesting strong Peierls stress control due to the crystal structure. No voids, bubbles or dislocation walls where observed in the vacuum dried sample. The sodium-doped sample had a homogeneous high dislocation density. The water-added sample has a significantly lower, relatively uniform dislocation density. Bubbles associated with dislocations are seen in every grain. Dislocations were either present in loops around bubbles or as straight dislocations with small bubbles spaced along the dislocation line. Some of the long straight dislocations are aligned parallel to the c-axis. Sub-grains where very frequent, sometimes form cells of about 2 p,m in diameter with straight edges. Analysis of dislocations show 1/3 < a > and [c] dislocations in sub-grain walls and free 1/3 < a > dislocations on prism planes. There is clear evidence for dislocation climb with sub-grain walls, dislocation cells, dislocation junctions and dislocation debris of small loops. The major difference between vacuum dried and water-added samples are the homogeneity of the microstructure and evidence for climb in the water-added sample. Glide is clearly difficult, with a high Peierls stress in the vacuum dried sample as shown by areas of very low and very high dislocation density and the crystallographic control of dislocation line direction. The sodium-doped sample indicates that nucleation was easy by the high homogenous dislocation density, but no climb recovery has taken place. The density is high and the dislocations are strongly interacting causing tangles; no evidence for crystallographic control can be observed at these levels of strain. The activation energy for creep in Heavitree quartzite decreases with inferred water content of the specimens form 185 kJ mol(-1) for vacuum dried to 151 for 0.4 wt% water-added samples. Analysis of diffusion data for oxygen under hydrothermal conditions and inferred diffusion data for the hydrogarnet defect and dislocation velocity suggests activation energies for these processes are similar to the activation energy for the dislocation creep of Heavitree quartzite and other quartz aggregates. For data from the previously published experiments with the highest stress resolution there is a correlation between the A pre-factor in the power law creep equation and the activation energy for creep. It is speculated that the correlation may be due to variable hydrogarnet defect concentrations.
ISSN: 0031-9201

hal-00413112
https://hal.archives-ouvertes.fr/hal-00413112
DOI : 10.1016/j.pepi.2008.07.009

Éditeur(s) : HAL CCSD Bureau de recherches géologiques et minières
Résumé : National audience
Les tremblements de Terre sont sans doute l’un des phénomènes les plus catastrophiques associés à la dynamique de notre planète. Leur occurrence peut être associée d’une part au chargement lent et progressif des failles dû au mouvement des plaques tectoniques, mais également à la proximité d’autres séismes qui peuvent localement provoquer une déstabilisation du milieu. Les séismes sont classiquement interprétés dans le cadre de la théorie du cycle sismique (Fig. 1). La période asismique, correspondant au chargement séculaire des contraintes sur le plan des failles, est appelée période inter-sismique. Sa durée, entre 50 et 1000 ans, dépend du contexte géodynamique et notamment de la vitesse de chargement. La phase co-sismique correspond au séisme, i.e. à la phase de nucléation et de propagation de la rupture sismique. La période de temps associée est extrêmement courte et varie suivant les séismes entre quelques secondes à plusieurs minutes pour les méga-tremblements de terre comme celui de Sumatra en 2004 ou plus récemment celui du Japon en 2011. Enfin, suite à la rupture sismique, on considère une phase post-sismique qui correspond à un réajustement mécanique rapide du milieu qui peut s’effectuer sur plusieurs semaines, mois ou même années. La courte échelle de temps des observations sismologiques ou géodésiques (<100 ans) par rapport à la durée d’un cycle sismique (plusieurs centaines d’années) est un facteur limitant. Ainsi, aucun cycle sismique complet n’a pour l’instant pu être documenté.
ISSN: 0292-8477

insu-00913121
https://hal-insu.archives-ouvertes.fr/insu-00913121
https://hal-insu.archives-ouvertes.fr/insu-00913121/document
https://hal-insu.archives-ouvertes.fr/insu-00913121/file/geochronique_cattinetal.pdf

