Éditeur(s) : HAL CCSD
Résumé : French Guiana is a region located on the Guiana Shield in South America. Is presents at the same time a high originality in biodiversity, a good state of conservation and a strong correlation to Amazonian carbon stocks. Knowledge on evolution of the forest structure of French Guiana is however still insufficient to bring an optimal management at territory scale. Availability as never seen before of remote sensing data at high spatial resolution such as LiDAR, on large coverage, offers the opportunity to assess the forest resource in French Guiana. The work done during this thesis aim mostly to study the structure and the variations of the canopy height, the factors determining its variability and the consequences of forest logging activities. The data used during this thesis come from an airborne LiDAR and field data from Office National des Forêts (ONF). This thesis manuscript is divided in three parts. The first part introduces the problem and sets the objectives of the thesis. The second part takes the so-called "article" form, that is, the different chapters that compose it are scientific articles published or in the course of publication, it is composed of three studies (I) A study on the gaps detection and environmental determinants on the gap sizes distribution in natural forest: How to characterize the gap size distribution and are there environmental determinants that influence the statistical distribution of gap size? This article has been submitted in Biogeoscience. (ii) A study of the control of the environment on the canopy height structure and variations at different spatial resolutions. Which spatial scales are relevant for analyzing the environmental determinants of canopy height changes in tropical forests from remote sensing data? How can the environment help or not map the height of the canopy in the rainforest? This article was accepted for publication in Remote Sensing. (iii) a third study where we quantified the effects of Reduced Impact Logging (RIL) on the structure and variation of canopy height. What are the effects of logging on canopy height variations and gap size distribution? This article will be submitted for publication in a Forest Ecology and Management journal. In the last part, after a synthesis of the main results, we propose a conclusion.
La Guyane française est une région située sur le Plateau des Guyanes en Amérique du sud. Elle présente à la fois une grande originalité en termes de biodiversité, un bon état de conservation et une forte contribution au stock de carbone Amazonien. Les connaissances sur l’évolution de la structure forestière de la Guyane française restent cependant insuffisantes pour offrir une gestion optimale à l’échelle du territoire. La disponibilité sans précédent de données de télédétection à très haute résolution spatiale telles que le LiDAR , sur de larges couvertures nous offre l'opportunité d’évaluer la ressource forestière de la Guyane Française. Les travaux réalisés dans le cadre de cette thèse visent prioritairement à étudier la structure et les variations de la hauteur de canopée, les facteurs déterminant sa variabilité ainsi que les conséquences des activités d’exploitation forestière. Les données utilisées au cours de la thèse proviennent d’un LiDAR aéroporté et des données de terrains de l'Office National des Forêts (ONF). Ce manuscrit de thèse est divisé en trois grandes parties. La première partie introduit la problématique et fixe les objectifs de la thèse. La seconde partie prend la forme dite « sur article », c'est-à-dire que les différents chapitres qui la compose sont des articles scientifiques publiés ou en cours de publication, elle est composée de trois études. (i) Une étude concernant la détection des trouées et des déterminants environnementaux sur la distribution de tailles des trouées en forêt non exploitée : Comment caractériser la distribution de taille des trouées et est-ce qu’il y a des déterminants environnementaux qui influencent la distribution statistique de taille de trouées? Cet article à été soumis dans Biogeoscience. (ii) Une étude du contrôle de l'environnement sur la structure et les variations de la hauteur de canopée à différentes résolutions spatiales. Quelles échelles spatiales sont pertinentes pour analyser les déterminants environnementaux des variations de hauteur de la canopée en forêt tropicale à partir des données de télédétection ? Comment l’environnement peut aider, ou pas, à cartographier la hauteur de la canopée en forêt tropicale ? Cet article à été accepté pour publication dans Remote Sensing. (iii) Une troisième étude où nous avons quantifié les effets de l’exploitation à faible impact (EFI) sur la structure et la variation de la hauteur de canopée. Quelles sont les effets de l’exploitation forestière sur les variations de hauteur de canopée et sur la distribution de taille des trouées ? Cet article sera soumis pour publication dans une revue scientifique (Forest Ecology and Management). Dans la dernière partie, après une synthèse des principaux résultats, nous proposons des pistes de développement.
https://tel.archives-ouvertes.fr/tel-01527553

NNT : 2016YANE0006
tel-01527553
https://tel.archives-ouvertes.fr/tel-01527553
https://tel.archives-ouvertes.fr/tel-01527553/document
https://tel.archives-ouvertes.fr/tel-01527553/file/these-youven-goulamoussene2.pdf

