Éditeur(s) : Caribbean Volunteer Expeditions Caribbean Volunteer Expeditions ( Corning, NY )

Droits : All rights reserved by the source institution.

Éditeur(s) : Caribbean Volunteer Expeditions Caribbean Volunteer Expeditions ( Corning, NY )

Droits : All rights reserved by the source institution.

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 American Society for Microbiology
Résumé : International audience
A number of men receiving prolonged suppressive HAART still shed HIV in semen. To investigate whether this seminal shedding may be due to poor drug penetration and/or viral production by long-lived cells within male genital tissues, we analyzed semen and reproductive tissues from macaques chronically infected with SIVmac251 submitted to HAART for 4 months, intensified over the last seven weeks with an integrase inhibitor. We showed that a subset of treated animals continued shedding SIV in semen despite efficient HAART. This shedding was not associated with low antiretroviral drug concentrations in semen, or in testis, epididymis, seminal vesicles and prostate. HAART had no significant impact on SIV RNA in the urethra, whereas it drastically reduced SIV RNA levels in the prostate and vas deferens, and to a lesser extent in the epididymis and seminal vesicle. The only detectable SIV RNA positive cells within the male genital tract after HAART were urethral macrophages. SIV DNA levels in genital tissues were not decreased by HAART, suggesting the presence throughout the male genital tract of non-productively infected cells. In conclusion, our results demonstrate that 4 months of HAART induced variable and limited control of viral infection in the male reproductive organs, particularly the urethra, and suggest that infected long-lived cells in the male genital tract may be involved in persistent seminal shedding during HAART. These results pave the way for further investigations of male genital organs infection in long term treated infected individuals. A substantial subset of men receiving prolonged suppressive HAART in the blood still harbor HIV in semen, and cases of sexual transmission have been reported. To understand the origin of this persistence, we analyzed the semen and male reproductive tissues from SIV-infected macaques treated by HAART. We demonstrated that persistent seminal shedding was not linked to poor drug penetration in semen or semen-producing prostate, seminal vesicle, epididymis and testis. We revealed that HAART decreased SIV RNA to various extents in all male genital organs, with the exception of the urethra, in which SIV RNA+ macrophages were observed despite HAART. Importantly also, HAART did not impact SIV DNA levels in the male genital organs. These results suggest that infection of male genital organs, and particularly the urethra, could be involved in the release of virus in semen during HAART.
ISSN: 0022-538X

hal-01139816
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01139816
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01139816/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01139816/file/Detection%20of%20SIV%20in%20Semen%2C%20Urethra%2C%20and%20Male%20Reproductive%20Organs%20during%20Efficient%20Highly%20Active%20Antiretroviral%20Therapy.pdf
PUBMEDCENTRAL : PMC4442442

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : International audience
The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positively to precipitation when rainfall is < 2000 mm yr(-1) (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall < 2000 mm yr(-1).
ISSN: 1726-4170

hal-01557759
https://hal.univ-lorraine.fr/hal-01557759
https://hal.univ-lorraine.fr/hal-01557759/document
https://hal.univ-lorraine.fr/hal-01557759/file/bg-13-2537-2016.pdf
DOI : 10.5194/bg-13-2537-2016

Éditeur(s) : HAL CCSD American Public Health Association
Résumé : International audience
Sickle cell disease (SCD) is a significant problem in the Caribbean, where many individuals have African and Asian forebears. However, reliable prevalence data and specific health care programs for SCD are often missing in this region. Closer collaboration between Caribbean territories initiated in 2006 to set up strategies to promote better equity in the health care system for SCD patients led to the formation of CAREST: the Caribbean Network of Researchers on Sickle Cell Disease and Thalassemia. We present the effectiveness of collaborations established by CAREST to promote SCD newborn screening programs and early childhood care, to facilitate health worker training and approaches for prevention and treatment of SCD complications, and to carry out inter-Caribbean research studies.
ISSN: 0090-0036

hal-01668331
https://hal.univ-antilles.fr/hal-01668331
DOI : 10.2105/AJPH.2016.303078

