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 Nature Publishing Group
Résumé : International audience
Treacher Collins/Franceschetti syndrome (TCS; OMIM 154500) is a disorder of craniofacial development belonging to the heterogeneous group of mandibulofacial dysostoses. TCS is classically characterized by bilateral mandibular and malar hypoplasia, downward-slanting palpebral fissures, and microtia. To date, three genes have been identified in TCS:,TCOF1, POLR1D, and POLR1C. We report a clinical and extensive molecular study, including TCOF1, POLR1D, POLR1C, and EFTUD2 genes, in a series of 146 patients with TCS. Phenotype-genotype correlations were investigated for 19 clinical features, between TCOF1 and POLR1D, and the type of mutation or its localization in the TCOF1 gene. We identified 92/146 patients (63%) with a molecular anomaly within TCOF1, 9/146 (6%) within POLR1D, and none within POLR1C. Among the atypical negative patients (with intellectual disability and/or microcephaly), we identified four patients carrying a mutation in EFTUD2 and two patients with 5q32 deletion encompassing TCOF1 and CAMK2A in particular. Congenital cardiac defects occurred more frequently among patients with TCOF1 mutation (7/92, 8%) than reported in the literature. Even though TCOF1 and POLR1D were associated with extreme clinical variability, we found no phenotype-genotype correlation. In cases with a typical phenotype of TCS, 6/146 (4%) remained with an unidentified molecular defect.
ISSN: 1098-3600

hal-01134364
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01134364
DOI : 10.1038/gim.2015.29
PUBMED : 25790162

Éditeur(s) : HAL CCSD
Résumé : International audience
Astrocytes send out long processes that are terminated by endfeet at the vascular surface and regulate vascular functions as well as homeostasis at the vascular interface. To date, the astroglial mechanisms underlying these functions have been poorly addressed. Here we demonstrate that a subset of messenger RNAs is distributed in astrocyte endfeet. We identified, among this transcriptome, a pool of messenger RNAs bound to ribosomes, the endfeetome, that primarily encodes for secreted and membrane proteins. We detected nascent protein synthesis in astrocyte endfeet. Finally, we determined the presence of smooth and rough endoplasmic reticulum and the Golgi apparatus in astrocyte perivascular processes and endfeet, suggesting for local maturation of membrane and secreted proteins. These results demonstrate for the first time that protein synthesis occurs in astrocyte perivascular distal processes that may sustain their structural and functional polarization at the vascular interface.
Cell Discovery

hal-01545319
https://hal.archives-ouvertes.fr/hal-01545319
DOI : 10.1038/celldisc.2017.5

Éditeur(s) : Pergamon-elsevier Science Ltd
Résumé : We report rare earth element (REE) and neodymium (Nd) isotope data for the organic fraction of sediments collected from various depositional environments, i.e. rivers (n=25), estuaries (n=18), open-ocean settings (n=15), and cold seeps (n=12). Sedimentary Organic Matter (SOM) was extracted using a mixed hydrogen peroxide/nitric acid solution (20%-H2O2 – 0.02M-HNO3), after removal of carbonate and oxy-hydroxide phases with dilute hydrochloric acid (0.25M-HCl). A series of experimental tests indicate that extraction of sedimentary organic compounds using H202 may be complicated occasionally by partial dissolution of sulphide minerals and residual carbonates. However, this contamination is expected to be minor for REE because measured concentrations in H2O2 leachates are about two-orders of magnitude higher than in the above mentioned phases. The mean REE concentrations determined in the H2O2 leachates for samples from rivers, estuaries, coastal seas and open-ocean settings yield relatively similar levels, with ΣREE = 109 ± 86 ppm (mean ± s; n=58). The organic fractions leached from cold seep sediments display even higher concentration levels (285 ± 150 ppm; mean ± s; n=12). The H2O2 leachates for most sediments exhibit remarkably similar shale-normalized REE patterns, all characterized by a mid-REE enrichment compared to the other REE. This suggests that the distribution of REE in leached sedimentary organic phases is controlled primarily by biogeochemical processes, rather than by the composition of the source from which they derive (e.g. pore, river or sea- water). The Nd isotopic compositions for organic phases leached from river sediments are very similar to those for the corresponding detrital fractions. In contrast, the SOM extracted from marine sediments display εNd values that typically range between the εNd signatures for terrestrial organic matter (inferred from the analysis of the sedimentary detrital fractions) and marine organic matter (inferred from the analysis of local surface seawater). A notable exception is the case of organic matter (OM) fractions leached from cold seep sediment samples, which sometimes exhibit εNd values markedly different from both terrigenous and surface seawater signatures. This suggests that a significant fraction of organic compounds in these sediments may be derived from chemosynthetic processes, recycling pore water REE characterized by a distinct isotopic composition. Overall, our results confirm that organic matter probably plays an important role in the oceanic REE budget, through direct scavenging and remineralization within the water column. Both the high REE abundances and the shape of shale-normalized patterns for leached SOM also suggest that OM degradation in sub-surface marine sediments during early diagenesis could control, to a large extent, the distribution of REE in pore waters. Benthic fluxes of organic-bound REE could hence substantially contribute to the exchange processes between particulates and seawater that take place at ocean margins. Neodymium isotopes could provide useful information for tracing the origin (terrestrial versus marine) and geographical provenance of organic matter, with potential applications in paleoceanography. In particular, future studies should further investigate the potential of Nd isotopes in organic compounds preserved in sedimentary records for reconstructing past variations of surface ocean circulation.
Geochimica Et Cosmochimica Acta (0016-7037) (Pergamon-elsevier Science Ltd), 2014-09 , Vol. 140 , P. 177-198

