Éditeur(s) : HAL CCSD Elsevier
Résumé : DNA metabarcoding on soil samples is increasingly used for large-scale and multi-taxa biodiversity studies. However, DNA extraction may be a major bottleneck for such wide uses. It should be cost/time effective and allow dealing with large sample volumes so as to maximise the representativeness of both micro- and macro-organisms diversity. Here, we compared the performances of a fast and cheap extracellular DNA extraction protocol with a total DNA extraction method in retrieving bacterial, eukaryotic and plant diversity from tropical soil samples of ca. 10 g. The total DNA extraction protocol yielded more high-quality DNA. Yet, the extracellular DNA protocol provided similar diversity assessments although it presented some differences in clades relative abundance and undersampling biases. We argue that extracellular DNA is a good compromise between cost, labor, and accuracy for high throughput DNA metabarcoding studies of soil biodiversity.
ISSN: 0038-0717

hal-01532638
https://hal.archives-ouvertes.fr/hal-01532638
DOI : 10.1016/j.soilbio.2016.01.008
PRODINRA : 384522

Éditeur(s) : HAL CCSD Cushman Foundation for Foraminiferal Research
Résumé : International audience
Benthic foraminifera are heterotrophic protists that utilize different trophic mechanisms and nutritional resources. They exhibit a wide range of trophic behaviours: selective (grazing) and indiscriminate herbivory, symbiosis, carnivory, parasitism, uptake of dissolved organic matter, passive suspension feeding and, most commonly, deposit feeding. The benthic foraminifera Ammonia tepida, previously known as an herbivore, fed as a carnivore in laboratory experiments where mobile metazoans were provided. We observed predation on the three types of metazoans provided: nematodes, copepods, and a larval gastropod. This foraminifera used its pseudopodial network to entrap the invertebrates, which were then stripped of their soft internal tissues within 24 hours. Our experiments are the first to demonstrate that Ammonia tepida, despite its limited motility, is able to utilize larger mobile animals as a food source. The great abundance of small metazoans in most marine environments suggests that they are a food source for foraminifera. Further study of foraminiferal feeding strategies will enhance our understanding of their role in marine communities.
ISSN: 0096-1191

hal-01248040
https://hal.archives-ouvertes.fr/hal-01248040
https://hal.archives-ouvertes.fr/hal-01248040/document
https://hal.archives-ouvertes.fr/hal-01248040/file/dupuy%20et%20al%202010.pdf

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
BACKGROUND: We aimed to assess, for the first time, the nature of the indoor air contamination of hospitals. METHODS AND FINDINGS: More than 40 volatile organic compounds (VOCs) including aliphatic, aromatic and halogenated hydrocarbons, aldehydes, alcohols, ketones, ethers and terpenes were measured in a teaching hospital in France, from sampling in six sampling sites--reception hall, patient room, nursing care, post-anesthesia care unit, parasitology-mycology laboratory and flexible endoscope disinfection unit--in the morning and in the afternoon, during three consecutive days. Our results showed that the main compounds found in indoor air were alcohols (arithmetic means ± SD: 928±958 µg/m³ and 47.9±52.2 µg/m³ for ethanol and isopropanol, respectively), ethers (75.6±157 µg/m³ for ether) and ketones (22.6±20.6 µg/m³ for acetone). Concentrations levels of aromatic and halogenated hydrocarbons, ketones, aldehydes and limonene were widely variable between sampling sites, due to building age and type of products used according to health activities conducted in each site. A high temporal variability was observed in concentrations of alcohols, probably due to the intensive use of alcohol-based hand rubs in all sites. Qualitative analysis of air samples led to the identification of other compounds, including siloxanes (hexamethyldisiloxane, octamethyltrisiloxane, decamethylcyclopentasiloxane), anesthetic gases (sevoflurane, desflurane), aliphatic hydrocarbons (butane), esters (ethylacetate), terpenes (camphor, α-bisabolol), aldehydes (benzaldehyde) and organic acids (benzoic acid) depending on sites. CONCLUSION: For all compounds, concentrations measured were lower than concentrations known to be harmful in humans. However, results showed that indoor air of sampling locations contains a complex mixture of VOCs. Further multicenter studies are required to compare these results. A full understanding of the exposure of healthcare workers and patients to complex mixtures of chemical compounds can then be related to potential health outcomes.
ISSN: 1932-6203