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Retreatment with pegylated interferon (peg-IFN) and ribavirin (RBV) results in poor sustained virological response (SVR) rates in human immunodeficiency virus (HIV)/hepatitis C virus (HCV)-coinfected patients. There are limited data regarding the use of telaprevir plus peg-IFN/RBV in this population. HIV type 1-infected patients who previously failed ≥12 weeks of peg-IFN/RBV for HCV genotype 1 coinfection were enrolled in a single-arm, phase 2 trial. Patients with cirrhosis and previous null response were excluded. Authorized antiretrovirals were tenofovir, emtricitabine, efavirenz, atazanavir, and raltegravir. All patients received peg-IFN alfa-2a (180 µg/week) plus RBV (1000-1200 mg/day) for 4 weeks, followed by telaprevir (750 mg or 1125 mg every 8 hours with efavirenz) plus peg-IFN/RBV for 12 weeks and peg-IFN/RBV for 32-56 weeks according to virological response at week 8. The primary endpoint was the SVR rate at 24 weeks after the end of treatment (SVR24). Sixty-nine patients started treatment; SVR24 was achieved in 55 (80% [95% confidence interval, 68%-88%). SVR24 was not influenced by baseline fibrosis stage, IL28B genotype, antiretroviral regimen, HCV subtype, CD4 cell count, previous response to HCV treatment, HCV RNA level, or HCV RNA decline at week 4. HCV treatment was discontinued for adverse events (AEs) in 20% of patients, including cutaneous (4%), psychiatric (4%), hematological (6%), and other AEs (6%). Peg-IFN or RBV dose reduction was required in 23% and 43% of patients, respectively. Seventy percent of patients required erythropoietin, blood transfusions, or RBV dose reduction for anemia. Two patients died during the study. No HIV breakthrough was observed. Despite a high discontinuation rate related to toxicity, a substantial proportion of treatment-experienced HIV-coinfected patients achieved SVR24 with a telaprevir-based regimen. Clinical Trials Registration. NCT01332955.
ISSN: 1058-4838

hal-01118447
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118447
PUBMED : 25139963
DOI : 10.1093/cid/ciu659

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : The diamond anvil cell (DAC) is a fundamental device used to explore the properties of materials under extreme pressure and temperature (P/T) conditions. In the past years, simultaneous high P/T DAC experiments using the resistively heated DAC (RH-DAC) techniques have been developed for studying materials properties in a wide P/T range. However, the mechanical instability of metallic gaskets used for sample confinement at high P/T conditions remains a limiting factor for exploiting the accessible P/T range of the RH-DAC. In this study, we present a new gasket configuration that overcomes these limitations. It is based on an amorphous boron-epoxy mixture inserted in a rhenium gasket. We show how these gasket inserts stabilize the sample chamber over a wide P/T range, allowing monitoring sample properties using X-ray diffraction and absorption spectroscopy up to 50GPa and 1620K.
ISSN: 0895-7959

hal-01608425
https://hal.archives-ouvertes.fr/hal-01608425
DOI : 10.1080/08957959.2016.1245297
PRODINRA : 387347

