Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : 4 pages
International audience
This article documents the addition of 268 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Alburnoides bipunctatus, Chamaerops humilis, Chlidonias hybrida, Cyperus papyrus, Fusarium graminearum, Loxigilla barbadensis, Macrobrachium rosenbergii, Odontesthes bonariensis, Pelteobagrus vachelli, Posidonia oceanica, Potamotrygon motoro, Rhamdia quelen, Sarotherodon melanotheron heudelotii, Sibiraea angustata, Takifugu rubripes, Tarentola mauritanica, Trimmatostroma sp. and Wallago attu. These loci were cross-tested on the following species: Alburnoides fasciatus, Alburnoides kubanicus, Alburnoides maculatus, Alburnoides ohridanus, Alburnoides prespensis, Alburnoides rossicus, Alburnoides strymonicus, Alburnoides thessalicus, Alburnoides tzanevi, Carassius carassius, Fusarium asiaticum, Leucaspius delineatus, Loxigilla noctis dominica, Pelecus cultratus, Phoenix canariensis, Potamotrygon falkneri, Trachycarpus fortune and Vimba vimba.
ISSN: 1755-098X

hal-00823716
https://hal.archives-ouvertes.fr/hal-00823716
DOI : 10.1111/1755-0998.12095
PUBMED : 23521844

Éditeur(s) : HAL CCSD Institute of Physics: Open Access Journals
Résumé : International audience
The Amazon river basin has been recently affected by extreme climatic events, such as the exceptional drought of 2005, with significant impacts on human activities and ecosystems. In spite of the importance of monitoring freshwater stored and moving in such large river basins, only scarce measurements of river stages and discharges are available and the signatures of extreme drought conditions on surface freshwater dynamics at the basin scale are still poorly known. Here we use continuous multisatellite observations of inundation extent and water levels between 2003 and 2007 to monitor monthly variations of surface water storage at the basin scale. During the 2005 drought, the amount of water stored in the river and floodplains of the Amazon basin was ~130 km3 (~70%) below its 2003-7 average. This represents almost a half of the anomaly of minimum terrestrial water stored in the basin as estimated using the Gravity Recovery and Climate Experiment (GRACE) data.
Environmental Research Letters

hal-00779275
https://hal.archives-ouvertes.fr/hal-00779275
https://hal.archives-ouvertes.fr/hal-00779275/document
DOI : 10.1088/1748-9326/7/4/044010

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

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

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
BACKGROUND: The use of pesticides and the related environmental contaminations can lead to human exposure to various molecules. In early-life, such exposures could be responsible for adverse developmental effects. However, human health risks associated with exposure to complex mixtures are currently under-explored. OBJECTIVE: THIS PROJECT AIMS AT ANSWERING THE FOLLOWING QUESTIONS: What is the influence of exposures to multiple pesticides on the metabolome? What mechanistic pathways could be involved in the metabolic changes observed? METHODS: Based on the PELAGIE cohort (Brittany, France), 83 pregnant women who provided a urine sample in early pregnancy, were classified in 3 groups according to the surface of land dedicated to agricultural cereal activities in their town of residence. Nuclear magnetic resonance-based metabolomics analyses were performed on urine samples. Partial Least Squares Regression-Discriminant Analysis (PLS-DA) and polytomous regressions were used to separate the urinary metabolic profiles from the 3 exposure groups after adjusting for potential confounders. RESULTS: The 3 groups of exposure were correctly separated with a PLS-DA model after implementing an orthogonal signal correction with pareto standardizations (R2 = 90.7% and Q2 = 0.53). After adjusting for maternal age, parity, body mass index and smoking habits, the most statistically significant changes were observed for glycine, threonine, lactate and glycerophosphocholine (upward trend), and for citrate (downward trend). CONCLUSION: This work suggests that an exposure to complex pesticide mixtures induces modifications of metabolic fingerprints. It can be hypothesized from identified discriminating metabolites that the pesticide mixtures could increase oxidative stress and disturb energy metabolism.
ISSN: 1932-6203

inserm-00863407
http://www.hal.inserm.fr/inserm-00863407
http://www.hal.inserm.fr/inserm-00863407/document
http://www.hal.inserm.fr/inserm-00863407/file/journal.pone.0064433.pdf
PUBMED : 23704985

