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 European Geosciences Union
Résumé : International audience
Measurements of branch xylem density, D_x, were made for 1466 trees representing 503 species, sampled from 80 sites across the Amazon basin. Measured values ranged from 240 kg m^?3 for a Brosimum parinarioides from Tapajos in West Pará, Brazil to 1130 kg m^?3 for an Aiouea sp. from Caxiuana, Central Pará, Brazil. Analysis of variance showed significant differences in average D_x across the sample plots as well as significant differences between families, genera and species. A partitioning of the total variance in the dataset showed that geographic location and plot accounted for 33% of the variation with species identity accounting for an additional 27%; the remaining "residual" 40% of the variance accounted for by tree to tree (within species) variation. Variations in plot means, were, however, hardly accountable at all by differences in species composition. Rather, it would seem that variations of xylem density at plot level must be explained by the effects of soils and/or climate. This conclusion is supported by the observation that the xylem density of the more widely distributed species varied systematically from plot to plot. Thus, as well as having a genetic component branch xylem density is a plastic trait that, for any given species, varies according to where the tree is growing and in a predictable manner. Exceptions to this general rule may be some pioneers belonging to Pourouma and Miconia and some species within the genera Brosimum, Rinorea and Trichillia which seem to be more constrained in terms of this plasticity than most species sampled as part of this study.
ISSN: 1810-6277

hal-00298004
https://hal.archives-ouvertes.fr/hal-00298004
https://hal.archives-ouvertes.fr/hal-00298004/document
https://hal.archives-ouvertes.fr/hal-00298004/file/bgd-5-2003-2008.pdf

Éditeur(s) : American Geophysical Union
Résumé : [1] A multiproxy integrated chronological framework, based on oxygen and carbon stable isotope stratigraphy, biostratigraphy (foraminifera and nannoplankton bioevents and foraminifer assemblage-based climate cyclicity), magnetostratigraphy, sapropel stratigraphy, and C-14 AMS radiometric dates, has been achieved for borehole PRAD1-2, collected in 185.5 m water depth in the central Adriatic. This work was carried out within the European Community project Profiles across Mediterranean Sedimentary Systems (PROMESS1). The 71.2 m long borehole spans a time interval between late MIS 11 and MIS 1 (the last 370 ka), showing a chronological resolution of 500 and 250 years per cm during interglacial and glacial intervals, respectively. At present, this record is the most expanded and continuous marine record available for the Adriatic Basin. Several orbital cycles can be recognized in the PRAD1-2 record: the 100 ka glacial-interglacial fluctuations and the 23 ka precession-related cycles, which in turn control the deposition of sapropel layers. An integrated analysis of short-term oscillations within the Last Glaciation interval (MIS 4-MIS 2) allowed the identification of the Adriatic signature of Dansgaard-Oeschger events, showing the potential to achieve a more refined chronostratigraphic framework for the top part of the PRAD1-2 record. Finally, the age model obtained by this study allowed the chronological integration of the main foraminifera bioevents detected in the borehole as well as of the volcanoclastic layers present in the upper part of the record. Despite its proximal location, PRAD1-2 presents a continuous record and shows the potential to be consistently correlated both with deep-sea and continental records in the Mediterranean region and beyond.
Geochemistry Geophysics Geosystems (1525-2027) (American Geophysical Union), 2008 , Vol. 9 , P. NIL_107-NIL_127

Droits : 2008 American Geophysical Union
http://archimer.ifremer.fr/doc/2008/publication-3605.pdf
DOI:10.1029/2007GC001713
http://archimer.ifremer.fr/doc/00000/3605/

Éditeur(s) : HAL CCSD
Résumé : International audience
Women who drink light-to-moderately during pregnancy have been observed to have lower risk of unfavourable pregnancy outcomes than abstainers. This has been suggested to be a result of bias. In a pooled sample, including 193 747 live-born singletons from nine European cohorts, we examined the associations between light-to-moderate drinking and preterm birth, birth weight, and small-for-gestational age in term born children (term SGA). To address potential sources of bias, we compared the associations from the total sample with a sub-sample restricted to first-time pregnant women who conceived within six months of trying, and examined whether the associations varied across calendar time. In the total sample, drinking up to around six drinks per week as compared to abstaining was associated with lower risk of preterm birth, whereas no significant associations were found for birth weight or term SGA. Drinking six or more drinks per week was associated with lower birth weight and higher risk of term SGA, but no increased risk of preterm birth. The analyses restricted to women without reproductive experience revealed similar results. Before 2000 approximately half of pregnant women drank alcohol. This decreased to 39% in 2000–2004, and 14% in 2005–2011. Before 2000, every additional drink was associated with reduced mean birth weight, whereas in 2005–2011, the mean birth weight increased with increasing intake. The period-specific associations between low-to-moderate drinking and birth weight, which also were observed for term SGA, are indicative of bias. It is impossible to distinguish if the bias is attributable to unmeasured confounding, which change over time or cohort heterogeneity. © 2017, Springer Science+Business Media B.V.
ISSN: 03932990

hal-01647159
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01647159
DOI : 10.1007/s10654-017-0323-2
PUBMED : 29027084