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
BACKGROUND: Thrombophilias are common disorders that increase the risk of pregnancy-associated venous thromboembolism and pregnancy loss and can also increase the risk of placenta-mediated pregnancy complications (severe pre-eclampsia, small-for-gestational-age infants, and placental abruption). We postulated that antepartum dalteparin would reduce these complications in pregnant women with thrombophilia. METHODS: In this open-label randomised trial undertaken in 36 tertiary care centres in five countries, we enrolled consenting pregnant women with thrombophilia at increased risk of venous thromboembolism or with previous placenta-mediated pregnancy complications. Eligible participants were randomly allocated in a 1:1 ratio to either antepartum prophylactic dose dalteparin (5000 international units once daily up to 20 weeks' gestation, and twice daily thereafter until at least 37 weeks' gestation) or to no antepartum dalteparin (control group). Randomisation was done by a web-based randomisation system, and was stratified by country and gestational age at randomisation day with a permuted block design (block sizes 4 and 8). At randomisation, site pharmacists (or delegates) received a randomisation number and treatment allocation (by fax and/or e-mail) from the central web randomisation system and then dispensed study drug to the local coordinator. Patients and study personnel were not masked to treatment assignment, but the outcome adjudicators were masked. The primary composite outcome was independently adjudicated severe or early-onset pre-eclampsia, small-for-gestational-age infant (birthweight <10th percentile), pregnancy loss, or venous thromboembolism. We did intention-to-treat and on-treatment analyses. This trial is registered with ClinicalTrials.gov, number NCT00967382, and with Current Controlled Trials, number ISRCTN87441504. FINDINGS: Between Feb 28, 2000, and Sept 14, 2012, 292 women consented to participate and were randomly assigned to the two groups. Three women were excluded after randomisation because of ineligibility (two in the antepartum dalteparin group and one in the control group), leaving 146 women assigned to antepartum dalteparin and 143 assigned to no antepartum dalteparin. Some patients crossed over to the other group during treatment, and therefore for on-treatment and safety analysis there were 143 patients in the dalteparin group and 141 in the no dalteparin group. Dalteparin did not reduce the incidence of the primary composite outcome in both intention-to-treat analysis (dalteparin 25/146 [17.1%; 95% CI 11.4-24.2%] vs no dalteparin 27/143 [18.9%; 95% CI 12.8-26.3%]; risk difference -1.8% [95% CI -10.6% to 7.1%)) and on-treatment analysis (dalteparin 28/143 [19.6%] vs no dalteparin 24/141 [17.0%]; risk difference +2.6% [95% CI -6.4 to 11.6%]). In safety analysis, the occurrence of major bleeding did not differ between the two groups. However, minor bleeding was more common in the dalteparin group (28/143 [19.6%]) than in the no dalteparin group (13/141 [9.2%]; risk difference 10.4%, 95% CI 2.3-18.4; p=0.01). INTERPRETATION: Antepartum prophylactic dalteparin does not reduce the occurrence of venous thromboembolism, pregnancy loss, or placenta-mediated pregnancy complications in pregnant women with thrombophilia at high risk of these complications and is associated with an increased risk of minor bleeding. FUNDING: Canadian Institutes of Health Research, Heart and Stroke Foundation of Canada, and Pharmacia and UpJohn.
ISSN: 0923-7577

hal-01258557
http://hal.univ-brest.fr/hal-01258557
DOI : 10.1016/S0140-6736(14)60793-5
PUBMED : 25066248

Éditeur(s) : HAL CCSD Saint-Maurice (Val de Marne) : Institut de veille sanitaire
Résumé : International audience
ISSN: 0245-7466

Droits : info:eu-repo/semantics/OpenAccess
hal-01675363
https://hal.archives-ouvertes.fr/hal-01675363
https://hal.archives-ouvertes.fr/hal-01675363/document
https://hal.archives-ouvertes.fr/hal-01675363/file/BEH_lepto.pdf

