Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699
Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted consequences. With the purpose to identify and quantify crop-wild gene flow in chicory, we analysed introgression in 19 wild chicory populations and 16 accessions of chicory varieties and landraces distributed across Northern, Central and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North-South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin. The results indicated, however, that the structuring between the two groups of wild and cultivated types was weak. As crop and wild recipients are genetically close and genes are transferred between the two types rather frequently, focus on mitigating crop-wild gene flow should be increased, before transgenic varieties are cultivated openly.
ISSN: 0925-9864

hal-01032184
https://hal.archives-ouvertes.fr/hal-01032184
DOI : 10.1007/s10722-008-9375-1

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
TMPRSS2/ERG fusion resulting in ERG overexpression occurs in 30 to 50% of prostate cancer (PCa) in Caucasian patients, but its prognostic relevance remains controversial. In the present study, we investigated ERG expression in all stages of PCa progression, and evaluated the prognostic impact of ERG status in clinically localized PCa (CLC) and in castration resistant disease (CRPC). ERG and AR expressions were evaluated by immunohistochemistry on tissue microarrays containing samples of high grade PIN (n = 57), CLC surgically treated (n = 299, including 185 Caucasians and 114 African-Caribbeans), metastases (n = 17), and CRPC (n = 41). In Caucasians, ERG expression significantly increased from high grade PIN (17.5%) to pT2 (27%) and pT3 CLC (43%), then to metastases (53%). In CLC, stainings for ERG and AR were correlated, and ERG expression was less frequent in African-Caribbeans compared to Caucasians (11.5% vs. 33%). In Caucasians CLC, ERG was associated with longer recurrence free survival, after adjusting for classical prognostic markers. In CRPC, ERG was expressed in 29% of cases, and was associated with a longer overall survival. Our results confirm that ERG expression is less frequent in PCa from patients of African descent. Although ERG expression increases during PCa natural history, positive ERG status is associated with better outcome in both CLC and CRPC. This paradox could be explained in part by the fact that ERG expression is AR dependant, then ERG positive cancers are likely to progress in a rich androgen environment, with a better response to androgen suppression.
ISSN: 0270-4137

hal-01118555
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118555
DOI : 10.1002/pros.22863
PUBMED : 25175352