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
ObjectivesTo compare the efficacy, in current clinical practice, of ă first regimens containing abacavir with lamivudine (ABC/3TC) or ă tenofovir with emtricitabine (TDF/FTC) in patients with baseline viral ă load 100000 HIV-1 RNA copies/mL. ă MethodsUsing a prospective cohort, we selected all patients starting a ă first HIV regimen based either on ABC/3TC or on TDF/FTC. The propensity ă score (PS) method was used to limit the indication bias due to the ă observational nature of the data. Adjusting and weighting methods via PS ă were used to compare the effectiveness of a first regimen containing ă ABC/3TC or TDF/FTC. The primary outcome was treatment failure by month ă 12 (M12). ă ResultsOverall, 2781 patients started an antiretroviral (ARV) regimen ă with ABC/3TC or TDF/FTC each in combination with efavirenz, boosted ă atazanavir or boosted darunavir. Among the 2472 uncensored patients ă before M12, 962 (39%) had a baseline viral load 100000 copies/mL of ă whom 294 were in treatment failure at or before M12. Our analyses showed ă no difference between ABC/3TC and TDF/FTC in the risk of treatment ă failure at M12 in patients starting an ARV regimen with a high viral ă load (100000 copies/mL). ă ConclusionsUsing a large prospectively collected cohort of patients ă seeking care in France, we found no evidence that ABC/3TC based regimens ă led to more failures than TDF/FTC based ones in patients with high ă baseline viral loads.
ISSN: 1464-2662

hal-01482656
https://hal.archives-ouvertes.fr/hal-01482656
DOI : 10.1111/hiv.12306

Éditeur(s) : HAL CCSD University of Arizona
Résumé : International audience
ISSN: 0033-8222

hal-00481872
https://hal.archives-ouvertes.fr/hal-00481872

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We describe an experimental system including monitoring of temperature, pressure, pH, oxidation reduction potential and optical density at 600 nm, designed for studying the role of microorganisms on the geological sequestration Of CO2 and its transformation into solid carbonate phases. Measurements were performed in an artificial ground water (AGW) supplemented with urea (2 g.l(-1)) and equilibrated at controlled temperatures with a gaseous phase before bacterial inoculation. We used the ureolytic strain Bacillus pasteurii as a model carbonate precipitating bacteria and showed that it can successfully promote strong pH increases by ureolysis in the AGW equilibrated with CO2 pressures of up to I bar. Increasing salinities (5.8,13.5 and 35.0 g.l(-1)) have a positive effect on the rate of pH increase, whereas the effect of increasing temperatures (30,35 and 38 degrees C) is less important. Calcium is also shown to have a specific positive influence on the rate of ureolysis. The number of viable cells present in solution decreases greatly during the carbonate precipitation event but the population partially recovers once precipitation is over.
ISSN: 0009-2541

hal-00445282
https://hal.archives-ouvertes.fr/hal-00445282
DOI : 10.1016/j.chemgeo.2008.12.012