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : International audience
Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life-history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow-barred Spanish mackerel (Scomberomorus commerson), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo-West Pacific range using control-region sequences (including previously published datasets), cytochrome-b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (Clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (Clade I). Such a high level of genetic divergence suggested the occurrence of two sister-species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele-frequency differences were found between local populations in the southwestern Pacific, both at the mitochondrial locus (ΦST=0.282-0.609) and at microsatellite loci (^θ=0.202-0.313). Clade II consisted of four deeply divergent subclades (9.0-11.8% nucleotide divergence for the control region; 0.3-2.5% divergence at the cytochrome b locus). Mitochondrial sub-clades within Clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within Clade II was present throughout the central Indo-West Pacific; that haplogroup was found to be sister-group to an haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal.
Biological Journal of the Linnean Society

ird-00759711
http://hal.ird.fr/ird-00759711
http://hal.ird.fr/ird-00759711/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : In order to address the question of the processes involved during shear zone nucleation, we present a petro-structural analysis of millimetre-scale shear zones within the Roffna rhyolite (Suretta nappe, Eastern central Alps). Field and microscopic evidences show that ductile deformation is localized along discrete fractures that represent the initial stage of shear zone nucleation. During incipient brittle deformation, a syn-kinematic metamorphic assemblage of white mica + biotite + epidote + quartz precipitated at ca. 8.5 ± 1 kbar and 480 ± 50 °C that represent the metamorphic peak conditions of the nappe stacking in the continental accretionary wedge during Tertiary Alpine subduction. The brittle to ductile transition is characterized by the formation of two types of small quartz grains. The Qtz-IIa type is produced by sub-grain rotation. The Qtz-IIb type has a distinct CPO such that the orientation of c-axis is perpendicular to the shear fracture and basal and rhombhoedric slip systems are activated. These Qtz-IIb grains can either be formed by recrystallization of Qtz-IIa or by precipitation from a fluid phase. The shear zone widening stage is characterized by a switch to diffusion creep and grain boundary sliding deformation mechanisms. During the progressive evolution from brittle nucleation to ductile widening of the shear zone, fluid–rock interactions play a critical role, through chemical mass-transfer, metasomatic reactions and switch in deformation mechanisms.
ISSN: 0191-8141

hal-01355954
https://hal.archives-ouvertes.fr/hal-01355954
DOI : 10.1016/j.jsg.2016.02.015

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
BACKGROUND: African Americans with head and neck squamous cell carcinoma (HNSCC) have a lower survival rate than whites. This study investigated the functional importance of ancestry-informative single-nucleotide polymorphisms (SNPs) in HNSCC and also examined the effect of functionally important genetic elements on racial disparities in HNSCC survival. METHODS: Ancestry-informative SNPs, RNA sequencing, methylation, and copy number variation data for 316 oral cavity and laryngeal cancer patients were analyzed across 178 DNA repair genes. The results of expression quantitative trait locus (eQTL) analyses were also replicated with a Gene Expression Omnibus (GEO) data set. The effects of eQTLs on overall survival (OS) and disease-free survival (DFS) were evaluated. RESULTS: Five ancestry-related SNPs were identified as cis-eQTLs in the DNA polymerase beta (POLB) gene (false discovery rate [FDR]<0.01). The homozygous/heterozygous genotypes containing the African allele showed higher POLB expression than the homozygous white allele genotype (P<.001). A replication study using a GEO data set validated all 5 eQTLs and also showed a statistically significant difference in POLB expression based on genetic ancestry (P=.002). An association was observed between these eQTLs and OS (P<.037; FDR<0.0363) as well as DFS (P=.018 to.0629; FDR<0.079) for oral cavity and laryngeal cancer patients treated with platinum-based chemotherapy and/or radiotherapy. Genotypes containing the African allele were associated with poor OS/DFS in comparison with homozygous genotypes harboring the white allele. CONCLUSIONS: Analyses show that ancestry-related alleles could act as eQTLs in HNSCC and support the association of ancestry-related genetic factors with survival disparities in patients diagnosed with oral cavity and laryngeal cancer. (C) 2016 American Cancer Society.
ISSN: 0008-543X

hal-01519253
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01519253
DOI : 10.1002/cncr.30457
PUBMED : 27906459

Éditeur(s) : HAL CCSD
Résumé : International audience
The presence of photosynthetic zooxanthellae (dinoflagellates) in the tissue of many cnidarians is the main reason for their ecological success (i.e. coral reefs). It could also be the main cause of their demise, as the worldwide bleaching of reef-building coral is nothing less than the breakdown of this symbiotic association. The stability of this relationship is the principal marker for the biomonitoring of cnidarian health. We have therefore developed a new, simple method to isolate zooxanthellae in a few steps using NaOH solution. The protocol was validated in three symbiotic cnidarian species: a sea anemone, a gorgonian and a coral. Our method allows the isolation of intact and viable zooxanthellae with better yields than classic methods, especially for species with a calcareous skeleton. Moreover, the isolated zooxanthellae were free of host nucleic contaminants, facilitating subsequent specific molecular analyses.
Journal of Experimental Biology

hal-01546180
https://hal.archives-ouvertes.fr/hal-01546180
DOI : 10.1242/jeb.074955

