Éditeur(s) : ISTPM
Résumé : Après une présentation rapide du procédé et de ses caractéristiques essentielles, divers aspects de la microbiologie des denrées ionisées sont passés en revue, en particulier le problème de Clostridium botulinum type E. Les principales applications potentielles sont brièvement décrites à savoir la radurisation des produits de la pêche à l'état frais ou congelé, la désinsectisation du poisson séché, la radicidation des farines de poisson. En conclusion, la faisabilité et les perspectives d'utilisation pour les produits de la pêche sont examinées.
Science et Pêche (0036-8350) (ISTPM), 1984-12 , Vol. 350 , P. 3-12

Droits : Ifremer
http://archimer.ifremer.fr/doc/1984/publication-7042.pdf
http://archimer.ifremer.fr/doc/00000/7042/

Éditeur(s) : HAL CCSD Elsevier
Résumé : Vegetation phenology is the study of the timing of seasonal events that are considered to be the result of adaptive responses to climate variations on short and long time scales. In the field of remote sensing of vegetation phenology, phenological metrics are derived from time series of optical data. For that purpose, considerable effort has been specifically focused on developing noise reduction and cloud-contaminated data removal techniques to improve the quality of remotely-sensed time series. Comparative studies between time series composed of satellite data acquired under clear and cloudy conditions and from radiometric data obtained with high accuracy from ground-based measurements constitute a direct and effective way to assess the operational use and limitations of remote sensing for predicting the main plant phenological events. In the present paper, we sought to explicitly evaluate the potential use of MODerate resolution Imaging Spectroradiometer (MODIS) remote sensing data for monitoring the seasonal dynamics of different types of vegetation cover that are representative of the major terrestrial biomes, including temperate deciduous forests, evergreen forests, African savannah, and crops. After cloud screening and filtering, we compared the temporal patterns and phenological metrics derived from in situ NDVI time series and from MODIS daily and 16-composite products. We also evaluated the effects of residual noise and the influence of data gaps in MODIS NDVI time series on the identification of the most relevant metrics for vegetation phenology monitoring. The results show that the inflexion points of a model fitted to a MODIS NDVI time series allow accurate estimates of the onset of greenness in the spring and the onset of yellowing in the autumn in deciduous forests (RMSE <= one week). Phenological metrics identical to those provided with the MODIS Global Vegetation Phenology product (MDC12Q2) are less robust to data gaps, and they can be subject to large biases of approximately two weeks or more during the autumn phenological transitions. In the evergreen forests, in situ NDVI time series describe the phenology with high fidelity despite small temporal changes in the canopy foliage. However, MODIS is unable to provide consistent phenological patterns. In crops and savannah, MODIS NDVI time series reproduce the general temporal patterns of phenology, but significant discrepancies appear between MODIS and ground-based NDVI time series during very localized periods of time depending on the weather conditions and spatial heterogeneity within the MODIS pixel. In the rainforest, the temporal pattern exhibited by a MODIS 16-day composite NDVI time series is more likely due to a pattern of noise in the NDVI data structure according to both rainy and dry seasons rather than to phenological changes. More investigations are needed, but in all cases, this result leads us to conclude that MODIS time series in tropical rainforests should be interpreted with great caution. (C) 2013 Elsevier Inc. All rights reserved.
ISSN: 0034-4257

hal-01032407
https://hal.archives-ouvertes.fr/hal-01032407
DOI : 10.1016/j.rse.2013.01.010

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

Résumé : Monitoring n° 18 of PENLY nuclear power - plant takes in account studies between March and September 2004. Hydrology, microbiology, phytoplankton, zooplankton and fishing are studied. his power-plant has been in opération for fifteen years.
La surveillance n° 18 sur le site de PENLY couvre la période de mars à septembre 2004. Les domaines étudiés sont l'hydrologie, la microbiologie, le plancton végétal et animal et le domaine halieutique. L'année 2004 est la quinzième année de fonctionnement de la centrale.

