Éditeur(s) : Elsevier
Résumé : Because Vibrio aestuarianus is known to cause serious infections in Pacific oyster Crassostrea gigas, a real-time PCR assay was developed targeting the dnaJ gene of this bacterium. Only V. aestuarianus strains isolated from C. gigas mortality events in different geographic areas and the reference strain tested positive, whereas no amplification products was obtained with type strains belonging to 23 other species of Vibrio. Sensitivity and reproducibility of the method were assessed using either seawater or oyster homogenate samples spiked with one V aestuarianus strain. All these samples were stored at -20 degrees C in order to mimic retrospective or grouped natural sample analysis without quantification bias due to prolonged freezing. Analysis of standard curves revealed excellent correlation values between light microscopy cell enumerations and PCR Threshold Cycle (Ct) values, and acceptable PCR reaction efficiencies for all type of samples. Quantification curves of both sample types were equivalent, with a detection level as low as 1.6 V. aestuarianus cells in the PCR reaction tube, corresponding to 1.6.10(2) cells ml(-1) and 1.6.10(2) cells mg(-1) in seawater and entire oyster samples, respectively, taking into account the dilution factor used for appropriate template DNA preparation. Comparison of PCR assay reproducibility according to the complexity of samples revealed that seawater samples gave more reproducible quantification measures than samples from oyster homogenate, with precision of measured Ct values inferior to 0.4 and 0.6 respectively at 99% confidence. Use of the real-time PCR assay allowed us to monitor V. aestuarianus load in oysters naturally infected with this pathogen. Furthermore, we were able to detect V aestuarianus in samples of seawater in which oysters had been reared and in algal cultures used for feeding oysters. Because of the rapidity and reliability of the real-time PCR assay method used in this study, just a few hours are needed compared with the two days required using the classic culture method, this technique will be particularly valuable in mollusc pathology laboratories, for monitoring the source and course of infections by V. aestuarianus in pathogenesis and epidemiologic studies, as well as for designing appropriate prophylactic control measures. (C) 2009 Elsevier B.V. All rights reserved.
Journal of Microbiological Methods (0167-7012) (Elsevier), 2009-05 , Vol. 77 , N. 2 , P. 191-197

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6447.pdf
DOI:10.1016/j.mimet.2009.01.021
http://archimer.ifremer.fr/doc/00000/6447/

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
The basis of this study is a new bathymetric map of the northeast Atlantic compiled from previously published maps made from conventional echosounder data, plus all Sea Beam data acquired on board the R/V JEAN CHARCOT since 1977. As most of the Sea Beam data have been obtained on the continental margin from Porcupine Seabight to the south of the Iberian Peninsula, a precise picture of the continental slope is given. A statistical analysis of the canyons, based on 750 measurements, reveals that many of the canyons present sharp changes in their direction, indicating a structural control mainly linked to the late Hercynian trends, especially around the Iberian Peninsula. Nevertheless, the paths of canyons may merely reflect recent gravity processes, as in the Porcupine Seabight. Canyons locally follow the directions of listric and associated transecting faults (Permian to Triassic and upper Jurassic to lower Cretaceous), as on the Celtic
ISSN: 0278-7407

hal-01261558
https://hal.archives-ouvertes.fr/hal-01261558
https://hal.archives-ouvertes.fr/hal-01261558/document
https://hal.archives-ouvertes.fr/hal-01261558/file/Lallemand1986-Tectonics.pdf
DOI : 10.1029/TC005i007p01125

Éditeur(s) : Paris : Librairie Larousse
Siècle(s) traité(s) : 19
Droits : Domaine public
Provenance : Communauté d'agglomération de La Rochelle. Médiathèque Michel-Crépeau
Permalien : http://www.manioc.org/patrimon/MMC16023-2
MMC16023-2

Éditeur(s) : Paris : Librairie J. B. Baillière et fils
Extrait de : Hygiène des pays chauds

Droits : Domaine public
Provenance : Université de Nantes. Service commun de la documentation
Permalien : http://www.manioc.org/patrimon/NAN13009
NAN13009

