Éditeur(s) : HAL CCSD Inter-Research
Résumé : International audience
Many large groupers form spawning aggregations, returning to the same spawning sites in consecutive spawning seasons. Connectivity between spawning aggregations is thus assured by larval dispersal. This study looks into the genetic structure and gene flow among spawning aggregations of a large grouper, the gulf coney Hyporthodus acanthistius, in the northern Gulf of California. First, using the mitochondrial control region and 11 microsatellites, we calculated FST metrics and conducted a Bayesian clustering analysis to determine structure among 5 spawning aggregations. Shallow genetic structure was found, separating the southernmost spawning aggregate from the remainder. Second, we used the results from the structure analysis and local water circulation patterns to delineate 3 distinct models of gene flow. The best-supported model, in which the southernmost spawning aggregate formed one group and all other spawning aggregates were nested into a second group, was the one that was consistent with water circulation during the species’ spawning season. Larval retention within a seasonal anticyclonic gyre that formed during the gulf coney’s spawning season may be responsible for the patterns found. This study highlights the importance of local oceanographic conditions in dictating the structure among spawning aggregations even at small geographic scales and contributes to informed management plans for this overexploited grouper.
Marine Ecology Progress Series

hal-01301199
https://hal-univ-perp.archives-ouvertes.fr/hal-01301199
DOI : 10.3354/meps10637

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Gulf of Cadiz lies astride the complex plate boundary between Africa and Eurasia west of the Betic-Rif mountain belt. We report on the results of recent bathymetric swathmapping and multi-channel seismic surveys carried out here. The seafloor is marked by contrasting morphological provinces, spanning the SW Iberian and NW Moroccan continental margins, abyssal plains and an elongate, arcuate, accretionary wedge. A wide variety of tectonic and gravitational processes appear to have shaped these structures. Active compressional deformation of the wedge is suggested by folding and thrusting of the frontal sedimentary layers as well as basal duplexing in deeper internal units. There is evidence for simultaneous gravitational spreading occurring upslope. The very shallow mean surface and basal slopes of the accretionary wedge (1° each) indicate a very weak decollement layer, geometrically similar to the Mediterranean Ridge accretionary complex. Locally steep slopes (up to 10°) indicate strongly focused, active deformation and potential gravitational instabilities. The unusual surface morphology of the upper accretionary wedge includes “raft-tectonics” type fissures and abundant sub-circular depressions. Dissolution and/or diapiric processes are proposed to be involved in the formation of these depressions.
ISSN: 0264-8172

insu-00401683
https://hal-insu.archives-ouvertes.fr/insu-00401683
DOI : 10.1016/j.marpetgeo.2007.11.008

Éditeur(s) : HAL CCSD
Résumé : This thesis has been conducted on a fractured crystalline basement located in Ploemeur (South of Brittany, France). The detailed study of this basement requires a good understanding of their internal structures, namely their intrinsic properties, flow mode, density and fractures distribution. This work is focused on the petrophysical characterization of the granitic formations. Physical properties were determined from downhole geophysical measurements and images, and petrophysical measurements with thin sections made for each mini-core in the laboratory. Fresh-altered schist and fresh-altered granite separated by a normal angle fault are the main lithology of the Ploemeur crystalline basement. The results showed that the petrophysical properties were function of both porosity variation and degree of alteration and that the pore-space topology was found to be porositydependent. This thesis introduces a new formula between electrical resistivity and porosity. In addition, the laboratory measurements of Ploemeur revealed that seismic wave velocity was a function not only of porosity, but also of the predominant pore type. In general, the pore aspect ratio inverted from velocity measurements were classified roughly into crack shape. In the Ploemeur crystalline basement, the downhole geophysical measurements and images were used to measure changes in physical and chemical properties in the borehole fluid and the bedrock surrounding the boreholes. The effective integration of different geophysical methods, hydrogeological tests and lithological description was the best way to characterize the fractures in the crystalline basement, and is critical for a suitable estimation of fluid circulation.
Le socle cristallin fracturé, situé à Ploemeur (Bretagne sud, France) est l'objet de ce travail de thèse. L'étude détaillée du socle nécessite une bonne compréhension de la structure interne, à savoir les propriétés intrinsèques, le mode d'écoulement, la densité et la distribution des fractures. Ce travail de thèse est consacré à la caractérisation pétrophysique des formations granitiques. Les propriétés physiques ont été déterminées à partir de l'interprétation des données de mesures de géophysique en forage, des images de paroi du puits et des mesures pétrophysiques réalisées sur carottes en laboratoire. Afin de replacer les mesures dans leur contexte lithologique, une lame mince a été analysée pour chaque mini-carotte. Les formations lithologiques rencontrées dans le socle cristallin de Ploemeur sont des schistes et granites sains et altérés, ces deux lithologies étant séparées par une zone de faille. Les résultats ont montré que les propriétés pétrophysiques des roches étaient fonction à la fois de la variation de la porosité et du degré d'altération des roches et que la topologie de l'espace poreux était fortement dépendante de la porosité. Cette thèse introduit une nouvelle formule entre la résistivité électrique et la porosité. De plus, les mesures en laboratoire sur les échantillons de Ploemeur révèlent que les vitesses sismiques ne sont pas seulement fonction de la quantité de porosité, mais aussi fonction de facteur de forme. Ce dernier a été calculé sur les échantillons du socle de Ploemeur à partir des vitesses acoustiques. Les résultats ont montré que la porosité est de forme fissurale. L'intégration des données issues des images optiques et acoustiques, des mesures de géophysique en forage, et de la description des carottes a permis d'étudier de façon détaillée la géologie et l'hydrodynamique du socle de Ploemeur. L'intégration effective de ces différentes méthodes avec les tests hydrogéologiques ressort comme la meilleure façon de caractériser les fractures et les circulations en eau dans le socle.
https://tel.archives-ouvertes.fr/tel-00444175

Droits : info:eu-repo/semantics/OpenAccess
tel-00444175
https://tel.archives-ouvertes.fr/tel-00444175
https://tel.archives-ouvertes.fr/tel-00444175/document
https://tel.archives-ouvertes.fr/tel-00444175/file/thesebelghoul.pdf