Éditeur(s) : HAL CCSD
Résumé : The present study addresses the question of increasing need in water supply. One line of research consists in investigating karst aquifers that represent significant water supplies for the areas around the Mediterranean. This work aims at developing a methodology of predictive evaluation of karst distribution and karst thickness within the carbonate massifs. It is based on the study of the Tethysian carbonate platform from the area of Montpellier, South of France. This area underwent a polyphased, complex, tectonic evolution, involving successive karst forming events. The approach is based on the relationships between eustacy and geodynamics, on one hand, and base-level variation recorded within palaeokarsts, on the other hand. Sedimentary fill of palaeokarsts allows to identify distinct karstification phases and sometimes to date them. It is a marker of base-level variations, which we attempt to quantify, that is responsible for karst formation and karst filling and sealing. For three palaeokarsts of regional extent, we analyze : karst sedimentary-fill, the distribution along upstream-downstream profile, the vertical extension of palaeokarsts, indicative of the base-level lowering. - The " Bauxite palaeokarst " results from the two-stage evolution of the " Isthme Durancien " : i) Bauxitic weathering of the Neocomian cover over the southern Massif Central , related to an inversion during Barremian ; ii) ≥1600 m uplift and exhumation during Aptian-Albian, inducing erosion of alterites, upstream, and deposition of detrital bauxites, downstream. - The " Early Paleocene palaeokarsts with marine sedimentary-fill " indicate base level variations of more than 350m in the upstream area. It is suggested here that such base-level variations, exceeding eustacy and recorded in tabular undeformed series, result from desiccation-flooding events in an endoreic silled basin. - The " Miocene palaeokarst with Cevennes-sourced sediment-fill " records a Serravalian-Tortonian base-level drop, depicted by canyon incision in the hinterland of the Gulf of Lion Margin. Uplift values of ≥ 400m upstream, about 250m in an intermediate area and 10's of m downstream, are measured. The present 3D geometry and distribution of carbonate massifs (exposed and covered) are modeled in the study area, from the Cevennes to the Mediterranean. The 3D geological model integrates seismic reflection, borehole and gravimetric data. Tectonic restoration of a N-S section, extracted from the 3D model, allows to reconstruct paleo-base-levels with respect with the carbonate massifs, at different stages of deformation and successive phases of karstification. The 3D paleo-flows through carbonates across the study area, are thus constrained, especially during the Messinian desiccation stage. Application of the results to hydrogeology leads to the following : - Uplift of upstream hinterland (Cretaceous, Miocene) produces large amplitude karsts, but they do not make significant reservoirs. - Karstification responsible for the development of important and deep karst reservoirs is related to desiccation of endoreic basins (early Paleocene and Messinian). - Theses two events have produced two main deep karst reservoirs, with a gravimetric signature : (1) Upstream of Montpellier Thrust, between Pic St Loup, Les Matelles Fault and Hérault Basin, a deep karsts developed over 900m thickness in the Malm limestone, during Paleocene. (2) Downstream (south) of Montpellier Thrust, the coastal karsts extend offshore over more than 10km, they are sealed by a thick Miocene to Quaternary cover, and they result from the Messinian event.
Cette étude s'inscrit dans un contexte de demande croissante en ressources en eau, conduisant à mieux contraindre et estimer la distribution des aquifères karstifiés qui représentent une ressource importante, notamment sur le pourtour méditerranéen. Le but de ce travail est d'élaborer une méthode prédictive de la distribution de la karstification et de l'épaisseur de massifs carbonatés karstifiés, notamment pour les karsts profonds. La méthodologie est développée à partir de l'étude des karsts de la plateforme carbonatée téthysienne du Languedoc montpelliérain; région qui a subi une histoire tectonique complexe et polyphasée, entrainant des phases de karstification successives. Elle est basée sur la compréhension des relations entre eustatisme, géodynamique et niveau de base, enregistrées par les paléokarsts de la région. Le remplissage sédimentaire des paléokarsts permet d'identifier les épisodes de karstification et de les dater ; c'est un marqueur des variations -que l'on cherche à quantifier- du niveau de base local responsable de la formation et du comblement des karsts. On analyse 3 paléokarsts d'extension régionale dont on peut étudier : le remplissage karstique, la distribution le long de profils amont-aval et l'extension verticale indicatrice de l'amplitude de l'abaissement du niveau de base dont il est issu. On en déduit les causes géodynamiques à l'origine de leur formation: - Le " paléokarst des bauxites " à remplissage caractéristique, résulte de l'évolution en 2 phases de " l'Isthme Durancien " : altération bauxitique de la couverture néocomienne sur le sud du Massif Central, liée à une inversion au Barrémien, suivi d'une surrection ≥ 1600m à l'Aptien-Albien, causant l'érosion des altérites en amont et le dépôt des bauxites détritiques en aval. - Le " paléokarst à remplissage marin paléocène inférieur " indique des variations du niveau de base local ≥350m dans la zone amont sud-cévenole. On propose que ces variations de niveau de base d'amplitude très supérieures aux variations eustatiques et dans une zone faiblement déformée, résultent d'assèchements et d'ennoiements d'un bassin endoréique à seuil. - Le " paléokarst à remplissage détritique d'origine cévenole ", enregistre la chute du niveau de base au Serravalien-Tortonien, qui se traduit par l'incision de canyons dans l'arrière-pays de la marge du Golfe du Lion. On détermine une surrection de plus de 400 mètres à l'amont, près de 250m dans les blocs faillés intermédiaires et quelques dizaines de mètres dans la zone avale. En parallèle, on établit la géométrie et la distribution actuelles des massifs carbonatés dans la zone d'étude (y compris sous couverture), en construisant un modèle géologique 3D, des Cévennes à la Méditerranée. On intègre les données de sismique réflexion, de forages et les données gravimétriques. La restauration tectonique séquentielle d'une coupe Nord-Sud extraite du modèle géologique permet d'appréhender la position des paléo-niveaux de base par rapport aux massifs carbonatés, pour chaque époque de karstification. On déduit l'organisation 3D des paléo-écoulements à travers la géométrie complexe des massifs carbonatés languedociens, notamment pendant l'évènement messinien. En terme d'évaluation de la ressource en eau, on déduit que: - Les surrections de l'arrière-pays (Crétacé " moyen ", Miocène) produisent des karsts de grande amplitude, mais ne constituent pas de réservoirs significatifs. - La karstification à l'origine de réservoirs exploitables importants et profonds est créée par l'assèchement de bassins endoréiques, qui ont affecté la région au Paléocène inférieur et au Messinien . - Ces deux évènements sont à l'origine de deux principaux réservoirs karstiques profonds qui ont une signature gravimétrique : (1) En amont du chevauchement de Montpellier, entre le Pic Saint Loup, la faille des Matelles et le bassin de l'Hérault, le karst profond se développe sur une épaisseur atteignant 900m, et est attribuée à l'événement du Paléocène. (2) Au Sud du chevauchement de Montpellier les karsts côtiers s'étendent jusqu'à plus de 10 km au large, scellés par une épaisse couverture Miocène et Plio-Quaternaire, et résultent de l'événement Messinien.
https://tel.archives-ouvertes.fr/tel-00936257