Éditeur(s) : HAL CCSD
Résumé : 15 pages
A Stochastic Differential Equation appearing in the statistical theory of turbulence is extended in random environment by assuming that its two parameters are switched by an unobserved continuoustime Markov chain whose states represent the states of the environment. A Dirichlet process is placed as a prior on the space of the sample paths of this chain, leading to a hierarchical Dirichlet model whose estimation is done both on simulated data and on real data of wind speed measured at the entrance of a mangrove ecosystem.
https://hal.archives-ouvertes.fr/hal-00455050

hal-00455050
https://hal.archives-ouvertes.fr/hal-00455050
https://hal.archives-ouvertes.fr/hal-00455050/document
https://hal.archives-ouvertes.fr/hal-00455050/file/CSDA06_Srik_Hal.pdf

Éditeur(s) : Paris : Imprimerie royale
Siècle(s) traité(s) : 19
Droits : Domaine public
Provenance : Collectivité territoriale de Martinique. Bibliothèque Schoelcher
Permalien : http://www.manioc.org/patrimon/SCH13142
SCH13142

Éditeur(s) : HAL CCSD Wiley
Résumé : 1- We examined among- and within-species effects of seed mass for seedling establishment from seed to 5 years of age in a field experiment at Paracou, French Guiana. 2- Six seeds of each of eight species were weighed and planted into each of 120 plots (1 m2) throughout closed-canopy forest along 12 100-m transects in 1998. 3- We described the microhabitat of each planting site using principal components derived from measurements of light availability, soil moisture, carbon and nitrogen content, and soil phosphorus availability. Although both survival and relative growth rate (RGR) increased with increasing light availability, no other microhabitat variable significantly affected seedling performance. Nor did the magnitude of microhabitat effects on survival or RGR differ among species. 4- Larger-seeded species were more likely to survive from germination to 1 year as well as from 1 to 5 years of age. RGR for seedling height during the first year post-germination was not related to seed mass, but smaller-seeded species did grow slightly faster thereafter. Path analyses revealed that correlations between seed mass and performance were explained in part because larger seeds produced larger initial seedlings, which tended to survive better but grow more slowly. 5- We also analysed within-species effects of seed mass for the larger-seeded Eperua grandiflora and Vouacapoua americana (both Caesalpiniaceae). Larger seeds produced larger seedlings in both species, but larger seeds survived better only for Eperua. Larger seedlings grew more slowly in both species, but did not offset the early (Eperua) and later (Vouacapoua) positive direct effects of seed mass on RGR that may represent contrasting strategies for reserve deployment. 6- Our results demonstrate that seed size influences performance within and among species in part because of indirect effects of initial seedling size. However, we suggest that traits tightly correlated with seed mass at the species level, such as specific leaf area, leaf longevity and photosynthetic capacity, may also contribute to interspecific performance differences.
ISSN: 0022-0477

hal-01031089
https://hal.archives-ouvertes.fr/hal-01031089
DOI : 10.1111/j.1365-2745.2005.01041.x

Éditeur(s) : HAL CCSD
Résumé : Staphylococcus aureus is an opportunistic pathogen of humans and warm-blooded animals. It is foundin healthy carriage and can cause a wide range of infections in its hosts. The epithelial surface is theprincipal site of staphylococcal infection. The pathogens have evolved sophisticated mechanisms tohijack the main function of the host cells, thus promoting their invasion and colonization. Amongstthese effects are, alteration of host cell apoptosis, promotion of cell proliferation or conversely,inhibition of cell growth. Using human cervix cancer HeLa and mammary gland bovine MAC-Tepithelial cells, we studied the cytopathic effect of S. aureus and its ability to affect host cell cycle.Using microscopic examination, we found that S. aureus induced the cytopathic effect resulting in theenlargement of the host cells 72 hours post infection. Our experiments showed that the proliferationrate of the epithelial cells was slowed down in S. aureus-infected culture. Three different S. aureusstrains from human and animal origins were used and showed similar effect on both human and bovinecells. Microscopic analysis of DAPI-stained cells revealed huge decrease of mitotic indexes in infectedHeLa and Mac-T cells, synchronized by Double Thymidine Block. Using flow cytometry analysis, wefound that S. aureus induces G2/M phase delay in synchronous HeLa cells. By Western blot analysis,we showed that the G2/M phase delay was associated with accumulation of inactive phosphorylatedcyclin-dependent kinase Cdk1/cdc2, a key inducer of mitosis entry, and dephosphorylation of corehistone H3, an important component of the epigenetic landscape.These results suggest that the delay in G2/M phase transition of the infected epithelial cells may beone of the mechanisms employed by S. aureus to survive and to propagate inside the host. A fullcomprehension of the mechanisms associated to S. aureus-host cell interactions will undoubtedly helpto discover novel targets to treat staphylococcal infections.
EMBO
Villars sur Ollon, Switzerland