Éditeur(s) : HAL CCSD
Résumé : Les dossiers thématiques d'Agropolis, n° 11
Dans le contexte actuel de contraintes climatiques et socioéconomiques, les agricultures des zones sèches doivent évoluer afin de s’adapter et de répondre à un double défi : produire plus pour satisfaire les besoins alimentaires importants de populations en croissance, mais aussi produire mieux de façon viable et durable. Pour cela, les agricultures de ces zones doivent évoluer vers des modes de production à la fois plus productifs, économes en ressources naturelles et résistants aux aléas climatiques.Dans ce cadre, l’ingénierie écologique propose de nouvelles alternatives de gestion des systèmes agro-sylvo-pastoraux caractéristiques des régions arides et semi-arides d’Afrique subsaharienne. Ceci implique de maitriser la complexité des systèmes étudiés et de s’inspirer à la fois du fonctionnement des écosystèmes naturels de référence à la région agroécologique concernée — les savanes pour les zones sèches ouest-africaines — et des pratiques traditionnelles et savoir-faire locaux issus d’une longue adaptation face aux contraintes environnementales.À partir des expériences ouest-africaines notamment, différentes options pratiques sont exposées dans ce dossier. On pourra ainsi agir sur la biodiversité des organismes, que ce soit les plantes ou les microorganismes du sol par exemple, favoriser le recyclage des matières organiques et des éléments nutritifs pour les plantes qui sont associées, maitriser les cycles de l’eau et, enfin, agir sur l’organisation des paysages pour favoriser un meilleur contrôle des ravageurs de culture.Cependant, développer une telle approche demande une vision intégrée du fonctionnement et de l’évolution des systèmes agro-sylvo-pastoraux. Les questions sociales — le foncier, l’urbanisation et les migrations — et économiques — les marchés des denrées de première nécessité, la pauvreté, etc. — sont des déterminants essentiels qu’il convient de prendre en compte pour le développement durable des populations dans les zones sèches en Afrique subsaharienne.
https://hal.archives-ouvertes.fr/hal-01585038

hal-01585038
https://hal.archives-ouvertes.fr/hal-01585038

Éditeur(s) : HAL CCSD American Association for the Advancement of Science
Résumé : International audience
Sediments cored along the southwestern Iberian margin during Integrated Ocean Drilling Program Expedition 339 provide constraints on Mediterranean Outflow Water (MOW) circulation patterns from the Pliocene epoch to the present day. After the Strait of Gibraltar opened (5.33 million years ago), a limited volume of MOW entered the Atlantic. Depositional hiatuses indicate erosion by bottom currents related to higher volumes of MOW circulating into the North Atlantic, beginning in the late Pliocene. The hiatuses coincide with regional tectonic events and changes in global thermohaline circulation (THC). This suggests that MOW influenced Atlantic Meridional Overturning Circulation (AMOC), THC, and climatic shifts by contributing a component of warm, saline water to northern latitudes while in turn being influenced by plate tectonics.
ISSN: 0036-8075

hal-01054316
https://hal.archives-ouvertes.fr/hal-01054316
DOI : 10.1126/science.1251306

Éditeur(s) : HAL CCSD European Centre for Disease Prevention and Control
Résumé : International audience
In 2002, the French Food Safety Agency drew attention to the lack of information on the prevalence of human cryptosporidiosis in the country. Two years later, the ANOFEL Cryptosporidium National Network (ACNN) was set up to provide public health authorities with data on the incidence and epidemiology of human cryptosporidiosis in France. Constituted on a voluntary basis, ACNN includes 38 hospital parasitology laboratories (mainly in university hospitals). Each laboratory is engaged to notify new cases of confirmed human cryptosporidiosis, store specimens (e.g. stools, duodenal aspirates or biopsies) and related clinical and epidemiological data, using data sheet forms. From January 2006 to December 2009, 407 cryptosporidiosis cases were notified in France and 364 specimens were collected. Of the notified cases, 74 were children under four years of age, accounting for 18.2%. HIV-infected and immunocompetent patients represented 38.6% (n=157) and 28% (n=114) of cases, respectively. A marked seasonal pattern was observed each year, with increased number of cases in mid to late summer and the beginning of autumn. Genotyping of 345 isolates from 310 patients identified C. parvumin 168 (54.2%) cases, C. hominis in 113 (36.4%) and other species in 29 (9.4%), including C. felis (n=15), C. meleagridis (n=4), C. canis (n=4), Cryptosporidium chipmunk genotype (n=1), Cryptosporidium rabbit genotype (n=1) and new Cryptosporidium genotypes (n=4). These data represent the first multisite report of laboratory-confirmed cases of cryptosporidiosis in France.
ISSN: 1560-7917

hal-00926813
https://hal-unilim.archives-ouvertes.fr/hal-00926813
PUBMED : 20739000