Éditeur(s) : HAL CCSD
Résumé : 38 pages
Rapport
The Chicxulub impact crater, México, is unique. It is the only known terrestrial impact structure that has been directly linked to a mass extinction event and the only terrestrial impact with a global ejecta layer. Of the three largest impact structures on Earth, Chicxulub is the best preserved. Chicxulub is also the only known terrestrial impact structure with an intact, unequivocal topographic peak ring. Chicxulub’s role in the Cretaceous/Paleogene (K-Pg) mass extinction and its exceptional state of preservation make it an important natural laboratory for the study of both large impact crater formation on Earth and other planets and the effects of large impacts on the Earth’s environment and ecology. Our understanding of the impact process is far from complete, and despite more than 30 years of intense debate, we are still striving to answer the question as to why this impact was so catastrophic.During International Ocean Discovery Program (IODP) Expedition 364, Paleogene sediments and lithologies that make up the Chicxulub peak ring were cored to investigate (1) the nature and formational mechanism of peak rings, (2) how rocks are weakened during large impacts, (3) the nature and extent of post-impact hydrothermal circulation, (4) the deep biosphere and habitability of the peak ring, and (5) the recovery of life in a sterile zone. Other key targets included sampling the transition through a rare midlatitude section that might include Eocene and Paleocene hyperthermals and/or the Paleocene/Eocene Thermal Maximum (PETM); the composition and character of the impact breccias, melt rocks, and peak-ring rocks; the sedimentology and stratigraphy of the Paleocene–Eocene Chicxulub impact basin infill; the chronology of the peak-ring rocks; and any observations from the core that may help us constrain the volume of dust and climatically active gases released into the stratosphere by this impact. Petrophysical property measurements on the core and wireline logs acquired during Expedition 364 will be used to calibrate geophysical models, including seismic reflection and potential field data, and the integration of all the data will calibrate impact crater models for crater formation and environmental effects. The proposed drilling directly contributes to IODP Science Plan goals:Climate and Ocean Change: How resilient is the ocean to chemical perturbations? The Chicxulub impact represents an external forcing event that caused a 75% level mass extinction. The impact basin may also record key hyperthermals within the Paleogene.Biosphere Frontiers: What are the origin, composition, and global significance of subseafloor communities? What are the limits of life in the subseafloor? How sensitive are ecosystems and biodiversity to environmental change? Impact craters can create habitats for subsurface life, and Chicxulub may provide information on potential habitats for life, including extremophiles, on the early Earth and other planetary bodies. Paleontological and geochemical studies at ground zero will document how large impacts affect ecosystems and effects on biodiversity.Earth Connections/Earth in Motion: What are the composition, structure and dynamics of Earth’s upper mantle? What mechanisms control the occurrence of destructive earthquakes, landslides, and tsunami? Mantle uplift in response to impacts provides insight into dynamics that differ between Earth and other rocky planets. Impacts generate earthquakes, landslides, and tsunami, and scales that generally exceed plate tectonic processes yield insight into effects, the geologic record, and potential hazards.IODP Expedition 364 was a Mission Specific Platform expedition to obtain subseabed samples and downhole logging measurements from the sedimentary cover sequence and peak ring of the Chicxulub impact crater. A single borehole was drilled into the Chicxulub impact crater on the Yucatán continental shelf, recovering core from 505.7 to 1334.73 m below seafloor with ~99% core recovery and acquiring downhole logs for the entire depth.
International Ocean Discovery Program

hal-01639520
https://hal.archives-ouvertes.fr/hal-01639520
DOI : 10.14379/iodp.pr.364.2017

Éditeur(s) : HAL CCSD Geological Society of America
Résumé : International audience
Lakes are major depositional systems for which the related depositional processes have long been considered relatively simple. Breaking this statement, this study presents a detailed analysis of deposits in Lake Saint-Jean, the third largest natural lake in Québec. In addition to postglacial deltaic and coastal depositional systems fringing the lake, current-controlled features such as a large subaqueous prograding wedge and three sediment drifts have been identifi ed in its central portion based on two-dimensional (2-D) acoustic high-resolution subbottom profiles. The large subaqueous prograding wedge is a 4-km-long and up to 15-m-thick heterolithic shelf-like construction in the southeastern part of the lake. The three sediment drifts are 0.1–0.5-km-long and 2–5-mthick mud mounds distributed on the lake floor in the central portion of the lake. Diatom analyses and radiocarbon dating show that the development of these current-controlled features occurred during the lacustrine phase, after the disconnection with the postglacial marine Laflamme Gulf at 8.5 cal. k.y. B.P. Depositional facies show evidence of recurrent bottom-current activity. Related deposits alternate with pelagic sedimentation stages characterized by the settling of mud and biogenic accumulations. We investigated the origin of bottom currents using a numerical simulation (SYMPHONIE, an oceanographic model), with the aim of modeling wind-induced lake-scale water circulation. Simulations suggest that the subaqueous prograding wedge and the three sediment drifts result from wind-induced bottom currents generated by storm events having wind speed greater than 10 m s–1. Such strong winds are able to significantly affect sedimentation in the central portion of Lake Saint-Jean. Theresulting wind-induced sedimentary features were integrated into a refi ned lacustrine depositional model that summarizes the evolution of a group of water bodies referred to as “wind-driven water bodies.” This study applies a new tool for lake strata characterization and highlights the potential diffi cultyin differentiating them from marine deposits in the geological record.
ISSN: 0016-7606

insu-01184724
https://hal-insu.archives-ouvertes.fr/insu-01184724
DOI : 10.1130/B31145.1