Éditeur(s) : HAL CCSD European Geosciences Union
Résumé : The fixation of carbon in tropical forests mainly occurs through the production of wood and leaves, both being the principal components of net primary production. Currently field and satellite observations are independently used to describe the forest carbon cycle, but the link between satellite-derived forest phenology and field-derived forest productivity remains opaque. We used a unique combination of a MODIS enhanced vegetation index (EVI) dataset, a wood production model based on climate data and direct litterfall observations at an intra-annual timescale in order to question the synchronism of leaf and wood production in tropical forests. Even though leaf and wood biomass fluxes had the same range (respectively 2.4 +/- 1.4 and 2.2 +/- 0.4 Mg C ha(-1) yr(-1)), they occurred separately in time. EVI increased with leaf renewal at the beginning of the dry season, when solar irradiance was at its maximum. At this time, wood production stopped. At the onset of the rainy season, when new leaves were fully mature and water available again, wood production quickly increased to reach its maximum in less than a month, reflecting a change in carbon allocation from short-lived pools (leaves) to long-lived pools (wood). The time lag between peaks of EVI and wood production (109 days) revealed a substantial decoupling between the leaf renewal assumed to be driven by irradiance and the water-driven wood production. Our work is a first attempt to link EVI data, wood production and leaf phenology at a seasonal timescale in a tropical evergreen rainforest and pave the way to develop more sophisticated global carbon cycle models in tropical forests.
ISSN: 1726-4170

hal-01268497
https://hal.archives-ouvertes.fr/hal-01268497
DOI : 10.5194/bg-10-7307-2013
PRODINRA : 256018

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Gibraltar arc, spans a complex portion of the Africa-Eurasia plate boundary marked by slow oblique convergence and intermediate and deep focus seismicity. The seemingly contradictory observations of a young extensional marine basin surrounded by an arcuate fold-and-thrust belt, have led to competing geodynamic models (delamination and subduction). Geophysical data acquired in the past decade provide a test for these models and support a narrow east-dipping, subduction zone. Seismic refraction studies indicate oceanic crust below the western Gulf of Cadiz. Tomography of the upper mantle reveals a steep, east-dipping high P-wave velocity body, beneath Gibraltar. The anisotropic mantle fabric from SKS splitting shows arc-parallel "fast directions", consistent with toroidal flow around a narrow, westward retreating subducting slab. The accompanying WSW advance of the Rif-Betic mountain belt has constructed a thick pile of deformed sediments, an accretionary wedge, characterized by west-vergent thrust anticlines. Bathymetric swath‐mapping images an asymmetric embayment at the deformation front where a 2 km high basement ridge has collided. Subduction has slowed significantly since 5 Ma, but deformation of recent sediments and abundant mud volcanoes suggest ongoing activity in the accretionary wedge. Three possible origins for this deformation are discussed; gravitational spreading, overall NW-SE convergence between Africa and Iberia and finally a WSW tectonic push from slow, but ongoing roll-back subduction. In the absence of arc volcanism and shallow dipping thrust type earthquakes, evidence in favor of present-day subduction can only be indirect and remains the object of debate. Continued activity of the subduction offers a possible explanation for great (M > 8.5) earthquakes known to affect the area, like the famous 1755 Great Lisbon earthquake. Recent GPS studies show SW motion of stations in N Morocco at velocities of 3-6 mm/yr indicating the presence of an independent block, a "Rif-Betic-Alboran" microplate, situated between Iberia and Africa.
ISSN: 0040-1951

insu-00769762
https://hal-insu.archives-ouvertes.fr/insu-00769762
DOI : 10.1016/j.tecto.2012.08.038

