Résumé : Ce rapport clôture une collaboration, entreprise courant 97, entre l’Agence Nationale pour la Valorisation de la Recherche (ANVAR), l’Agence Française de Sécurité Sanitaire des Aliments(AFSSA), le Syndicat National des Aquaculteurs Marins (SFAM) et l’Institut Français de Recherche pour l’Exploitation de la Mer (IFREMER). Deux lignées de nodavirus infectant le bar ont été mises en évidence avec une pathogénie variable selon l'âge et les facteurs extérieurs. Ce virus s’est montré d’une résistance exceptionnelle aux facteurs tant physiques que chimiques. Les diagnostics existants ont été adaptés ou réabordés sous un angle différent. Une étude épidémiologique a été réalisée chez les producteurs. La vaccination par peptides synthétiques a permis de sélectionner un peptide potentiellement protecteur et des essais de vaccin par injection des plasmides directement chez le poisson ont été réalisés. La désinfection et l’inactivation du virus ont donné des bons résultats.

Droits : 2002 Ifremer, Afssa, Anvar
http://archimer.ifremer.fr/doc/00167/27874/26120.pdf
http://archimer.ifremer.fr/doc/00167/27874/26121.pdf
http://archimer.ifremer.fr/doc/00167/27874/

Éditeur(s) : HAL CCSD
Résumé : 20 pp
We first analyze some atmospheric parameters measured in 2004 at the top of La Soufrière volcano: wind speed, pressure and temperature. Next, we study the stochastic process of the wind speed modulus which is of interest for prediction of pollution induced by the plume. We fit to the data various models : FARIMA, periodic trend plus multifractional Brownian noise, multifractal continuous cascades. The estimations show that they evoluate during some transition phases in response to environment changes. Thus, we finally suggest, for future works, some settings that should be more appropriate: time series with regime changes and stochastic processes in random environment.
https://hal.archives-ouvertes.fr/hal-00165572

hal-00165572
https://hal.archives-ouvertes.fr/hal-00165572
https://hal.archives-ouvertes.fr/hal-00165572/document
https://hal.archives-ouvertes.fr/hal-00165572/file/Windsouf_v11.pdf

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
ISSN: 1935-2727

hal-01447691
https://hal.archives-ouvertes.fr/hal-01447691
DOI : 10.1371/journal.pntd.0005254
PUBMED : 28081120

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
ISSN: 1752-0894

hal-01667978
https://hal.archives-ouvertes.fr/hal-01667978
DOI : 10.1038/s41561-017-0028-x

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Line transect surveys are widely used in neotropical rainforests to estimate the population abundance of medium- and large-sized vertebrates. The use of indices such as Encounter Rate has been criticized because the probability of animal detection may fluctuate due to the heterogeneity of environmental conditions among sites. In addition, the morphological and behavioral characteristics (biological traits) of species affect their detectability. In this study, we compared the extent to which environmental conditions and species' biological traits bias abundance estimates in terra firme rainforests in French Guiana. The selected environmental conditions included both physical conditions and forest structure covariates, while the selected biological traits included the morphological and behavioral characteristics of species. We used the distance sampling method to model the detection probability as an explicit function of environmental conditions and biological traits and implemented a model selection process to determine the relative importance of each group of covariates. Biological traits contributed to the variability of animal detectability more than environmental conditions, which had only a marginal effect. Detectability was best for large animals with uniform or disruptive markings that live in groups in the canopy top. Detectability was worst for small, solitary, terrestrial animals with mottled markings. In the terra firme rainforests which represent ~80% of the Amazonia and Guianas regions, our findings support the use of relative indices such as the encounter rate to compare population abundance between sites in species-specific studies. Even though terra firme rainforests may appear similar between regions of Amazonia and the Guianas, comparability must be ensured, especially in forests disturbed by human activity. The detection probability can be used as an indicator of species' vulnerability to hunting and, thus, to the risk of local extinction. Only a few biological trait covariates are required to correctly estimate the detectability of the majority of medium- and large-sized vertebrates. Thus, a biological trait model could be useful in predicting the detection probabilities of rare, uncommon or localized species for which few data are available to fit the detection function.
ISSN: 1051-0761

hal-01555267
https://hal.archives-ouvertes.fr/hal-01555267
DOI : 10.1002/eap.1549
PRODINRA : 396614
PUBMED : 28419598