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
AIMS: Virus detection has often been difficult due to a low concentration in water. In this study, we developed a new procedure based on concentration of virus particles on an innovative support: poly-L-lysine dendrigrafts (DGL), coupled with directed nucleic acid extraction and real-time PCR quantification. METHODS AND RESULTS: This method was evaluated using the bacteriophage MS2 as a model virus. This virus exhibited the size and structural properties of human pathogenic enteric viruses and has often been used to assess new supports of concentration. Moreover, this bacteriophage is also a faecal contamination indicator. In this study, many water filtration conditions were tested (volume of water, concentration, etc.), and more than 80% of bacteriophage were recovered after filtration on polymer, in most conditions. We demonstrated that the method was linear (slope = 0*99 ± 0*04 and Y intercept when x = -0*02 ± 0*28), valid (as manipulators, tested concentrations, volumes of sample and batch of polymer did not have any influence on concentration) and sensitive (allowing to concentrate up to 16,600-fold 1 l of sample and to detect and quantify down to 750 GC l(-1) and 7500 GC l(-1), respectively). CONCLUSIONS: To conclude, this support exhibits high interest to retain viruses and to allow to detect low concentration of virus in water. SIGNIFICANCE AND IMPACT OF THE STUDY: This study gives valuable advance in the methods of concentration and diagnosis of virus in water.
Journal of Applied Microbiology

hal-00828987
https://hal.archives-ouvertes.fr/hal-00828987
DOI : 10.1111/jam.12209
PUBMED : 23551794

Éditeur(s) : Springer
Résumé : The transforming growth factor (TGF)-beta superfamily is a group of important growth factors involved in multiple processes such as differentiation, cell proliferation, apoptosis and cellular growth. In the Pacific oyster Crassostrea gigas, the oyster gonadal (og) TGF-beta gene was recently characterized through genome-wide expression profiling of oyster lines selected to be resistant or susceptible to summer mortality. Og TGF-beta appeared specifically expressed in the gonad to reach a maximum when gonads are fully mature, which singularly contrasts with the pleiotropic roles commonly ascribed to most TGF-beta family members. The function of og TGF-beta protein in oysters is unknown, and defining its role remains challenging. In this study, we develop a rapid bacterial production system to obtain recombinant og TGF-beta protein, and we demonstrate that og TGF-beta is processed by furin to a mature form of the protein. This mature form can be detected in vivo in the gonad. Functional inhibition of mature og TGF-beta in the gonad was conducted by inactivation of the protein using injection of antibodies. We show that inhibition of og TGF-beta function tends to reduce gonadic area. We conclude that mature og TGF-beta probably functions as an activator of germ cells development in oyster.
Marine Biotechnology (1436-2228) (Springer), 2011-10 , Vol. 13 , N. 5 , P. 971-980

Droits : Springer Science+Business Media, LLC 2011
http://archimer.ifremer.fr/doc/00042/15371/13438.pdf
DOI:10.1007/s10126-010-9361-4
http://archimer.ifremer.fr/doc/00042/15371/

Éditeur(s) : Université de la Polynésie Française
Résumé : The ontogeny of osmoregulation was studied in the blue shrimp Litopenaeus stylirostris in New Caledonia. The implication of branchial organs in ionic regulation was first demonstrated in juveniles by immunolocalization of three ion transporting proteins ( namely NKA, co-transporter NKCC1 and CFTR ) and ionocyte detection was done by means of electron microscopy. The role of the main ion transporting enzyme, NKA, was subsequently investigated during post-embryonic development using an integrative approach associating physiological, histological, immunological and biomolecular studies. Results obtained allowed us to propose a model of the osmoregulatory pattern in L. stylirostris based on weak regulation in the early stages, then progressively this species acquires the adult pattern of hyper-hypo-regulation after metamorphosis with the concurrent development of epipodites and gills. Strong NKA immunofluorescence and abundance of NKA transcripts in these two tissues compared to others organs suggest their functional implication in osmoregulatory processes. The results of this study allow us to increase our knowledge of the penaeid shrimp osmoregulation and to propose zootechnical measures to improve the animal physiological comfort. These propositions have been already tested during larval rearing trials, leading a two-fold-growth in 19 days-old postlarvae.
L’étude de l’ontogenèse de l’osmorégulation a été entreprise chez la crevette bleue Litopenaeus stylirostris en Nouvelle-Calédonie. L’implication des tissus de la cavité branchiale dans la régulation ionique a été déterminée au préalable chez des juvéniles par immunolocalisation de trois transporteurs protéiques d’ions, ( la NKA, le co-transporteur NKCC1 et le CFTR ) et par la détection de ionocytes en microscopie électronique. Le rôle de la NKA a été particulièrement étudié et son implication a été examinée au cours du développement post-embryonnaire par une approche intégrative associant des études physiologiques, histologiques, immunologiques et moléculaires. Cette démarche nous a permis de proposer un modèle d’osmorégulation chez L. stylirostris: de faible régulatrice dans les premiers jours de sa vie, cette espèce évolue vers l’hyper-hypo-régulation après la métamorphose avec le développement progressif des épipodites et des branchies. L’immunofluorescence prononcée de la NKA ainsi que l’abondance des transcrits du gène codant la NKA dans les tissus de ces deux organes suggèrent leur implication fonctionnelle dans l’ionorégulation. Les résultats de ce travail nous ont permis d’accroître nos connaissances sur l’osmorégulation chez les pénéidés et de proposer des améliorations zootechniques visant à augmenter leur confort physiologique. Ces préconisations ont fait l’objet de premiers essais en conditions d’élevage et se sont traduites par un doublement de la croissance des post-larves de 19 jours.

