Éditeur(s) : HAL CCSD
Résumé : International audience
In all vertebrate species, estrogens play a crucial role in the development, growth, and function of reproductive and nonreproductive tissues. A large number of natural or synthetic chemicals present in the environment and diet can interfere with estrogen signaling; these chemicals are called endocrine disrupting chemicals (EDCs) or xenoestrogens. Some of these compounds have been shown to induce adverse effects on human and animal health, and some compounds are suspected to contribute to diverse disease development. Because xenoestrogens have varying sources and structures and could act in additive or synergistic effects when combined, they have multiple mechanisms of action. Consequently, an important panel of in vivo and in vitro bioassays and chemical analytical tools was used to screen, evaluate, and characterize the potential impacts of these compounds on humans and animals. In this paper, we discuss different molecular actions of some of the major xenoestrogens found in food or the environment, and we summarize the current models used to evaluate environmental estrogens.
Int J Endocrinol

Droits : info:eu-repo/semantics/OpenAccess
inserm-00863365
http://www.hal.inserm.fr/inserm-00863365
http://www.hal.inserm.fr/inserm-00863365/document
http://www.hal.inserm.fr/inserm-00863365/file/501851.pdf
PUBMED : 23737774

Résumé : This study contributes to inventory programme on emerging pollutants in French waters and to the general reflection which will enable to update the list of relevant substnaces to be included in the new monitoring programmes to come. This work concerns the coastal part of the inventory programme on marine waters and sediments of France and five overseas french departments (OFD). In this goal, passive sampling techniques and direct extraction techniques have been tested through the implementation of in situ systems integrators POCIS (Polar Organic Chemical Integrative Sampler) and the extraction by SBSE bars (Stir bar sorptive extraction) directly in the waters sampled. Finally, analyzes of sediment completed the acquisition of data. Arount 40 stations were sampled for shore waters and sediments were collected from 7 stations in France and 5 stations in the OFD (one station/OFD). In analytical terms, 1054 analyzes were carried out on POCIS membranes and only 64 data exceeded the limit of detection (LD), 12726 analyzes came from SBSE extractions and 304 were above the LD and 1536 analyzes in sediment showed that 237 data were above the limit of quantification (LQ). Finally, 169 different substances were investigated and 68 of them were detected at least once in water or sediment. The lack of replicates for POCIS analyzes and those in the sediment limited the statistical treatment of data. The results were used to determine the level of contamination, the detection frequency (FD), the distribution of substances between France and OFD, the comparison with environmental thresholds (the PNEC) and the origin/use of the substances. In littoral waters, 32 substances were identified and 19 were quantified. In the sediment, 47 substances were quantified. Nine substances were detected in both water and sediment. In France, the 15 substances that were quantified at higher frequencies (> 50 %, one out of 2 sites) were quantified in sediments. These are the congeners of PAHs (11 substances), organic forms of tin (2 substances), diethyl lead and 209 PBDE congener. In the OFD, the 22 substances that were quantified at higher frequencies (> 50 %, one out of 2 sites) were measured in sediments. These are congeners of PAHs (13 substances) , alkylphenols ( 3 molecules: the mono and diethoxyate nonylphenol and the 4-ter butylphenol ), the organic forms of tin (2 substances), products of metabolism insecticide DDT ( 2 products), diethyl lead and the 209 PBDE congener. The study of the highest concentrations distribution of substances between France and OFD shows that the 5 (among 19 molecules) highest concentrations in water and the 6 (among 47 molecules) highest concentrations in sediments are found in OFD. Reference to PNEC indicates that four pesticides in water and 11 different substances in sediments exceed the environmental thresholds. Substances with highest detection frequency are found in the sediment. The distribution of data by use or nature of the substance shows that plasticizers and pesticides predominate in raw water, both in France and overseas departments while PAHs in sediments dominate in France and in OFD.