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Tapajós Domain in the Amazonian Craton comprises hundreds of gold occurrences mainly hosted by Paleoproterozoic granitic rocks, whose geotectonic evolution and deformation style are poorly understood. The Tocantinzinho granite hosts a large amount of gold, forming the largest gold deposit known in the Tapajós Domain. The Tocantinzinho area is formed by plutonic rocks cut by subvolcanic rocks shallowly emplaced and constrained by NW-SE strike-slip faults, probably in a transtensive site. The magmatism started with the emplacement of huge granodiorite that presently formed the basement country rocks (2007–1997Ma), it was followed by the Tocantinzinho granite magmatism (1989–1979 Ma), and the coeval to late andesite emplacement. Petrological and textural evidence suggest the complex and synchronous occurrence of tectonics and few magmatic events expressed by the emplacement of successive granite, aplite, pegmatite, andesite, and dacite. The magmatic event finished with the cooling of this set of rocks below c. 320 °C, at c. 1950 Ma. The cooling rates vary from c. 3.6–14.7°C/Ma, with an average of 7.5°C/Ma, indicating no important vertical exhumations. The elongated geometry of the Tocantinzinho granite and related rocks, features of solid-state deformation within granites and syntectonic deformation of some andesite dikes imply the existence of wrench type tectonic control. The I-type signature of these rocks, their high-K calc-alkaline and metaluminous to peraluminous affinities combined with the tectonic style indicate a post-collisional tectonic setting. Based on geochemical and structural constrains, the rocks from the Tocantinzinho area are interpreted as a part of the Creporizão Suite and probably represent the first expressions of this syn-to late-tectonic magmatism in the region. A continuous and progressive process of magmatic emplacement controlled by tectonics will be proposed and discussed in conclusion.
ISSN: 0895-9811

hal-01526936
https://hal.archives-ouvertes.fr/hal-01526936
DOI : 10.1016/j.jsames.2017.02.003

Éditeur(s) : Springer
Résumé : The light response curve methodology for microphytobenthic biofilms was studied by comparing the two most usual approaches used in pulse amplitude modulated (PAM) fluorometry. The non-sequential light curve (N-SLC) method is characterized by independent measures of the photosynthetic activity across a light gradient whereas the rapid light curve (RLC) method consists of successive measures on the same sample exposed to a stepwise increase of light intensities. Experiments were carried out on experimental microphytobenthic biofilms prepared from natural assemblages and acclimated to dark conditions. In preliminary experiments, N-SLCs were constructed from fluorescence induction curves performed at 12 different photon flux densities (PFDs). A minimum of 50 s of illumination was necessary to reach a stable light response curve; shorter illumination times resulted in underestimating the physiological parameters (alpha the light utilization coefficient in light-limited conditions and rETR(max) the maximum rate of photosynthesis efficiency) of the light response curve. For the comparison between N-SLCs and RLCs, the same time of illumination (50 s) was used for each light step of RLCs so that N-SLCs differed from RLCs only by the way the amount of light was delivered, i.e., a light dose accumulation for RLC. The experimental results showed the difference between the two photobiological response curves. In the lower range of PFDs, RLCs exhibited a larger value of alpha; in this light-limited part of the response curve the incremental increase of PFDs limited the development of NPQ and resulted in a better optimization of electron transport rate for RLC. In the higher range of PFDs, the trend was reversed and the RLC showed a lower value of rETR(max) than the N-SLC did; this is attributed to the light dose accumulation which likely led to a more efficient dispersion of energy, as illustrated by a higher non-photochemical quenching (NPQ). In conclusion, these results confirm that parameters derived from both methods differ in their value and do not bear the same physiological information.
Marine Biology (0025-3162) (Springer), 2007-11 , Vol. 153 , N. 1 , P. 91-101