hal-01454214
https://hal.archives-ouvertes.fr/hal-01454214
PRODINRA : 171657

Éditeur(s) : Université de Paris 6 – Pierre et Marie Curie
Résumé : Since 1997, a new pathology seasonally occurs in new caledonian shrimp farms during the warm season and was named Summer Syndrome. Diseased Litopenaeus stylirostris shrimp suffer from a septicemic vibriosis which was attributed to V. nigripulchritudo. Preliminary studies based on a collection of V. nigripulchritudo strains have brought to light different virulence levels according to experimental infections results; three virulence statuses were defined: highly (HP), moderately (MP) and non pathogenic (NP). The aim of this work was to genetically characterize virulent V. nigripulchritudo strains. In a first step the genetic diversity of 58 V. nigripulchritudo strains was analyzed by MLST and AP-PCR, revealing a cluster of HP and MP strains, characterized by a low genetic variability and that includes all Summer Syndrome-associated isolates. This confirms the emergence of one cluster of pathogenic V. nigripulchritudo simultaneously with the emergence of the Summer Syndrome ; in a second step, 368 genetic markers of virulence were identified by a Suppressive Subtractive Hybridization performed between the genomes of a HP strain and a genetically close, NP isolate; the distribution of the screened SSH fragments was studied in 58 V. nigripulchritudo isolates by macro-array: 78 DNA fragments were selected, allowing to characterize clusters identified and pathogenic statuses; 13 are specific of the HP strains involved in Summer Syndrome. Interestingly, 10 of these markers are carried by a plasmid pSFn1 that contains sequences highly similar to those of a plasmid pAK1, detected in Vibrio shilonii, a coral pathogen. The origin and consequences of this plasmid acquisition are discussed.
Depuis 1997, les élevages de crevettes en Nouvelle-Calédonie sont confrontés à une nouvelle maladie, le Syndrome d'été, une vibriose septicémique dont l'agent étiologique est Vibrio nigripulchritudo. Les résultats d'infection expérimentale sur une collection de souches, ont montré l'existence de trois pathotypes distincts : hautement (HP), moyennement (MP) et non pathogène (NP). L'étude du polymorphisme génétique de 58 souches par typage moléculaire en MLST et AP-PCR, a mis en évidence un groupe phylogénétique particulier caractérisé par un très faible degré de variabilité génétique (confirmant l'émergence de ce groupe en parallèle à l'émergence du Syndrome d'été) et constitué uniquement de souches HP (dont toutes celles associées au Syndromed'été) et de souches MP. Afin d'identifier des marqueurs génétiques de la virulence des souches responsables du Syndrome d'été, et parmi ces marqueurs des gènes codant potentiellement pour des effecteurs de la virulence, une approche soustractive par SSH a été développée entre une souche HP de type Syndrome d'été et une souche NP : 368 marqueurs génétiques ont ainsi été mis en évidence ; la distribution de ces marqueurs a été étudiée chez les 58 souches de la collection par une approche en macroarray : 78 marqueurs ont été sélectionnés, qui permettent de caractériser les différents groupes phylogénétiques et les différents pathotypes, dont 13 fragments spécifiques des souches HP type Syndrome d'été. Parmi ces 13 fragments, 10 ont été localisés sur le plasmide pSFn1 qui a été entièrement séquencé. Ce même plasmide a été purifié uniquement des souches HP de type Syndrome d'été. Par ailleurs, une très forte homologie a été mise en évidence entre pSFn1 et pAK1, un autre plasmide également séquencé et retrouvé chez la souche V. shilonii AK1, responsable du blanchiment du corail Oculina patagonica en Méditerranée. Ces résultats ont ouvert la discussion sur le rôle de pSFn1 dans la virulence de V. nigripulchritudo.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2008/these-3906.pdf
http://archimer.ifremer.fr/doc/00000/3906/