tel-00936257
https://tel.archives-ouvertes.fr/tel-00936257
https://tel.archives-ouvertes.fr/tel-00936257/document
https://tel.archives-ouvertes.fr/tel-00936257/file/thA_se_husson_couleurs.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Background Experimental evidence suggests that developmental exposure to persistent organic pollutants (POP) and to some non persistent pesticides may disrupt metabolic regulation of glucose metabolism and insulin secretion, and thereby contribute to the current epidemic of obesity and metabolic disorders. Quasi-experimental situations of undernutrition in utero have provided some information. However, the evidence in humans concerning the role of the prenatal environment in these disorders is contradictory, and little is known about long-term outcomes, such as type 2 diabetes, of prenatal exposure. Objectives Our aim was to evaluate the effects of prenatal exposure to POP and organophosphate pesticides on fetal markers of glucose metabolism in a sample of newborns from the Pelagie mother–child cohort in Brittany (France). Methods Dialkylphosphate (DAP) metabolites of organophosphate pesticides were measured in maternal urine collected at the beginning of pregnancy. Cord blood was assayed for polychlorinated biphenyl congener 153 (PCB153), p,p′-dichlorodiphenyl dichloroethene (DDE) and other POP. Insulin and adiponectin were determined in cord blood serum (n=268). Results A decrease in adiponectin and insulin levels was observed with increasing levels of DDE, but only in girls and not boys. Adiponectin levels were not related to the concentrations of other POP or DAP metabolites. Decreasing insulin levels were observed with increasing PCB153 concentrations. Insulin levels increased with DAP urinary levels. Additional adjustment for BMI z-score at birth modified some of these relations. Conclusions Our observations bring support for a potential role of organophosphate pesticides and POP in alterations to glucose metabolism observable at birth
ISSN: 0013-9351

hal-01259218
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01259218
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01259218/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01259218/file/Prenatal%20exposure%20to%20persistent%20organic%20pollutants%20and%20organophosphate%20pesticides%2C%20and%20markers%20of%20glucose%20metabolism%20at%20birth.pdf
DOI : 10.1016/j.envres.2016.01.005

Éditeur(s) : HAL CCSD American Association of Petroleum Geologists
Résumé : International audience
We describe the structure, microstructure, and petrophysical properties of fault rocks from two normal fault zones formed in low-porosity turbiditic arkosic sandstones, in deep diagenesis conditions similar to those of deeply buried reservoirs. These fault rocks are characterized by a foliated fabric and quartz-calcite sealed veins, which formation resulted from the combination of the (1) pressure solution of quartz, (2) intense fracturing sealed by quartz and calcite cements, and (3) neoformation of synkinematic white micas derived from the alteration of feldspars and chlorite. Fluid inclusion microthermometry in quartz and calcite cements demonstrates fault activity at temperatures of 195degC to 268degC. Permeability measurements on plugs oriented parallel with the principal axes of the finite strain ellipsoid show that the Y axis (parallel with the foliation and veins) is the direction of highest permeability in the foliated sandstone (10-2 md for Y against 10-3 md for X, Z, and the protolith, measured at a confining pressure of 20 bars). Microstructural observations document the localization of the preferential fluid path between the phyllosilicate particles forming the foliation. Hence, the direction of highest permeability in these fault rocks would be parallel with the fault and subhorizontal, that is, perpendicular to the slickenlines representing the local slip direction on the fault surface. We suggest that a similar relationship between kinematic markers and fault rock permeability anisotropy may be found in other fault zone types (reverse or strike-slip) affecting feldspar-rich lithologies in deep diagenesis conditions.
ISSN: 0149-1423

hal-00903428
https://hal.archives-ouvertes.fr/hal-00903428
DOI : 10.1306/03071312127

