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

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

Éditeur(s) : HAL CCSD Institute of Electrical and Electronics Engineers (IEEE) Institute of Electrical and Electronics Engineers
Résumé : International audience
Conventional quantitative electron probe microanalysis of actinides requires the use of reference standard samples. However, for such elements, standards are generally not available. To overcome this difficulty, standardless methods of analysis are used, in which the x-ray intensity emitted by the standard is calculated. To be reliable, such calculations require accurate knowledge of physical data such as the x-ray production cross section. However, experimental data of this quantity are not always available for actinide elements. In the present work, experimental L and M x-ray production cross sections were measured for elements uranium and lead. Measurements were performed with two electron microprobes using wavelength-dispersive spectrometers using thin self-supporting targets. Experimental results are compared with calculated cross sections obtained from different analytical formulae, and, whenever possible, with experimental data obtained from the literature.
ISSN: 0018-9499

hal-01122820
https://hal.archives-ouvertes.fr/hal-01122820
DOI : 10.1109/TNS.2014.2321016

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
People are exposed to multiple pollutants, especially indoors, in particular through ingestion of indoor settled dust. In the perspective of a cumulative risk assessment, a multi-residue analytical method based on pressurized liquid extraction (PLE) and gas chromatography/tandem mass spectrometry (GC/MS/MS) was developed for the simultaneous analysis in indoor dust of several classes of semi-volatile organic compounds (SVOCs) of health concern, from trace to highly concentrated compounds, including musk fragrances, organochlorines (OCs), organophosphates (OPs), polycyclic aromatic hydrocarbons (PAHs), polybromodiphenylethers (PBDEs), polychlorobiphenyls (PCBs), phthalates and pyrethroids. The method was validated in terms of limits of quantification (LOQ), and accuracy and precision via spiking experiments on an inert material (Celite(®) 545) and replicate analysis of the standard reference material SRM 2585 supplied by the National Institute of Standards and Technology (NIST). Method LOQs for 200 mg samples of sieved dust were 26 ng g(-1) for PCBs and some OCs, 65 ng g(-1) for musks, OPs, PAHs, PBDEs, pyrethroids, other OCs and some phthalates, 132 ng g(-1) for butylbenzylphthalate (BBP), 197 ng g(-1) for tributylphosphate and 1579 ng g(-1) for other phthalates. Quadratic calibration curves were established for each compound by analyzing at least five calibration solutions and exhibited determination coefficients higher than 0.999. The method was successfully applied to the SRM 2585 and seven real indoor dust samples. The results obtained on SRM 2585 demonstrate both excellent reproducibility and agreement with the indicative, reference or certified values and provide, for the first time, indicative concentrations for chlorpyrifos, diazinon, diisononylphthalate (DiNP) and tetramethrin. The results obtained on real dust samples illustrate the ability of the proposed method to quantify a wide range of SVOCs in a single analysis, making it appropriate for environmental monitoring programs or large-scale studies with a large number of samples.
ISSN: 0021-9673

hal-00994493
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00994493
DOI : 10.1016/j.chroma.2014.02.004
PUBMED : 24598454

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : Absolute Mα and Mβ X-ray intensities were measured for the elements Pt, Au, Pb, U, and Th by electron impact for energies ranging from 6 to 38 keV. Experimental data were obtained by measuring the X-ray intensity emitted from bulk samples with an electron microprobe using high-resolution wavelength-dispersive spectrometers. Recorded X-ray intensities were converted into absolute X-ray yields by evaluation of the detector efficiency and then compared with X-ray intensities calculated by means of Monte Carlo simulations. Simulated Mα and Mβ X-ray intensities were found to be in good agreement with the measurements, allowing their use in standardless quantification methods. A procedure and a software program were developed to accurately obtain virtual standard values. Standardless quantifications of Pb and U were tested on standards of PbS, PbTe, PbCl2, vanadinite, and UO2.
ISSN: 0003-2700

hal-01217495
https://hal.archives-ouvertes.fr/hal-01217495
DOI : 10.1021/acs.analchem.5b01443