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

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Hepatocellular carcinoma (HCC) is a particularly severe disease characterized by a high rate of recurrence and death even after surgical resection. Molecular characterization of HCC helps refine prognosis and may facilitate the development of improved therapy. Phosphatidylinositol 4-kinases have recently been identified as cellular factors associated with cancer. Also, phosphatidylinositol 4-kinase type IIIα (PI4KA) is necessary for the propagation of the hepatitis C virus, a major etiological factor for HCC. METHODS: Reverse transcription, quantitative real-time PCR was used to assay PI4KA mRNA. The expression levels were investigated both in a collection of molecularly and clinically characterized hepatic tissues from 344 patients with diverse liver diseases and in human hepatocyte cell lines whose proliferative and differentiation status was controlled by specific culture conditions. Analytical microarray data for 60 HCC and six normal liver tissue samples were exploited to study correlations between PI4KA mRNA levels and cell proliferation markers in vivo. Postoperative disease-specific survival and time to recurrence in a set of 214 patients with HCC were studied by univariate and multivariate analyses. RESULTS: PI4KA mRNA was more abundant in HCC than normal healthy tissues. This upregulation correlated significantly with both poor differentiation and the active proliferation rate in HCC. These associations were confirmed with in vitro models. Moreover, patients with HCC who had been treated by surgical resection and had higher PI4KA mRNA concentrations in their tumor tissue exhibited a higher risk of tumor recurrence (median time: 20 months versus 49 months, P = 0.0012) and shorter disease-specific survival (first quartile time: 16 months versus 48 months, P = 0.0004). Finally, the abundance of PI4KA mRNA proved to be an independent prognostic marker of survival for cases of HCC (hazard ratio = 2.36, P = 0.0064). CONCLUSIONS: PI4KA mRNA could be used as a new molecular marker to improve established prognostic models for HCC. These findings also indicate possible new lines of research for the development of innovative therapeutic approaches targeting PI4KA.
ISSN: 1471-2407

inserm-00934294
http://www.hal.inserm.fr/inserm-00934294
http://www.hal.inserm.fr/inserm-00934294/document
http://www.hal.inserm.fr/inserm-00934294/file/1471-2407-14-7.pdf
DOI : 10.1186/1471-2407-14-7

Éditeur(s) : HAL CCSD Wiley
Résumé : While attention on logging in the tropics has been increasing, studies on the long-term effects of silviculture on forest dynamics and ecology remain scare and spatially limited. Indeed, most of our knowledge on tropical forests arises from studies carried out in undisturbed tropical forests. This bias is problematic given that logged and disturbed tropical forests are now covering a larger area than the so-called primary forests. A new network of permanent sample plots in logged forests, the Tropical managed Forests Observatory (TmFO), aims to fill this gap by providing unprecedented opportunities to examine long-term data on the resilience of logged tropical forests at regional and global scales. TmFO currently includes 24 experimental sites distributed across three tropical regions, with a total of 490 permanent plots and 921ha of forest inventories.
ISSN: 1402-2001

hal-01204230
https://hal.archives-ouvertes.fr/hal-01204230
DOI : 10.1111/avsc.12125
PRODINRA : 323838

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Ash flow tuffs, or ignimbrites have been recently proposed to be a good material for palaeointensity determination. In this paper, we present a multidisciplinary study, combining geochronology, petrology, rock magnetism and palaeomagnetism, carried out on Oligocene to Early Miocene ignimbrites and related flows from the southern part of the Sierra Madre Occidental. Two new 40Ar/39Ar ages were determined for ignimbrites; 20.4 ± 0.2 Ma (the youngest age obtained so far in this area) and 29.2 ± 0.5 Ma. Density measurements, as a proxy for welding, proved to be extremely useful to estimate the emplacement temperature and the origin of the magnetizations carried by the ignimbrites. After alternating field and thermal demagnetizations, the mean palaeomagnetic pole (Lat = 66.8°N; Long = 180.5°E; Kappa = 142; A95 = 6.3°), calculated for the period 28-31 Ma, is in close agreement with our only Miocene determination. Comparison with the North America Synthetic Apparent Polar Path indicates a net counter-clockwise vertical axis rotation of about 10 ± 4° compared to stable North America, which occurred likely during the last extensional episode in the Late Miocene (ca. 12-9 Ma). Palaeointensity estimates, obtained with the Thellier-Coe method, are mainly questionable and should not be used for global interpretation. Therefore, these ignimbrites are not a viable material for reliable palaeointensity determinations.
ISSN: 0956-540X

hal-00854457
https://hal.archives-ouvertes.fr/hal-00854457
DOI : 10.1093/gji/ggt079