Éditeur(s) : HAL CCSD
Résumé : Sand intrusions (or injectites) are most often the product of post-depositional remobilization of sand leading to its injection into the surrounding rocks. While injectites were recognized for the first time nearly 200 years ago, their emplacement process has been studied for a couple of decades only, since the concepts of deep sea depositional environments have allowed us to better understand their emplacement processes. However, these processes are still relatively poorly understood. Our approach is based on the study of injectites in the Lower Congo Basin from seismic and well data, which we compare to a fossil system in the SE France basin. We have shown that: (1) In buried turbidite channel systems draping deposits on the channel flanks and terraces of channels have the same geophysical signature as 'wing-like' injectites. Finally, the only criterion for identifying seismic injectites is the presence of bedding-discordant seismic reflections, and in the best case the associated uplift of the overlying seismic reflectors. (2) Seismic-scale conical and saucer-shaped sand injectites have been identified in the Lower Congo Basin. The remobilization is likely due to overpressuring induced by the buoyancy effect of hydrocarbons trapped in the margins of a lobe buried underneath 160 m of sediment, followed by the sudden injection of fluidized sand associated with fault reactivation of faults (with a possible role of nearby salt diapirs). (3) A network of injectites (dykes, sills/wings and laccoliths) was formed in the Vocontian basin during the late Albian and/or early Cenomanian, from a lower-middle Albian turbidite channel. The emplacement is probably due to the early compartmentalization of the channel during its burial and the increase of the sedimentation rate generating overpressure; and the subsequent large influx of deep fluids triggering injection. The injection of sand was polyphased: a first episode formed the sills and another emplaced the dykes. Sills/wings and dykes propagated about 2 km laterally away from the parent sand body and about 200 m up to the surface, revealing a much more extended lateral than vertical reach, contrary to the classically accepted idea from the interpretation of seismic data. (4) The emplacement of this large network of injectites was governed by hydrofracturing. Therefore, its morphology is dependent on the host rock heterogeneity (isotropy, fractures), the paleo-stress orientation (ó3 = NW-SE) and the burial depth of the source (300-600 m) at the time of injection. The study of this fossil network allows us to define the relationship between morphology of the injected network and stress state at the time of injection. This relationship can be extrapolated to constrain the morphology of subsurface networks beyond seismicvisibility. (5) Sands injected into low permeability lithologies bear evidence to a major event of fluid escape in the studied basin, but also channeled fluids long after their formation. In this way, injectites both attest to specific episodes of fluid migration in sedimentary basins and contribute to long-lived re-routing of migrating fluids once emplaced. The injection of sand is associated with the sudden escape of fluids, probably resulting from a significant tectonic and/or sedimentary event; in addition, the architecture of injectite networks is governed by the local paleo-stress and heterogeneity in the host rock. Consequently, characterizing injectite networks is an important step in understanding the plumbing systems of continental margins, i.e. the post-depositional evolution of sedimentary basins.
Les intrusions sableuses (ou injectites) sont le plus souvent le produit de la remobilisation post-dépositionnelle des sédiments et de l'injection du sable dans les roches environnantes. Bien que reconnues pour la première fois il y a près de 200 ans, elles ne sont réellement étudiées que depuis quelques dizaines d'années, depuis que les concepts sur les environnements de dépôt dans les domaines marins profonds nous permettent de mieux comprendre les processus de mise en place. Cependant, ces processus restent encore aujourd'hui relativement mal compris. Notre approche repose sur l'étude d'injectites dans le bassin du Bas-Congo a partir de données de sismique et de puits que nous comparerons a un système fossile dans le bassin du SE de la France. Nous avons montre que : (1) Dans des systèmes de chenaux turbiditiques enfouis, les dépôts de drapage sur les marges et terrasses de chenaux présentent la même signature géophysique que les injectites de type "wing". Finalement, le seul critère sismique d'identification des injectites est la présence de réflexions sismiques sécantes vis-a-vis de la stratigraphie associée dans le meilleur des cas au soulèvement des réflecteurs sismiques sus-jacents. (2) Des injectites d'échelle sismique en forme de cône et d'assiette ont été identifiées dans le bassin du Bas-Congo. La remobilisation résulte probablement des pressions anormales induites par l'effet de flottabilité des hydrocarbures piégés dans les marges d'un lobe enfoui sous 160 m de sédiment, puis de l'injection soudaine du sable fluidise associée a la réactivation de failles (possible rôle des diapirs de sel a proximité). (3) Un réseau d'injectites (dykes, sills/wings et laccolites) s'est formé dans le bassin Vocontien entre la fin de l'Albien supérieur et/ou le début du Cénomanien, depuis un chenal turbiditique de l'Albien inférieur-moyen. La mise en place résulte probablement de la compartimentalisation précoce du chenal au cours de son enfouissement et de l'augmentation du taux de sédimentation générant la surpression et de l'apport ulterieur d'importante quantité de fluides profonds déclenchant l'injection. L'injection du sable a été polyphasée : une première injection a formé des sills et une suivante des dykes. Les sills/wings et les dykes se sont propagés latéralement au chenal source sur environ 2 km et vers la surface sur environ 200 m, mettant en évidence une forte remobilisation latérale plutôt que verticale, contrairement a l'idée classiquement admise a partir de l'interprétation des données sismiques. (4) La formation de ce large réseau d'injectites a été gouvernée par des mécanismes d'hydrofracturation. Par conséquent, sa morphologie a été dépendante des hétérogenéités de la roche hôte (milieu isotrope, fracture), des directions de paléo-contraintes (ƒÐ3 = NWSE) et de la profondeur d'enfouissement de la source (300-600 m) au moment de l'injection. L'étude de ce réseau fossile permet de définir les relations entre morphologie du réseau injecté et état de contraintes au moment de l'injection. Cette relation peut être extrapolée de façon à contraindre la morphologie des réseaux de subsurface au-delà de la visibilité sismique. (5) Les sables injectés dans des lithologies de faible perméabilité témoignent d'un épisode d'échappement de fluide important dans les bassins étudiés mais ont aussi guide les fluides longtemps après leur formation. Les injectites contribuent ainsi a l'initiation épisodique et la pérennisation de migrations de fluides dans les bassins sedimentaires. Le processus d'injection est associé a l'échappement brutal de fluides, résultant vraisemblablement d'un évènement tectonique et/ou sédimentaire important, et l'architecture des réseaux d'injectites est gouverné par les paléo-contraintes locales et les hétérogénéités de la roche hôte. Par conséquent, la caractérisation des réseaux d'injectites est une étape importante dans la compréhension de la plomberie des marges, c'est-a-dire l'évolution post-dépôt des bassins sédimentaires.
https://tel.archives-ouvertes.fr/tel-01011486

tel-01011486
https://tel.archives-ouvertes.fr/tel-01011486
https://tel.archives-ouvertes.fr/tel-01011486/document
https://tel.archives-ouvertes.fr/tel-01011486/file/These_Monnier_2013_banalisee.pdf