Droits : 2011 The author, Univ. Polynésie Française
http://archimer.ifremer.fr/doc/00052/16314/13816.pdf
http://archimer.ifremer.fr/doc/00052/16314/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Molds and allergens are common indoor biocontaminants. The aims of this study were to assess the concentrations of common molds in indoor air and floor dust and the concentrations of house dust mite, cat and dog allergens in mattress dust in French dwellings, and to assess predictors of these concentrations. A sample of 150 houses in Brittany (western France) was investigated. Airborne Cladosporium and Penicillium were detected in more than 90% of the dwellings, Aspergillus in 46% and Alternaria in only 6% of the housings. Regarding floor dust samples, Cladosporium and Penicillium were detected in 92 and 80% of the housings respectively, Aspergillus in 49% and Alternaria in 14%. House dust mite allergens Der p1 and Der f1 were detected in 90% and 77% of the mattress dust samples respectively and Can f1 and Fel d1 in 37% and 89% of the homes. Airborne and dustborne mold concentrations, although not statistically correlated (except for Aspergillus) shared most of their predictors. Multivariate linear models for mold levels, explaining up to 62% of the variability, showed an influence of the season, of the age of the dwelling, of aeration habits, presence of pets, smoking, signals of dampness, temperature and relative humidity. Allergens in the dust of the mattress were strongly related to the presence of pets and cleaning practices of bedsheets, these factors accounting for 60% of the variability. This study highlights ubiquitous contamination by molds and underlines complex interaction between outdoor and indoor sources and factors
ISSN: 0048-9697

hal-01165440
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01165440
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01165440/file/Molds%20and%20allergens%20in%20French%20dwellings%20rev2_clean%20version.pdf
DOI : 10.1016/j.scitotenv.2015.06.039
PUBMED : 26094801

Résumé : Ifremer launched and coordinated the development of a strategy for the REBENT network (REseau BENThique) in 2000 to monitor the aftermath of the "Erika" oil spill in December 1999. Its aim is to provide consistent baseline knowledge about coastal benthic habitats and constitute a monitoring tool to detect changes at various scales over time and space. Sector-based seabed habitat mapping in shallow water (< 50 m deep), is currently being conducted throughout Brittany's coastal waters through a combination of geoacoustic marine systems and ground-truthing using biological grab sampling and seabed observations. Sedimentological and biological results on Glenan area emphasize a great diversity of subtidal habitats and marine species recognized. Sidescan imagery accentuates the complexity of the communities structure in a marine environment distinguished by strong and regulary roughness of the sea. Maerl biocenose is present at the nord-east of the archipelago. Progressively it gives way to mud sediment colonized by Amphiura filiformis and Haploops in the deeper channel. To the west and the south, substratum types are more coarse, occasionally mobiles, composed of essentially sand community with Nephtys and gravelly sand community with Branchiostoma lanceolatum.
Le Rebent (Réseau benthique), initié en 2000 à la suite de la catastrophe de l'Erika, a pour objectif de suivre les habitats benthiques côtiers et de détecter les changements à différentes échelles de temps et d'espace. L'approche sectorielle dans les petits fonds (< 50 m) des côtes bretonnes combine, des moyens de prospection acoustique, afin de délimiter les principaux types de substrats, avec des prélèvements et des observations biologiques pour caractériser les peuplements macrobenthiques. Les résultats des analyses sédimentologiques et faunistiques montrent autour de l'archipel des Glénan, une grande diversité d'habitats et d'espèces reconnues. L'imagerie acoustique fait ressortir la complexité de leur structuration dans un environnement marin soumis à de fortes et régulières périodes d'agitation. La biocénose de maërl occupe le nord-est de l'archipel. Elle laisse place progressivement aux sédiments envasés à Amphiura filiformis et aux vases à Haploops dans le fond du chenal. A l'ouest et au sud, les subtrats sont plus grossiers, essentiellement sableux à Nephtys et sablo-graveleux à Branchiostoma lanceolatum, épisodiquement mobiles.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/rapport-2301.pdf
http://archimer.ifremer.fr/doc/2006/sup-2301.pdf
http://archimer.ifremer.fr/doc/00000/2301/

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : Sites of monomethylmercury (MMHg) production in Amazonian regions have been identified in hydraulic reservoirs, lake sediments and wetlands, but tailings ponds have not yet received sufficient attention for this purpose. This work evidenced high MMHg production within the water column and the interstitial water of two tailings ponds of French Guiana Au mines located; (i) in a small scale exploitation (Combat) where Hg was used for Au amalgamation, and (ii) in an industrial on-going Au mine (Yaoni) processing without Hg. The (MMHg)(D) maximum (2.5 ng L-1) occurred in the oxic water column above the sediment-water interface (SWI) of the most recent tailings pond (Combat), where the substrate was fresh, the redox transition was sharp and the pool of total Hg was large. In the Yaoni pond, the (MMHg)(D) maximum concentration (1.4 ng L-1) was located at the SWI where suboxic conditions prevailed. Using the (MMHg)(D) concentration as a proxy for Hg methylation rates, the present results show that Hg methylation may occur in various redox conditions in tailings ponds, and are favored in areas where the organic matter regeneration is more active. A 3-month long laboratory experiment was performed in oxic and anoxic boxes filled with high turbidity waters from the Combat Au mine to simulate tailings ponds. Slaked lime was added in an experimental set (2 mg L-1)and appeared to be very efficient for the reduction of suspended particulate matter (SPM) to environmentally acceptable concentrations. However, at the end of the experiment, large (MMHg)(D) concentrations were monitored under treated anoxic conditions with the (MMHg)(D) maximum located at the SWI above the Fe-reducing zones. No (MMHg)(D) was detected in oxic experiments. The use of slaked lime for SPM decantation appears to be an efficient and non-onerous process for Au miners to avoid Hg methylation in tailings ponds when it is combined with rapid drainage of the mine waters. A subsequent human intervention is however necessary for the recovery of soil structure through the cover of dried ponds with organic rich materials and reforestation to avoid the stagnation of rain waters and the occurrence of anoxia. (C) 2010 Elsevier Ltd. All rights reserved.
Applied Geochemistry (0883-2927) (Pergamon-elsevier Science Ltd), 2011-02 , Vol. 26 , N. 2 , P. 222-229