Cette étude contribue au programme d’inventaire des substances chimiques émergentes dans les eaux françaises et à la réflexion qui doit permettre d’actualiser la liste des substances pertinentes à surveiller de manière régulière dans le cadre des nouveaux programmes de surveillance. Ce travail concerne la partie littorale de l’inventaire, sur les eaux brutes et les sédiments de la métropole et des 5 DOM. Dans ce cadre, des techniques d’échantillonnage passif (EP) et d’extraction directe ont été testées grâce à la mise en place in situ de systèmes intégrateurs POCIS (Polar Organic Chemical Integrative Sampler) et à l’extraction par des barres SBSE (Stir Bar Sorptive Extraction) directement dans les eaux échantillonnées. Enfin des analyses de sédiments ont complété l’acquisition des données. L’eau d’une quarantaine de stations a été échantillonnée et des sédiments ont été prélevés sur 7 stations en métropole et dans 5 stations dans les DOM (une station par DOM). En termes analytiques, 1054 analyses ont été réalisées sur les membranes POCIS et 64 dépassaient la limite de détection (LD), 12726 analyses ont concerné les extractions par SBSE pour 304 résultats situés au dessus de la LD et 1536 analyses effectuées dans le sédiment ont donné 237 valeurs supérieures à la limite de quantification (LQ). Au bilan 169 substances différentes ont été recherchées et 68 d’entre elles ont été détectées au moins une fois dans l’eau brute ou le sédiment. L’absence de réplicats pour les analyses POCIS et celles dans le sédiment a limité le traitement statistique des données. Les résultats ont permis de déterminer le niveau de contamination, la fréquence de détection (FD), la distribution métropole/DOM des substances, la comparaison avec les seuils environnementaux (PNEC) et l’origine des substances. Dans l’eau 32 substances ont été identifiées et 19 ont été quantifiées. Dans le sédiment 47 substances sont quantifiées .Neuf substances sont détectées à la fois dans l’eau et le sédiment. En métropole, les 15 substances quantifiées aux plus hautes fréquences (> 50%, soit un site sur 2) sont quantifiées dans les sédiments. Ce sont les congénères de la famille des HAP (11 substances), des formes organiques de l’étain (2 substances), le plomb diéthyle et le congénère 209 des PBDE. Dans les DOM, les 22 substances quantifiées aux plus hautes fréquences (> 50%, soit un site sur 2) sont mesurées dans les sédiments. Ce sont des congénères de la famille des HAP dans (13 substances), des alkylphénols (3 substances : nonylphénols mono et diéthoxylés et 4-ter butylphénol), des formes organiques de l’étain (2 substances), des produits de métabolisation de l’insecticide DDT (2 produits), du plomb diéthyle et du congénère 209 des PBDE. L’étude de la répartition des plus fortes concentrations entre la métropole et les DOM montre que les 5 (sur 19) concentrations les plus élevées mesurées dans l’eau et les 6 (sur 47) plus fortes concentrations mesurées dans les sédiments sont trouvées dans les DOM. Les substances mesurées aux fortes fréquences sont observées dans le sédiment. La référence à la PNEC indique le dépassement de la norme pour 4 pesticides dans l’eau brute et 11 substances diverses dans les sédiments. L’exploitation des données par usage ou nature des substances montre que les plastifiants et les pesticides sont majoritaires dans les eaux brutes, à la fois en métropole et dans les DOM alors que ce sont les HAP qui dominent dans les sédiments, en métropole et dans les DOM.