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Mosha and North Tehran faults correspond to the nearest seismic sources for the northern part of the Tehran megacity. The present-day structural relationships and the kinematics of these two faults, especially at their junction in Lavasanat region, is still a matter of debate. In this paper, we present the results of a morphotectonic analysis (aerial photos and field investigations) within the central part of the Mosha and eastern part of the North Tehran faults between the Mosha valley and Tehran City. Our investigations show that, generally, the traces of activity do not follow the older traces corresponding to previous long-term dip-slip thrusting movements. The recent faulting mainly occurs on new traces trending E-W to ENE-WSW affecting Quaternary features (streams, ridges, risers, and young glacial markers) and cutting straight through the topography. Often defining en-echelon patterns (right- and left-stepping), these new traces correspond to steep faults with either north- or south-dipping directions, along which clear evidences for left-lateral strike-slip motion are found. At their junction zone, the two sinistral faults display a left-stepping en-echelon pattern defining a positive flower structure system clearly visible near Ira village. Further west, the left-lateral strike-slip motion is transferred along the ENE-WSW trending Niavaran fault and other faults. The cumulative offsets associated with this left-lateral deformation is small compared with the topography associated with the previous Late Tertiary thrusting motion, showing that it corresponds to a recent change of kinematics.
ISSN: 0040-1951

hal-00617778
https://hal.archives-ouvertes.fr/hal-00617778
DOI : 10.1016/j.tecto.2010.09.013

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Longmen Shan range is one of the major topographic and structural features of the easternmargin of the Tibetan Plateau. With an impressive topographic gradient and low convergence rates across the range this region has raised important questions concerning the dynamics of plateaumargin settings, such as the long-term mechanisms of topographic evolution. The investigation of the distribution in space and time of denudation can provide critical insight into such dynamics and shed light on still unresolved controversies. For that purpose, we present a new dataset that documents the intensity and distribution of denudation processes across this plateaumargin through field survey of fluvial incision markers, quantitative geomorphology and cosmogenic nuclide derived basin-wide erosion rates. Erosion is < 0.5 mm/year in the frontal region of the Longmen Shan and between 0.5 and 1 mm/year further west, with a gradual decrease when reaching the northern headwaters of the Min Jiang watershed, adjacent to the beginning of the Tibetan Plateau. The spatialdistribution of denudation inferred from the various methods we use suggests that most of the differential uplift in the Central Longmen Shan is accommodated by the Beichuan Fault and frontal structures located in the foothills. The denudation pattern seems also to reflect the large-scale propagation of erosion from the Sichuan Basin toward the Plateau. This suggests that the Longmen Shan range is submitted to the combined influences of slow thrusting activity on the frontal structures and progressive westward regressiveerosion as a probable response to a pulse of uplift of the Tibetan PlateauEasternmargin, that started 10 Ma ago.
ISSN: 0040-1951

hal-01564192
https://hal.archives-ouvertes.fr/hal-01564192
DOI : 10.1016/j.tecto.2009.10.026

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Macrophages (MΦ), well-known to play an important role in immune response, also respond to environmental toxic chemicals such as diesel exhaust particles (DEP). Potential effects of DEPs towards MΦ polarization, a key hall-mark of MΦ physiology, remain however poorly documented. This study was therefore designed to evaluate the effects of a reference DEP extract (DEPe) on human MΦ polarization. Human blood monocytes-derived MΦ were incubated with IFNγ+LPS or IL-4 to obtain M1 and M2 subtypes, respectively; a 24 h exposure of polarizing MΦ to 10 μg/ml DEPe was found to impair expression of some macrophagic M1 and M2 markers, without however overall inhibition of M1 and M2 polarization processes. Notably, DEPe treatment increased the secretion of the M1 marker IL-8 and the M2 marker IL-10 in both MΦ subtypes, whereas it reduced lipopolysaccharide-induced IL-6 and IL-12p40 secretion in M1 MΦ. In M2 MΦ, DEPe exposure led to a reduction of CD200R expression and of CCL17, CCL18 and CCL22 secretion, associated with a lower chemotaxis of CCR4-positive cells. DEPe activated the Nrf2 and AhR pathways and induced expression of their reference target genes such as Hmox-1 and cytochrome P-4501B1 in M1 and M2 MΦ. Nrf2 or AhR silencing through RNA interference prevented DEPe-related down-regulation of IL-6. AhR silencing also inhibited the down-secretion of IL-12p40 and CCL18 in M1- and M2-DEPe-exposed MΦ, respectively. DEPs are therefore likely to alter expression of some M1 and M2 markers in an AhR- and Nrf2-dependent manner; such regulations may contribute to deleterious immune effects of atmospheric DEP.
ISSN: 1932-6203

hal-01122723
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122723
PUBMED : 25710172
DOI : 10.1371/journal.pone.0116560