Droits : 2010 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/00030/14117/12133.pdf
DOI:10.1016/j.apgeochem.2010.11.022
http://archimer.ifremer.fr/doc/00030/14117/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
A shallow field experimental site for CO2 injection was established at Maguelone (Languedoc, France), in order to test in an integrated manner a suite of surface and downhole hydrogeophysical monitoring methods. The objective is to improve monitoring of gas transport in the shallow subsurface and to determine the sensitivity of CO2 monitoring systems for leakage detection. The site offers a natural laboratory to study the processes associated with CO2 injection in a clastic and clay-rich context saturated with saline fluids. Prior to CO2 injection, three nitrogen (N2) injections were undertaken in 2012 to measure the site response to neutral gas injection. In 2013, a volume of 111 m3 (mass of 220 kg) of CO2 was injected during 3.5 h at 15 m depth. During each experiment, the gas plumes were successfully detected from pressure monitoring, time-lapse induction logging and downhole resistivity monitoring with dipole–dipole array. Increases in resistivity are attributed to free gas propagation (either N2 or CO2) whereas decreases in resistivity correlate with CO2 dissolution in the pore fluid. Chemical analyses confirm this hypothesis with a decrease in pH and an increase in the concentration of dissolved species in the latter case.
ISSN: 1750-5836

hal-01355943
https://hal.archives-ouvertes.fr/hal-01355943
DOI : 10.1016/j.ijggc.2015.12.005

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This study investigated the clinical epidemiology and resistance mechanisms of Acinetobacter baumannii and characterised the clonal diversity of carbapenem-resistant A. baumannii (CRAB) during an ICU-associated outbreak at Cayenne Hospital, French Guiana. All non-duplicate A. baumannii isolates from 2008 to 2014 were tested for antibiotic susceptibility by disk diffusion. Multilocus sequence typing, pulsed-field gel electrophoresis (PFGE) and characterisation of carbapenemase-encoding genes were performed on CRAB. Of the 441 A. baumannii isolates, most were from males (54.0%) and were detected mainly from the ICU (30.8%) and medicine wards (21.8%). In the ICU, strains were mainly isolated from the respiratory tract (44.1%) and bloodstream (14.0%), whereas in medicine wards they mainly were from wound/drainage (36.5%) and bloodstream (25.0%). A. baumannii showed the greatest susceptibility to piperacillin/tazobactam (92.7%), imipenem (92.5%), colistin (95.6%) and amikacin (97.2%), being lower in the ICU and medicine wards compared with other wards. An outbreak of OXA-23-producing CRAB occurred in the 13-bed ICU in 2010. CRAB strains were more co-resistant to other antimicrobials compared with non-CRAB. Molecular genetics analysis revealed five sequence types [ST78, ST107 and ST642 and two new STs (ST830 and ST831)]. Analysis of PFGE profiles indicated cross-transmissions of CRAB within the ICU, between the ICU and one medicine ward during transfer of patients, and within that medicine ward. This study provides the first clinical and molecular data of A. baumannii from French Guiana and the Amazon basin. The ICU was the highest risk unit of this nosocomial outbreak of OXA-23-producing CRAB, which could subsequently disseminate within the hospital.
ISSN: 0924-8579

hal-01506828
https://hal.archives-ouvertes.fr/hal-01506828
PUBMED : 27236843

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : Three methods for automatic detection of mesoscale coherent structures are applied to Sea Level Anomaly (SLA) fields in the South Atlantic. The first method is based on the wavelet packet decomposition of the SLA data, the second on the estimation of the Okubo-Weiss parameter and the third on a geometric criterion using the winding-angle approach. The results provide a comprehensive picture of the mesoscale eddies over the South Atlantic Ocean, emphasizing their main characteristics: amplitude, diameter, duration and propagation velocity. Five areas of particular eddy dynamics were selected: the Brazil Current, the Agulhas eddies propagation corridor, the Agulhas Current retroflexion, the Brazil-Malvinas confluence zone and the northern branch of the Antarctic Circumpolar Current (ACC). For these areas, mean propagation velocities and amplitudes were calculated. Two regions with long duration eddies were observed, corresponding to the propagation of Agulhas and ACC eddies. Through the comparison between the identification methods, their main advantages and shortcomings were detailed. The geometric criterion presents the best performance, mainly in terms of number of detections, duration of the eddies and propagation velocities. The results are particularly good for the Agulhas Rings, which have the longest lifetimes of all South Atlantic eddies.
Ocean Science (1812-0784) (Copernicus Gesellschaft Mbh), 2011 , Vol. 7 , N. 3 , P. 317-334