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The southernmost part of the Ryukyu subduction, where the Philippine Sea Plate is subducting under the Eurasian Plate, is known to be a very seismically active region of transition from a north-dipping subduction along the Ryukyu subduction to an ~ SE-NW collision along the Taiwanese orogenic wedge. In this paper, we will focus on the Ryukyu forearc area close to Taiwan where the deformation is paroxysmal. In order to decipher the nature of the seismic deformation in this region, a three month passive experiment, combining 22 Ocean Bottom Seismometers and 51 onland stations, has been led. Starting from an a-priori heterogeneous model, we have obtained 801 well-located earthquake hypocenters, a precise P-wave tomography model and 14 focal mechanisms. The seismicity along the Ryukyu forearc is mainly located not only in the vicinity of the Interplate Seismogenic Zone (ISZ) but also within both the subducting PSP and the overriding plate. Seismicity within the upper-plate is essentially localized east of Nanao basin where NW-SE extension occurs, and northwest of the Hoping basin where strike-slip dominates. As revealed by both the P-wave velocity structure and the newly derived seismicity, we argue that a sub-vertical step offsetting the subducting PSP around 10 km may support the presence of a trench-parallel tear. The PSP also undergoes extension in its upper part that is probably caused by buckling and slab pull. The P-wave velocity structure reveals three other major features: (1) a continuity between the Central Range and the Ryukyu Arc with a shallower Moho (~ 30 km depth) between ~ 122.3°N and ~ 122.5°N along the Ryukyu Arc, (2) high P-wave velocities along the eastern side of the Central Range and, (3) two bodies with similar high crustal velocities (6.5-7.0 km/s) at 12-18 km depths, embedded within the Ryukyu arc basement, just north of Hoping Basin and north of the Nanao Basin.
ISSN: 0040-1951

hal-00795521
https://hal.archives-ouvertes.fr/hal-00795521
DOI : 10.1016/j.tecto.2012.04.011

Éditeur(s) : HAL CCSD Lippincott, Williams & Wilkins
Résumé : International audience
The aim of the study was to investigate the impact of first-line combined antiretroviral therapy (cART) regimen on the course of CD8 + T-cell counts in human immunodeficiency virus (HIV)-infected patients. A retrospective observational study conducted on the French DAT'AIDS Cohort of HIV-infected patients. We selected 605 patients initiating a first-line cART between 2002 and 2009, and which achieved a sustained undetectable HIV plasma viral load (pVL) for at least 12 months without cART modification. The evolution of CD8 + T-cell counts according to cART regimen was assessed. CD8 + T-cell counts were assessed in 572 patients treated with 2NRTIs+1PI/r (n= 297), 2NRTIs+1NNRTI (n= 207) and 3NRTIs (n= 68). In multivariate analysis, after 12 months of follow-up, the 3NRTIs regimen was associated with a significantly smaller decrease of CD8 + T-cell count compared with NNRTI-containing regimens (–10.2 cells/mL in 3NRTIs vs –105.1 cells/mL; P=0.02) but not compared with PI-containing regimens (10.2 vs –60.9 cells/mL; P=0.21). After 24 months, the 3NRTIs regimen was associated with a smaller decrease of CD8 + T-cell count and % compared with PI/r-and NNRTI-containing regimens (0.2 in 3NRTIs vs –9.9 with PI/r-regimens, P=0.001, and vs –11.1 with NNRTI-regimens, p < 0.0001). A focus analysis on 11 patients treated with an INSTI-containing cART regimen during the study period showed after 12 months of follow-up, a median decrease of CD8 + T-cell count of –155 [inter quartile range: –302; –22] cells/mL. Our data highlight the fact that cART regimens have differential effects on CD8 pool down regulation. Abbreviations: cART = combined antiretroviral therapy, HIV = human immunodeficiency virus, INSTI = integrase strand transfer inhibitor, NNRTI = non-nucleotide reverse transcriptase inhibitor, NRTI = nucleotide reverse transcriptase inhibitor, PI/r = Ritonavir-boosted protease inhibitor, pVL = plasma viral load.
ISSN: 0025-7974

inserm-01408002
http://www.hal.inserm.fr/inserm-01408002
http://www.hal.inserm.fr/inserm-01408002/document
http://www.hal.inserm.fr/inserm-01408002/file/2016%2C%20Poizot-Martin%20-%20First-line%20cART%20regimen%20impacts%20the%20course%20of%20CD8%2B%20T-cell%20counts%20in%20HIV-infected%20patients.pdf
DOI : 10.1097/MD.0000000000005087