Droits : 2007 Springer
http://archimer.ifremer.fr/doc/2007/publication-3331.pdf
DOI:10.1007/s00227-007-0787-9
http://archimer.ifremer.fr/doc/00000/3331/

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
ISSN: 0305-1048

hal-01146849
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146849
DOI : 10.1093/nar/gkv350
PUBMED : 25897122

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

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Accumulating evidence suggests that developmental exposure to environmental chemicals may modify the course of brain development, ultimately leading to neuropsychiatric / neurodegenerative disorders later in life. In the present study, we assessed the impact of one of the most frequently used pesticides in both residential and agricultural applications - the synthetic pyrethroid cypermethrin (CYP) - on developmental neurotoxicity (DNT). Female mice were perinatally exposed to low doses of CYP (5 and 20 mg/kg body weight) from gestation to postnatal day 15. Behavioral analyses were performed during the offspring's early life and during adulthood. Postnatal analyses revealed that perinatal exposure to CYP disturbed motor development without modifying sensory and communicative skills. We found that later in life, CYP-exposed offspring expressed maladaptive behaviors in response to highly challenging tasks and abnormal sociability. Transcriptomic analyses performed in the offspring's brain at the end of the exposure, highlighted mitochondrial dysfunction as a relevant pathomechanism underlying CYP-induced DNT. Interestingly, several genes involved in proteostasis maintenance were also shown to be dysregulated suggesting that alterations in biogenesis, folding, trafficking and degradation of proteins may significantly contribute to CYP-related DNT. From a regulatory perspective, this study highlights that behavioral and transcriptomic analyses are complementary tools providing useful direction for better DNT characterization, and as such, should be used together more systematically.
ISSN: 1932-6203

hal-01616489
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01616489
DOI : 10.1371/journal.pone.0184475
PUBMED : 29020013

Éditeur(s) : HAL CCSD Météo et Climat
Résumé : International audience
Les risques hydrométéorologiques sont au coeur du programme de recherche HyMeX sur le cycle de l'eau en Méditerranée. HyMeX a pour ambition d'améliorer leur prévision, de mieux connaître leur variabilité à l'échelle pluriannuelle et de renseigner sur leur évolution, dans le contexte du changement climatique. À cette fin, deux campagnes de mesures dédiées à ces événements extrêmes (SOP1 : pluies intenses et crues rapides ; SOP2 : vents forts et formation d'eaux denses) sont organisées en Méditerranée nord-occidentale, entre septembre 2012 et mars 2013.
ISSN: 0026-1181

hal-00829760
https://hal.archives-ouvertes.fr/hal-00829760
DOI : 10.4267/2042/48793

Éditeur(s) : HAL CCSD Météo et Climat
Résumé : International audience
D'initiative française, le projet international HyMeX a pour objectif d'améliorer la compréhension du cycle de l'eau en Méditerranée, de sa variabilité, de l'échelle de l'événement météorologique aux échelles saisonnières et interannuelles, et de ses caractéristiques sur une décennie, dans un contexte de changement global. Le projet est motivé par le rôle déterminant des processus de mésoéchelle, couplés entre l'atmosphère, la mer et la terre, sur la variabilité du système climatique et sur le déclenchement d'événements hydrométéorologiques extrêmes (précipitations et inondations, vents forts et convection océanique, canicules et sécheresses). Le projet vise enfin à évaluer les conséquences de ces événements extrêmes sur la vulnérabilité sociale et économique de cette région et sa capacité d'adaptation.
ISSN: 0026-1181

hal-00828758
https://hal.archives-ouvertes.fr/hal-00828758
https://hal.archives-ouvertes.fr/hal-00828758/document
https://hal.archives-ouvertes.fr/hal-00828758/file/meteo_2013_80_23%20%281%29.pdf
DOI : 10.4267/2042/48792