Droits : Author(s) 2011. This work is distributed under the Creative Commons Attribution 3.0 License. EGU
http://archimer.ifremer.fr/doc/00039/15051/12378.pdf
DOI:10.5194/os-7-317-2011
http://archimer.ifremer.fr/doc/00039/15051/

Éditeur(s) : EDP Sciences
Résumé : From April 2003 to April 2004 monthly sea surveys were conducted around 2 fish aggregating devices (FADs) moored at 2000 and 2500 m depth in Martinique (Lesser Antilles). The use of a dual frequency splitbeam echosounder combined with an underwater camera and fishing methods allowed assessment of average space and time distribution of pelagic fish aggregated beneath the FADs, as well as identification of their overall size and species composition. At daytime, 4 fish aggregations were identified at each FAD, representing 4 distinct types: i) an aggregation of small juvenile tuna (mean fork length, FL: 30 cm) observed very close to the surface in 25% of daytime periods; ii) a small surface aggregation dominated by carangids, Caranx crysos, present in 65% of daytime periods; iii) a large sub-surface aggregation observed during all daytime periods: this aggregation appeared to be primarily comprised of 58 cm FL blackfin tuna (Thunnus atlanticus), mixed with yellowfin (Thunnus albacares) and skipjack (Katsuwonus pelamis) tunas of the same size; and iv) sub-surface scattered large predators (mainly blue marlin, Makaira nigricans) present in 10% of daytime periods. A smaller sub-surface aggregation comprised of medium tuna mixed with "extranatants" (fishes which remain within 10 to 50 m of a FAD) was observed in 75% of night-time periods, whereas unidentified scattered fishes were detected from 70 to 400 m depth. The low daytime vulnerability of medium sub-surface tunas to applied line techniques leads us to assume that their feeding motivation was low during daytime. These tunas could preferentially feed on mesopelagic organisms during night-time and transition periods around Martinican moored FADs. Local fishermen mainly targeted the large scattered predators using very small tunas as living bait. The sub-surface tuna aggregation hence appeared to be currently unexploited by local fisheries, though it represented the large majority of the pelagic biomass around the moored FADs.
Des campagnes scientifiques mensuelles ont été menées autour de 2 dispositifs de concentration de poissons ancrés à 2000-2500 m de profondeur, en Martinique d'avril 2003 à avril 2004. L'utilisation combinée d'un échosondeur monofaisceau multifréquence, d'une caméra vidéo sous-marine et de techniques de pêche conventionnelles a permis de déterminer la distribution spatio-temporelle moyenne des poissons agrégés autour des DCP ancrés ainsi que la composition générale des agrégations. Les techniques de vidéo sous-marine ont joué un rôle majeur dans l'identification des espèces et l'observation de leur comportement. De jour; quatre types d'agrégations ont été définis : i) une agrégation de thonidés juvéniles (longueur à la fourche, LF, moyenne : 30 cm) observée très près de la surface durant 25 % des périodes diurnes échantillonnées ii) une petite agrégation composée essentiellement de Caranx crysos présente en surface lors de 65 % des phases diurnes iii) une grande agrégation de thons observée en sub-surface lors de toutes les phases diurnes; cette agrégation était constituée essentiellement de thons noirs (Thunnus atlanticus) de 58 cm LF, associés de façon saisonnière à des albacores (Thunnus albacares) et des listaos (Katsuwonus pelamis) de taille similaire iv) des grands prédateurs assez dispersés (essentiellement le marlin bleu, Makaira nigricans), observés lors de 10 % des phases diurnes. Une agrégation de sub-surface, aux dimensions plus réduites et composée de thons et "d'extranatants" (poissons restant à distance de 10 à 50 m du DCP) a été observée lors de 75 % des périodes nocturnes; ainsi que des organismes non-identifiés dispersés entre 70 et 400 m de profondeur. La faible vulnérabilité diurne des thons de sub-surface aux techniques de ligne utilisées indique qu'ils ne se nourrissent pas activement durant la journée. Ces poissons pourraient se nourrir préférentiellement d'organismes mésopélagiques durant les phases de transition et nocturnes autour des DCP ancrés. La pêcherie artisanale martiniquaise n'exploite qu'une faible part des ressources agrégées autour des DCP ancrés. Les principales espèces-cibles sont les grands prédateurs capturés de jour en utilisant des thonidés juvéniles comme appât vivant. L'agrégation de thons de sub-surface représente la grande majorité de la biomasse autour des DCP mais elle est quasiment inexploitée par les pêcheries locales.
Aquatic Living Resources (0990-7440) (EDP Sciences), 2007-10 , Vol. 20 , N. 4 , P. 357-366