Éditeur(s) : HAL CCSD
Résumé : Water vapour is highly variable in the atmosphere with concentration reaching saturation in the tropics and with dry areas over elevated continental region. Good knowledge of the amount of integrated water vapour in the air is necessary to predict phase changes and in particular precipitation. Water vapour variability measurements are still insufficient with standard observing systems. Moreover accurate GPS antenna positioning is affected by the refractivity index variation in the troposphere. Consequently, vertical positioning component estimation is difficult. This variation is directly linked to distribution of variables such as pressure, temperature and humidity along the path between satellite and receiver. Here we study more specifically heavy rains et notably Cevenols events. This thesis work consists to check the GPS measurement validity to quantify water vapour in comparison with measurements from radiosoundings and meteorological model outputs. GPS observations and flux surface information have been analysed to see if water vapour quantification by GPS allowed characterising heavy rain events (cumulative rainfall amount greater than 150 mm). Then, we tested the GPS data assimilation impact on cumulative precipitation forecasts using the high resolution Meteo France AROME model (2.5 km). Finally the quality and the contribution of GPS measurement on sea is evaluated for water vapour measurement. This study has been realised in the framework of VAPIMED experiment.
La vapeur d'eau varie largement dans l'atmosphère avec des concentrations allant de la saturation dans les tropiques à des zones presque sèches au-dessus des zones continentales élevées. Une bonne connaissance du contenu en vapeur d'eau dans l'air est nécessaire pour la prévision des changements de phases, notamment les précipitations. La mesure de la variabilité de la vapeur d'eau est une lacune des systèmes d'observation. Par ailleurs, il est apparu que le positionnement précis des antennes GPS était affecté par la variation de l'indice de réfraction dans la troposphère, ce qui rend particulièrement difficile l'estimation de la composante verticale. Cette variation est directement liée à la distribution des variables pression, température et humidité sur les trajets satellite-récepteur. On s'intéresse ici à l'étude des précipitations intenses et notamment aux épisodes Cévenols. Ce travail de thèse consiste à vérifier la validité de la mesure GPS pour la quantification de la vapeur d'eau en la comparant avec des mesures issues de radiosondage et des sorties de modèle météorologique. On cherche à analyser si la quantification de vapeur d'eau par GPS permet de caractériser les forts événements précipitants (cumuls supérieurs à 150 mm) à l'aide d'observations conjointes sur les flux de surface. On étudie ensuite l'impact de l'assimilation de données GPS issues d'un réseau GPS dense sur la prévision des cumuls de pluies dans le modèle à hauterésolution (2.5 km) AROME de Météo France. Finalement on évalue la qualité et l'apport de la mesure de vapeur d'eau par GPS en mer dans le cadre d'une campagne de mesure VAPIMED).
https://tel.archives-ouvertes.fr/tel-00444081

Droits : info:eu-repo/semantics/OpenAccess
tel-00444081
https://tel.archives-ouvertes.fr/tel-00444081
https://tel.archives-ouvertes.fr/tel-00444081/document
https://tel.archives-ouvertes.fr/tel-00444081/file/These_KBoniface.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
People are exposed to multiple pollutants, especially indoors. In the perspective of a cumulative risk assessment, a multi-residue analytical method was developed to assess the contamination of indoor suspended particulate matter by 55 semi-volatile organic compounds (SVOCs) including musk fragrances, organochlorines (OCs), organophosphates (OPs), polycyclic aromatic hydrocarbons (PAHs), polybromodiphenylethers (PBDEs), polychlorobiphenyls (PCBs), phthalates and pyrethroids. It is based on thermal desorption (TD) coupled with gas chromatography/mass spectrometry (GC/MS). Once the thermal desorption conditions were optimized, the method was validated in terms of quantification limits and accuracy using a standard reference material (SRM 2585). Instrumental quantification limits were 10pg (some OCs, some pyrethroids, musk fragrances, OPs, PAHs, PBDEs and PCBs), 100pg (phthalates and other OCs) and 1000pg (other pyrethroids) corresponding respectively to method quantification limits of 1, 10, and 100pg/m(3) for a sampled air volume of 20m(3). Calibration quadratic curves for ranges of 10-1000, 100-10,000, and 1000-100,000pg, depending on the substance, exhibit determination coefficients above 0.999. Recoveries were between 61 and 96% for chlorinated pesticides, PAHs, PBDEs and PCBs present in the SRM 2585. A test of the method on indoor particulate matter samples (PM(10)) collected on quartz fiber filters in French dwellings demonstrated its ability to quantify SVOCs from a small amount of PM.
ISSN: 0021-9673

hal-00732133
https://hal.archives-ouvertes.fr/hal-00732133
DOI : 10.1016/j.chroma.2012.07.025
PUBMED : 22840824