Éditeur(s) : HAL CCSD Linnean Society of London
Résumé : International audience
Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life-history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow-barred Spanish mackerel (Scomberomorus commerson), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo-West Pacific range using control-region sequences (including previously published datasets), cytochrome-b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (Clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (Clade I). Such a high level of genetic divergence suggested the occurrence of two sister-species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele-frequency differences were found between local populations in the southwestern Pacific, both at the mitochondrial locus (ΦST=0.282-0.609) and at microsatellite loci (^θ=0.202-0.313). Clade II consisted of four deeply divergent subclades (9.0-11.8% nucleotide divergence for the control region; 0.3-2.5% divergence at the cytochrome b locus). Mitochondrial sub-clades within Clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within Clade II was present throughout the central Indo-West Pacific; that haplogroup was found to be sister-group to an haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal.
ISSN: 0024-4066

ird-00759711
http://hal.ird.fr/ird-00759711
http://hal.ird.fr/ird-00759711v2/document
http://hal.ird.fr/ird-00759711/file/FauvelotBorsa_Scomberomorus%20commerson%20p%20HAL.pdf

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Two genome-wide association studies (GWASs) recently highlighted the HLA-DRA and HLA-DRB5 genes as associated with Parkinson disease (PD). However, because HLA-DRA displays a low level of polymorphisms and HLA-DRB5 is only present in approximately 20% of the population, these findings are difficult to interpret. Our aims were: (1) to replicate and investigate in greater detail the association between PD and the HLA-DR region; (2) to identify PD-associated HLA alleles; and (3) to perform a meta-analysis of our top finding. As part of 2 French population-based case-control studies of PD including highly ethnically homogeneous participants, we investigated the association between PD and 51 Single-nucleotide polymorphisms (SNPs) in the HLA-DR region. HLA-DRB1 alleles were imputed using the HLA(*) IMP software. HLA typing was performed in a subsample of the participants. We performed a meta-analysis of our top finding based on 4 GWAS data sets. Among 499 cases and 1123 controls, after correction for multiple testing, we found an association with rs660895 (OR/minor allele, 0.70; 95% CI, 0.57-0.87) within the HLA-DRB1 gene, which encodes the most polymorphic HLA-DR chain (DRβ). A meta-analysis (7996 cases, 36455 controls) confirmed this association (OR, 0.86; 95% CI, 0.82-0.91; P < .0001). SNP-based imputation of HLA alleles showed an inverse association between PD and the HLA-DRB1(*) 04 allele. We replicated an association between PD and the HLA-DR region and provided further insight into the loci and alleles involved. The highly polymorphic HLA-DRB1 locus contains rs660895, which represents a more legitimate candidate than previous ones. Our finding is in agreement with the hypothesis of an immune component in PD pathophysiology. © 2012 Movement Disorder Society.
ISSN: 0885-3185

inserm-00721562
http://www.hal.inserm.fr/inserm-00721562
http://www.hal.inserm.fr/inserm-00721562/document
http://www.hal.inserm.fr/inserm-00721562/file/Table1.pdf
http://www.hal.inserm.fr/inserm-00721562/file/Table2.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
Background: We examined the association between exposure during pregnancy to trihalomethanes, the most common water disinfection by-products, and birth outcomes in a European cohort study (Health Impacts of Long-Term Exposure to Disinfection By-Products in Drinking Water). We took into account exposure through different water uses, measures of water toxicity, and genetic susceptibility. Methods: We enrolled 14,005 mothers (2002-2010) and their children from France, Greece, Lithuania, Spain, and the UK. Information on lifestyle- and water-related activities was recorded. We ascertained residential concentrations of trihalomethanes through regulatory records and ad hoc sampling campaigns and estimated route-specific trihalomethane uptake by trimester and for whole pregnancy. We examined single nucleotide polymorphisms and copy number variants in disinfection by-product metabolizing genes in nested case-control studies. Results: Average levels of trihalomethanes ranged from around 10 μg/L to above the regulatory limits in the EU of 100 μg/L between centers. There was no association between birth weight and total trihalomethane exposure during pregnancy (β = 2.2 g in birth weight per 10 μg/L of trihalomethane, 95% confidence interval = 3.3, 7.6). Birth weight was not associated with exposure through different routes or with specific trihalomethane species. Exposure to trihalomethanes was not associated with low birth weight (odds ratio [OR] per 10 μg/L = 1.02, 95% confidence interval = 0.95, 1.10), small-for-gestational age (OR = 0.99, 0.94, 1.03) and preterm births (OR = 0.98, 0.9, 1.05). We found no gene-environment interactions for mother or child polymorphisms in relation to preterm birth or small-for-gestational age. Conclusions: In this large European study, we found no association between birth outcomes and trihalomethane exposures during pregnancy in the total population or in potentially genetically susceptible subgroups. © 2016 Wolters Kluwer Health, Inc.
Epidemiology

