Éditeur(s) : HAL CCSD Mineralogical Society of America
Résumé : International audience
Accessory phases are important hosts of trace elements; allanite may contain >90% of the REE in a bulk rock. The mobility and redistribution of several trace elements, notably HREE, Th, U, and Y is thus controlled by reactions involving allanite and other REE phases, as well as several rock-forming minerals. As these elements are commonly concentrated in mature elastic sediments, a suite of impure quartzite was studied. Two eclogite facies samples from the Monometamorphic Cover Complex of the Sesia Zone (Western Italian Alps) are presented in some detail, as they reveal a remarkably rich spectrum of reaction relationships that involve REE phases.;Two allanite-forming reactions were inferred from textures and phase compositions;(1) monazite + Ca-silicate(?) + fluid -> allanite + apatite + thorite;;(2) monazite + thorite + Ca-silicate(?) + fluid -> Th-rich allanite + auerlite +/- apatite.;Petrographic observations and thermodynamic models suggest that allanite entered the HP assemblage at similar to 530 degrees C and 17-18 kbar during prograde metamorphism.;In one sample, allanite is rimmed by epidote rich in Y and HREE that grew at the expense of xenotime. Two net transfer reactions were derived;(3) xenotime + allanite + fluid -> Y-rich epidote + apatite + thorite;;(4) xenotime + allanite + fluid -> Y-rich epidote + aeschynite + thorite + (phosphate?).;Textural relationships and trace element analyses of coexisting allanite/monazite and xenotime/Y-rich epidote reveal systematic partitioning of the REE. Partition coefficients for the HREE are compatible with equilibrium fractionation, whereas those for the LREE show patterns that seem to be inherited from the precursor phases, in this case zircon with variable LREE composition.
ISSN: 0003-004X

hal-00745674
https://hal.archives-ouvertes.fr/hal-00745674
DOI : 10.2138/am.2012.3832

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This work relates to the characterisation of the predominant gill protein of the white clam, Codakia orbicularis (Linné, 1758), which harbours endosymbiotic sulphur-oxidising chemoautotrophic bacteria. Total RNA was extracted from the clam to perform 3'rapid amplification of cDNA ends (3'RACE) using degenerate oligonucleotides prepared from a partial sequence of a predominant protein of about 14kDa, termed codakine. The partial peptide sequence was obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and Edman degradation. Clones isolated from the cDNA library and containing the gene of interest were used in polymerase chain reaction (PCR). The PCR and RACE-PCR products were sequenced to determine the entire coding DNA sequence of codakine. BLAST analysis revealed about 23% to 29% sequence identity between codakine and various animal C-type lectins that are often involved in symbiosis and immune defences. Codakine also contains the motifs and domains of Ca(2+)-dependent C-type lectins, and in particular the tripeptide EPN motif frequently found in mannose-binding lectins (MBLs). Analysis of the protein by affinity chromatography on a mannose-agarose column is consistent with the findings that codakine is a dimeric Ca(2+)-dependent MBL of about 29kDa. Based on the present results, it is hypothesised that this novel C. orbicularis gill protein is involved in the recognition of symbiotic and pathogenic bacteria.
ISSN: 1050-4648

hal-00746015
https://hal.univ-antilles.fr/hal-00746015
DOI : 10.1016/j.fsi.2006.06.013
PUBMED : 17169576

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 Wiley
Résumé : International audience
BACKGROUND: The RH blood group system has many RHCE variant alleles that have arisen through gene conversion or nucleotide changes. Two probands, with red blood cells (RBCs) that were D+C+E-c+(w) e+ were sent to our laboratories to resolve the weak c expression. STUDY DESIGN AND METHODS: Hemagglutination tests were performed by automated and manual procedures. Genomic DNA analysis was performed by sequencing of Exons 1 to 10 of RHCE and RHD. RESULTS: The probands' RBCs did not react with standard monoclonal anti-E reagents from Bio-Rad, Diagast, DiaMed, Immucor, Ortho, and Quotient. The RBCs reacted variably with anti-c reagents from Diagast, DiaMed, Immucor, or Ortho and did not react with the Quotient anti-c reagent. Surprisingly, sequencing results of RHCE showed the presence of C/G at Position 676 (E/e polymorphism) and the association of the E polymorphism with a 734T>C transition in Exon 5 of the RHCE, encoding a Leu245Pro amino acid substitution in the mature RhcE polypeptide. Replacement of leucine 245 by proline in the eighth transmembrane domain of the RhcE protein may have a steric effect on the protein such that most anti-E reagents do not bind and the interaction between anti-c and c antigen is also affected. CONCLUSION: We report a novel RHCE*cE allele, RHCE*cE734C, which was assigned the provisional ISBT allele name RHCE*cE.14 or RHCE*03.14. It was found in two probands whose RBCs had weakened c expression and typed E- with conventional anti-E reagents. These data, once again, highlight the fact that the genotype does not always reflect the phenotype.
ISSN: 0041-1132