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
This study aimed to evaluate the repeated sequence REP-529 compared to the B1 gene for the molecular diagnosis of toxoplasmosis by quantitative PCR (qPCR) in routine diagnosis.Over a ten-year period (2003-2013), all patients prospectively diagnosed with a positive REP-529 qPCR result for toxoplasmosis were included. All DNA samples (76 samples from 56 patients) were simultaneously tested using the two qPCR methods (REP-529 and B1).The mean Ct obtained with the B1 qPCR was significantly higher (+4.71 cycles) than that obtained with REP-529 qPCR (p<0.0001). Thirty-one out of 69 extracts (45.6%) positive with REP-529 qPCR were not amplified with the B1 qPCR (relative sensitivity 54.4%, compared to REP-529), yielding false negative results on 15/28 placentas, 5 cord blood, 2 amniotic fluids, 4 cerebrospinal fluids, 1 aqueous humor, 2 lymph node punctures and 1 abortion product. This defect in sensitivity would have left 20/56 patients undiagnosed, distributed as follows: 12/40 congenital toxoplasmosis, 4/5 cerebral toxoplasmosis, 2/8 patients with retinochoroiditis, and both patients with chronic lymphadenopathy. This poor performance of B1 qPCR could be related to low parasite loads, since the mean Toxoplasma quantification in extracts with B1 false negative results was 0.4 parasite/reaction.These results clearly show the superiority of the REP-529 sequence in the diagnosis of toxoplasmosis by PCR suggest that this target should be adopted as part of standardization of the PCR assay.
ISSN: 0095-1137

hal-01118293
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118293
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118293/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118293/file/A%2010-Year%20Retrospective%20Comparison%20of%20Two%20Target%20Sequences-belaz2015.pdf
PUBMEDCENTRAL : PMC4365238

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In order to perform a human and ecological risk assessment of pharmaceutical products (PPs) in natural waters, it is necessary to accurately quantify a broad variety of PPs at low concentrations. Although numerous currently implemented analytical methodologies, less is known about the preservation of PPs in natural water samples within the period before analysis (holding time, storage conditions). This paper is the first literature review about the stability of PPs in natural waters (surface and groundwaters) during sample storage. The current work focuses on a comparison of the performances of the available preservation techniques (filtration, container materials, storage temperature, preservative agents, etc.) for PPs in samples. All 58 reviewed PPs may be successfully stabilized during 7 days in surface waters by at least one appropriate methodology regarding temperature, acidic and non-acidic preservatives. When temperature is not a sufficient preservation parameter f! or some PPs (hormones and fluoxetine) its combination with the addition of chemical agents into the samples may prolong the integrity of the PPs during storage in surface water. There is a strong need to use standard protocols to assess and compare the stability of PPs in environmental water matrices during storage as well as during analytical preparation or analysis (European criteria 2002/657/EC). Since the stability of PPs during sample storage is a critical parameter that could call into question the quality of the data provided for the concentrations, the design of stability studies should rigorously take into account all critical parameters that could impact the concentrations of the PPs with time.
Talanta

insu-00839186
https://hal-insu.archives-ouvertes.fr/insu-00839186
DOI : 10.1016/j.talanta.2013.01.042

Éditeur(s) : HAL CCSD Institute of Electrical and Electronics Engineers
Résumé : International audience
: A new set-up for exposure of human cells in vitro at 37°C to pulse-modulated 300 MHz and 500 MHz signals of future magnetic resonance imaging (MRI) systems is designed, built up, and characterized. Two dipole antennas, specifically designed for ultra high field MRI, are used as radiating structures. The electromagnetic (EM) field distribution inside the incubator containing the cells is computed, and it is shown to be in a good agreement with measurements. The electric field at the cell level is quantified numerically. Local, 1g average, and averaged over the culture medium volume SAR are provided along with the standard deviation values for each well. Temperature increments are measured inside the culture medium during the exposure using an optical fiber thermometer. Then we identify the pulse parameters corresponding to the thermal threshold of 1°C, usually considered as a threshold for thermally-induced biological effects. For these parameters, the induction of heat shock proteins is assessed to biologically verify a potential thermal response of cells. The data demonstrate that, under the considered experimental conditions, exposure to pulsemodulated radiations emulating typical ultra high field MRI signals, corresponding to temperature increments below 1°C, does not trigger any heat shock response in human brain cells.
ISSN: 0018-9294

hal-00874329
https://hal.archives-ouvertes.fr/hal-00874329
DOI : 10.1109/TBME.2013.2270371
PUBMED : 23799680