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The base of the Faro contouritic drift (IODP Site U1386) on the northern margin of the Gulf of Cádiz (Algarve margin) is characterized by two sequences of frequent gravity deposits with different ages and compositions. Among these gravity deposits, several relatively thick debrites (up to 12 m) have been observed and studied in detail.Sedimentological analyses have been performed and because of non-turbulent behavior of debris flows, detailed micropaleontological studies could be realized. Planktonic foraminifera thus allowed establishing a detailed biostratigraphy of these deposits. Benthic foraminifer and ostracod assemblages were used to evaluate the origin of the sediment composing these debris flows and estimate their run-out distance.These debrites are dated from Early Pliocene and early Pleistocene, and were deposited in a mesobathyal environment. They comprise silty mud clasts and matrixes with sand content up to 34%. The Early Pliocene debrites are bioclast-rich whereas the Early Pleistocene debrite is enriched in terrigenous particles. The data indicates that these debrites were triggered on the continental shelf and traveled less than 100 km, eroding the seafloor all along their path for the Early Pliocene debrites and only the first part of their path for the early Pleistocene debrite. Matrixes originate from failure areas whereas eroded sediments along the flow pathway are incorporated into the flow as clasts.High abundance of shelf fauna during the Early Pliocene and great supply of terrigenous particles from rivers during the early Pleistocene in the south-western Iberian margin have favored gravity flows from the continental shelf to the slope. The contouritic paleo-moat of the Faro drift has been a determining channeling feature for gravity flows along the Algarve margin during the early Pleistocene, testifying of the strong interaction between MOW circulation and down-slope processes. Tectonic and diapiric activities were significant during Early Pliocene and early Pleistocene on the Algarve margin and could have been triggering parameters of failures related to these debris flows.
ISSN: 0025-3227

hal-01356172
https://hal.archives-ouvertes.fr/hal-01356172
DOI : 10.1016/j.margeo.2015.08.018

Éditeur(s) : HAL CCSD American Society of Tropical Medicine and Hygiene
Résumé : International audience
From September 2013 to July 2014, several gold miners working in the tropical forest consulted the Maripasoula Health Center in French Guiana for edema and findings consistent with right cardiac failure. Of the 42 cases of beriberi that were diagnosed, one patient died. The laboratory and clinical investigation demonstrated vitamin B1 deficiency in most of the patients tested. Furthermore, 30 of 42 patients responded favorably to 500 mg of intravenous or intramuscular thiamine supplementation. In addition, dietary investigation showed insufficient thiamine intake in these patients. We concluded that patients had acquired beriberi because of diet restrictions, hard labor, and infectious diseases, notably malaria. In 2016, cases were still being reported. We recommend screening for compatible symptoms in gold miners, thiamine supplementation, and nutritional intervention
ISSN: 0002-9637

inserm-01503899
http://www.hal.inserm.fr/inserm-01503899
http://www.hal.inserm.fr/inserm-01503899/document
http://www.hal.inserm.fr/inserm-01503899/file/2017%2C%20Mosnier%20-%20A%20Large%20Outbreak%20of%20Thiamine%20Deficiency%20among%20Illegal%20Gold%20Miners%20in%20French%20Guiana.pdf
DOI : 10.4269/ajtmh.15-0906

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
CD95 ligand (CD95L) is expressed by immune cells and triggers apoptotic death. Metalloprotease-cleaved CD95L (cl-CD95L) is released into the bloodstream but does not trigger apoptotic signaling. Hence, the pathophysiological role of cl-CD95L remains unclear. We observed that skin-derived endothelial cells from systemic lupus erythematosus (SLE) patients expressed CD95L and that after cleavage, cl-CD95L promoted T helper 17 (Th17) lymphocyte transmigration across the endothelial barrier at the expense of T regulatory cells. T cell migration relied on a direct interaction between the CD95 domain called calcium-inducing domain (CID) and the Src homology 3 domain of phospholipase C gamma 1. Th17 cells stimulated with cl-CD95L produced sphingosine-1-phosphate (S1P), which promoted endothelial transmigration by activating the S1P receptor 3. We generated a cell-penetrating CID peptide that prevented Th17 cell transmigration and alleviated clinical symptoms in lupus mice. Therefore, neutralizing the CD95 non-apoptotic signaling pathway could be an attractive therapeutic approach for SLE treatment.
ISSN: 1074-7613

hal-01359568
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01359568
DOI : 10.1016/j.immuni.2016.06.028
PUBMED : 27438772