Éditeur(s) : HAL CCSD American Society for Investigative Pathology
Résumé : International audience
Based on both experimental and clinical data, tamoxifen has been proposed to have cardiovascular benefits, although the mechanism(s) contributing to that protective effect are still poorly understood. In vitro experiments demonstrated that tamoxifen elicits its transcriptional effect through estrogen receptor (ER) α, but other targets can participate in its actions. However, although tamoxifen selectively activates the activating function (AF)-1 of ERα, we recently showed that this ERα subfunction is dispensable for the atheroprotective action of 17β-estradiol (E2), the main ligand of ERs. The goal of the present work is to determine to which extent ERα and its AF-1 mediate the vasculoprotective action of tamoxifen. Our data confirm that tamoxifen exerts an atheroprotective action on low density lipoprotein receptor (LDL-r(-/-)) female mice, but, in contrast to E2, it fails to accelerate reendothelialization after carotid electric injury. Tamoxifen and E2 elicit differences in gene expression profiles in the mouse aorta. Finally, the atheroprotective action of tamoxifen is abrogated in ERα(-/-)LDL-r(-/-) mice and in LDL-r(-/-) mice selectively deficient in ERαAF-1 (ERαAF-1(0/0)LDL-r(-/-)). Our results demonstrate, for the first time to our knowledge, that tamoxifen mediates its actions in vivo through the selective activation of ERαAF-1, which is sufficient to prevent atheroma, but not to accelerate endothelial healing.
ISSN: 0002-9440

hal-00874317
https://hal.archives-ouvertes.fr/hal-00874317
DOI : 10.1016/j.ajpath.2013.03.010
PUBMED : 23669343

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
The Convective and Orographically-driven Precipitation Study (COPS) carried out in summer 2007 over northeastern France and southwestern Germany provided a fairly comprehensive description of the low-troposphere water-vapour field, thanks in particular to the deployment of two airborne differential absorption lidar systems. These lidar observations were assimilated using the 3D-Var assimilation system of the Application of Research to Operations at MEsoscale (AROME) numerical weather prediction mesoscale model. The assimilation was carried out for the period 4 July-3 August by running a three-hour forward intermittent assimilation cycle. First, the impact of the lidar observations was assessed by comparing the analyses with a set of more than 200 independent soundings. The lidar observations were found to have a positive impact on the analyses by reducing the dry bias in the first 500 m above ground level and by diminishing the root-mean-square error by roughly 15% in the first km. Then the impact of the lidar observations was assessed by comparing the precipitation forecasts (obtained with and without the lidar observations for the period 15 July-2 August) with the gridded precipitation observations provided by the Vienna Enhanced Resolution Analysis. In general, the impact was found to be positive but not significant for the 24 h precipitation and positive and significant for the 6 h precipitation, with an improvement lasting up to 24 h. Some selected case studies show that the improvement was obtained through a better depiction of convection initiation or through a more accurate positioning of the precipitation systems
ISSN: 0035-9009

hal-00659497
https://hal.archives-ouvertes.fr/hal-00659497
DOI : 10.1002/qj.1864

Éditeur(s) : HAL CCSD Société géologique de France
Résumé : The Mesozoic series of the southern units of the Pyrenean Empordà thrust sheets (Montgrí and Figueres nappes, Catalonia, Spain) were finally emplaced over the autochthonous basement and its Cenozoic cover during Eocene times. However, they have originally been folded by the "Laramian" compressional event (Late Cretaceous/Early Paleocene), while they were still in their root zone more than 50 km to the N-NE. Postdating the Santonian, the emersion of the Cretaceous tectorogen induced karst formation at the expense of Berriasian to Santonian limestone sequences. Karst cavities of this paleokarst 1 (lapiaz and canyons) were subsequently coated with a fine, red or black, Microcodium-bearing, continental silt, and infilled with marine chaotic breccias. Following a new episode of emersion then erosion, the original paleokarst 1 was cross-cut by newly formed cavities of the paleokarst 2, filled with Lutetian-Bartonian marine breccias. Both types of marine breccias (Paleocene then Eocene in age) are now relatively well dated by means of planktonic foraminifera (Globigerinacea) occurring within the argillaceous-sandy matrix, and for the older ones, within the argillaceous-sandy or carbonate, finely laminated, interbedded hemipelagites, that mark the top of marine sequences tens of centimetres thick. The relationships of the "Laramian" and "Pyrenean" compressional tectonic events, occurring from latest Cretaceous to Bartonian, with the development of paleokarsts 1 and 2 are analysed in the perspective of the progressive southwards emplacement of the Montgrí thrust sheet, during Eocene time.
EISSN: 1777-5817