Droits : 2014 ONEMA, Ifremer
http://archimer.ifremer.fr/doc/00259/36994/35483.pdf
http://archimer.ifremer.fr/doc/00259/36994/

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

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

Éditeur(s) : 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) : HAL CCSD MDPI
Résumé : International audience
Tetherin (BST2/CD317) has been recently recognized as a potent interferon-induced antiviral molecule that inhibits the release of diverse mammalian enveloped virus particles from infected cells. By targeting an immutable structure common to all these viruses, the virion membrane, evasion of this antiviral mechanism has necessitated the development of specific countermeasures that directly inhibit tetherin activity. Here we review our current understanding of the molecular basis of tetherin's mode of action, the viral countermeasures that antagonize it, and how virus/tetherin interactions may affect viral transmission and pathogenicity.
ISSN: 1999-4915

hal-01121799
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01121799
PUBMED : 21994744
DOI : 10.3390/v3050520
PUBMEDCENTRAL : PMC3185764

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The tropical to warm-temperate marine brown macroalgal genus Lobophora (Dictyotales, Phaeophyceae) recently drew attention because of its striking regional diversity. In this study we reassess Lobophora global species diversity, and species distributions, and explore how historical factors have shaped current diversity patterns. We applied a series of algorithmic species delineation techniques on a global mitochondrial cox3 dataset of 598 specimens, resulting in an estimation of 98–121 species. This diversity by far exceeds traditional diversity estimates based on morphological data. A multi-locus time-calibrated species phylogeny using a relaxed molecular clock, along with DNA-confirmed species distribution data was used to analyse ancestral area distributions, dispersal-vicariance-founder events, and temporal patterns of diversification under different biogeographical models. The origin of Lobophora was estimated in the Upper Cretaceous (−75 to −60 MY), followed by gradual diversification until present. While most speciation events were inferred within marine realms, founder events also played a non-negligible role in Lobophora diversification. The Central Indo-Pacific showed the highest species diversity as a result of higher speciation events in this region. Most Lobophora species have small ranges limited to marine realms. Lobophora probably originated in the Tethys Sea and dispersed repeatedly in the Atlantic (including the Gulf of Mexico) and Pacific Oceans. The formation of the major historical marine barriers (Terminal Tethyan event, Isthmus of Panama, Benguela upwelling) did not act as important vicariance events. Long-distance dispersal presumably represented an important mode of speciation over evolutionary time-scales. The limited geographical ranges of most Lobophora species, however, vouch for the rarity of such events.
ISSN: 1055-7903

hal-01535635
http://hal.upmc.fr/hal-01535635
http://hal.upmc.fr/hal-01535635/document
http://hal.upmc.fr/hal-01535635/file/Vieira_2017_Historical.pdf
DOI : 10.1016/j.ympev.2017.03.007

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
The first studies of the 16S rRNA gene diversity of the bacterial symbionts found in lucinid clams did not clarify how symbiotic associations had evolved in this group. Indeed, although species-specific associations deriving from a putative ancestral symbiotic association have been described (coevolution scenario), associations between the same bacterial species and various host species (opportunistic scenario) have also been described. Here, we carried out a comparative molecular analysis of hosts, based on 18S and 28S rRNA gene sequences, and of symbionts, based on 16S rRNA gene sequences, to determine as to which evolutionary scenario led to modern lucinid/symbiont associations. For all sequences analyzed, we found only three bacterial symbiont species, two of which are harbored by lucinids colonizing mangrove swamps. The last symbiont is the most common and was found to be independent of biotope or depth. Another interesting feature is the similarity of ctenidial organization of lucinids from the Philippines to those described previously, with the exception that two bacterial morphotypes were observed in two different species (Gloverina rectangularis and Myrtea flabelliformis). Thus, there is apparently no specific association between Lucinidae and their symbionts, the association taking place according to which bacterial species is present in the environment.
ISSN: 0168-6496

hal-00743766
https://hal.univ-antilles.fr/hal-00743766
DOI : 10.1111/j.1574-6941.2010.00989.x