Droits : 2005 Ifremer
http://archimer.ifremer.fr/doc/2005/rapport-1030.pdf
http://archimer.ifremer.fr/doc/00000/1030/

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
Toxoplasmosis is a life-threatening infection in immunocompromised patients (ICPs). The definite diagnosis relies on parasite DNA detection, but the incidence and burden of disease are ill-known in HIV-negative patients. A three-year retrospective study was conducted in 15 reference laboratories from the network of the French National Reference Center for Toxoplasmosis, to record the frequency of Toxoplasma DNA detection in ICPs, to review the molecular methods used for diagnosis and the prevention measures implemented in transplant patients. During the study period, out of 31,640 PCR performed in ICPs, 610 were positive (323 patients). Blood (n=337), cerebrospinal fluid (n=101) and aqueous humor (n=100) samples were more frequently positive. Chemoprophylaxis schemes in transplant patients differed between centers. PCR follow-up of allogeneic hematopoietic stem-cell transplant (allo-HSCT) patients was implemented in 8/15 centers. Data from 180 patients (13 centers) were further analyzed regarding clinical setting and outcome. Only 68/180 (38%) patients were HIV+; the remaining 62% consisted in 72 HSCT, 14 solid-organ transplants, and 26 miscellaneous immunodeficiencies. Cerebral toxoplasmosis and disseminated toxoplasmosis were most frequently observed in HIV and transplant patients, respectively. Of 72 allo-HSCT patients with a positive PCR, 23 were asymptomatic; all were diagnosed in centers performing systematic blood PCR follow-up, and received specific treatment. Overall survival of allo-HSCT patients at two months was better in centers with PCR follow-up than in other centers (p<0.01). This study provides updated data on the frequency of toxoplasmosis in HIV-negative ICPs and suggests that regular PCR follow-up of allo-HSCT patients could guide pre-emptive treatment and improve outcome.
ISSN: 0095-1137

hal-01134189
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01134189
DOI : 10.1128/JCM.03282-14
PUBMED : 25762774

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

Résumé : Le Laboratoire Côtier de La Tremblade est implanté géographiquement dans le premier bassin ostréicole d'Europe (30 000 tonnes produites et 60 000 tonnes commercialisées chaque année). L'ostréiculture est une activité économique très importante en terme d'emplis, qui doit cohabiter sur un même littoral avec le tourisme et l'agriculture générant parfois des conflits d'usages (gestion de l'eau, qualité de l'eau). Les avis donnés à l'Administration ou aux collectivités locales s'appuient sur les résultats de la surveillance ou ceux émanant des études spécifiques comme les études microbiologiques locales. Les activités, les responsabilités de chacun dans le cadre ce de mandat, figurent dans le Manuel Qualité du Laboratoire. Enfin, l'assistance technique à la profession conchylicole, en matière environnementale ou de préparation à la mise en marché des coquillages revêt des formes multiples : formations données, distribution de fiches pratiques, fourniture de renseignements, interface entre professionnels et laboratoires de recherche, études spécifiques.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00074/18538/16085.pdf
http://archimer.ifremer.fr/doc/00074/18538/