Siècle(s) traité(s) : 19
Droits : Domaine public
Provenance : Université des Antilles. Service commun de la documentation
Permalien : http://www.manioc.org/patrimon/HASH015cec1d83692f3063aead21
HASH015cec1d83692f3063aead21

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
One of the main difficulties encountered when characterizing the hydrodynamic properties of a fractured aquifer is to identify the preferential flow paths within it. Different methods may be applied to determine the variability of the permeability at the borehole scale and to image the structure of the main flow zones between boreholes. In this paper, we compare the information obtained from different measurement techniques performed in a set of three 100 m depth wells (well-to-well spacing: 5­10 m) in a fractured crystalline rock setting. Geophysical logging and borehole-wall imaging are used to identify open and closed fractures intersecting the boreholes and their orientation. The comparison with flowmeter and single packer tests shows that few of the fractures interpreted as open from geophysical logs are significantly transmissive. Cross-borehole connectivity is first investigated from single packer tests with pressure monitoring in adjacent boreholes. To determine fracture zone connectivity, we propose a methodology simply based on the variation with packer depth of the ratio of the drawdown in the observation well and the drawdown in the pumping well. The results are compared to the analysis of cross-borehole flowmeter tests. We show that both methods provide consistent results with a similar level of information on connectivity.
ISSN: 0022-1694

insu-00221380
https://hal-insu.archives-ouvertes.fr/insu-00221380
DOI : 10.1016/j.jhydrol.2007.07.007

Éditeur(s) : HAL CCSD
Résumé : 27 pages
Cascade Stochastic Differential Equation (SDE), a continuous time model for energy dissipation in turbulence, is a generalization of the Yaglom discrete cascade model. We extend this SDE to a model in random environment by assuming that its two parameters are switched by a continuous time Markov chain whose states represent the states of the environment. Moreover, a Dirichlet process is placed as a prior on the space of sample paths of this chain. We propose a Bayesian estimation method of this model which is tested both on simulated data and on real data of wind speed measured at the entrance of the mangrove ecosystem in Guadeloupe.
https://hal.archives-ouvertes.fr/hal-00286131

hal-00286131
https://hal.archives-ouvertes.fr/hal-00286131
https://hal.archives-ouvertes.fr/hal-00286131/document
https://hal.archives-ouvertes.fr/hal-00286131/file/Srik11_PhysicaDDspace.pdf

Éditeur(s) : Port-au-Prince, Haïti : Imprimerie La Presse
Siècle(s) traité(s) : 20
Provenance : Conseil départemental de la Guadeloupe. La Médiathèque Caraïbe
Permalien : http://www.manioc.org/patrimon/LAM18023
LAM18023

Éditeur(s) : HAL CCSD SAGE Publications
Résumé : International audience
A multiproxy analysis of lacustrine sediments cored in Grand-Case Pond at Saint-Martin, north of the Lesser Antilles archipelago, reveals three distinct climatic periods for the last 3700 years. From 3700 to ~2500 yr cal. BP and from 1150 yr cal. BP to the present, carbonate mud deposition occurred in connection with pond lowstands. These periods were also punctuated by severe drought events, marked by gypsum laminae, and hurricane landfalls, leading to marine sand inputs into the pond. The intermediate time interval, from 2500 to 1150 yr cal. BP, is typified by black organic mud deposition, suggesting that hypoxic to anoxic conditions prevailed at the pond bottom. These were probably linked with a perennial pond highstand and reflect more uniform and wetter climatic conditions than today. The carbon isotopic composition of the ostracod Perissocytheridea bisulcata shows that the lowest δ13C values are recorded during the hypoxic periods, as a consequence of bacterial recycling of isotopically depleted organic matter. Such a climatic history agrees closely with that documented from other records in the Caribbean area, such as the Cariaco Basin, central coast of Belize or Barbados. By constrast, discrepancies seem to emerge from the comparison between hurricane activity recorded at Saint-Martin on the one hand and Vieques (Puerto Rico) on the other hand. We explain this apparent contradiction by a balance between two distinct storm paths in response to latitudinal shifts of the Intertropical Convergence Zone (ITCZ). Stronger storm activity over the Gulf coast and the inner Caribbean Sea is favoured by a southern position of the ITCZ in connection with dry climatic conditions. Plausible links with the North Atlantic Oscillation (NAO) are also suggested.
ISSN: 0959-6836