Droits : EDP Sciences, IFREMER, IRD 2007
http://archimer.ifremer.fr/doc/2007/publication-3634.pdf
DOI:10.1051/alr:2008004
http://archimer.ifremer.fr/doc/00000/3634/

Éditeur(s) : HAL CCSD
Résumé : International audience
BACKGROUND AND AIM: The impact of basal core promoter (BCP) and precore (PC) mutants of the hepatitis B virus (HBV) on liver disease severity remains controversial. The aim of the present study was to screen BCP and PC mutations in 252 HBV surface antigen (HBsAg) positive carriers in France and to assess relationships between these mutations and severe fibrosis. METHODS: Direct sequencing of the precore/core gene was used to detect A1762T/G1764A and G1757A mutations in the BCP and G1896A and G1899A mutations in the PC region. RESULTS: The prevalences of A1762T/G1764A, G1757A, G1896A, and G1899A mutations were 34.1%, 38.7%, 54.9%, and 29.3% (P < 0.001), respectively. The independent predictors of severe fibrosis (>/=F3 Metavir) were older age (P < 0.001), male gender (P = 0.012), elevated alanine aminotransferase (P < 0.001), and the double A1762T/G1764A mutant with no other mutations (P = 0.011). Interestingly, the association of the G1899A mutation with the double A1762T/G1764A mutant significantly counteracted the deleterious effect of the sole double A1762T/G1764A mutant (odds ratio [OR] = 0.28 vs. OR = 3.55, respectively, P = 0.028). CONCLUSIONS: Patients with the A1762T/G1764A mutation have a higher risk of severe fibrosis. The G1899A mutation is a protective factor against severe fibrosis that counteracted the deleterious effect of the A1762T/G1764A mutation. Finally, host phenotypic and HBV genotypic markers independently predict fibrosis severity.
Journal of gastroenterology and hepatology

hal-01477209
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01477209
DOI : 10.1111/jgh.13338
PUBMED : 26992056

Éditeur(s) : HAL CCSD ACM
Résumé : International audience
Applications over wireless sensor networks are growing quickly. Traditional software development tools are not well adapted to this technology. In particular, adequate testing methodologies are required. Many issues have not been formally addressed as energy-conservation, congestion control, reliability data dissemination, security. In this paper, we present a pragmatic approach to detect some kind of anomalies based on defined scenarios on wireless sensor networks. A scenario is considered as a set of events which should happen on the network in an ordered way. We discuss a formal architecture able to perform these scenarios over the wireless sensor networks and to raise alarms if necessary. This methodology has been implemented on a prototype and has been experimented with various examples. This contribution is a first attempt for a formal testing methodology for wireless sensor networks.
Proceedings of the 6th ACM workshop on QoS and security for wireless and mobile networks

Droits : info:eu-repo/semantics/OpenAccess
hal-00596118
https://hal.archives-ouvertes.fr/hal-00596118
https://hal.archives-ouvertes.fr/hal-00596118/document
https://hal.archives-ouvertes.fr/hal-00596118/file/Q2sWinet_10.pdf
DOI : 10.1145/1868630.1868641

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September-October (autumn) and lowest in April-May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3-5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters. See also the Perspective by Massana
ISSN: 0962-1083

hal-01545321
https://hal.archives-ouvertes.fr/hal-01545321
DOI : 10.1111/mec.13160

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Virus detection has often been difficult due to a low concentration in water. In this study, we developed a new procedure based on concentration of virus particles on an innovative support: poly-L-lysine dendrigrafts (DGL), coupled with directed nucleic acid extraction and real-time PCR quantification. Methods and Results: This method was evaluated using the bacteriophage MS2 as a model virus. This virus exhibited the size and structural properties of human pathogenic enteric viruses and has often been used to assess new supports of concentration. Moreover, this bacteriophage is also a faecal contamination indicator. In this study, many water filtration conditions were tested (volume of water, concentration, etc.), and more than 80% of bacteriophage were recovered after filtration on polymer, in most conditions. We demonstrated that the method was linear (slope = 0 99 0 04 and Y intercept when x = 0 02 0 28), valid (as manipulators, tested concentrations, volumes of sample and batch of polymer did not have any influence on concentration) and sensitive (allowing to concentrate up to 16 600-fold 1 l of sample and to detect and quantify down to 750 GC l 1 and 7500 GC l 1, respectively). Conclusions: To conclude, this support exhibits high interest to retain viruses and to allow to detect low concentration of virus in water. Significance and Impact of the Study: This study gives valuable advance in the methods of concentration and diagnosis of virus in water.
Journal of Applied Microbiology

hal-00932328
https://hal.archives-ouvertes.fr/hal-00932328
DOI : 10.1111/jam.12209