Résumé : La tuberculose (TB), maladie infectieuse contagieuse, est causée par une mycobactérie appartenant au complexe Mycobacterium tuberculosis (MTBC). Malgré de nombreuses campagnes de vaccination par le BCG (Bacilles de Calmette et Guérin) et les traitements antituberculeux, on observe une réémergence de la maladie depuis les années 80. Ce bouleversement s’explique par la coïnfection avec le virus du VIH/SIDA, la désorganisation des systèmes de santé et par l’apparition des bactéries résistantes aux principaux antibiotiques antituberculeux. Dans ce contexte une meilleure connaissance des mouvements et de l’évolution des clones circulants du bacille tuberculeux permettrait de détecter plus rapidement et de façon plus pertinente l’émergence d’épidémies. Le contrôle et la surveillance de la maladie représentent des moyens essentiels pour lutter contre l’expansion mondiale de la tuberculose. C’est ainsi que l’unité de la Tuberculose et des Mycobactéries de l’Institut Pasteur de la Guadeloupe (IPG) a mis en place une base de données de profils génotypiques pour l’étude de l’épidémiologie globale de la tuberculose. Dans le cadre de cette thèse, nous décrirons les méthodes de bioinformatique qui ont été utilisées pour la gestion et l’exploitation de la 6ème version (SITVIT2) de cette base de données des génotypes pour mieux comprendre l’évolution et la dissémination mondiale du bacille tuberculeux. Cette base intègre aussi plusieurs marqueurs moléculaires tels que les MIRU-VNTRs (« mycobacterial interspersed repetitive units-variable number of tandem repeats ») et le Spoligotype43 servant à mieux décrire et identifier les familles de profils génotypiques du MTBC. La banque de données SITVIT2 ne cesse d’évoluer, et elle contient actuellement des informations épidémiologiques sur 111 635 isolats cliniques. Cette base de données est consultable en ligne à l’adresse suivante : http://www.pasteur-guadeloupe.fr:8081/SITVIT2/. Nous avons également réalisé une base de données nommée SITVITBovis qui est dédiée à la tuberculose bovine. Cette base de données sera accessible à l’adresse : http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis/. Parallèlement au développement et à la gestion des bases de données, ce travail de thèse s’est appuyé sur plusieurs études épidémiologiques et phylogéographiques mettant en corrélation les données disponibles sur la résistance aux médicaments ou les caractéristiques démographiques (dont le sexe, l’âge, le statut VIH, et l’origine du patient). Notre initiative de recherche permet ainsi d’améliorer la caractérisation phylogénétique détaillée des lignées du MTBC, ainsi que l’épidémiologie des clones en circulation, afin d’élaborer une cartographie géographique des isolats cliniques prédominants pour les bacilles tuberculeux principalement impliqués dans la maladie, à l’échelle nationale, régionale et mondiale. La superposition ultérieure de ces cartes avec des données sociopolitiques, économiques et démographiques obtenues auprès de Systèmes d’information géographique (SIG) ont permis de dresser un portrait précis des disparités actuelles par pays ou sous-région. Cette thèse représente une importante collaboration avec plusieurs équipes de chercheurs travaillant également dans le domaine de l’épidémiologie moléculaire de la tuberculose. L’objectif à long terme de ce travail, est d’optimiser la structure de la base, et de pérenniser l’enrichissement de celle-ci (notamment par l’automatisation et la facilité de la saisie de données). Une représentation optimale et une meilleure accessibilité des données de la base conforteraient les efforts faits pour le contrôle et la surveillance de la TB dans monde.
Tuberculosis (TB) is a contagious infectious disease caused by mycobacteria belonging to the Mycobacterium tuberculosis complex (MTBC). Despite numerous campaigns of vaccination by the BCG (Bacillus Calmette-Guérin) vaccine, and TB treatments, there was a resurgence of the disease since the 80s. This disruption is due to coinfection with HIV/AIDS, disorganization of health systems and the emergence of bacteria resistant to anti-TB drugs. In this context, a better understanding of the movements and changes of circulating clones of tubercle bacilli would detect faster and more relevant emerging epidemics. The control and monitoring of the disease are essential means to fight against the worldwide spread of tuberculosis. Thus the TB and Mycobacteria unit of the Pasteur Institute of Guadeloupe (IPG) has developed a database of genotypic profiles for the study of global epidemiology of tuberculosis.In this thesis, we discuss the Bioinformatical methods that have been used for the management and development of the 6th version (SITVIT2) of this database of genotypes to better understand the evolution and global dissemination of the tubercle bacillus. The database also includes several molecular markers such as MIRU-VNTRs (mycobacterial interspersed repetitive units- variable number of tandem repeats) and Spoligotype43 allowing a better description and identification of the families of genotypic profiles of Mycobacterium tuberculosis complex. SITVIT2 database is constantly evolving, and it currently contains epidemiological information on 111,635 clinical isolates. This database is available online at the following address: http://www.pasteur-guadeloupe.fr:8081/SITVIT2/. We also developed a database named "SITVITBovis", which is dedicated to bovine tuberculosis. This database will be accessible at: http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis/.Alongside the development and management of databases, this work was based on several epidemiological and phylogeographic studies correlating data on drug resistance or demographic characteristics (including sex, age, HIV status, and the origin of the patient). Our research initiative is thus focused to further improve in depth phylogenetic characterization of MTBC lineages, as well as the epidemiological analysis of circulating clones to generate evidence-based geographical mapping of predominant clinical isolates of tubercle bacilli causing the bulk of the disease both at country and regional level. Further superposition of these maps with socio-political, economical and demographical available through Geographic Information Systems (GIS) allows to have a precise view of prevailing disparities at the level of country or sub-region. This thesis represents an important collaboration with several researchers teams also working in the field of molecular epidemiology of tuberculosis.The long-term goal of this work is to further optimize the database structure, and sustain enriching it (including automation and ease of data entry). Optimum performance and accessibility of data in the database would reinforce efforts to control and surveillance of TB in the world.