hal-00839022
https://hal.archives-ouvertes.fr/hal-00839022
DOI : 10.1111/j.1537-2995.2012.03860.x
PUBMED : 22958092

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The equilibrium phase relations of a mafic durbachite (53 wt.% SiO2) from the TA (TM) ebi pluton, representative of the Variscan ultrapotassic magmatism of the Bohemian Massif (338-335 Ma), have been determined as a function of temperature (900-1,100A degrees C), pressure (100-200 MPa), and H2O activity (1.1-6.1 wt.% H2O in the melt). Two oxygen fugacity ranges were investigated: close to the Ni-NiO (NNO) buffer and 2.6 log unit above NNO buffer (a dagger NNO + 2.6). At 1,100A degrees C, olivine is the liquidus phase and co-crystallized with phlogopite and augite at 1,000A degrees C for the whole range of investigated pressure and water content in the melt. At 900A degrees C, the mineral assemblage consists of augite and phlogopite, whereas olivine is not stable. The stability field of both alkali feldspar and plagioclase is restricted to low pressure (100 MPa) at nearly water-saturated conditions (< 3-4 wt.% H2O) and T < 900A degrees C. A comparison between experimental products and natural minerals indicates that mafic durbachites have a near-liquidus assemblage of olivine, augite, Ti-rich phlogopite, apatite and zircon, followed by alkali feldspar and plagioclase, similar to the mineral assemblage of minette magma. Natural amphibole, diopside and orthopyroxene were not reproduced experimentally and probably result from sub-solidus reactions, whereas biotite re-equilibrated at low temperature. The crystallization sequence olivine followed by phlogopite and augite reproduces the sequence inferred in many mica-lamprophyre rocks. The similar fractionation trends observed for durbachites and minettes indicate that mafic durbachites are probably the plutonic equivalents of minettes and that K- and Mg-rich magmas in the Bohemian Massif may have been generated from partial melting of a phlogopite-clinopyroxene-bearing metasomatized peridotite. Experimental melt compositions also suggest that felsic durbachites can be generated by simple fractionation of a more mafic parent and mixing with mantle-derived components at mid crustal pressures.
ISSN: 0010-7999

hal-00618418
https://hal.archives-ouvertes.fr/hal-00618418
DOI : 10.1007/s00410-009-0430-5

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
The deeply branching Deinococcus-Thermus lineage is recognized as one of the most extremophilic phylum of bacteria. In previous studies, the presence of Deinococcus-related bacteria in the hot arid Tunisian desert of Tataouine was demonstrated through combined molecular and culture-based approaches. Similarly , Thermus-related bacteria have been detected in Tunisian geothermal springs. The present work was conducted to explore the molecular diversity within the Deinococcus-Thermus phylum in these extreme environments. A set of specific primers was designed in silico on the basis of 16S rRNA gene sequences, validated for the specific detection of reference strains, and used for the polymerase chain reaction (PCR) amplification of metagenomic DNA retrieved from the Tataouine desert sand and Tunisian hot spring water samples. These analyses have revealed the presence of previously undescribed Deino-coccus-Thermus bacterial sequences within these extreme environments. The primers designed in this study thus represent a powerful tool for the rapid detection of Deinococcus-Thermus in environmental samples and could also be applicable to clarify the biogeography of the Deinococcus-Thermus phylum.
ISSN: 2045-8827