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Objective: The first aim of this study was to evaluate the antimicrobial resistance of Enterobacteriaceae in different water environments of Guadeloupe and especially those impacted by waste water treatment plants (WWTP) effluents. The second objective was to characterize the genetic basis for antibiotic resistance of extended-spectrum beta-lactamase (ESBL) and AmpC beta-lactamase producing Enterobacteriaceae isolates (ESBLE and AmpCE).Methods: We have collected 70 surface waters (river and sea samples) impacted or not by WWTP and 18 waste waters from 2 WWTPs in 2012 and 2013. We i) determined the total and resistant bacterial counts and ii) tested isolated Enterobacteriaceae for their antimicrobial susceptibility. We also studied the genetic basis for antibiotic resistance of ESBLE and AmpCE, and the genetic background of Escherichia coli.Results: In rivers, contamination with Escherichia coli and antibiotic resistant coliforms (ARC) increased from the source to the mouth. Highest levels of river contamination with E. coli (9.26 x 105 MPN/100mL) and ARC (2.26 x 108 CFU/mL) were observed in surface water sampled near the discharge. A total of 246 Enterobacteriaceae strains resistant to antibiotics were isolated, mostly from waste waters and from river water collected near the discharge. Among these strains, 33 were Extended Spectrum Beta Lactamase (ESBLE) and 8 E. coli were AmpC beta-lactamase producers. All the ESBLE were isolated from waste waters or from river water collected near the discharge. The blaCTX-M gene was present in 29 of the 33 ESBLE strains, with 24 belonging to group 1. Numerous strains (68.7%) showed more than one acquired antibiotic resistance mechanism. E. coli strains belonged to different phylogenetic groups; among the B2 group, most strains belonged to the ST131 clone.Conclusion: Our results demonstrated that many human activities can supply antibiotic-resistant bacteria in surface water. Nevertheless, WWTPs were the most important supplier of ESBLE in water environment of Guadeloupe.
ISSN: 1932-6203

Droits : http://creativecommons.org/licenses/by/
hal-01485327
http://hal.upmc.fr/hal-01485327
http://hal.upmc.fr/hal-01485327/document
http://hal.upmc.fr/hal-01485327/file/journal.pone.0173155.pdf
DOI : 10.1371/journal.pone.0173155.t002

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Oceanic larvae of the European (Anguilla anguilla) and American (A. rostrata) eels have to cross the Atlantic Ocean from the Sargasso Sea to European or North American coasts before entering continental habitats. In some European rivers, eel recruitment is now < 1% of levels in the 1980s. A better understanding of the effects of anthropogenic pressures and environmental fluctuations on eel larvae and subsequent recruitment is a prerequisite to build efficient management plans. The present paper provides insight into the critical oceanic phase of the eel life cycle with a focus on the duration of the larval migration whose estimates varies between 7 months and more than 2 years in both species. Does this range correspond to a natural variability in larval duration or does it stem from methodological artefacts? We first review the different methods used to estimate the duration of larval migration and critically describe their possible sources of misinterpretation. We then evaluate the consistency of these methods with the current knowledge about the ecology and physiology of eel larvae and the physical oceanography. While a moderate discrepancy in migration duration was found between methods for the American eel, the discrepancy was large in the European eel. In this species, otolith microstructure studies indicated migration durations between 7 and 9 months, while other methods pointed to durations of about 2 years. We show that estimates in favour of a long migration duration seem more robust to methodological caveats than methods estimating short durations of migration.
Fish And Fisheries (1467-2960) (Wiley-blackwell Publishing, Inc), 2010-09 , Vol. 11 , N. 3 , P. 289-306

Droits : 2010 Blackwell Publishing Ltd.
http://archimer.ifremer.fr/doc/00011/12208/9033.pdf
DOI:10.1111/j.1467-2979.2010.00362.x
http://archimer.ifremer.fr/doc/00011/12208/