hal-00405328
https://hal.archives-ouvertes.fr/hal-00405328
DOI : 10.2113/gssgfbull.178.1.15

Éditeur(s) : HAL CCSD Météo et Climat
Résumé : International audience
The Convective and Orographically- induced Precipitation Study (COPS) is a coordinated international project, comprised of an observational field campaign and a research programme aiming to advance the quality of fore- casts of orographically-induced pre- cipitation by four-dimensional obser- vations and modelling of its life cycle. The COPS field campaign took place during June-July-August 2007 over eastern France and south-western Germany. Its main objective was to provide an unprecedented comprehen- sive set of in situ and remotely-sensed meteorological observations of the entire depth of the troposphere. After a short overview of the project, the paper focuses on the French contribution to the COPS field phase, describes the experimental setup and highlights some key observations.
L’étude des précipitations convectives induites par l’orographie (Cops selon l’acronyme anglais) est un projet inter- national coordonné qui comprend une campagne d’observations de terrain et un programme scientifique et qui vise à améliorer la qualité des prévisions des précipitations orographiques convectives à la fois par l’observation quadridimensionnelle et la modélisa- tion de leur cycle de vie. La campagne de terrain s’est déroulée en juin-juillet- août 2007 sur l’est de la France et le sud-ouest de l’Allemagne. Son objectif majeur était de fournir un jeu d’obser- vations météorologiques, in situ et à distance, aussi complet que possible et sur toute la profondeur de la colonne troposphérique.Après une brève revue d’ensemble du projet, l’article se concentre sur la contribution française à la campagne Cops, décrit le dispositif expérimental mis en œuvre et met en valeur quelques observations clés.
ISSN: 0026-1181

insu-01504075
https://hal-insu.archives-ouvertes.fr/insu-01504075
https://hal-insu.archives-ouvertes.fr/insu-01504075/document
https://hal-insu.archives-ouvertes.fr/insu-01504075/file/meteo_2009_64_32.pdf
DOI : 10.4267/2042/23632

Éditeur(s) : HAL CCSD Centre National de la Recherche Scientifique
Résumé : International audience
ISSN: 1142-2904

hal-00476106
https://hal.archives-ouvertes.fr/hal-00476106

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : International audience
We provide new constraints on the modes of mantle exhumation and denudation in the pre-orogenic Pyrenees by investigating the poorly known peridotites located east of the Lherz body, in eastern Ariè ge (Vicdessos, Urs, Bestiac, Caussou and Prades main peridotitic bodies). We show that: (1) numerous peridotite bodies, not described so far, are constituted by decametric to sub-metric outcrops scattered between and around the main outcrops identified by Monchoux (1970); (2) most of the peridotites form blocks and lenses of various sizes, from millimetric monocrystalline grains to hectometric olistoliths, embedded in debris flows involving mainly Mesozoic metasediments; these peridotites can therefore be linked to the S-type peridotites of Lagabrielle et al. (2010), and share similarities with the peridotites of Lherz region (Clerc et al., 2012). All originated from tectono-sedimentary processes associated with mantle exhumation in relation with extreme thinning and breakoff of the continental basement; (3) the various petrographic characters of these peridotites and their heterogeneity in serpentinisation degree imply a peculiar mode of exhumation, which merges mantle fragments inherited from different structural levels; (4) the lack of tectonic structures such as faults and shear planes associated with the ultramafic-rich breccia formation and the presence of neoformation of metamorphic minerals within the matrix preclude their origin as cataclasites related to the Latest Cretaceous and Tertiary Pyrenean contractional deformation. The peridotites of eastern Ariè ge are indisputable witnesses of the presence of an inverted hyper-extended Cretaceous passive margin forming the current North Pyrenean zone. The geometry of the extensional system was complex and probably associated with strike-slip faults and transcurrent motion. ß 2016 The Authors. Published by Elsevier Masson SAS on behalf of Acadé mie des sciences. This is an open access article under the CC BY-NC-ND license (http://creativecommons. org/licenses/by-nc-nd/4.0/).
ISSN: 1631-0713