Droits : http://creativecommons.org/licenses/by/
hal-01560945
https://hal-amu.archives-ouvertes.fr/hal-01560945
https://hal-amu.archives-ouvertes.fr/hal-01560945/document
https://hal-amu.archives-ouvertes.fr/hal-01560945/file/Theodorakopoulos-2013.pdf
DOI : 10.1002/mbo3.119

Éditeur(s) : Pêche thonière et dispositifs de concentration de poissons, Caribbean-Martinique, 15-19 Oct 1999
Résumé : A development programme for the promotion of FADs in Sao Tome and Principe has implemented an original interactive approach by granting a predominant place to the initiative of the target group and its participation in decision making. The appropriation process of the innovative fads by the beneficiaries takes place in three stages described herewith. the technical research phase. This consists of formally describing an idea in reply to an expressed or potential need. The envisaged fad type is developed and tested by the project's agents in order to obtain a technically appropriate prototype.- the research and adjustment phase. The fad is given to a small number of people to be used in real-life conditions. Reaction surveys will enable its pertinence to be tested and its adaptation to normal conditions of use. This second phase results in the production of a technically and socio-economically appropriated fad. - the diffusion-perpetuation phase. This entails i) identification of the sequences of the various stages, ii) definition and grouping of contributions by the various parties, iii) production of educational auxiliaries, iv) initiating actions for user awareness and demonstration, v) staff training, vi) monitoring of the fad "socialisation", vii) solving funding problems.Original Abstract: Un projet visant, entre autres, la promotion de DCP pour la peche artisanale fonctionne a Sao Tome et Principe depuis 1993. Le processus d'appropriation daune telle innovation par les beneficiaires comprend trois etapes ici decrites. La phase de recherche technique. Il s'agit d'instrumentaliser une idee en reponse a un besoin exprime ou potentiel. L'innovation envisagee est mise au point et testee par les agents du projet en milieu controle de facon a obtenir un prototype techniquement approprie. La phase de recherche-developpement: l'outil est confie a un petit nombre de personnes pour une utilisation en conditions reelles. C'est une phase de mise au point interactive, seule susceptible de provoquer une reelle appropriation par les recipiendaires. Des enquetes de reaction permettront de tester sa pertinence et de l'adapter aux conditions normales d'utilisation. Cette seconde phase debouche sur la production d'un outil de reference approprie techniquement et socio-economiquement. La phase de diffusion-perennisation: il s'agira la : i) d'identifier les sequences d'intervention, ii) d'identifier et de regrouper les apports des differentes parties, iii) de definir et de produire les auxiliaires pedagogiques (manuels, affiches, radio), iv) d'entreprendre des actions de sensibilisation et de demonstration, v) de former les personnels, vi) de veiller a la socialisation de l'innovation, pour les outils collectifs, vii) de resoudre le probleme du financement.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00042/15306/12641.pdf
http://archimer.ifremer.fr/doc/00042/15306/