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
The brown algal genus Padina (Dictyotales, Phaeophyceae) is distributed worldwide in tropical and temperate seas. Global species diversity and distribution ranges, however, remain largely unknown. Species-level diversity was reassessed using DNA-based, algorithmic species delineation techniques based on cox3 and rbcL sequence data from 221 specimens collected worldwide. This resulted in estimates ranging from 39 to 61 putative species (ESUs), depending on the technique as well as the locus. We discuss the merits, potential pitfalls, and evolutionary and biogeographic significance of algorithmic species delineation. We unveil patterns whereby ESUs are in all but one case restricted to either the Atlantic or Indo-Pacific Ocean. Within ocean basins we find evidence for the vast majority of ESUs to be confined to a single marine realm. Exceptions, whereby ESUs span up to three realms, are located in the Indo-Pacific Ocean. Patterns of range-restricted species likely arise by repeated founder events and subsequent peripatric speciation, hypothesized to dominate speciation mechanisms for coastal marine organisms in the Indo-Pacific. Using a three-gene (cox3, psaA and rbcL), relaxed molecular clock phylogenetic analysis we estimated divergence times, providing a historical framework to interpret biogeographic patterns.
ISSN: 0022-3646

hal-01545323
https://hal.archives-ouvertes.fr/hal-01545323
DOI : 10.1111/jpy.12027

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

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

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]Aim[/b][br/] Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species.[br/] [br/] [b]Location[/b][br/] Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America.[br/] [br/] [b]Methods[/b][br/] Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH-psbA and trnC-ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times.[br/] [br/] [b]Results[/b][br/] Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation-by-distance process or exhibit a phylogeographical signal.[br/] [br/] [b]Main conclusions[/b][br/] The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.
ISSN: 0305-0270

hal-01032395
https://hal.archives-ouvertes.fr/hal-01032395
DOI : 10.1111/j.1365-2699.2011.02678.x

Éditeur(s) : HAL CCSD Wiley
Résumé : The routes through which Norway spruce recolonized the Alps after the last ice age were investigated at the genetic level. Seven populations along the Alpine range plus one Apennine population were characterized for seven sequence-characterized amplified region (SCAR) loci, detecting an overall FST = 0.118. This rather high value for forest species reflects an uneven distribution of genetic variability, and was analysed through different statistical methods. Alternative hypotheses were tested under the isolation-by-distance model and using the analysis of molecular variance (amova) frame. We conclude that the hypothesis of the existence of a glacial refugium in the Apennines should be rejected, while a putative relict population is identified in the Maritime Alps. The Alpine range of Norway spruce appears to be split in two parts across a north-south line. The results are discussed in comparison with data based on morphological markers, isozymes, chloroplast microsatellites and mitochondrial markers.
ISSN: 0962-1083

hal-01031243
https://hal.archives-ouvertes.fr/hal-01031243
DOI : 10.1046/j.1365-294x.2000.00911.x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.
ISSN: 1462-2912

hal-01191731
http://hal.upmc.fr/hal-01191731
http://hal.upmc.fr/hal-01191731/document
http://hal.upmc.fr/hal-01191731/file/Massana_2015_Marine_protist.pdf
DOI : 10.1111/1462-2920.12955