Éditeur(s) : Elsevier
Résumé : Genetic variation was surveyed at 11 microsatellite loci and at 517 bp of the mitochondrial control region to investigate the presence of genetic stock structure in swordfish (Xiphias gladius) in four proximal localities of the southwest Indian Ocean. One aim of this study was to serve as a preliminary examination for congruency of structure detected by these two genetic markers, prior to conducting a more comprehensive basin-wide survey of the Indian Ocean and nearby surrounding areas. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences both revealed a great homogeneity between samples. Genetic diversity detected at the regional scale was not significantly higher than detected at the local scale. Results suggest that the southwest Indian Ocean globally functions as a unique panmictic population. However, some discrete genetic differences appeared that could possibly indicate influence from a second genetic pool in the northern part of the Indian Ocean. This structure appeared to be sex-dependent with genetic differences higher among female than among male samples. This result may indicate a higher level of spawning area fidelity for females with a subsequent sampling bias tending to homogenise male genotypic distributions. (c) 2009 Elsevier B.V. All rights reserved.
Fisheries Research (0165-7836) (Elsevier), 2009-05 , Vol. 97 , N. 3 , P. 263-269

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6455.pdf
DOI:10.1016/j.fishres.2009.03.004
http://archimer.ifremer.fr/doc/00000/6455/

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Cytochrome P450 aromatase (P450arom; aromatase) is a microsomal enzyme involved in the production of endogeneous sex steroids by converting testosterone into oestradiol. Aromatase is the product of the cyp19a1 gene and plays a crucial role in the sexual differentiation of the brain and in the regulation of reproductive functions. In the brain of mammals and birds, expression of cyp19a1 has been demonstrated in neuronal populations of the telencephalon and diencephalon. By contrast, a wealth of evidence established that, in teleost fishes, aromatase expression in the brain is restricted to radial glial cells. The present study investigated the precise neuroanatomical distribution of cyp19a1 mRNA during brain development in Xenopus laevis (late embryonic to juvenile stages). For this purpose, we used in situ hybridisation alone or combined with the detection of a proliferative (proliferating cell nuclear antigen), glial (brain lipid binding protein, Vimentin) or neuronal (acetylated tubulin; HuC/D; NeuroβTubulin) markers. We provide evidence that cyp19a1 expression in the brain is initiated from the very early larval stage and remains strongly detected until the juvenile and adult stages. At all stages analysed, we found the highest expression of cyp19a1 in the preoptic area and the hypothalamus compared to the rest of the brain. In these two brain regions, cyp19a1-positive cells were never detected in the ventricular layers. Indeed, no co-labelling could be observed with radial glial (brain lipid binding protein, Vimentin) or dividing progenitors (proliferating cell nuclear antigen) markers. By contrast, cyp19a1-positive cells perfectly matched with the distribution of post-mitotic neurones as shown by the use of specific markers (HuC/D, acetylated tubulin and NeuroβTubulin). These data suggest that, similar to that found in other tetrapods, aromatase in the brain of amphibians is found in post-mitotic neurones and not in radial glia as reported in teleosts.
ISSN: 0953-8194

hal-00994513
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00994513
DOI : 10.1111/jne.12142
PUBMED : 24612124

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : No efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary. We developed a method to compare genome-wide diversity estimates while taking into account-and factoring out-variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels. An approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers. RaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots. RaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms).
ISSN: 1286-4560

hal-01032413
https://hal.archives-ouvertes.fr/hal-01032413
DOI : 10.1007/s13595-013-0302-z

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01224215
http://hal.upmc.fr/hal-01224215
http://hal.upmc.fr/hal-01224215/document
http://hal.upmc.fr/hal-01224215/file/Genome%20Biol%20Evol-2015-Boon-505-21.pdf
DOI : 10.1093/gbe/evv002