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
During the treatment process of drinking water, disinfectants (chlorine, ozone, chlorine dioxide) react on water containing organic matter and bromide to produce disinfection by-products at trace levels. Among them, five of the nine existing halo-acetic acids (HAAs) are commonly found in drinking water (monochloroacetic acid (MCAA), dichloroacetic acid (DCAA), monobromoacetic acid (MBAA), dibromoacetic acid (DBAA), and Trichloroacetic acid (TCAA)), including four classified in the 2B IARC group of potential carcinogens (BCAA, DBAA, DCAA, TCAA). With respect to drinking water quality, guidelines are proposed by WHO (2006) and water quality standards are imposed in many countries such as less than 100 μg/L for the sum of the five HAAs by US EPA (1998) and Canadian Health Department (2008). For this purpose, two analytical methods are commonly used, GC/MS with derivatization and LC/MS, UV or conductivity. A new method, based on two-dimensional ion chromatography (IC 2D) with suppressed conductivity is proposed. This method presents the main advantage of offering a quick implementation compared to GC or LC methods: direct injection, slight maintenance, lower cost of investment, by leading to good performances (specificity and sensitivity). The use of two different selectivity columns, and the fractionation on the first dimension canceling interferences, improves the specificity. The sensitivity is enabled by interfacing a preconcentration column between the two different internal diameter columns. The analytical conditions are optimized for the analysis of nine HAAs. The performances of the method are evaluated. The optimized method applied to natural water samples demonstrates its ability to quantify HAAs at trace levels in drinking water.
Microchemical Journal

hal-00877151
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00877151
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00877151/document
DOI : 10.1016/j.microc.2013.07.012

Éditeur(s) : HAL CCSD
Résumé : Land-use changes have deep consequences on species diversity, community structure and ecosystem functioning. Consequently, many works have tried to understand the effects of such changes on the diversity and functional properties of organisms. It has been demonstrated that species traits are oftenly more important than the identity of species per se in order to account understand the ecological roles of species. Besides, while the majority of assessments about land-use change effects on ecosystem functioning have focused on primary producers, the contribution of other organisms is essential to maintain the functioning and resilience of ecosystems.Ants are interesting organisms to track land-use changes due to their abundance, ubiquity and ecological dominance. Ants are present in most of terrestrial biomes and participate in several ecosystem processes through their consumption of food resources. They are also easy to sample and standard methods exist to provide accurate comparisons between studies. While a number of studies have demonstrated abrupt changes in ant species composition along environmental gradients, only a reduced number of such studies have tried to understand how ant community changes affect ecosystem processes. Moreover, the traits responsible for the stability of ant communities in response to land-use changes are little known. It is therefore necessary to develop a methodology that enables a proper identification of ant participation to different ecosystem processes and their contribution to ecosystems’ resistance and resilience.In this thesis I aim to bring some light about i) how land-use changes affect ant community structure? ii) what traits are responsible of the ecological success of a species or it’s extinction from a given environment? iii) how changes in the species or trait composition affect the participation intensity of ants in different ecosystem processes ?
Les perturbations d’origine anthropique sont à l’origine de l’érosion de la biodiversité avec des conséquences sur la structure des communautés et pour le fonctionnement des écosystèmes. La vitesse de ces changements a stimulé de nombreuses recherches portant sur les effets de ces modifications sur la biodiversité des organismes et leurs propriétés fonctionnelles. En effet il a été montré que les traits des espèces sont plus importants que leur identité elle-même pour tenir compte de leurs rôles écologiques. Même si la majorité de ces travaux ont étudié la réponse des producteurs primaires sur les écosystèmes terrestres, la contribution d’autres organismes est toutefois essentielle pour maintenir un fonctionnement et une résilience des écosystèmes corrects.Les fourmis sont des organismes cibles intéressants pour étudier de telles modifications du fait de leur abondance et de leur dominance écologique. En effet elles ont une distribution cosmopolite et participent à de nombreuses fonctions dans l’écosystème terrestre. Elles sont également faciles à étudier et des méthodes d’échantillonnage standard existent. Bien que de nombreuses recherches aient démontré des modifications dans la composition spécifique des fourmis dans des gradients environnementaux, un nombre réduit d’entre elles ont étudié la contribution de ces organismes sur le fonctionnement des écosystèmes. De plus, les traits responsables de la stabilité des communautés de fourmis en réponse à ces modifications sont encore peu connus. Il est donc nécessaire de développer une méthodologie capable d‘identifier la participation des fourmis dans des processus écosystémiques permettant également de quantifier leur activité afin de comprendre comment ces organismes agissent sur les capacités de résistance et résilience des écosystèmes.Ainsi, cette thèse vise mettre en lumière i) en quoi la simplification des habitats liée aux activités humaines a des répercussions sur les communautés de fourmis, ii) quels sont les traits responsables du succès écologique d’une espèce ou de son déclin au sein d’un environnement donné, et iii) comment ces variations en composition spécifique impactent l’intensité de participation des fourmis aux processus écosystémiques.
https://hal.archives-ouvertes.fr/tel-01389102