Éditeur(s) : HAL CCSD Mineralogical Society of America
Résumé : International audience
To constrain the crystallization of alkaline and volatile-rich lavas present in intraplate settings, we studied the petrological features and the geochemical composition of major, trace, and volatile elements of mineral and bulk-rock of two sodalite-bearing phonolites: (1) haüyne-plagioclase-bearing Si-K-rich phonolite from Laacher See (Germany) and (2) nosean-nepheline-bearing Si-poor phonolite from Saghro (Morocco). In haüyne-bearing phonolites (55–59 wt% SiO2, K > Na, Na+K/Al = 0.96–1.08), we found that the low silica and low sodium activity promoted the early crystallization of S-rich haüyne (13.7–13.9 wt% SO3, 0.4 wt% Cl) + S-rich apatite (0.7–0.9 wt% SO3), titanite, and rare pyrrhotite followed by clinopyroxene-plagioclase-sanidine at relatively low pressure and temperature (P = 250 MPa and T = 850 °C) and oxidized condition (ΔNNO-NNO+1, where NNO is nickel-nickel oxide buffer). The crystallization of haüyne occurred at fluid-undersaturated conditions from a silicate melt with 6 wt% H2O, 0.17–0.23 wt% Cl, 0.11–0.4 wt% S, and 0.07–0.14 wt% F. Nosean-bearing phonolites from Saghro are silica-poor and peralkaline (52–54 wt% SiO2, Na > K, Na+K/Al = 1.2) and crystallized at higher P and T (300 MPa and 950 °C) and more reduced conditions (NNO) compared to haüyne-bearing phonolites. The incongruent reaction to form nosean requires high silica and Na2O activity. The mineral assemblage and composition suggest early crystallization of nepheline followed by nosean (7.8–8.8 wt% SO3; 1–1.1 wt% Cl). The sequence of crystallization is: clinopyroxene + nepheline + S-poor apatite (<0.04 wt% SO3) + pyrrhotite followed by nosean and titanite. Nosean-bearing magmas are fluid-undersaturated with relatively low volatile content (4 wt% H2O, <0.25 wt% Cl, <0.056 wt% S, 0.08–0.1 wt% F), although Cl may have exsolved during ascent and formed a fluid phase (NaCl-bearing).Both haüyne- and nosean-bearing phonolites are last equilibrated at relatively low pressure and high temperature. Haüyne and nosean crystallized at oxidized and volatile-rich pre-eruptive conditions. They record the volatile concentrations at depth and may be used as oxybarometer. The incongruent reactions involved to form haüyne and nosean suggest that phonolitic magmas became more oxidized during crystallization. The initial volatile concentrations in basanite/nephelinite magmas, from partial melting of volatile-bearing K2O-rich mantle rock, should have been one important factor influencing the crystallization of haüyne-bearing Si-K-rich phonolite and nosean-bearing Si-poor phonolite in intracontinental setting.
ISSN: 0003-004X

hal-01278067
https://hal.archives-ouvertes.fr/hal-01278067
DOI : 10.2138/am-2015-5318

Éditeur(s) : HAL CCSD Wiley
Résumé :  
The symbiotic interactions between Frankia strains and their associated plants from the Casuarinaceae under controlled conditions are well documented but little is known about these interactions under natural conditions. We explored the symbiotic interactions between eight genotypically characterized Frankia strains and five Casuarinaceae species in long-term field trials. Characterization of strains was performed using the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) for the nifD-nifK intergenic transcribed spacer (ITS) and 16S-23S ITS. Assessments of the symbiotic interactions were based on nodulation patterns using nodule dry weight and viability, and on actual N-2 fixation using the delta N-15 method. The PCR-RFLP patterns showed that the analyzed strains belonged to the same genotypic group (CeD group), regardless of the host species and environment of origin. The nodule viability index is introduced as a new tool to measure the viability of perennial nodules and to predict their effectiveness. The host Casuarinaceae species was a key factor influencing both the actual N-2-fixing activity of the associated Frankia strain and the viability of nodules within a location. This is the first study providing information on the symbiotic interactions between genotypically characterized Frankia strains and actinorhizal plants under natural conditions. The results revealed a way to improve a long-term management of the Casuarinaceae symbiosis.
ISSN: 0031-9317

hal-01032134
https://hal.archives-ouvertes.fr/hal-01032134
DOI : 10.1111/j.1399-3054.2007.00856.x

Éditeur(s) : HAL CCSD American Society of Tropical Medicine and Hygiene
Résumé : International audience
We investigated infection of rodents and shrews by Leptospira spp. in two localities of Cambodia (Veal Renh, Kaev Seima) and in four types of habitat (forests, non-flooded lands, lowland rain-fed paddy fields, houses) during the wet and the dry seasons. Habitat preference was common, and rodent and shrew species were found only in houses or in rain-fed paddy fields or in forests. Among 649 small mammals trapped belonging to 12 rodent species and 1 shrew species, 71 of 642 animals tested were carriers of Leptospira according to the 16S ribosomal RNA marker used. Rodent infection was higher in low-slope locations, corresponding to rain-fed paddy fields, especially in the rainy season and in Kaev Seima. Rodents (Rattus exulans) and shrews (Suncus murinus) inhabiting households showed significantly low levels of infections, whereas rodents living in and near to forests (shrubby wasteland, orchards) showed high levels of infection.
American Journal of Tropical Medicine and Hygiene

pasteur-00808144
https://hal-riip.archives-ouvertes.fr/pasteur-00808144
DOI : 10.4269/ajtmh.2012.11-0349
PUBMED : 22665613