http://www.theses.fr/2014AGUY0791/document

Éditeur(s) : Public Library Science
Résumé : Studying the larval dispersal of bottom-dwelling species is necessary to understand their population dynamics and optimize their management. The black-lip pearl oyster (Pinctada margaritifera) is cultured extensively to produce black pearls, especially in French Polynesia's atoll lagoons. This aquaculture relies on spat collection, a process that can be optimized by understanding which factors influence larval dispersal. Here, we investigate the sensitivity of P. margaritifera larval dispersal kernel to both physical and biological factors in the lagoon of Ahe atoll. Specifically, using a validated 3D larval dispersal model, the variability of lagoon-scale connectivity is investigated against wind forcing, depth and location of larval release, destination location, vertical swimming behavior and pelagic larval duration (PLD) factors. The potential connectivity was spatially weighted according to both the natural and cultivated broodstock densities to provide a realistic view of connectivity. We found that the mean pattern of potential connectivity was driven by the southwest and northeast main barotropic circulation structures, with high retention levels in both. Destination locations, spawning sites and PLD were the main drivers of potential connectivity, explaining respectively 26%, 59% and 5% of the variance. Differences between potential and realistic connectivity showed the significant contribution of the pearl oyster broodstock location to its own dynamics. Realistic connectivity showed larger larval supply in the western destination locations, which are preferentially used by farmers for spat collection. In addition, larval supply in the same sectors was enhanced during summer wind conditions. These results provide new cues to understanding the dynamics of bottom-dwelling populations in atoll lagoons, and show how to take advantage of numerical models for pearl oyster management.
Plos One (1932-6203) (Public Library Science), 2014-04 , Vol. 9 , N. 4 , P. e95050

Droits : 2014 Thomas 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/00197/30843/29210.pdf
DOI:10.1371/journal.pone.0095050
http://archimer.ifremer.fr/doc/00197/30843/

Éditeur(s) : Gauthier-Villars
Résumé : Long tropical instability waves are described at around 3-4 degrees N based on results of a simulation performed with a general circulation model for the Atlantic Ocean. This description is in agreement with earlier observations of organized undulations of the summer thermal front associated with anti-cyclonic eddies propagating westward at 30-40 km/day along 3-4 degrees N from 10 to 40 degrees W through the Atlantic basin. However, the simulation indicated the presence of long waves in early boreal winter. In this respect, satellite observations during short cold events in winter show thermal front undulations similar to those associated with long wave propagations. The simulation clearly demonstrated large vertical movements between the surface and a depth of 70 m, associated with anti-cyclonic eddies at around 3 degrees N. These vertical movements could commonly reach the thermocline in the central part of the Atlantic basin (10-20 degrees W). In this region, long instability waves could subsequently affect biological production by ''eddy pumping''. During the PIRAL cruise at 4 degrees N-20 degrees W in June 1986, remarkably high chlorophyll concentrations (the highest values in our data bank for the equatorial Atlantic and typical of a very productive zone) were associated with currents similar to those of an anticyclonic eddy and characterized by a surface temperature distribution typical of the long instability wave pattern. These high chlorophyll concentrations may have resulted from ''eddy pumping'' and/or strong meridian advection since each of these mechanisms is associated with long instability waves.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1994 , Vol. 17 , N. 6 , P. 585-596

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00099/21034/18660.pdf
http://archimer.ifremer.fr/doc/00099/21034/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
During compressive events, deformation in sedimentary basins is mainly accommodated by thrust faulting and related fold growth. Thrust faults are generally rooted in the basement and may act as conduits or barriers for crustal fluid flow. Most of recent studies suggest that fluid flow through such discontinuities is not apparent and depends on the structural levels of the thrust within the fold-and-thrust belt. In order to constrain the paleofluid flow through the Jaca thrust-sheet-top basin (Paleogene southwest-Pyrenean fold-and-thrust belt) this study compares on different thrust faults located at different structural levels. The microstructures in the different fault zones studied are similar and consist of pervasive cleavage, calcite shear veins (SV1), extension veins (EV1) and late dilatation veins (EV3). In order to constrain the nature and the source of fluids involved in fluid-rock interactions within fault zones, a geochemical approach, based on oxygen and carbon stable isotope and trace element compositions of calcite from different vein generations and host rocks was adopted. The results suggest a high complexity in the paleohydrological behaviors of thrust faults providing evidence for a fluid-flow compartmentalization within the basin. Previous studies in the southern part of the Axial Zone (North of the Jaca basin) indicates a circulation of deep metamorphic water, probably derived from the Paleozoic basement, along fault zones related to the major basement Gavarnie thrust. In contrast, in northern part of the Jaca basin, the Monte Perdido thrust fault is affected by a closed hydrological fluid system involving formation water during its activity. The Jaca and Cotiella thrust faults, in turn, both located more to the south in the basin, are characterized by a composite fluid flow system. Indeed, stable isotope and trace element compositions of the first generations of calcite veins suggest a relatively closed paleohydrological system, whereas the late calcite vein generations, which are probably associated with the late tectonic activity of the basin, support a contribution of both meteoric and marine waters. Based on these results, a schematic fluid-flow model is presented. This model allows visualization of three main fluid flow compartments along a N-S transect.
ISSN: 0264-8172

hal-00963606
https://hal.archives-ouvertes.fr/hal-00963606
DOI : 10.1016/j.marpetgeo.2013.09.005