Droits : http://creativecommons.org/licenses/by-nc-nd/
insu-01280502
https://hal-insu.archives-ouvertes.fr/insu-01280502
https://hal-insu.archives-ouvertes.fr/insu-01280502/document
https://hal-insu.archives-ouvertes.fr/insu-01280502/file/1-s2.0-S1631071316000043-main.pdf
DOI : 10.1016/j.crte.2015.12.003

Éditeur(s) : HAL CCSD Wiley-VCH Verlag
Résumé : International audience
Deciphering the assembly history of the Milky Way is a formidable task, which becomes possible only if one can produce high-resolution chrono-chemo-kinematical maps of the Galaxy. Data from large-scale astrometric and spectroscopic surveys will soon provide us with a well-defined view of the current chemo-kinematical structure of the Milky Way, but will only enable a blurred view on the temporal sequence that led to the present-day Galaxy. As demonstrated by the (ongoing) exploitation of data from the pioneering photometric missions CoRoT, Kepler, and K2, asteroseismology provides the way forward: solar-like oscillating giants are excellent evolutionary clocks thanks to the availability of seismic constraints on their mass and to the tight age-initial-mass relation they adhere to. In this paper we identify five key outstanding questions relating to the formation and evolution of the Milky Way that will need precise and accurate ages for large samples of stars to be addressed, and we identify the requirements in terms of number of targets and the precision on the stellar properties that are needed to tackle such questions. By quantifying the asteroseismic yields expected from PLATO for red-giant stars, we demonstrate that these requirements are within the capabilities of the current instrument design, provided that observations are sufficiently long to identify the evolutionary state and allow robust and precise determination of acoustic-mode frequencies. This will allow us to harvest data of sufficient quality to reach a 10% precision in age. This is a fundamental pre-requisite to then reach the more ambitious goal of a similar level of accuracy, which will only be possible if we have to hand a careful appraisal of systematic uncertainties on age deriving from our limited understanding of stellar physics, a goal which conveniently falls within the main aims of PLATO's core science.
ISSN: 0004-6337

hal-01541393
https://hal.archives-ouvertes.fr/hal-01541393
ARXIV : 1706.3778
BIBCODE : 2017AN....338..644M
DOI : 10.1002/asna.201713385

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
In the mid-afternoon of 15 July 2007, during the Convective and Orographically induced Precipitation Study (COPS), in a very warm and dry environment, an isolated, short-lived, deep convective system developed over the southern Black Forest. Most of the high-resolution, convection-permitting models involved in COPS were unable to capture this event whereas the Meso-NH forecast was quite skilful. To assess the Meso-NH performance further, the model results were carefully checked against the various and numerous COPS observations. In full agreement with clear-air radar observations, model results underlined the triggering role of a low-level convergence line that developed in the lee of the Feldberg. The main departure from the observations was found to be in the low-level moisture fields, which appeared significantly moister in the model than in the observations and also slightly moister than in the other models. Sensitivity studies showed that this departure from the observations was strongly controlled by the initial surface moisture conditions. When the surface moisture was reduced by 20% or replaced by the value derived from a different analysis, the evolution of the planetary boundary layer was more accurately represented while the storm evolution was still correctly captured. These results demonstrate that the quality of the initial forecast cannot be ascribed to the moist bias of the model. It could therefore be hypothesized that the key parameters for a satisfactory forecast of this event lie more in the ability of the model to reproduce the dynamical forcing accurately than in the characteristics of the air-mass instability.
ISSN: 0035-9009