halshs-00758748
https://halshs.archives-ouvertes.fr/halshs-00758748
https://halshs.archives-ouvertes.fr/halshs-00758748/document
https://halshs.archives-ouvertes.fr/halshs-00758748/file/Malaize_et_al._2011_cor.pdf
DOI : 10.1177/0959683611400198

Éditeur(s) : Paris : Morizot
Résumé : Nouvelle édition
Il manque les tomes : 1:Histoire de la géographie 3:Asie(suite) 8:Europe(suite) et Table générale Chaque tome concernant des pays précis , ils sont indépendant les uns des autres
Description : Nouvelle édition continuée jusqu'à nos jours, d'après les documents scientifiques les plus récents, les derniers voyages et les dernières découvertes par V.-A. Malte-Brun fils,...

Droits : Domaine public
Provenance : Collectivité territoriale de Guyane. Bibliothèque Alexandre-Franconie
Permalien : http://www.manioc.org/patrimon/FRA11193
FRA11193

Date de création : 1870-01-01

Éditeur(s) : London : Bell & Daldy
Siècle(s) traité(s) : 19
Droits : Domaine public
Provenance : Collectivité territoriale de Guyane. Bibliothèque Alexandre-Franconie
Permalien : http://www.manioc.org/patrimon/FRA11002
FRA11002

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Pathogenic agents can be very hard to detect, and usually they do not cause illness for several hours or days. To improve the speed and the accuracy of detection tests and satisfy the needs of early diagnosis, molecular biology methods such as PCR are now used. However, selecting a proper target gene and designing good primers is often not easy. We present a dedicated website, http://patho-genes.org, where we provide every sequence, functional annotation, published primer and relevant article for every annotated gene of major pathogenic bacterial species listed as key agents to be used for a bioterrorism attack. Each published primer was analysed to determine its melting temperature, its specificity and its coverage (i.e. its sensitivity against every allele of its target gene). Data generated have been organized in the form of data sheet for each gene, which are available through multiple browser panels and query systems.
ISSN: 1751-7915

hal-01546181
https://hal.archives-ouvertes.fr/hal-01546181
DOI : 10.1111/j.1751-7915.2012.00353.x

Éditeur(s) : Elsevier
Résumé : The Danube Canyon is a large shelf-indenting canyon that has developed seaward of the late Pleistocene paleo-Danube valley. Mechanisms of canyon evolution and factors that controlled it are revealed by analyzing the morphology and the sedimentary structure of the canyon, as well as the main features of the continental margin around the canyon. This is based on investigation by swath bathymetry in the canyon area combined with different types of seismic data. The canyon is a major erosional trough with a flat bottom cut by an entrenched axial thalweg. The thalweg path varies from highly meandering to fairly straight in relation to the local gradient. Segments of the canyon are characterized by specific morphology, orientation and gradient along the axial thalweg. We interpret these segments in terms of canyon maturity. The sedimentary structure of the canyon documents an older phase of erosion followed by partial infilling, and thus attests for repeated cycles of canyon development. Canyon morphology is interpreted as a result of erosive sediment flows along the entrenched axial thalweg that caused downcutting into the canyon bottom and instability of the canyon walls, and hence enlargement of the canyon and expansion by headward erosion. During the last lowstand level of the Black Sea the canyon was located in an area of high sediment supply close to the paleo-Danube River mouths. This is indicated by buried fluvial channels on the shelf and by a wave-cut terrace associated with a water level situated about - 90 m below the present level. We infer that erosive flows in the canyon resulted from hyperpycnal currents at the river mouths, probably favored by the low salinity environment that characterized the Black Sea during lowstand times. Other mechanisms could have contributed to trigger sediment failure along the canyon, such as instability related to the presence of shallow gas, or the effect of a deep fault.
Marine Geology (0025-3227) (Elsevier), 2004-05 , Vol. 206 , N. 1-4 , P. 249-265