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

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

Éditeur(s) : HAL CCSD
Résumé :   Diplôme : DEA
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
As part of a programme of degraded soils rehabilitation, and in order to follow the biological processes connected with the soils reconstitution, it is a requisite to determine indicators able to account for the evolution of the soil. These indicators can he found on structural and/or functional characteristics of the bacterial communities, such as soil respiration, denitrification or genetic diversity. Theses descriptors are able to characterize the global community or targeted communities chosen for their importance in the ecosystem functioning. In this work, we tried to know whether soil bacteria genetic diversity was able to be a relevant indicator of the soil evolution in a rehabilitated sequence. This diversity is apprehended via a molecular technique: ARISA. A chronosequence situated on a gold mine, already experimented as part of a programme of degraded zones rehabilitation, was at our disposal. Results show that ARISA is a very sensitive technique, able to account for the bacterial community heterogeneity in a soil but unable, at the parcel scale, to discriminate the treatments nor to account for the evolution in lime of planted treatments. Lastly, the advantage of this indicator of genetic diversity may arise from its confrontation to other indicators (functional, for example).
Dans le cadre de la revégétalisation d'un sol dégradé et afin de pouvoir suivre les processus biologiques liés à la reconstitution des sols, il est nécessaire de déterminer des indicateurs pouvant rendre compte de l'évolution de l'état du sol. Ces indicateurs peuvent être fondés sur des caractéristiques fonctionnelles et/ou structurales des communautés bactériennes telles que la respiration, la dénitrification ou la diversité génétique. Ces descripteurs peuvent analyser la communauté globale ou des communautés cibles choisies pour leur importance dans le fonctionnement de l'écosystème. L'objectif de ce stage était de savoir si la diversité génétique des bactéries du sol pouvait être un indicateur de l'évolution des sols au sein d'une séquence de revégétalisation. Cette diversité est appréhendée par une technique de biologie moléculaire : l'ARISA. On dispose d'une chronoséquence située sur une mine d'or étudiée dans le cadre d'un programme de réhabilitation des zones dégradées. Les résultats montrent que l'ARISA est une technique très sensible, qui rend bien compte de l’hétérogénéité des communautés bactériennes présentes dans un sol mais est incapable, à l’échelle de la parcelle, de discriminer ni les traitements ni de rendre compte de l'évolution dans le temps de ces parcelles. Enfin, l'intérêt de cet indicateur de diversité génétique pourra résulter de sa confrontation avec d'autres indicateurs (fonctionnels par exemple).
https://hal.archives-ouvertes.fr/hal-01189155

hal-01189155
https://hal.archives-ouvertes.fr/hal-01189155
PRODINRA : 9464

Éditeur(s) : HAL CCSD Wiley
Résumé : [b]Aim[/b][br/] [br/] The phylogeographical history of Neotropical species can be difficult to reconstruct because of superimposed Neogene and Quaternary histories, and because of taxonomic uncertainty. We analysed range-wide genetic diversity in a widespread pioneer tree species, Jacaranda copaia (Aubl.) D. Don, to characterize phylogeographical structure, date the evolutionary relationships among lineages, and evaluate the role of dispersal and vicariance in establishing the present geographical range.[br/] [br/] [br/] [b]Location[/b][br/] [br/] Guiana Shield; central, southern and western Amazon Basin; Chocó region; Central America.[br/] [br/] [br/] [b]Methods[/b][br/] [br/] We analysed nine nuclear simple sequence repeat loci (nuSSR), eight chloroplast SSRs (cpSSR), and two cpDNA intergenic sequences in 341 adult trees. Genetic differentiation at nuSSRs was inferred using Bayesian clustering. Dating of chloroplast lineage divergence was obtained using a range of published mutation rates and Bayesian coalescence analyses. Population divergence dating was performed using an isolation-with-migration model for eight loci (one cp sequence and seven nuSSRs).[br/] [br/] [br/] [b]Results[/b][br/] [br/] Nuclear SSR variation identified three geographically overlapping clusters (nu-1, nu-2, nu-3). Twelve cpDNA haplotypes were clustered into two haplogroups (cp-1, cp-2) with the central Amazon harbouring the highest diversity. Molecular dating analysis suggests that cpDNA haplotype diversification started around the end of the Pliocene (2.61 Ma on average), whereas population divergence was more recent and occurred during the mid-Quaternary (point estimates between 357 and 436 ka).[br/] [br/] [br/] [b]Main conclusions[/b][br/] [br/] The genetic variation of J. copaia in the Neotropics was shaped mainly by Pleistocene events. Chloroplast diversity did not display the expected cis/trans Andean disjunction, indicating recent dispersal. Nuclear variation revealed that separate regions share a recent history, with a centre of diversity in the central Amazon Basin. The geographical pattern of diversity is congruent with the distribution of the two subspecies, J. copaia copaia and J. copaia spectabilis, and evidence of nuSSR admixture between the two taxa supports their classification as subspecies.
ISSN: 0305-0270

hal-01032410
https://hal.archives-ouvertes.fr/hal-01032410
DOI : 10.1111/j.1365-2699.2012.02797.x