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting. The ISME Journal (2012) 6, 2199-2218; doi:10.1038/ismej.2012.84; published online 2 August 2012
ISSN: 1751-7362

hal-01546179
https://hal.archives-ouvertes.fr/hal-01546179
DOI : 10.1038/ismej.2012.84

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Tyrrhenian Sea is usually interpreted to be a Neogene back-arc basin that opened by continental rifting and oceanic spreading caused by the eastward migration of the Apennine subduction system during Miocene and Pliocene times. Rifting of the southern Tyrrhenian Sea started first along the Eastern Sardinian margin during the middle to late Miocene times, including the Messinian. The "METYSS" project aims at better constraining the relationships between crustal tectonics, salt tectonics and sedimentation from Messinian times to present-day. The "METYSS 1" cruise (2009) allowed to acquire about 1200 km of HR seismic-reflection profiles along the Eastern Sardinian margin, Western Tyrrhenian Sea. This data set clearly illustrates that this area has been highly dissected during the rifting stage by N-S trending normal faults delineating ridges and basins, as previously described. The Messinian seismic markers (UU and MU) locally display fan-shaped stratal geometries, but the mechanism responsible for such geometries, salt tectonics or rifting, has yet to be carefully deciphered. We also mapped the spatial distribution of the mobile salt. The highly variable thickness of the small confined salt basins may be related to the initial pre-Messinian basin geometry, to the fact that salt deposition was syn-rift or to salt movement. Southeastward, salt tectonics is vigorous in unconfined basins and appears to have started early during the UU deposition. More surprisingly, our data demonstrate that some of the major faults have been significantly reactivated during the post-rift period, up to late Quaternary time, as shown by bathymetric scarps and associated debris flows. Moreover, some of this post-rift deformation can be evidenced within the Plio-Quaternary sequence by a regional unconformity. The post-Miocene deformation style varies greatly between different areas of the margin, and can also be strongly influenced by the presence or absence of mobile Messinian salt.
ISSN: 0040-1951

hal-00996665
https://hal.archives-ouvertes.fr/hal-00996665
DOI : 10.1016/j.tecto.2013.12.015

Éditeur(s) : Colloque IMBC - International Marine Biotechnology Conference
Résumé : Since 1997, a new pathology seasonally occurs in new caledonian shrimp farms during the warm season. Diseased Litopenaeus stylirostris shrimp suffer from a systemic vibriosis which was attributed to highly pathogenic Vibrio nigripulchritudo. At the present time, only two farms among 17 are affected by the so called "summer syndrome". In such a context it appears urgent to develop reliable diagnostic tools to detect V. nigripulchritudo strains and to differentiate highly virulent strains from non virulent ones in order to understand the mechanisms of infection and overcome disease spreading. Multilocus Sequencing Typing (MLST) analysis on 24 bacterial strains isolated in geographically distinct shrimp farms highlighted the existence of a cluster A containing only strains displaying moderate to high virulence. Since experimental infection procedure for virulence status determination is material intensive and time consuming, and MLST method not accurate enough to inform on the virulence status of strains, it appeared of great interest to develop other diagnostic tools. Two phylogenetically closed strains, one highly virulent SFn1 and the other non-virulent SFn118 were selected in order to characterize genes specific of the virulent strain by Substractive Suppression Hybridization (SSH). Firstly, a total of 622 DNA fragments specific of SFn1 were sequenced, characterized and further used as probes in a DNA macroarray. Testing 24 strains, hybridization profiles were found to be strongly correlated with both MLST genotypes and bacterial virulence status. A total of 96 representative probes were secondly selected to validate macroarray results on 34 more additionnal strains, allowing identification of genetic markers of virulence. Most of DNA fragments specific of highly virulent strains associated to summer syndrome were found to be bore by a plasmid successfully isolated in the laboratory. In next future, these results would permit the development of relevant diagnostic tools useful for accurate epidemiological survey of the summer syndrome.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/acte-3398.pdf
http://archimer.ifremer.fr/doc/00000/3398/