hal-00874694
https://hal.archives-ouvertes.fr/hal-00874694
https://hal.archives-ouvertes.fr/hal-00874694/document
https://hal.archives-ouvertes.fr/hal-00874694/file/VOC_Contamination-accepted.pdf
DOI : 10.1371/journal.pone.0055535

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The strikingly complex structural organization of the mammalian testis in vivo creates particular difficulties for studies of its organization, function and regulation. These difficulties are particularly pronounced for investigations of the molecular communication networks within the seminiferous tubules that govern spermatogenesis. The use of classical molecular and cell biology approaches to unravel this complexity has proved problematic, due to difficulties in maintaining differentiated germ cells in vitro, in particular. The lack of a suitable testing ground has led to a greater reliance on high-quality proteomic and genomic analyses as a prelude to the in vitro antx1d in vivo testing of hypotheses. In this study, we highlight the options currently available for research, as used in our laboratory, in which proteomic and integrative genomic strategies are applied to the study of spermatogenesis in mammals. We will comment on results providing insight into the molecular mechanisms underlying normal and pathological spermatogenesis and new perspectives for the treatment of male infertility in humans. Finally, we will discuss the relevance of our strategies and the unexpected potential and perspectives they offer to teams involved in the study of male reproduction, within the framework of the Human Proteome Project. SIGNIFICANCE: Integrative genomics is becoming a powerful strategy for discovering the biological significance hidden in proteomic datasets. This work introduces some of the integrative genomic concepts and works used by our team to gain new insight into mammalian spermatogenesis, a remarkably sophisticated process. We demonstrate the relevance of these integrative approaches to understand the cellular cross talks established between the somatic Sertoli cells and the germ cell lineage, within the seminiferous epithelium. Our work also contributes to new knowledge on the pathophysiology of testicular function, with promising clinical applications. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
ISSN: 1874-3919

hal-01063931
https://hal.archives-ouvertes.fr/hal-01063931
DOI : 10.1016/j.jprot.2014.04.013
PUBMED : 24751586

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : The acquisition of reliable data sets representative of hydrological regimes and their variations is a critical concern for water resource assessment. For the subsurface, traditional approaches based on probe measurements, core analysis, and well data can be laborious, expensive, and highly intrusive, while only yielding sparse data sets. For this study, an innovative field survey, merging relative microgravimetry, magnetic resonance soundings, and hydrological measurements, was conducted to evaluate both surface and subsurface water storage variations in a semiarid Sahelian area. The instrumental setup was implemented in the lower part of a typical hillslope feeding to a temporary pond. Weekly measurements were carried out using relative spring gravimeters during 3 months of the rainy season in 2009 over a 350 × 500 m2 network of 12 microgravity stations. Gravity variations of small to medium amplitude (≤220 nm s−2) were measured with accuracies better than 50 nm s−2, revealing significant variations of the water storage at small time (from 1 week up to 3 months) and space (from a couple of meters up to a few hundred meters) scales. Consistent spatial organization of the water storage variations were detected, suggesting high infiltration at the outlet of a small gully. The comparison with hydrological measurements and magnetic resonance soundings involved that most of the microgravity variations came from the heterogeneity in the vadose zone. The results highlight the potential of time lapse microgravity surveys for detecting intraseasonal water storage variations and providing rich space-time data sets for process investigation or hydrological model calibration/evaluation
ISSN: 0043-1397

hal-00857351
https://hal.archives-ouvertes.fr/hal-00857351
DOI : 10.1002/wrcr.20235