Éditeur(s) : HAL CCSD MDPI
Résumé : International audience
Marine micro-and macroorganisms are well known to produce metabolites with high biotechnological potential. Nearly 40 years of systematic prospecting all around the New Caledonia archipelago and several successive research programs have uncovered new chemical leads from benthic and planktonic organisms. After species identification, biological and/or pharmaceutical analyses are performed on marine organisms to assess their bioactivities. A total of 3582 genera, 1107 families and 9372 species have been surveyed and more than 350 novel molecular structures have been identified. Along with their bioactivities that hold promise for therapeutic applications, most of these molecules are also potentially useful for cosmetics and food biotechnology. This review highlights the tremendous marine diversity in New Caledonia, and offers an outline of the vast possibilities for natural products, especially in the interest of pursuing collaborative fundamental research programs and developing local biotechnology programs.
EISSN: 1660-3397

Droits : http://creativecommons.org/licenses/by/
hal-01292225
http://hal.upmc.fr/hal-01292225
http://hal.upmc.fr/hal-01292225/document
http://hal.upmc.fr/hal-01292225/file/marinedrugs-14-00058.pdf
DOI : 10.3390/md14030058

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Hepatocellular carcinoma (HCC) is a particularly severe disease characterized by a high rate of recurrence and death even after surgical resection. Molecular characterization of HCC helps refine prognosis and may facilitate the development of improved therapy. Phosphatidylinositol 4-kinases have recently been identified as cellular factors associated with cancer. Also, phosphatidylinositol 4-kinase type IIIα (PI4KA) is necessary for the propagation of the hepatitis C virus, a major etiological factor for HCC. METHODS: Reverse transcription, quantitative real-time PCR was used to assay PI4KA mRNA. The expression levels were investigated both in a collection of molecularly and clinically characterized hepatic tissues from 344 patients with diverse liver diseases and in human hepatocyte cell lines whose proliferative and differentiation status was controlled by specific culture conditions. Analytical microarray data for 60 HCC and six normal liver tissue samples were exploited to study correlations between PI4KA mRNA levels and cell proliferation markers in vivo. Postoperative disease-specific survival and time to recurrence in a set of 214 patients with HCC were studied by univariate and multivariate analyses. RESULTS: PI4KA mRNA was more abundant in HCC than normal healthy tissues. This upregulation correlated significantly with both poor differentiation and the active proliferation rate in HCC. These associations were confirmed with in vitro models. Moreover, patients with HCC who had been treated by surgical resection and had higher PI4KA mRNA concentrations in their tumor tissue exhibited a higher risk of tumor recurrence (median time: 20 months versus 49 months, P = 0.0012) and shorter disease-specific survival (first quartile time: 16 months versus 48 months, P = 0.0004). Finally, the abundance of PI4KA mRNA proved to be an independent prognostic marker of survival for cases of HCC (hazard ratio = 2.36, P = 0.0064). CONCLUSIONS: PI4KA mRNA could be used as a new molecular marker to improve established prognostic models for HCC. These findings also indicate possible new lines of research for the development of innovative therapeutic approaches targeting PI4KA.
ISSN: 1471-2407

inserm-00934294
http://www.hal.inserm.fr/inserm-00934294
http://www.hal.inserm.fr/inserm-00934294/document
http://www.hal.inserm.fr/inserm-00934294/file/1471-2407-14-7.pdf
DOI : 10.1186/1471-2407-14-7