hal-01392115
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01392115
DOI : 10.1097/EDE.0000000000000544
PUBMED : 27468006

Éditeur(s) : Elsevier
Résumé : Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.
Developmental & Comparative Immunology (0145-305X) (Elsevier), 2006 , Vol. 30 , N. 3 , P. 283-288

Droits : 2005 Elsevier Ltd All rights reserved
http://archimer.ifremer.fr/doc/2006/publication-2332.pdf
DOI:10.1016/j.dci.2005.04.003
http://archimer.ifremer.fr/doc/00000/2332/

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : Nucleotide diversity was assessed within nine candidate genes (in total 4.6 kb) for the time of bud burst in nine sessile oak (Quercus petraea) populations distributed in central and northern Europe. The sampled populations were selected on the basis of their contrasting time of bud burst observed in common garden experiments (provenance tests). The candidate genes were selected according to their expression profiles during the transition from quiescent to developing buds and/or their functional role in model plants. The overall nucleotide diversity was large (pi(tot) - 6.15 x 10(-3); pi(silent) - 11.2 x 10(-3)), but population differentiation was not larger than for microsatellites. No outlier single-nucleotide polymorphism (SNP), departing from neutral expectation, was found among the total of 125 SNPs. These results contrasted markedly with the significant associations that were observed between the candidate genes and bud burst in segregating populations. Quantitative trait loci (QTLs) for bud burst were identified for 13 year*site seasonal observations in a cloned mapping pedigree. Nineteen QTLs were detected, and QTLs located on linkage groups 2, 5 and 9 contributed repeatedly to more than 12% of the phenotypic variation of the trait. Eight genes were polymorphic in the two parents of the pedigree and could be mapped on the existing genetic map. Five of them located within the confidence intervals of QTLs for bud burst. Interestingly, four of them located within the three QTLs exhibiting the largest contributions to bud burst.
ISSN: 0018-067X

hal-01032156
https://hal.archives-ouvertes.fr/hal-01032156
DOI : 10.1038/hdy.2009.170

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
We investigated the characteristics of the sulfur-oxidizing symbiont hosted in the gills of Codakia orbicularis, a bivalve living in shallow marine tropical environments. Special attention was paid to describing the heterogeneity of the population by using single-cell approaches including flow cytometry (FCM) and different microscopic techniques and by analyzing a cell size fractionation experiment. Up to seven different subpopulations were distinguished by FCM based on nucleic acid content and light side scattering of the cells. The cell size analysis of symbionts showed that the symbiotic population was very heterogeneous in size, i.e., ranging from 0.5 to 5 _m in length, with variable amounts of intracellular sulfur. The side-scatter signal analyzed by FCM, which is often taken as a proxy of cell size, was greatly influenced by the sulfur content of the symbionts. FCM revealed an important heterogeneity in the relative nucleic acid content among the subclasses. The larger cells contained exceptionally high levels of nucleic acids, suggesting that these cells contained multiple copies of their genome, i.e., ranging from one copy for the smaller cells to more than four copies for the larger cells. The proportion of respiring symbionts (5-cyano-2,3-ditolyl-terazolium chloride positive) in the bacteriocytes of Codakia revealed that around 80% of the symbionts hosted by Codakia maintain respiratory activity throughout the year. These data allowed us to gain insight into the functioning of the symbionts within the host and to propose some hypotheses on how the growth of the symbionts is controlled by the host.
ISSN: 0099-2240

hal-00716079
https://hal.univ-antilles.fr/hal-00716079
DOI : 10.1128/AEM.01683-06