Résumé : in mollusc hatcheries. Consequently, we assessed themost commonly used species to establish their growth and size profiles, their cytomorphological, biochemical, biomolecular identification as well as their cytometer signs, and also their ability to grow under extreme conditions of temperature and salinity. This work aimed at matching the conformity of the strains used in Argenton (dispatched to most of the French commercial hatcheries) to those of a referenced culture collection. A previous screening preceded this study, because of the 45 species and/or clones held originally, Argenton kept no more than 15 species. As most of the latter are also represented in referenced collection, our strains are therefore correctly identified. On the other hand, the combination of several approaches (characteristic of growth and size, cytomorphological description, establishment of biochemical and biomolecular profiles) to discriminate the different species was broadly successful. Nevertheless, flow cytometer measurements were extremely variable from sample to sample, dueto their high sensitivity to the microalga's physiological state. Accordingly, we have developed a method of identification which could be transferred at a national or international level, to the Institutions in charge of microalgae collections. Furthermore, we achieved relevant data to establish an identity card for each of the microalgae suitable for mollusc hatcheries.
La caractérisation des microalgues fourrage constituait l'un des points perfectibles au regard de ce qui est appliquée en microbiologie. Nous avons alors cherché à définir, pour les espèces les plus utilisées en écloserie, leurs profils de croissance et de taille, leur caractéristiques cytomorphologique, cytofluorimétrique, biochimique et biomoléculaire, et enfin, précisé leur aptitude au développement sous des conditions extrêmes de température et de salinité (écotolérance). Ce travail avait pour but de vérifier, d'une part, la conformité des souches utilisées à l'écloserie d'Argenton (auprès de laquelle se fournissent la plupart des écloseries commerciales françaises) en comparant les espèces utilisées à celles issues d'une collection référencée. Un premier balayage avait été réalisé avant la mise en place de cette étude puisque sur les 45 espèces et clones détenus originellement, Argenton ne possédait plus que 15 espèces. La plupart de ces dernières ayant leur équivalent en collection référencée notre souchier est désormais parfaitement identifiée. D'autre part, la confrontation de plusieurs approches, caractéristique de la croissance et de taille, description cytomorphologique, établissement des profils biochimique et biomoléculaire, écotolérance, signature cytofluorimétrique, pour discriminer les différentes espèces de microalgues fourrage a été globalement couronnée de succès. Seule cette dernière technique n'a pas permis de caractériser les espèces entre elles, les paramètres mesurés en cytométrie de flux étant particulièrement sensibles à l'état physiologique des microalgues, très variable d'un échantillon à un autre. Nous disposons dorénavant d'une méthode d'identification qu'il serait souhaitable de transférer, au niveau national voire international, auprès des organismes en charge des collections. De plus, nous disposons dorénavant de données pertinentes pour établir pour chacune des microalgues d'intérêt aquacole une véritable carte d'identité.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2004/rapport-1546.pdf
http://archimer.ifremer.fr/doc/00000/1546/

Résumé : This synthesis report assesses the current state of the marine hydrobiological knowledge acquired in the surroundings of the Flamanville electronuclear site (north-west of Cotentin), in the framework of the various project and monitoring programs in the pelagic, benthic and halieutic domains carried out on this site since 1976. Each domain is divided, as much as necessary, into different study areas such as hydrobiology, phytoplankton, microbiology, crustacean larvae or macrophyte algae. For each area, a series of parameters, considered as representative of the evolution of this area, is studied. In this way, for the hydrological area, the sea water temperature and salinity, the mineral nutriment concentrations, the holagen compounds and the boron are monitored. The evolution of each of these parameters enabled us to draw the following conclusions. The vegetal and animal species' physiology is conditioned by climate changes. The study of the pluviometry and air temperature parameters shows that the 1986/2005 period is slightly less humid and warmer than the 1949/2005 period. This reflects also on the sea water temperature whose average values increase on a regular basis.
Ce rapport de synthèse fait le point sur l'état des connaissances hydrobiologiques marines acquises aux abords du site électronucléaire de Flamanville (nord-ouest Cotentin), dans le cadre des différents programmes de projet et de surveillance des domaines pélagique, benthique et halieutique, menés sur ce site depuis 1976. Chaque domaine est divisé, autant que nécessaire, en compartiments d'étude, tels que l'hydrologie, le phytoplancton, la microbiologie, les larves de crustacés ou les algues macrophytes. Pour chaque compartiment, une série de paramètres, jugés représentatifs de l'évolution de ce compartiment, est étudié. Ainsi, pour le compartiment hydrologique, sont suivis la température et la salinité de l'eau de mer, les concentrations en nutriments minéraux, les composés halogénés et le bore. Les évolutions de ces différents paramètres ont permis d'élaborer les conclusions suivantes. La physiologie des espèces animales et végétales est conditionnée par les changements climatiques. L'examen des paramètres pluviométrie et température de l'air montre que la période 1986/2005 est sensiblement plus humide et plus chaude que la période 1949/2005. Cela se répercute également sur la température de l'eau de mer dont les valeurs moyennes croissent régulièrement.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/rapport-6405.pdf
http://archimer.ifremer.fr/doc/00000/6405/