Éditeur(s) : HAL CCSD
Résumé : International audience
Up-to-date estimates of the health outcomes of preterm children are needed for assessing perinatal care, informing parents, making decisions about care, and providing evidence for clinical guidelines. To determine survival and neonatal morbidity of infants born from 22 through 34 completed weeks' gestation in France in 2011 and compare these outcomes with a comparable cohort in 1997. The EPIPAGE-2 study is a national, prospective, population-based cohort study conducted in all maternity and neonatal units in France in 2011. A total of 2205 births (stillbirths and live births) and terminations of pregnancy at 22 through 26 weeks' gestation, 3257 at 27 through 31 weeks, and 1234 at 32 through 34 weeks were studied. Cohort data were collected from January 1 through December 31, 1997, and from March 28 through December 31, 2011. Analyses for 1997 were run for the entire year and then separately for April to December; the rates for survival and morbidities did not differ. Data are therefore presented for the whole year in 1997 and the 8-month and 6-month periods in 2011. Survival to discharge and survival without any of the following adverse outcomes: grade III or IV intraventricular hemorrhage, cystic periventricular leukomalacia, severe bronchopulmonary dysplasia, retinopathy of prematurity (stage 3 or higher), or necrotizing enterocolitis (stages 2-3). A total of 0.7% of infants born before 24 weeks' gestation survived to discharge: 31.2% of those born at 24 weeks, 59.1% at 25 weeks, and 75.3% at 26 weeks. Survival rates were 93.6% at 27 through 31 weeks and 98.9% at 32 through 34 weeks. Infants discharged home without severe neonatal morbidity represented 0% at 23 weeks, 11.6% at 24 weeks, 30.0% at 25 weeks, 47.5% at 26 weeks, 81.3% at 27 through 31 weeks, and 96.8% at 32 through 34 weeks. Compared with 1997, the proportion of infants surviving without severe morbidity in 2011 increased by 14.4% (P < .001) at 25 through 29 weeks and 6% (P < .001) at 30 through 31 weeks but did not change appreciably for those born at less than 25 weeks. The rates of antenatal corticosteroid use, induced preterm deliveries, cesarean deliveries, and surfactant use increased significantly in all gestational-age groups, except at 22 through 23 weeks. The substantial improvement in survival in France for newborns born at 25 through 31 weeks' gestation was accompanied by an important reduction in severe morbidity, but survival remained rare before 25 weeks. Although improvement in survival at extremely low gestational age may be possible, its effect on long-term outcomes requires further studies. The long-term results of the EPIPAGE-2 study will be informative in this regard.
ISSN: 2168-6211

hal-01258705
http://hal.univ-brest.fr/hal-01258705
PUBMED : 25621457
DOI : 10.1001/jamapediatrics.2014.3351

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.
ISSN: 2041-1723

hal-01545322
https://hal.archives-ouvertes.fr/hal-01545322
DOI : 10.1038/ncomms3091

Éditeur(s) : HAL CCSD MDPI
Résumé : International audience
Lead in childhood is well known to be associated with poor neurodevelopment. As part of a study on maternal anemia and offspring neurodevelopment, we analyzed blood lead level (BLL) with no prior knowledge of lead exposure in 225 mothers and 685 offspring 1 to 2 years old from Allada, a semi-rural area in Benin, sub-Saharan Africa, between May 2011 and May 2013. Blood samples were analyzed by inductively coupled plasma mass spectrometry. Environmental assessments in households and isotopic ratio measurements were performed for eight children with BLL extgreater 100 µg/L. High lead levels (BLL extgreater 50 µg/L) were found in 44% of mothers and 58% of children. The median BLL was 55.1 (interquartile range 39.2-85.0) and 46.6 (36.5-60.1) µg/L, respectively. Maternal BLL was associated with offspring's consumption of piped water and animals killed by ammunition. Children's BLL was associated with presence of paint chips in the house and consumption of animals killed by ammunition. In this population, with 98% of children still breastfed, children's BLL was highly associated with maternal BLL on multivariate analyses. Environmental measures and isotopic ratios supported these findings. Offspring may be highly exposed to lead in utero and probably via breastfeeding in addition to lead paint exposure
ISSN: 1660-4601

hal-01296778
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01296778
DOI : 10.3390/ijerph13030316
PUBMED : 26978384