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Geochronological studies of samples from continuous crustal sections of fossil intra-oceanic arcs are paramount for determining the precise timing of major processes that took place during the building of an oceanic island-arc crust. In this study, laser ablation ICP-MS U-Pb zircon (and conventional Rb-Sr) analyses pinpoint the timing of major events responsible for crustal growth of the Kohistan paleo-island arc (Northern Pakistan). Inheritance in magmatic rocks is evidence for recycling of intra-arc material and indicates that the Kohistan arc may have formed as early as 135 +/- 4 Ma. One older inherited grain indicates that the arc developed on a young oceanic lithosphere whose remnants include a c. 175 Ma old component. An interesting consequence is that intra-oceanic arc magmas can yield inherited zircons, which can be much older than the arc system itself without requiring recycling back into the mantle by subduction processes. In the case of the Kohistan arc, ante-arc Neotethys oceanic lithosphere was tapped by arc magmas during their way upward into the arc crust. The oldest magmatic ages measured in this study fall in the range 101-102 Ma (100.9 +/- 0.6 and 102.1 +/- 0.4 Ma). This period corresponds to arc build-up and thickening of the arc crust. Leucogranitic melts dated at 89.9 +/- 0.4 Ma and 90.9 +/- 1.0 Ma are considered as produced by dehydration/melting reaction accompanying granulitisation of the thickened lower arc crust. A maximum age for this event is 97.7 +/- 0.7 Ma, the age of emplacement of a garnet meta-tonalite affected by granulite facies metamorphism. Magmatic activity was still ongoing during and after the granulitisation as testified by emplacement of a diorite and a gabbro dated at 89.1 +/- 0.6 and 88.2 +/- 0.9 Ma respectively. The upper part of the metaplutonic sequence contains diorite samples dated at 84.6 +/- 0.5 Ma and 84.3 +/- 0.5 Ma and as young as 81.1 +/- 0.7 Ma. During this period, and based on the present day outcropping sequences, the mean crustal growth rate varied from 32 to 65 km(3)/km/Ma (volume per unit width along the strike of the arc) which is comparable to the range for present day arcs of the Western Pacific region. The correspondence of crustal growth rates observed for present-day island arcs and the good preservation of the crustal section in the Kohistan arc, make this area an exceptional natural laboratory to study arc related processes and to check models of continental crust formation by arc accretion.
ISSN: 0012-821X

hal-00644555
https://hal.archives-ouvertes.fr/hal-00644555
DOI : 10.1016/j.epsl.2011.07.016