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
AimThe global biodiversity crisis requires the identification of regions with high evolutionary potential, i.e. evolutionary hotspots (evospots). We created an analytical framework based on comparative phylogeography and coalescent methods to assess the dynamics of diversification and population persistence in the reef ecosystem of a little-studied region: the Southwestern Indian Ocean (SWIO).LocationCoral reefs of the SWIO, with comparative data from the Pacific Ocean.MethodsWe generated sequences of mitochondrial DNA (COI and 16S) for 10 widespread brittle-stars (345 specimens) from 21 localities (8 in the SWIO). We analysed them by combining comparative phylogeography approaches, coalescent-based methods, molecular clocks and the concept of evolutionarily significant units (ESUs) to draw conclusions about the drivers of biodiversity in the region.ResultsCryptic diversity was prevalent, increasing lineage diversity within the 10 nominal species by 70% within the SWIO and by 200% across the Indo-West Pacific. All seven new SWIO lineages meet the criteria for ESUs and at least six are biological species. We detected likely intraregional diversifications dating to the Plio-Pleistocene, supporting the SWIO as a generator of biodiversity. Geographical restriction of ESUs, long coalescent times (> 80 ka) and old in situ diversification (> 1 Ma) point to the persistence of populations over multiple glacio-eustatic cycles. We provide data suggesting demographic expansion during sea-level high stands. Regional connectivity was lower, and cryptic differentiation higher in lecithotrophs than in planktotrophs.Main conclusionsThe analytical framework based on a biodiversity survey makes it possible to identify evospots by assessing the potential of a region to maintain and generate biodiversity and by evaluating the evolutionary processes and potential drivers at play.
ISSN: 0305-0270

hal-01369697
http://hal.univ-reunion.fr/hal-01369697
DOI : 10.1111/jbi.12155

Éditeur(s) : HAL CCSD Elsevier
Résumé :  
The within-population spatial structure of genetic diversity is shaped by demographic processes, including historical accidents such as forest perturbations. Information drawn from the analysis of the spatial distribution of genetic diversity is therefore inherently linked to demographic-historical processes that ultimately determine the fate of populations. All adult trees and saplings in a 1.4-ha plot within a mixed Norway spruce (Picea abies [L.] Karst) stand were characterised by means of chloroplast (paternally inherited) markers, and a large sub-sample of these were genotyped at mitochondrial (maternally inherited) molecular markers. These data were used to analyse the spatial distribution of genetic variation and to compare the patterns corresponding to the two marker types. The plot presented non-homogeneous local stem density in the younger cohorts, and the indirect effect of this source of variation on the spatial genetic structure was investigated. Results suggest that (i) spatially limited seed dispersal induced patchiness in genotype distribution, while pollen flow had a homogenising effect; (ii) deviations from random spatial structure were stronger in the demographically most stable portions of the stand, while they were weaker where sudden bursts of regeneration occurred; (iii) spatially overlapping adult and sapling cohorts displayed the same spatial genetic structure (stronger on stable areas, weaker in portions of the stand undergoing events of intense regeneration), which was substantiated by the influence of local demographic processes. Regeneration dynamics as modulated by demography thus influences the distribution of genetic diversity within the stand both in the younger life stages and in the adult population.
ISSN: 0378-1127

hal-01032063
https://hal.archives-ouvertes.fr/hal-01032063
DOI : 10.1016/j.foreco.2008.03.023

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
With global climate change altering marine ecosystems, research on plankton ecology is likely to navigate uncharted seas. Yet, a staggering wealth of new plankton observations, integrated with recent advances in marine ecosystem modelling, may shed light on marine ecosystem structure and functioning. A EuroMarine foresight workshop on the “Impact of climate change on the distribution of plankton functional and phylogenetic diversity” (PlankDiv) identified five grand challenges for future plankton diversity and macroecology research: 1) What can we learn about plankton communities from the new wealth of high-throughput ‘omics’ data? 2) What is the link between plankton diversity and ecosystem function? 3) How can species distribution models be adapted to represent plankton biogeography? 4) How will plankton biogeography be altered due to anthropogenic climate change? and 5) Can a new unifying theory of macroecology be developed based on plankton ecology studies? In this review, we discuss potential future avenues to address these questions, and challenges that need to be tackled along the way.
ISSN: 2296-7745

hal-01545318
https://hal.archives-ouvertes.fr/hal-01545318
DOI : 10.3389/fmars.2017.00068