Éditeur(s) : Springer
Résumé : The great fecundity and very high larval mortality of most marine invertebrates and fish make possible substantial variance in the number of offspring contributed by adults to subsequent generations. The reproductive success of such organisms may thus resemble a sweepstakes lottery, in which a minority of progenitors succeeds in replacing an entire population, while the majority fails to procreate. One specific prediction of this hypothesis, that genetic diversity of newly settled cohorts should be less than that of the adult population, is tested in the present study. Microsatellite DNA markers were examined in naturally spawned juvenile European flat oysters Ostrea edulis (L.), collected over a 12-day period in 1993 from the western Mediterranean Sea, near Sete, France (43 degrees 32'N, 3 degrees 56'E) and grown out for a period of up to 10 months. Variation in these juveniles was compared to that in a pooled sample of adults collected in 1994 from two locations (Thau Lagoon and Port St. Louis) that had statistically homogeneous allelic frequencies. Though nearly twice as large as the pooled adult sample, the juvenile sample had only 60% of the adult allelic diversity. Analyses of linkage disequilibrium and kinship, as well as estimation of the effective number of parents, suggested that 10-20 adults produced this juvenile cohort. This observation supports the hypothesis of sweepstakes reproductive success and suggests that partial inbreeding may occur even in species with large populations and dispersing planktonic larvae.
Marine Biology (0025-3162) (Springer), 2007-03 , Vol. 150 , N. 6 , P. 1173-1182

Droits : 2007 Springer
http://archimer.ifremer.fr/doc/2007/publication-2616.pdf
DOI:10.1007/s00227-006-0441-y
http://archimer.ifremer.fr/doc/00000/2616/

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
Centropyge bispinosa is one of the most frequently coral reef fish exported through the aquarium trade. We developed fifteen microsatellite markers to evaluate possible distinct breeding stocks throughout its Indo-Pacific distribution range. Number of alleles varied from 2 to 50 per locus, observed and expected heterozygosities ranged from 0.486 to 0.953 and 0.482 to 0.974 respectively. Significant deviations from HWE were detected in two loci. Cross-amplifications were tested in four congener species: C. loriculus, C. bicolor, C. flavissima and C. vroliki. The 15 new microsatellite loci will be helpful tools for the identification of breeding units, connectivity studies, as well as phylogenetic relationships among pygmy angelfishes.
ISSN: 1877-7252

hal-01341716
https://hal-univ-perp.archives-ouvertes.fr/hal-01341716
DOI : 10.1007/s12686-014-0363-9

Éditeur(s) : HAL CCSD Ferrata Storti Foundation
Résumé : International audience
BackgroundRecent evidence suggests that autonomic nervous system activity could be involved in thepathophysiology of sickle cell disease, but it is unclear whether differences in autonomic nervoussystem activity are detectable during steady state in patients with mild and severe disease.The aim of the present study was to compare the autonomic nervous system activity, bloodrheology, and inflammation in patients with sickle cell anemia according to the frequency ofacute pain crisis.Design and MethodsTwenty-four healthy volunteers, 20 patients with sickle cell anemia with milder disease, and15 patients with sickle cell anemia with more severe disease were recruited. Milder disease wasdefined as having no pain crisis within the previous year. More severe disease was defined ashaving had within the previous year three or more pain crises which were documented by aphysician and required treatment with narcotics. The autonomic nervous system activity wasdetermined by spectral analysis of nocturnal heart rate variability. Blood viscosity determinationand measurements of several inflammatory markers (interleukin-6, soluble vascular celladhesion molecule-1, soluble CD40 ligand and sL-selectin) were made on blood samples collectedin steady-state conditions.ResultsResults showed that: 1) patients who had suffered more frequent pain crises had lowerparasympathetic activity and greater sympatho-vagal imbalance than both controls andpatients with milder disease. However, when adjusted for age, no significant difference wasdetected between the two sickle cell anemia patient groups; 2) patients who had suffered morefrequent pain crises had higher blood viscosity than patients with milder disease, and this wasnot dependent on age.ConclusionsResults from the present study indicate that both the autonomic nervous system activity andblood viscosity are impaired in patients with sickle cell anemia exhibiting high frequency ofpain crisis in comparison with those who did not experience a crisis within the previous year.
ISSN: 0390-6078

hal-01163973
https://hal.univ-antilles.fr/hal-01163973
DOI : 10.3324/haematol.2011.047365