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In French Guiana, severe cases of toxoplasmosis in immunocompetent patients are associated with atypical strains of Toxoplasma gondii linked to a wild neotropical rainforest cycle and a higher genetic diversity than usually observed for T. gondii isolates from anthropized environment. This raises the question of the impact of anthropization of the natural environment, on genetic diversity and on the population structure of T. gondii. However, few data are available on strains circulating in the anthropized areas from French Guiana. Seropositive animals originating mainly from anthropized sub-urban areas and punctually from wild environment in French Guiana were analyzed for T. gondii isolation and genotyping. Thirty-three strains were obtained by bioassay in mice and compared with 18 previously reported isolates chiefly originating from the Amazon rainforest. The genotyping analysis performed with 15 microsatellite markers located on 12 different chromosomes revealed a lower genetic diversity in the anthropized environment. Results were analyzed in terms of population structure by clustering methods, Neighbor-joining trees reconstruction based on genetic distances, F(ST,) Mantel's tests and linkage disequilibrium. They clearly showed a genetic differentiation between strains associated to the anthropized environment and those associated to the wild, but with some inbreeding between them. The majority of strains from the anthropized environment were clustered into additional lineages of T. gondii that are common in the Caribbean. In conclusion the two environmental populations "wild" and "anthropized" were genetically well differentiated. The anthropization of the environment seems to be accompanied with a decreased diversity of T. gondii associated with a greater structure of the populations. We detected potential interpenetration and genetic exchanges between these two environmental populations. As a higher pathogenicity in human of "wild" genotypes has been described, the interpenetration of both environments leads to hybridization between strains that may be at risk for human health.
ISSN: 1567-1348

pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/document
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/file/Mercier_et_al_IGE2011.pdf
DOI : 10.1016/j.meegid.2011.05.003

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
In cyclic females, FSH stimulates ovarian estradiol (E2) production and follicular growth up to the terminal stage. A transient elevation in circulating FSH and E2 levels occurs shortly after birth. But what could be the action of FSH on the ovary during this period, and in particular how it stimulates ovarian steroidogenesis without supporting terminal follicular maturation is intriguing. By experimentally manipulating FSH levels, we demonstrate in mice that the mid-infantile elevation in FSH is mandatory for E2 production by the immature ovary, but that it does not stimulate follicle growth. Importantly, FSH increases aromatase expression to stimulate E2 synthesis, however it becomes unable to induce cyclin D2, a major driver of granulosa cell proliferation. Besides, although FSH prematurely induces luteinizing hormone (LH) receptor expression in granulosa cells, LH pathway is not functional in these cells to induce their terminal differentiation. In line with these results, supplying infantile mice with a superovulation regimen exacerbates E2 production, but it does not stimulate the growth of follicles and it does not induce ovulation. Overall, our findings unveil a regulation whereby high postnatal FSH concentrations ensure the supply of E2 required for programming adult reproductive function without inducing follicular maturation before puberty.
ISSN: 2045-2322

hal-01516023
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01516023
DOI : 10.1038/srep46222
PUBMED : 28397811
PUBMEDCENTRAL : PMC5387682

Éditeur(s) : Interciencia
Résumé : Zooplankton abundance, biomass and composition were evaluated in various temporal scales in a seasonal coastal upwelling system at Margarita Island, Venezuela. Scales of temporal variation include weeks, months and seasons (relaxation, upwelling and transition). Seasons were delimitated by upwelling index and sea temperature. The sampling period comprise Sept/2002 - July/2003. Zooplankton samplings were made by horizontal trawls (1-10m depth), using 200,mu m nets, 2-6km from the coastal margin. Total abundance show important variation at week scales, with different patterns between locations, while seasonal differences of abundance are marginal. Biomass only shows seasonal variation due significant reduction in the transition season. Zooplankton assemblages show changes at scale of weeks, with different local patterns, and seasonal changes. Changes in assemblage between the relaxation and upwelling seasons include reduction (during upwelling) of abundance in copepods, cladocerans, salpidae, chaetognates, fish and crustacea larvae. Except by cirripedia larvae, those were important in the upwelling assemblages. Transition shows high variation, with reduction of biomass and assemblage composition similar to upwelling, except by an isolated event. Small scale variation in the zooplankton could be related to physical processes at small scales, eg. turbulence, local circulation, small eddies and filaments, and biological response. Additional sources of nutrient input, eg. riverine input and internal waves, could support local plankton productivity and abundance during relaxation. Detection of high variation in zooplankton abundance and composition at small scales, with local interaction, bring a new light over zooplankton estimation in time series in this system.
La abundancia, la biomasa y la composición del zooplancton costero fueron analizadas a varias escalas temporales en un área afectada por surgencia costera estacional (Isla de Margarita, Venezuela); considerando para ello escalas de semanas, meses y periodos, así como la variación local. La estimación del zooplancton fue realizada a partir de arrastres horizontales (1-10m de profundidad) utilizando redes de 200μ entre 2 y 6 km de la línea de costa, entre set/2002 y jul/2003. La abundancia total presentó alta variabilidad a escala de semanas, con patrones diferentes entre localidades, mientras que la diferencia entre periodos es marginal. La biomasa únicamente mostró variación a escala de periodos por una disminución durante el periodo de transición. La composición presentó fluctuaciones a escalas temporales pequeñas, con patrones de variación diferentes localmente, así como a escala de periodos. Los cambios en composición entre el periodo de relajación y el de surgencia incluyen disminución en la abundancia de copépodos, cladóceros, salpas, quetognatos, larvas de peces y crustáceos; excepto por las larvas de cirrípedos que forman un componente importante durante la surgencia. Se postula que procesos físicos a pequeña escala, como la turbulencia, la circulación local o la formación de pequeños giros o filamentos, y los procesos biológicos, condicionan esta elevada variabilidad a escalas pequeñas. La existencia de fuentes de enriquecimiento adicionales como aportes de ríos y ondas internas pudiera condicionar la presencia de elevada abundancia y biomasa, en especial durante periodos de relajación. Los cambios en composición resaltan la importancia del aporte de merozooplancton costero. Palabras clave / Biomasa / Escalas Temporales / Surgencia / Venezuela / Zooplancton Costero /
Interciencia (0378-1844) (Interciencia), 2014-02 , Vol. 39 , N. 2 , P. 122-128

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00187/29851/28297.pdf
http://archimer.ifremer.fr/doc/00187/29851/