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : Les îles sont devenues les principaux marchés mondiaux pour le tourisme balnéaire en profitant de leur richesse naturelle et culturelle. Dans le même temps, les îles sont des territoires fragiles avec des ressources limitées, raison pour laquelle un développement durable de l’activité touristique est une nécessité. L'étude de la consommation des ressources naturelles par le tourisme est une étape essentielle pour détecter les menaces que cette activité cause à l'environnement et donc la mise en œuvre de mesures plus durables. Dans cet article, nous analysons la consommation des ressources naturelles dans cinq régions touristiques de Minorque. Les données ont été recueillies auprès des fournisseurs, des établissements touristiques et au travail d’enquête terrain, ainsi cela nous a permis d'estimer la consommation d'eau et d'électricité, la production et la collecte des déchets pour les études de cas. Les consommations élevées d’eau et de déchets observés indiquent la nécessité d'entreprendre des actions. D'autre part, les résultats montrent que les coûts environnementaux les plus élevés proviennent des établissements touristiques fondés sur la faible densité de ménage.
Islands have become world’s leading markets for sun and sand tourism taking advantage of their natural and cultural richness. At the same time, islands are fragile territories with limited resources, reason why a sustainable development of tourism is a necessity. The study of natural resources consumption by tourism is an essential step to detect the threats that this activity is causing to the environment and thus implement measures to go towards a more sustainable direction. In this article we analyze the natural resources consumption in five tourist areas of Menorca. Data were gathered from supplier companies, tourist establishments and through fieldwork, and allowed us to estimate water and electricity consumption, generation and collection of waste for the case studies. The high observed ratios of water consumption as well as waste generation and collection ratios indicate the need to undertake actions. The results showed the higher environmental costs of tourism settlements based on low density of household.
Espagne
Minorque

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.6267
http://journals.openedition.org/etudescaribeennes/6267

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Two of the crucial aspects of human immunodeficiency virus (HIV) infection are (i) viral persistence in reservoirs (precluding viral eradication) and (ii) chronic inflammation (directly associated with all-cause morbidities in antiretroviral therapy (ART)-controlled HIV-infected patients). The objective of the present study was to assess the potential involvement of adipose tissue in these two aspects. Adipose tissue is composed of adipocytes and the stromal vascular fraction (SVF); the latter comprises immune cells such as CD4+ T cells and macrophages (both of which are important target cells for HIV). The inflammatory potential of adipose tissue has been extensively described in the context of obesity. During HIV infection, the inflammatory profile of adipose tissue has been revealed by the occurrence of lipodystrophies (primarily related to ART). Data on the impact of HIV on the SVF (especially in individuals not receiving ART) are scarce. We first analyzed the impact of simian immunodeficiency virus (SIV) infection on abdominal subcutaneous and visceral adipose tissues in SIVmac251 infected macaques and found that both adipocytes and adipose tissue immune cells were affected. The adipocyte density was elevated, and adipose tissue immune cells presented enhanced immune activation and/or inflammatory profiles. We detected cell-associated SIV DNA and RNA in the SVF and in sorted CD4+ T cells and macrophages from adipose tissue. We demonstrated that SVF cells (including CD4+ T cells) are infected in ART-controlled HIV-infected patients. Importantly, the production of HIV RNA was detected by in situ hybridization, and after the in vitro reactivation of sorted CD4+ T cells from adipose tissue. We thus identified adipose tissue as a crucial cofactor in both viral persistence and chronic immune activation/inflammation during HIV infection. These observations open up new therapeutic strategies for limiting the size of the viral reservoir and decreasing low-grade chronic inflammation via the modulation of adipose tissue-related pathways
ISSN: 1553-7366

Droits : http://creativecommons.org/licenses/by/
hal-01207287
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01207287
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01207287/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01207287/file/journal.ppat.1005153.pdf
DOI : 10.1371/journal.ppat.1005153

Éditeur(s) : HAL CCSD
Résumé : International audience
We present a new 3-D GPS velocity solution for 182 sites for the region encompassing the Western Alps, Pyrenees, and southern France. The velocity field is based on a Precise Point Positioning (PPP) solution, to which we apply a common-mode filter, defined by the 26 longest time series, in order to correct for network-wide biases (reference frame, unmodeled large-scale processes, etc.). We show that processing parameters, such as troposphere delay modeling, can lead to systematic velocity variations of 0.1–0.5 mm yr−1 affecting both accuracy and precision, especially for short (< 5 years) time series. A velocity convergence analysis shows that minimum time-series lengths of  ∼  3 and  ∼  5.5 years are required to reach a velocity stability of 0.5 mm yr−1 in the horizontal and vertical components, respectively. On average, horizontal residual velocities show a stability of  ∼  0.2 mm yr−1 in the Western Alps, Pyrenees, and southern France. The only significant horizontal strain rate signal is in the western Pyrenees with up to 4  ×  10−9 yr−1 NNE–SSW extension, whereas no significant strain rates are detected in the Western Alps (< 1  ×  10−9 yr−1). In contrast, we identify significant uplift rates up to 2 mm yr−1 in the Western Alps but not in the Pyrenees (0.1 ± 0.2 mm yr−1). A correlation between site elevations and fast uplift rates in the northern part of the Western Alps, in the region of the Würmian ice cap, suggests that part of this uplift is induced by postglacial rebound. The very slow uplift rates in the southern Western Alps and in the Pyrenees could be accounted for by erosion-induced rebound.
ISSN: 1869-9529

hal-01395116
https://hal.archives-ouvertes.fr/hal-01395116
https://hal.archives-ouvertes.fr/hal-01395116/document
https://hal.archives-ouvertes.fr/hal-01395116/file/nguyen2016.pdf
DOI : 10.5194/se-7-1349-2016