Droits : 2004 Elsevier B.V. All rights reserved
http://archimer.ifremer.fr/doc/2004/publication-476.pdf
DOI:10.1016/j.margeo.2004.03.003
http://archimer.ifremer.fr/doc/00000/476/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The base of the Faro contouritic drift (IODP Site U1386) on the northern margin of the Gulf of Cádiz (Algarve margin) is characterized by two sequences of frequent gravity deposits with different ages and compositions. Among these gravity deposits, several relatively thick debrites (up to 12 m) have been observed and studied in detail.Sedimentological analyses have been performed and because of non-turbulent behavior of debris flows, detailed micropaleontological studies could be realized. Planktonic foraminifera thus allowed establishing a detailed biostratigraphy of these deposits. Benthic foraminifer and ostracod assemblages were used to evaluate the origin of the sediment composing these debris flows and estimate their run-out distance.These debrites are dated from Early Pliocene and early Pleistocene, and were deposited in a mesobathyal environment. They comprise silty mud clasts and matrixes with sand content up to 34%. The Early Pliocene debrites are bioclast-rich whereas the Early Pleistocene debrite is enriched in terrigenous particles. The data indicates that these debrites were triggered on the continental shelf and traveled less than 100 km, eroding the seafloor all along their path for the Early Pliocene debrites and only the first part of their path for the early Pleistocene debrite. Matrixes originate from failure areas whereas eroded sediments along the flow pathway are incorporated into the flow as clasts.High abundance of shelf fauna during the Early Pliocene and great supply of terrigenous particles from rivers during the early Pleistocene in the south-western Iberian margin have favored gravity flows from the continental shelf to the slope. The contouritic paleo-moat of the Faro drift has been a determining channeling feature for gravity flows along the Algarve margin during the early Pleistocene, testifying of the strong interaction between MOW circulation and down-slope processes. Tectonic and diapiric activities were significant during Early Pliocene and early Pleistocene on the Algarve margin and could have been triggering parameters of failures related to these debris flows.
ISSN: 0025-3227

hal-01356172
https://hal.archives-ouvertes.fr/hal-01356172
DOI : 10.1016/j.margeo.2015.08.018

Éditeur(s) : HAL CCSD
Résumé : International audience
Background: Comparative analysis, which aims at investigating ecological and evolutionary patterns among species, may help at targeting reservoirs of zoonotic diseases particularly in countries presenting high biodiversity. Here, we developed a simple method to target rodent reservoirs using published studies screening microparasite infections. Methods: We compiled surveys of microparasites investigated in rodents trapped in Thailand. The data comprise a total of 17,358 rodents from 18 species that have been investigated for a total of 10 microparasites (viruses, bacteria and protozoans). We used residual variation of microparasite richness controlled for both rodent sample size and pathogens' screening effort to identify major rodent reservoirs and potential risky habitats. Results: Microparasite species richness was positively related to rodent sample size and pathogens' screening effort. The investigation of the residual variations of microparasite species richness showed that several rodent species harboured more pathogens than expected by the regression model. Similarly, higher pathogen richness than expected was observed in rodents living in non-flooded lands, forests and paddy fields. Conclusion: Our results suggest to target some rodent species that are not commonly investigated for pathogen screening or surveillance such as R. andamanensis or B. savilei, and that non-flooded lands and forests should be more taken into caution, whereas much surveys focused on paddy rice fields and households.
Infection Ecology and Epidemiology

ird-00714369
http://hal.ird.fr/ird-00714369
http://hal.ird.fr/ird-00714369v2/document
DOI : 10.3402/iee.v2iO.18637
IRD : fdi:010055557