Éditeur(s) : Amer Geophysical Union
Résumé : This study focuses on the improved estimation of mesoscale surface ocean circulation obtained by merging TOPEX/Poseidon (T/P) and ERS-1 and -2 altimeter measurements between October 1992 and May 1998. Once carefully intercalibrated and homogenized, these data are merged through an advanced global objective analysis method that allows us to correct for residual long wavelength errors and uses realistic correlation scales of ocean dynamics, The high-resolution (0.25 degrees x 0.25 degrees) merged T/P + ERS-1 and -2 sea level anomaly maps provide more homogeneous and reduced mapping errors than either individual data set and more realistic sea level and geostrophic velocity statistics than T/P data alone. Furthermore, the merged T/P + ERS-1 and -2 maps yield eddy kinetic energy (EKE) levels 30% higher than maps of T/P alone. They also permit realistic global estimates of east and north components of EKE and their seasonal variations, to study EKE sources better. A comparison of velocity statistics with World Ocean Circulation Experiment surface drifters in the North Atlantic shows very good agreement. Comparison with contemporary current meter data in various oceanic regimes also produces comparable levels of energy and similar ratios of northward and eastward energy, showing that the maps are suitable to studying anisotropy. The T/P + ERS zonal and meridional components of the mapped currents usually present comparable rms variability, even though the variability in the Atlantic is more isotropic than that in the Pacific, which exhibits strong zonal changes. The EKE map presents a very detailed description, presumably never before achieved at a global scale. Pronounced seasonal changes of the EKE are found in many regions, notably the northeastern Pacific, the northeastern and northwestern Atlantic, the tropical oceans, and the zonally extended bands centered near 20 degrees S in the Indian and western Pacific Oceans and at 20 degrees N in the northwestern nl Pacific.
Journal Of Geophysical Research-oceans (0148-0227) (Amer Geophysical Union), 2000-08 , Vol. 105 , N. C8 , P. 19477-19498

Droits : 2000 AGU
http://archimer.ifremer.fr/doc/00079/19033/16617.pdf
DOI:10.1029/2000JC900063
http://archimer.ifremer.fr/doc/00079/19033/

Éditeur(s) : Université Paris 7 – Denis Diderot
Résumé : Sea surface salinity (SSS) influences numerous oceanic phenomena, for instance surface water ventilation, deep water formation and thermohaline circulation. SSS also controls some ocean-atmosphere coupled processes, such as the intensity of freshwater flux and the penetration of heat flux and turbulence. Salinity is more difficult to measure than temperature from in situ surveys, which results in 20 times less data being currently available. Moreover, sea surface temperature (SST) is routinely estimated from satellites, which is not possible yet for SSS. Two space missions will fill this gap soon: SMOS from the European Space Agency and Aquarius/SAC-D from NASA and CONAE. To contribute to the SMOS project, we propose a method for estimating SSS from current satellite observations and for studying the mechanisms governing its variability. We developed a simplified model of the ocean mixed layer, based on the "slab mixed layer" formulation (Frankignoul et Hasselmann, 1977). This 2D horizontal model is implemented over the global ocean, using a near 100 km resolution, and integrated during a climatological year. Air-sea fluxes are taken from the ECMWF meteorological model (ERA40 reanalysis) and the surface currents are provided by altimeter data (SSALTO-DUACS analysis). The mixed layer depth (MLD) is derived from SST observations, using an original inversion technique. The MLD fields obtained from this inversion are well correlated to in situ estimates. This effective depth represents the air-sea fluxes penetration and ensures consistency between fluxes, les currents and SST. We first validate the simulation through examination of the heat balance in north-eastern Atlantic, by comparing to measurements and models from the POMME experiment. Then we study the salinity balance in the global domain, in terms of its geographical distribution and seasonal evolution. Equilibrium between the various processes appears generally more complex than for temperature. Noteworthy, the role of atmospheric flux is less predominant (22%), while geostrophic advection (33%) and diapycnal mixing (22%) contribute more strongly. Our results indicate this model succeeds in reconstructing SSS variability over most of the oceans. Daily SSS variations are also simulated, whereas they are not represented in current observed data at a global scale. Owing to its simplicity and fast computation, the model will be useful to the SMOS mission. It can help for the measurement calibration/validation and provide a first guess estimate to the sophisticated algorithm required for SSS restitution.
La salinité de surface des océans (SSS) influence de nombreux phénomènes océaniques, parmi lesquels la ventilation des eaux de surface, la formation d'eaux profondes et la circulation thermohaline. Elle détermine aussi certains processus couplés océan-atmosphère, notamment l'intensité du flux d'eau douce, la pénétration du flux de chaleur et de la turbulence. La mesure in situ de salinité est plus compliquée que celle de température, si bien qu'on dispose actuellement de 20 fois moins de données pour cette propriété. De plus, la température de surface (SST) est couramment estimée par satellite, ce qui n'est pas encore le cas de la SSS. Deux missions spatiales vont prochainement combler cette lacune : le satellite SMOS de l'Agence Spatiale Européenne et le satellite Aquarius/SAC-D de la NASA et de la CONAE. En préparation du projet SMOS, nous proposons une méthode pour estimer la SSS à partir des observations satellitaires actuelles et étudier les mécanismes de sa variabilité. Nous avons développé un modèle simplifié de couche mélangée océanique, basé sur la formulation "slab mixed layer" (Frankignoul et Hasselmann, 1977). Ce modèle 2D horizontal est implémenté sur l'océan global, avec une résolution proche de 100 km, et intégré au cours d'une année climatologique. Les flux air-mer proviennent du modèle météorologique ECMWF (réanalyse ERA40) et les courants de surface sont issus de l'altimétrie (analyse SSALTO-DUACS). La profondeur de la couche mélangée (MLD) est dérivée des observations de SST, grâce à une technique d'inversion originale. La MLD obtenue par inversion est bien corrélée aux estimations basées sur des données in situ. Cette profondeur effective représente la pénétration des flux air-mer et assure la cohérence entre les flux, les courants et la SST. La simulation est d'abord validée en examinant le bilan de chaleur dans l'Atlantique Nord-Est, par comparaison aux mesures et aux modèles de l'expérience POMME. Puis le bilan de salinité est étudié dans le domaine global, en termes de distribution géographique et d'évolution saisonnière. L'équilibre entre les différents processus est généralement plus complexe que pour la température. Notamment, le rôle du flux atmosphérique est moins prépondérant (22%), tandis que l'advection géostrophique (33%) et le mélange diapycnal (22%) contribuent fortement. Nos résultats montrent que ce modèle parvient à restituer la variabilité de la SSS sur la majeure partie des océans. Le modèle simule aussi les variations journalières de SSS, qui ne sont pas représentées à l'échelle globale dans les observations actuelles. Grâce à sa simplicité et à sa rapidité, le modèle pourra être utile dans le cadre de SMOS. Il pourra aider à la calibration/validation de la mesure et fournir une estimation a priori pour l'algorithme complexe nécessaire à la restitution de la SSS.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/these-2302.pdf
http://archimer.ifremer.fr/doc/00000/2302/