Éditeur(s) : HAL CCSD Météo et Climat
Résumé : International audience
Le premier volet du projet Cyprim vise à mieux identifier les précurseurs des cyclogenèses et des précipitations intenses en région méditerranéenne. Cet article en présente les principaux résultats. Il est question des ingrédients météorologiques à l'origine de ces systèmes, de la grande à la mésoéchelle, des causes des fortes intensités, localisations et parfois stationnarité des récipitations associées. Le coeur de l'article présente des méthodes d'identification des anomalies de tourbillon potentiel liées à l'occurrence d'événements précipitants intenses et dresse une climatologie de ces anomalies. Les perspectives d'exploitation de cette information pour améliorer la qualité des prévisions sont évoquées. ENGLISH VERSION: The first part of the CYPRIM project (Cyclogenesis and intense precipitations in the Mediterranean region) aims at a better identification of the precursor structures of cyclogenesis and heavy precipitation in the Mediterranean region. This article presents the main results. It mentions the meteorological ingredients from which these systems originate from the large to themesoscale, the reasons for large intensities, the localization and sometimes stationarity of the associated precipitations. The heart of the article shows methods for identifiying potential vorticity anomalies involved in the occurrence of heavy precipitation events and sets up a climatology of these anomalies.The perspectives of the usefulness of this information for improving forecast quality are discussed.
ISSN: 0026-1181

insu-00448250
https://hal-insu.archives-ouvertes.fr/insu-00448250
DOI : 10.4267/2042/28828

Éditeur(s) : HAL CCSD Elsevier
Résumé : Two peat sequences were sampled in the vicinity of the main mining districts of the Vosges Mountains: Sainte-Marie-aux-Mines and Plancher-les-Mines. Lead isotopic compositions and excess lead fluxes were calculated for each of these radiocarbon-dated sequences. Geochemical records are in very good agreement with the mining history of the area, well known over the last millennium. Except for an anomaly corresponding to the Middle Bronze Age which has not yet been resolved, there is no clear geochemical evidence of local metal production in the Vosges before the 10th century as excess lead deposition archived between 500 BC and 500 AD is attributed to long-range transport of polluted particulate matter. The approach described here can be applied to other mining districts where archaeological evidence is scarce or even lacking, but where past exploitation is suspected.
ISSN: 0375-6742

hal-00512409
https://hal.archives-ouvertes.fr/hal-00512409
DOI : 10.1016/j.gexplo.2010.05.004

Éditeur(s) : HAL CCSD Frontiers
Résumé : International audience
Glufosinate ammonium (GLA) is one of the most widely used herbicides in agriculture. As is the case for most pesticides, potential adverse effects of GLA have not been studied from the perspective of developmental neurotoxicity. Early pesticides exposure may weaken the basic structure of the developing brain and cause permanent changes leading to a wide range of lifelong effects on health and/or behavior. Here, we addressed the developmental impact of GLA by exposing female mice to low dose GLA during both pre- and postnatal periods and analyzed potential developmental and behavioral changes of the offspring during infancy and adulthood. A neurobehavioral test battery revealed significant effects of GLA maternal exposure on early reflex development, pup communication, affiliative behaviors, and preference for social olfactory cues, but emotional reactivity and emotional memory remained unaltered. These behavioral alterations showed a striking resemblance to changes seen in animal models of Autistic Spectrum Disorders. At the brain level, GLA maternal exposure caused some increase in relative brain weight of the offspring. In addition, reduced expression of Pten and Peg3 - two genes implicated in autism-like deficits - was observed in the brain of GLA-exposed pups at postnatal day 15. Our work thus provides new data on the link between pre- and postnatal exposure to the herbicide GLA and the onset of autism-like symptoms later in life. It also raises fundamental concerns about the ability of current safety testing to assess risks of pesticide exposure during critical developmental periods.
ISSN: 1662-5153

hal-01121829
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01121829
PUBMED : 25477793
DOI : 10.3389/fnbeh.2014.00390
PUBMEDCENTRAL : PMC4238406

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) : HAL CCSD International Union of Crystallography
Résumé : International audience
ISSN: 0021-8898

cea-01377306
https://hal-cea.archives-ouvertes.fr/cea-01377306
DOI : 10.1107/S0021889813027453

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
ISSN: 1752-0894

hal-01668923
https://hal.archives-ouvertes.fr/hal-01668923
DOI : 10.1038/s41561-017-0028-x