NNT : 2016YANE0004
tel-01389102
https://hal.archives-ouvertes.fr/tel-01389102
https://hal.archives-ouvertes.fr/tel-01389102v2/document
https://hal.archives-ouvertes.fr/tel-01389102/file/these.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We show how to introduce the Value at Risk (VaR) concept in the analysis of the adaptation of the shape of a soft bed to a flow knowing the Probability Density Function (PDF) of the responses of the shape to flow perturbations (bed receptivity). Our aim is to quantify our confidence on simulation scenarios by an available morphodynamic model for the shape. The approach permits to perform this task at low complexity as it does not require any sampling of the bed receptivity parameter space. The paper goes beyond stationarity for the variability of the bed receptivity by linking its dynamics to the bottom morphodynamics through an original transport equation for the local bed receptivity standard deviation. The approach has been applied to the analysis of bed morphodynamics based on minimization principles. The results show the importance of including uncertainty information during the coupling and not only eventually through simple margins on the results.
ISSN: 0045-7930

hal-01054937
https://hal.archives-ouvertes.fr/hal-01054937
https://hal.archives-ouvertes.fr/hal-01054937/document
https://hal.archives-ouvertes.fr/hal-01054937/file/paper_var_litto.pdf
DOI : 10.1016/j.compfluid.2013.10.021

Éditeur(s) : HAL CCSD
Résumé : International audience
This study assessed the usefulness of UV spectrophotometry for the monitoring of a yeast-based deoxygenation process proposed for ships' ballast water treatment to prevent the transfer of aquatic invasive species. Ten-day laboratory experiments using three treatment concentrations and different water types were conducted and resulted in complete oxygen depletion of treated waters. The treatment performance and quality of treated waters were determined by measuring the UV-visible absorbance spectra of water samples taken over time. Samples were also used for laboratory analysis of water quality properties. The UV absorbance spectra values were strongly correlated (r = 0.96) to yeast cell density in treated waters. The second-order derivative (D (2)) of the spectra varied greatly over time, and the spectrum profiles could be divided into two groups corresponding to the oxygenated and anoxic phases of the treatment. The D (2) value at 215 nm was strongly correlated (r = 0.94) to ammonia levels, which increased over time. The D (2) value at 225 nm was strongly correlated (r  extgreater 0.97) to DO concentration. Our results showed that UV spectrophotometry may provide a rapid assessment of the behavior and performance of the yeast bioreactor over time by quantifying (1) the density of yeast cells, (2) the time at which anoxic conditions were reached, and (3) a water quality index of the treated water related to the production of ammonia. We conclude that the rapidity of the technique confers a solid advantage over standard methods used for water quality analysis in laboratory and would permit the direct monitoring of the treatment performance on-board ships
Environmental Monitoring and Assessment

hal-01286253
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01286253
DOI : 10.1007/s10661-016-5209-3
PUBMED : 26944435