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Pituitary adenomas are currently classified by histological, immunocytochemical and numerous ultrastructural characteristics lacking unequivocal prognostic correlations. We investigated the prognostic value of a new clinicopathological classification with grades based on invasion and proliferation. This retrospective multicentric case-control study comprised 410 patients who had surgery for a pituitary tumour with long-term follow-up. Using pituitary magnetic resonance imaging for diagnosis of cavernous or sphenoid sinus invasion, immunocytochemistry, markers of the cell cycle (Ki-67, mitoses) and p53, tumours were classified according to size (micro, macro and giant), type (PRL, GH, FSH/LH, ACTH and TSH) and grade (grade 1a: non-invasive, 1b: non-invasive and proliferative, 2a: invasive, 2b: invasive and proliferative, and 3: metastatic). The association between patient status at 8-year follow-up and age, sex, and classification was evaluated by two multivariate analyses assessing disease- or recurrence/progression-free status. At 8 years after surgery, 195 patients were disease-free (controls) and 215 patients were not (cases). In 125 of the cases the tumours had recurred or progressed. Analyses of disease-free and recurrence/progression-free status revealed the significant prognostic value (p < 0.001; p < 0.05) of age, tumour type, and grade across all tumour types and for each tumour type. Invasive and proliferative tumours (grade 2b) had a poor prognosis with an increased probability of tumour persistence or progression of 25- or 12-fold, respectively, as compared to non-invasive tumours (grade 1a). This new, easy to use clinicopathological classification of pituitary endocrine tumours has demonstrated its prognostic worth by strongly predicting the probability of post-operative complete remission or tumour progression and so could help clinicians choose the best post-operative therapy.
ISSN: 0001-6322

hal-00875723
https://hal.archives-ouvertes.fr/hal-00875723
DOI : 10.1007/s00401-013-1084-y
PUBMED : 23400299

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : National audience
The sources of exposure during diseases due to Aspergillus fungi in cystic fibrosis patients are still poorly explored. We assessed home fungal exposure in patients suffering from cystic fibrosis and analysed its impact on the presence of Aspergillus biological markers, the colonisation of airways, as well as the sensitization and Aspergillus serology. Between March 2012 and August 2012, 34 patients benefited from a visit performed by a home environment medical adviser including sampling for mycological analysis. The number of colonies of Aspergillus was not significantly different in the various sampling sites (P = 0.251), but the number of non-Aspergillus colonies was much higher in the kitchen (P = 0.0045). Subsequently, home fungal exposure was compared between the groups “absence of Aspergillus-related markers” and “presence of Aspergillus-related markers”. Home exposure to Aspergillus (P = 0.453) and non-Aspergillus (P = 0.972) flora was not significant between the 2 groups. Within this series of 34 patients that should be expanded, we note an absence of clear relationship between home exposure and the Aspergillus-linked markers in patients suffering from cystic fibrosis. This result should be taken into account regarding too restrictive hygiene advices provided to families, given the fact that fungal exposure can also results from activities performed away from home.
La source d’exposition au cours des pathologies aspergillaires du patient atteint de mucoviscidose reste encore peu explorée. Nous avons évalué l’exposition fongique domiciliaire chez des patients atteints de mucoviscidose, et analysé son impact sur la présence de marqueurs biologiques aspergillaires, colonisation des voies aériennes, ainsi que sensibilisation et sérologie anti-aspergillaire. Trente-quatre patients ont bénéficié d’une visite par un conseiller médical en environnement intérieur entre mars et août 2012, comprenant des prélèvements à visée mycologique. Le nombre de colonies aspergillaires ne différait pas significativement d’un site de prélèvement à l’autre (p = 0,251), mais le nombre de colonies non aspergillaires était significativement plus important dans la cuisine (p = 0,0045). L’exposition fongique domiciliaire a ensuite été comparée entre les groupes « marqueurs aspergillaires absents » et « marqueurs aspergillaires présents ». L’exposition domiciliaire à une flore aspergillaire (p = 0,453) et non aspergillaire (p = 0,972) ne différait pas significativement entre les 2 groupes. Sur cette série de 34 patients qui mérite d’être élargie, on note une absence de lien évident entre l’exposition domiciliaire et la pathologie aspergillaire. Ce résultat doit rendre prudent sur des conseils d’hygiène parfois très contraignants donnés aux familles, l’exposition fongique étant également importante dans le cadre des activités extra-domiciliaires.
ISSN: 1156-5233

hal-01158660
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01158660
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01158660/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01158660/file/Exposition%20domiciliaire%20aux%20moisissures%20postprint%20MYCMED-S-14-00173.pdf
DOI : 10.1016/j.mycmed.2015.03.005