Éditeur(s) : HAL CCSD
Résumé : Subduction is one of the major geodynamical process active during the Earth evolution. The characterization of arc magmas, their evolution through space and time, and the relationship between arc magmatism and continental crust forming processes, constitute the main research topics in petrology and geochemistry since the last three decades. This study focuses on an exhumed portion of the Kohistan Arc (N Pakistan), which is an exceptional ‘in situ' laboratory to study and follow through time the processes active on subduction zones. Based on a pluri-geochemical approach, this study allows unraveling two major issues : 1/ The lack of a cogenetic relationship between the arc root (i.e. ultramafic rocks) and the overlying gabbroic crustal section. The Jijal ultramafic section does not bear a crustal origin and was emplaced at ~117 Ma via a magma-rock reaction between REE-depleted ‘boninite-like' melts and the pre-existing lithospheric mantle with Indian-MORB affinities; 2/ A three-stage geodynamical model covering the arc evolution through ~30 Ma. This model starts with the onset of the subduction followed by the building of the volcanic arc (1st stage). The 2nd stage corresponds to a major thermal event, characterized by abundant magma underplating and by granulitisation of the arc base. Recycling of the residual/cumulative lower crust into the convective asthenospheric mantle was efficient during this stage, and probably related to thermo-mechanical erosion processes. The last stage, between ~95 and 85 Ma, seals the end of the intra-oceanic subduction and corresponds to an “amagmatic” period. This step is followed by a voluminous, but short, magmatic pulse at ~85 Ma, occurring just before the arc-continent collision. At last, this study emphasizes the more mafic composition of the investigated crustal arc section when compared to the bulk continental crust. Nevertheless the arc section composition nicely fits with the lower continental crust average.
Les zones de subduction représentent des zones d'évolution clés dans la compréhension des processus géologiques majeurs actifs sur notre planète. En particulier, la caractérisation et l'évolution des magmas générés dans les zones d'arcs océaniques et la relation entre leur genèse et les processus de croissance crustale sont des axes primordiaux. Cette étude est focalisée sur la portion d'arc océanique exhumée du Kohistan (Nord Pakistan) qui constitue un laboratoire exceptionnel pour appréhender cette problématique. Basée sur une approche géochimique multi-méthodes (éléments majeurs et en trace, isotopes), cette étude a permis d'établir : 1/ l'absence de relation génétique directe entre les roches ultrabasiques de la racine de l'arc et la section crustale sus-jacente. La formation de la séquence ultrabasique de Jijal se produit à ~117 Ma via une réaction de type magma-roche entre des liquides de type boninitique (appauvris en terres rares), et le manteau lithosphérique de type MORB-Indien ; 2/ un modèle géodynamique en trois stades majeurs résumant l'évolution de l'arc océanique et de la subduction sur une période d'environ 30 Ma. Ce modèle débute par l'initiation de la subduction et la formation de l'arc volcanique s.s. (1er stade) ; le 2ème stade correspond à un évènement thermique majeur. Il est représenté par un sous-placage important de magmas et une granulitisation intense de la base de l'arc. Le recyclage de la croûte inférieure cumulative et résiduelle, dans le manteau sous-jacent, se produit durant cette étape vraisemblablement suite à des processus d'érosion thermo-mécanique. Le dernier stade, entre 95 Ma et 85 Ma, scelle la fin du fonctionnement de la zone de subduction et correspond à une période amagmatique suivie par une brève reprise du magmatisme avant la collision de l'arc après 85 Ma. Enfin, une modélisation numérique comparative avec la croûte continentale globale met en évidence la composition significativement plus basique de la croûte de l'arc insulaire du Kohistan. De fortes similitudes sont en revanche observées entre la section d'arc étudiée et la croûte continentale inférieure.
https://tel.archives-ouvertes.fr/tel-00437770

tel-00437770
https://tel.archives-ouvertes.fr/tel-00437770
https://tel.archives-ouvertes.fr/tel-00437770/document
https://tel.archives-ouvertes.fr/tel-00437770/file/thesedhuime.pdf

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

Éditeur(s) : HAL CCSD American Chemical Society
Résumé : International audience
2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), a carcinogenic heterocyclic aromatic amine formed in cooked meats, is metabolically activated to electrophilic intermediates that form covalent adducts with DNA and protein. We previously identified an adduct of PhIP formed at the Cys34 residue of human serum albumin following reaction of albumin with the genotoxic metabolite 2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]pyridine (HONH-PhIP). The major adducted peptide recovered from a tryptic/chymotryptic digest was identified as the missed-cleavage peptide LQQC*[SO2PhIP]PFEDHVK, a [cysteine-S-yl-PhIP]-S-dioxide linked adduct. In this investigation, we have characterized the albumin adduction products of N-sulfooxy-2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-sulfooxy-PhIP), which is thought to be a major genotoxic metabolite of PhIP formed in vivo. Targeted and data-dependent scanning methods showed that N-sulfooxy-PhIP adducted to the Cys34 of albumin in human plasma to form LQQC*[SO2PhIP]PFEDHVK at levels that were 8-10-fold greater than the adduct levels formed with N-(acetyloxy)-2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-acetoxy-PhIP) or HONH-PhIP. We also discovered that N-sulfooxy-PhIP forms an adduct at the sole tryptophan (Trp214) residue of albumin in the sequence AW*[PhIP]AVAR. However, stable adducts of PhIP with albumin were not detected in human hepatocytes. Instead, PhIP and 2-amino-1-methyl-6-(5-hydroxy)phenylimidazo[4,5-b]pyridine (5-HO-PhIP), a solvolysis product of the proposed nitrenium ion of PhIP, were recovered during the proteolysis, suggesting a labile sulfenamide linkage had formed between an N-oxidized intermediate of PhIP and Cys34 of albumin. A stable adduct was formed at the Tyr411 residue of albumin in hepatocytes and identified as a deaminated product of PhIP, Y*[desaminoPhIP]TK, where the 4-HO-tyrosine group bound to the C-2 imidazole atom of PhIP.
ISSN: 0893-228X

hal-01146777
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146777
DOI : 10.1021/acs.chemrestox.5b00075
PUBMED : 25815793