hal-00554400
https://hal.archives-ouvertes.fr/hal-00554400
DOI : 10.1002/qj.710

Éditeur(s) : HAL CCSD
Résumé : International audience
Continental erosion and weathering destroy parts of the stratigraphic record. Analyses of the sedimentary filling of paleokarsts help completing the geological record of regions that have been submitted to post-depositional, long-term, continental evolution. Jurassic carbonate platform of Languedoc (South of France) has undergone several karstification phases from Cretaceous to Neogene. Later incision of canyons through the carbonate massifs allows to observe paleokarsts over 400m depth, within the massifs. Paleokarsts are partly filled with sediments. Some have yielded marine bioclasts (echinoderms, radiolars), foraminifera and nannofossils; others are composed of polygenic detrital sediments, including sources from the upstream Paleozoic basement (Cevennes). The age of the filling of successive paleokarsts can be constrained by structural relationships and by biostratigraphy. These findings suggests 1) the marine elements of the karstic filling relate to a Late Cretaceous to Early Paleocene interval, while 2) the Paleozoic basement-sourced-sediments were trapped in the karst during Miocene to Present. Karstic sediment containing Early Paleocene foraminifera and nannofossils are found in paleokarsts cavities distributed across the entire thickness of the carbonate massif (≥350m). This requires base-level lowering and associated karstification, followed by base-level rise and karst filling of at least 350 m amplitude, respectively. The time interval corresponding to the occurrence of foraminifera and nannofossils in karsts covers 10 Myrs ; surprisingly, no equivalent marine sediments are preserved on the surface. In addition, analyses of the different forams species suggests several (up to 3) distinct karstification and marine filling cycles. Finally, sedimentological facies analysis of the karst filling reveals the following succession of processes: low energy settling of mudstone, high energy reworking, transport and deposition of silts and sandstones within the karst system. Integration of geological, paleontological and sedimentological data, leads to a polyphase scenario in response to repeated base-level variations, more than 350m amplitude. Such an amplitude excludes eustacy, and the improbable repeated sequence of uplift and subsidence rules out tectonics, as driving forces for base-level change, respectively. We propose that the high-amplitude base-level changes results from a succession of desiccation-flooding events of an endorheic, silled, basin during Early Paleogene. The later detrital assemblage sourced in the Cevennes occurs on perched paleosurfaces and in karst cavities across the whole 350m-deep canyon walls. When found on paleosurfaces, they correspond to the south-flowing Early Miocene fluvial drainage, and can be correlated downstream with the marine, well dated, Early Miocene, sediments. When found within the karst cavities, they correspond to successive base-level surfaces connected to the progressive incision of the canyon. This canyon incision is coeval with a Late Miocene uplift of the hinterland.
24th International Karstological School "Classical karst" : Paleokarst
Postojna, Slovenia

hal-01306683
https://hal-brgm.archives-ouvertes.fr/hal-01306683
https://hal-brgm.archives-ouvertes.fr/hal-01306683/document
https://hal-brgm.archives-ouvertes.fr/hal-01306683/file/Abstract_IKS.pdf

Éditeur(s) : HAL CCSD Landes Bioscience
Résumé : International audience
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Autophagy

hal-00735751
https://hal.archives-ouvertes.fr/hal-00735751
PUBMED : 22966490

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.
ISSN: 1755-098X

hal-01094222
https://hal-agroparistech.archives-ouvertes.fr/hal-01094222
DOI : 10.1111/j.1755-0998.2010.02916.x