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Clin Microbiol Infect ABSTRACT: Atypical Toxoplasma gondii strains, unrelated to archetypal clonal lineages (I, II, III), have been reported more frequently over the last decade in areas other than Europe and North America. A newly described form of toxoplasmosis, 'Amazonian toxoplasmosis' (AT), has been reported since 2002 in French Guiana. It is characterized by severe cases and atypical strains linked to a neotropical forest-based cycle. We report on the cases of AT that required intensive care management. We performed a prospective observational study on hospitalized adults in the Intensive Care Unit (ICU) from 2002 to 2008. Clinical and laboratory data, microbiological findings and outcomes were recorded. Data, including the ICU simplified acute physiology score and the pneumonia severity index, were calculated. Epidemiological risk factors for AT were assessed through questionnaires. Eleven non-immunodeficient patients were admitted to the ICU in Cayenne for life-threatening pneumonia associated with disseminated toxoplasmosis. Mechanical ventilation was necessary in seven patients, four of whom required immediate orotracheal intubation. Cardiac and ophthalmological abnormalities were found in five and four patients, respectively. One patient died from multiple organ failure. The genetic characterization of Toxoplasma DNA using six microsatellite markers revealed unique and atypical genotypes in eight patients. All patients presented epidemiological risk factors for AT. In French Guiana, significant T. gondii-related infectious syndrome associated with the lungs, a high level of LDH activity and the reported risk factors for AT was strongly suggestive of disseminated toxoplasmosis with a possible trend toward life-threatening pneumonia.
ISSN: 1198-743X

hal-00678752
https://hal-unilim.archives-ouvertes.fr/hal-00678752
DOI : 10.1111/j.1469-0691.2011.03648.x
PUBMED : 21958195

Résumé : A l’aube du XXIème siècle, l’enjeu pour la Martinique est de construire un modèle de développement endogène qui nécessite son intégration dans la Caraïbe. Un consensus existe pour cette orientation, tant au niveau des acteurs économiques que des gouvernances locales et nationales. Mais qu’en pense la population ? Sur le plan diplomatique, cette orientation se concrétise par une adhésion progressive de la Martinique aux différentes organisations communautaires caribéennes en qualité de membre à part entière. Toutes ces avancées s’opèrent dans un contexte socio-économique qui se caractérise pour la Martinique par une population en voie de vieillissement, un chômage structurel et un départ du territoire des jeunes diplômés. Dans cette perspective, le développement des échanges avec la Caraïbe va induire des flux matériels et immatériels, et pour les Martiniquais, des perspectives d’insertion professionnelle dans des pays de la Caraïbe qui ont des taux de chômage plus cléments. Ces éléments de contexte interrogent l’évolution de la société Martiniquaise dans un nouveau paysage international, qui va au-delà des accords politiques et diplomatiques, car il va induire des rencontres entre individus de culture et de pratiques professionnelles différentes, directement ou indirectement, matérialisées ou dématérialisées. Cette étude s’intéresse au point de vue des individus, au regard qu’ils portent sur ce qu’il convient de considérer comme un projet de société et aux moyens qu’ils ont d’y contribuer. Elle s’inscrit dans la perspective du développement de la mobilité professionnelle des Martiniquais dans la Caraïbe et elle fait des propositions sur les conditions de sa mise en œuvre. Elle interroge l’environnement dans lequel s’opèrent aujourd’hui les projets de mobilité professionnelle à l’international des Martiniquais et les représentations sociales qui sont en marche dans ce nouveau paradigme. Comment le Martiniquais peut-il devenir un citoyen caribéen sur un marché du travail élargi aux pays du bassin caribéen ?
At the turn of the century, the challenge for Martinique is to build a model of endogenous development that requires its integration in the Caribbean. There is consensus for this approach, both in terms of economic actors as local and national governance. But what the people think? On the diplomatic front, this orientation is reflected by a gradual accession of Martinique to different Caribbean community organizations as a full member. All these developments are taking place in a socioeconomic context characterized for Martinique by a population in the process of aging, structural unemployment, and a departure from the territory of graduates. In this perspective, the development of trade with the Caribbean will induce the material and immaterial flows and for Martinique, perspectives employability in Caribbean countries with more lenient unemployment. These contextual elements questioning the evolution of Martinican society in a new international landscape that goes beyond political and diplomatic agreements, as it will lead to encounters between individuals of different cultures and business practices, directly or indirectly, materialized or dematerialized. This study focuses on the perspective of individuals and the way they look at what should be regarded as a social project and how they contribute. It is part of a perspective of the development of professional mobility of Martinique in the Caribbean and on the conditions for its implementation. She questions the environment in which today operate occupational mobility projects internationally Martinicans and social representations that are running in this new paradigm. How can the Caribbean Martinique become a citizen on the broader labor market to the countries of the Caribbean basin?