Éditeur(s) : HAL CCSD Elsevier
Résumé : Recent evolutionary studies clearly indicate that evolution is mainly driven by changes in the complex mechanisms of gene regulation and not solely by polymorphism in protein-encoding genes themselves. After a short description of the cis-regulatory mechanism, we intend in this review to argue that by applying newly available technologies and by merging research areas such as evolutionary and developmental biology, population genetics, ecology and molecular cell biology it is now possible to study evolution in an integrative way. We contend that, by analysing the effects of promoter sequence variation on phenotypic diversity in natural populations, we will soon be able to break the barrier between the study of extant genetic variability and the study of major developmental changes. This will lead to an integrative view of evolution at different scales. Because of their sessile nature and their continuous development, plants must permanently regulate their gene expression to react to their environment, and can, therefore, be considered as a remarkable model for these types of studies. (C) 2010 Elsevier Ireland Ltd. All rights reserved.
ISSN: 0168-9452

hal-01032399
https://hal.archives-ouvertes.fr/hal-01032399
DOI : 10.1016/j.plantsci.2010.09.009

Éditeur(s) : HAL CCSD Lippincott, Williams & Wilkins
Résumé : International audience
Purpose of review Toxoplasmosis in immunocompromised patients is associated with a high mortality rate. Molecular techniques are important tools to diagnose acute disease in immunocompromised patients, but there are various methods with variable efficiency. Some of them have been validated for the diagnosis of congenital toxoplasmosis, but the impact of their use has not been evaluated in immunocompromised patients. Recent findings Toxoplasmosis is of increasing importance in non-HIV immunocompromised patients. In addition, the picture of disease shows greater severity in South America, both in immunocompetent study participants and in congenitally infected infants. These epidemiological differences could influence the sensitivity of diagnostic methods. This review analyzes recent data on molecular diagnosis and compares them with older ones, in light of progress gained in molecular techniques and of recent epidemiological findings. Most recent studies were conducted in South America and used PCR targeting the B1 gene. PCR on blood could allow diagnosing a significant proportion of patients with ocular toxoplasmosis in Brazil. Summary Quantitative PCR methods with specific probes should be used to improve sensitivity and warrant specificity. Performance of quantitative PCR targeting the repeated 529 bp sequence for the diagnosis of toxoplasmosis in immunocompromised patients needs evaluation in field studies in South America and in western countries.
ISSN: 0951-7375

hal-01390970
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01390970
DOI : 10.1097/QCO.0000000000000275
PUBMED : 27191201

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We propose a new geometric approach to describe the qualitative dynamics of chemical reactions networks. By this method we identify metastable regimes, defined as low dimensional regions of the phase space close to which the dynamics is much slower compared to the rest of the phase space. These metastable regimes depend on the network topology and on the orders of magnitude of the kinetic parameters. Benchmarking of the method on a computational biology model repository suggests that the number of metastable regimes is sub-exponential in the number of variables and equations. The dynamics of the network can be described as a sequence of jumps from one metastable regime to another. We show that a geometrically computed con-nectivity graph restricts the set of possible jumps. We also provide finite state machine (Markov chain) models for such dynamic changes. Applied to signal transduction models, our approach unravels dynamical and functional * corresponding author capacities of signalling pathways, as well as parameters responsible for speci-ficity of the pathway response. In particular, for a model of TGFβ signalling, we find that the ratio of TGFBR2 to TGFBR1 receptors concentrations can be used to discriminate between metastable regimes. Using expression data from the NCI60 panel of human tumor cell lines, we show that aggressive and non-aggressive tumour cell lines function in different metastable regimes and can be distinguished by measuring the relative concentrations of receptors of the two types.
ISSN: 0303-2647

hal-01379033
https://hal.inria.fr/hal-01379033
https://hal.inria.fr/hal-01379033/document
https://hal.inria.fr/hal-01379033/file/Samal_et_al_Biosystems_final.pdf
DOI : 10.1016/j.biosystems.2016.07.004