Éditeur(s) : Wiley-blackwell
Résumé : A new benthic dinoflagellate species, Prorocentrum bimaculatum sp. nov., is studied from Kuwaits marine sediments, based on detailed morphological and molecular data. Cells are large, oblong oval in shape. They are 49.955.3 mu m long and 38.443.2 mu m wide. The ornamentation of this new species is peculiar, and characterized by smooth valves with large pores (0.320.50 mu m) scattered on their surface, except in two circular patches of similar to 15 mu m in diameter, devoid of ornamentation and located on both sides of the valve centers. The periflagellar area is widely triangular, located in a moderate excavation of the right valve, and comprises nine platelets. The intercalary band of P. bimaculatum is smooth. The molecular phylogenetic position of this new taxon was inferred from SSU and LSU rDNA genes. In both phylogenetic analyses, P. bimaculatum branched with high support with Prorocentrum consutum and formed a clade sister to the one including P. lima and related species such as P. arenarium, P. belizeanum, P. hoffmannianum, and P. maculosum. From the phylogenetic study, since most species related to P. bimaculatum are known for their toxic effects and production of okadaic acid, this new species can be considered as a potential toxin producer, but this has to be analyzed.
Journal Of Phycology (0022-3646) (Wiley-blackwell), 2012-02 , Vol. 48 , N. 1 , P. 211-221

Droits : 2012 Phycological Society of America
http://archimer.ifremer.fr/doc/00066/17756/15698.pdf
DOI:10.1111/j.1529-8817.2011.01102.x
http://archimer.ifremer.fr/doc/00066/17756/

Éditeur(s) : Elsevier Science Bv
Résumé : The study was conducted to (1) estimate the effects of polyculture of blue shrimp Litopenaeus stylirostris with goldlined rabbitfish Siganus lineatus on production, environmental quality and water and sediment metabolism and (2) to determine if blue shrimp and goldlined rabbitfish polyculture is possible. The experiment was carried out for 12 weeks in a mesocosm system that consisted of 12 circular outdoor mesocosm fiberglass tanks (1.7 m2, 1275 L water volume). Shrimp (2.9 g) were randomly stocked at density of 15 shrimp.m− 2 without rabbitfish (control), with rabbitfish (25.5 g) at low density (1.2 fish.m− 2) (LDRB) and high density (2.4 fish.m− 2) (HDRB). Results indicated that goldlined rabbitfish S. lineatus did not affect shrimp growth performance. At the end of the experiment, the combined shrimp and rabbitfish yields in the LDRB (213 g.m− 2) treatment and the HDRB (295 g.m− 2) treatment were significantly greater (P < 0.05) than the shrimp yield in the control (143 g.m− 2). Most of the water and sediment parameters were similar among treatments. There was no significant difference (P > 0.05) in gross primary productivity and respiration between the HDRB treatment and the control. It was concluded that the polyculture of blue shrimp with goldlined rabbitfish is technically possible without degradation of the environment in the culture system.
Aquaculture (0044-8486) (Elsevier Science Bv), 2014-09 , Vol. 433 , P. 340-347

Droits : 2014 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/00198/30968/29344.pdf
DOI:10.1016/j.aquaculture.2014.06.014
http://archimer.ifremer.fr/doc/00198/30968/

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

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

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This manuscript reports on a novel field experiment carried out on a microtidal beach in Camargue, France. For the first time in the field, a comprehensive description of the groundwater dynamics under sandy beach swash zone is presented. A cross-shore network of 15 buried pressure sensors is combined with terrestrial LiDAR measurements to study the swash-groundwater dynamics. The presented data focus on the decay of a moderate storm which allows to monitor the evolution of the groundwater pressure field in response to the retreat of the swash zone. Both horizontal and vertical head gradients are measured within the porous sand soil to estimate the groundwater flow field using Darcy’s law. Time-averaged analysis demonstrates the presence of a rather consistent groundwater circulation pattern under the swash zone, shifting offshore with the swash zone. The main tendency is an offshore directed flow, with infiltration/exfiltration in the upper/lower parts of the swash zone. Time-resolved analysis highlights the typical groundwater response to swash events which consists mainly of an overall infiltration flow during the bed inundation by the swash tongue, a seaward flow during the swash retreat and, for long backwash events, a localized exfiltration flow under the next incoming uprush.
ISSN: 0309-1708

hal-01412450
https://hal.archives-ouvertes.fr/hal-01412450
DOI : 10.1016/j.advwatres.2016.09.009

Éditeur(s) : Ofioliti
Résumé : Serpentinisation of mantle rocks, leading to natural venting of hydrogen and methane, has been reported to occur at the global scale, wherever fluids percolate in ultramafic formations. Here we compare gas composition from two on-land, low-temperature, and hyper-alkaline springs hosted on ultramafic rocks in the ophiolite massifs of the Sultanate of Oman and the Ligurian Alps (Voltri Group, Genoa region, Northern Italy). These two settings exhibit similar chemical and mineralogical features but show diverse styles of gas venting. Commonly to all hyper-alkaline springs, gases are characterised by relatively high N-2, very low O-2 and CO2 concentrations, and a strong enrichment in H-2 and CH4. The comparison between Oman and Liguria highlights a high variability of the H-2/CH4 ratios whereby the gas phase of the Oman Ophiolite is enriched in H-2 whereas being CH4 enriched in the Voltri Ophiolite. These results combined with literature data define three groups that may reflect different stages of serpentinisation producing fluids from hydrogen-dominated to methane-dominated. The origin of these distinct groups might lie in the difference of the mineralogical composition of the rocks within which the fluids circulate, on the degree of alteration of the rocks and finally on the geological/metamorphic history of the ophiolite.
Ofioliti (0391-2612) (Ofioliti), 2013-12 , Vol. 38 , N. 2 , P. 143-156

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00175/28634/27059.pdf
DOI:10.4454/ofioliti.v38i2.423
http://archimer.ifremer.fr/doc/00175/28634/