http://www.theses.fr/2015AGUY0845/document

Résumé : A l’aube du XXIème siècle, l’enjeu pour la Martinique est de construire un modèle de développement endogène qui nécessite son intégration dans la Caraïbe. Un consensus existe pour cette orientation, tant au niveau des acteurs économiques que des gouvernances locales et nationales. Mais qu’en pense la population ? Sur le plan diplomatique, cette orientation se concrétise par une adhésion progressive de la Martinique aux différentes organisations communautaires caribéennes en qualité de membre à part entière. Toutes ces avancées s’opèrent dans un contexte socio-économique qui se caractérise pour la Martinique par une population en voie de vieillissement, un chômage structurel et un départ du territoire des jeunes diplômés. Dans cette perspective, le développement des échanges avec la Caraïbe va induire des flux matériels et immatériels, et pour les Martiniquais, des perspectives d’insertion professionnelle dans des pays de la Caraïbe qui ont des taux de chômage plus cléments. Ces éléments de contexte interrogent l’évolution de la société Martiniquaise dans un nouveau paysage international, qui va au-delà des accords politiques et diplomatiques, car il va induire des rencontres entre individus de culture et de pratiques professionnelles différentes, directement ou indirectement, matérialisées ou dématérialisées. Cette étude s’intéresse au point de vue des individus, au regard qu’ils portent sur ce qu’il convient de considérer comme un projet de société et aux moyens qu’ils ont d’y contribuer. Elle s’inscrit dans la perspective du développement de la mobilité professionnelle des Martiniquais dans la Caraïbe et elle fait des propositions sur les conditions de sa mise en œuvre. Elle interroge l’environnement dans lequel s’opèrent aujourd’hui les projets de mobilité professionnelle à l’international des Martiniquais et les représentations sociales qui sont en marche dans ce nouveau paradigme. Comment le Martiniquais peut-il devenir un citoyen caribéen sur un marché du travail élargi aux pays du bassin caribéen ?
At the turn of the century, the challenge for Martinique is to build a model of endogenous development that requires its integration in the Caribbean. There is consensus for this approach, both in terms of economic actors as local and national governance. But what the people think? On the diplomatic front, this orientation is reflected by a gradual accession of Martinique to different Caribbean community organizations as a full member. All these developments are taking place in a socioeconomic context characterized for Martinique by a population in the process of aging, structural unemployment, and a departure from the territory of graduates. In this perspective, the development of trade with the Caribbean will induce the material and immaterial flows and for Martinique, perspectives employability in Caribbean countries with more lenient unemployment. These contextual elements questioning the evolution of Martinican society in a new international landscape that goes beyond political and diplomatic agreements, as it will lead to encounters between individuals of different cultures and business practices, directly or indirectly, materialized or dematerialized. This study focuses on the perspective of individuals and the way they look at what should be regarded as a social project and how they contribute. It is part of a perspective of the development of professional mobility of Martinique in the Caribbean and on the conditions for its implementation. She questions the environment in which today operate occupational mobility projects internationally Martinicans and social representations that are running in this new paradigm. How can the Caribbean Martinique become a citizen on the broader labor market to the countries of the Caribbean basin?

http://www.theses.fr/2015AGUY0910/document