Éditeur(s) : Université de Bretagne Occidentale
Résumé : Several small pelagic fish species contribute remarkably to world catch. Their populations are, however, characterized by large biomass fluctuations strongly affecting fisheries. The fishing gears and methods used to capture small pelagics have evolved to exploit the highly developed shoaling behavior of these species. Hence, faced to modern fishing this gregarious behavior becomes a disadvantage for fish. Fish behavior may be affected by environmental conditions and by fishing, at the same time that behavior impacts fishing. In this study, we seek to characterize the aggregative systems of small pelagic fishes inhabiting the Bay of Biscay by analyzing "acoustic images", defined as the group of echoes (planktonic layers, shoals, isolated targets) detected on a transect section of a given length. We analyzed the species composition, the spatial distribution and the evolution over time of acoustic images. We also studied the hydrological conditions of the bay, as well as the small pelagics French fishery in order to look for correlations between hydrology, commercial catch and fish aggregation patterns observed by acoustics. We observed the same species or group of species forming different types of aggregation according to habitat. Conversely, the same type of aggregation, associated with a particular habitat, can be produced by different species. The most notorious change observed during the studied period relates to small clupeoids aggregations in the vicinity of the Gironde estuary, whose structure evolved toward a greater fragmentation of shoals (a large number of small size detections) since 2000. Concerning commercial catches, pelagic trawlers fishing in pairs mainly seek for anchovy in the coastal areas, single pelagic trawlers capture mackerel and horse mackerel in deeper waters while purse seiners target mostly sardine near their fishing ports. Because of the coarse spatial resolution of commercial fishing data and the effect of the application of an international fisheries agreement limiting the fishing activity of French pelagic trawlers during spring, only small correlations between captures and types of aggregation were observed.
La participation des petits poissons pélagiques dans les captures est remarquable. Leurs populations sont cependant caractérisées par des importantes fluctuations de biomasse, impactant fortement les pêcheries. Les méthodes et appareils de pêche utilisés pour capturer ces espèces ont évolué dans le sens d'exploiter le comportement grégaire très développé des petits pélagiques. Cette tendance à former de bancs devient alors désavantageuse pour le poisson face à la pêche moderne. Les conditions environnementales et la pêche peuvent affecter le comportement du poisson, en même temps que ce dernier est susceptible d'affecter l'activité halieutique. Le but de cette étude est de caractériser les systèmes agrégatifs des petits poissons pélagiques dans le golfe de Gascogne en étudiant des « images acoustiques », définies comme l'ensemble des échos (couches planctoniques, bancs, cibles isolées) détectés sur une section de radiale de longueur donnée. Nous analysons leur composition en espèces ainsi que leur distribution spatiale et leur évolution au cours du temps. Nous étudions aussi les conditions hydrologiques du golfe, ainsi que la pêcherie française de ces espèces afin de chercher des corrélations entre l'hydrologie, la capture commerciale et les types d'agrégations observés par acoustique. Nous avons observé qu'une espèce est capable de former des agrégations différentes en fonction de l'habitat, et inversement, le même type d'agrégation, associé à un habitat particulier, peut être produit par des espèces différentes. Le changement observé le plus évident concerne les agrégations de petits clupéiformes, dont la structure a évolué vers une plus grande fragmentation des détections (des petits bancs plus nombreux) depuis 2000. Par rapport à la pêche des professionnels, les chalutiers pélagiques en boeufs recherchent en priorité l'anchois dans la zone côtière, les pélagiques simples capturent le chinchard et le maquereau au large et les senneurs recherchent principalement la sardine à proximité des ports de pêche. À cause de la résolution spatiale trop sommaire des données de pêche et l'effet de l'application des accords internationaux limitant l'activité des chalutiers pélagiques au printemps, nous n'avons observé que peu des corrélations entre les captures et les types d'agrégation établis à partir de données issues des campagnes scientifiques.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2008/these-6083.pdf
http://archimer.ifremer.fr/doc/00000/6083/

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : International audience
Abstract Indoor fungal contamination has been associated with a wide range of adverse health effects, including infectious diseases, toxic effects and allergies. The diversity of fungi contributes to the complex role that they play in indoor environments and human diseases. Molds have a major impact on public health, and can cause different consequences in hospitals, homes and workplaces. This review presents the methods used to assess fungal contamination in these various environments, and discusses advantages and disadvantages for each method in consideration with different health risks. Air, dust and surface sampling strategies are compared, as well as the limits of various methods are used to detect and quantify fungal particles and fungal compounds. In addition to conventional microscopic and culture approaches, more recent chemical, immunoassay and polymerase chain reaction (PCR)-based methods are described. This article also identifies common needs for future multidisciplinary research and development projects in this field, with specific interests on viable fungi and fungal fragment detections. The determination of fungal load and the detection of species in environmental samples greatly depend on the strategy of sampling and analysis. Quantitative PCR was found useful to identify associations between specific fungi and common diseases. The next-generation sequencing methods may afford new perspectives in this area.
ISSN: 1040-841X

hal-00874670
https://hal.archives-ouvertes.fr/hal-00874670
DOI : 10.3109/1040841X.2013.777687
PUBMED : 23586944