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
In 2008 a fatal case of primary amoebic meningoencephalitis, due to the amoeboflagellate Naegleria fowleri, occurred in Guadeloupe, French West Indies, after a child swam in a bath fed with geothermal water. In order to improve the knowledge on free-living amoebae in this tropical part of France, we investigated on a monthly basis, the presence of Naegleria spp. in the recreational baths, and stream waters which feed them. A total of 73 water samples, 48 sediments and 54 swabs samples were collected from 6 sampling points between June 2011 and July 2012. The water samples were filtered and the filters transferred to non-nutrient agar plates seeded with a heat-killed suspension of Escherichia coli while sediment and swab samples were placed directly on these plates. The plates were incubated at 44°C for the selective isolation of thermophilic Naegleria. To identify the Naegleria isolates the internal transcribed spacers, including the 5.8S rDNA, were amplified by polymerase chain reaction and the sequence of the PCR products was determined. Thermophilic amoebae were present at nearly all collection sites. The pathogenic N. fowleri was the most frequently encountered thermophilic species followed by N. lovaniensis. The concentration of N. fowleri was rather low in most water samples, ranging from 0 to 22 per liter. Sequencing revealed that all N. fowleri isolates belonged to a common Euro-American genotype, the same as detected in the human case in Guadeloupe. These investigations need to be continued in order to counsel the health authorities about prevention measures, because these recreational thermal baths are used daily by local people and tourists.
ISSN: 1932-6203

pasteur-00782031
https://hal-riip.archives-ouvertes.fr/pasteur-00782031
https://hal-riip.archives-ouvertes.fr/pasteur-00782031/document
https://hal-riip.archives-ouvertes.fr/pasteur-00782031/file/article_naegleria_plos_one.pdf
DOI : 10.1371/journal.pone.0054414

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Tsavorite, the vanadian variety of green grossular, is a high value economic gemstone. It is hosted exclusively in the metasedimentary formations from the Neoproterozoic Metamorphic Mozambique Belt. The deposits are mined in Kenya, Tanzania and Madagascar and other occurrences are located in Pakistan and East Antarctica. They are located within metasomatized graphitic rocks such as graphitic gneiss and calc-silicates, intercalated with meta-evaporites. Tsavorite is found as primary deposits either in nodule (type I) or in quartz vein (type II), and in placers (type III). The primary mineralizations (types I and II) are controlled by lithostratigraphy and/or structure. For the African occurrences, the protoliths of the host-rocks were deposited at the beginning of the Neoproterozoic within a marine coastal sabkha environment, located at the margin of the Congo-Kalahari cratons in the Mozambique Ocean. During the East African-Antarctican Orogeny, the rocks underwent high amphibolite to granulite facies metamorphism and the formation of tsavorite deposits occurred between 650 and 550 Ma. The nodules of tsavorite were formed during prograde metamorphism, calcium coming from sulphates and carbonates, whereas alumina, silicates, vanadium and chromium probably came from clays and chlorite. The veins were formed during the deformation of the metasedimentary platform units which experienced shearing, leading to the formation of fault-filled veins. Metasomatism developed during retrograde metamorphism. The metasedimentary sequences are characterized by the presence of evaporitic minerals such as gypsum and anhydrite, and scapolite. Evaporites are essential as they provide calcium and permit the mobilization of all the chemical elements for tsavorite formation. The H2S-S8 metamorphic fluids characterized in primary fluid inclusions of tsavorites and the δ11B values of coeval dravite confirm the evaporitic origin of the fluids. The V2O3 and Cr2O3 contents of tsavorite range respectively from 0.05 to 7.5 wt.%, while their δ18O values are in the range of 9.5-21.1‰. The genetic model proposed for tsavorite is metamorphic, based on chemical reactions developed between an initial assemblage composed of gypsum and anhydrite, carbonates and organic matter deposited in a sabkha-like sedimentary basin.
ISSN: 0169-1368

hal-00853279
https://hal.archives-ouvertes.fr/hal-00853279
DOI : 10.1016/j.oregeorev.2013.01.016