Droits : 2014 Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00191/30250/28682.pdf
DOI:10.1016/j.gca.2014.05.016
http://archimer.ifremer.fr/doc/00191/30250/

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 Springer Verlag
Résumé : International audience
Bone Morphogenetic Protein 9 (BMP9) has been recently found to be the physiological ligand for the activin receptor-like kinase 1 (ALK1), and to be a major circulating vascular quiescence factor. Moreover, a soluble chimeric ALK1 protein (ALK1-Fc) has recently been developed and showed powerful anti-tumor growth and anti-angiogenic effects. However, not much is known concerning BMP9. This prompted us to investigate the human endogenous sources of this cytokine and to further characterize its circulating form(s) and its function. Analysis of BMP9 expression reveals that BMP9 is produced by hepatocytes and intrahepatic biliary epithelial cells. Gel filtration analysis combined with ELISA and biological assays demonstrate that BMP9 circulates in plasma (1) as an unprocessed inactive form that can be further activated by furin a serine endoprotease, and (2) as a mature and fully active form (composed of the mature form associated with its prodomain). Analysis of BMP9 circulating levels during mouse development demonstrates that BMP9 peaks during the first 3 weeks after birth and then decreases to 2 ng/mL in adulthood. We also show that circulating BMP9 physiologically induces a constitutive Smad1/5/8 phosphorylation in endothelial cells. Taken together, our results argue for the role of BMP9 as a hepatocyte-derived factor, circulating in inactive (40%) and active (60%) forms, the latter constantly activating endothelial cells to maintain them in a resting state.
ISSN: 1420-682X

hal-00681969
https://hal.archives-ouvertes.fr/hal-00681969
DOI : 10.1007/s00018-011-0751-1
PUBMED : 21710321

Éditeur(s) : HAL CCSD Elsevier
Résumé :  
Tree species-rich tropical rainforests are characterized by a highly variable quality of leaf litter input to the soil at small spatial scales. This diverse plant litter is a major source of energy and nutrients for soil microorganisms, particularly in rainforests developed on old and nutrient-impoverished soils. Here we tested the hypothesis that the variability in leaf litter quality produced by a highly diverse tree community determines the spatial variability of the microbial respiration process in the underlying soil. We analyzed a total of 225 litter-soil pairs from an undisturbed Amazonian rainforest in French Guiana using a hierarchical sampling design. The microbial respiration process was assessed using substrateinduced respiration (SIR) and compared to a wide range of quality parameters of the associated litter layer (litter nutrients, carbon forms, stoichiometry, litter mass and pH). The results show that the variability of both litter quality and SIR rates was more important at large than at small scales. SIR rates varied between 1.1 and 4.0 mg g_1 h_1 and were significantly correlated with litter layer quality (up to 50% of the variability explained by the best mixed linear model). Total litter P content was the individual most important factor explaining the observed spatial variation in soil SIR, with higher rates associated to high litter P. SIR rates also correlated positively with total litter N content and with increasing proportions of labile C compounds. However, contrary to our expectation, SIR rates were not related to litter stoichiometry. These data suggest that in the studied Amazonian rainforest, tree canopy composition is an important driver of the microbial respiration process via leaf litter fall, resulting in potentially strong plant-soil feedbacks. .
ISSN: 0038-0717

hal-01032139
https://hal.archives-ouvertes.fr/hal-01032139
DOI : 10.1016/j.soilbio.2011.01.018

Résumé : Les espaces naturels protégés sont aujourd’hui à l‘échelle mondiale l’une des principales politiques publiques mises en œuvre pour faire face à la destruction des écosystèmes. Leur nombre a beaucoup augmenté ces dernières années et les modes d’action qu’ils recouvrent se sont considérablement diversifiés. Pour autant, les écosystèmes continuent à se dégrader, et l’efficacité de ces dispositifs est souvent remise en cause. Cette thèse vise à analyser les facteurs influant sur l’efficacité des espaces protégés pour la conservation d’écosystèmes amazoniens encore peu dégradés. Elle étudie pour cela la mise en œuvre de dispositifs relevant de doctrines de gestion de l’environnement différentes, basées sur (i) la limitation réglementaire maximale des activités humaines impactantes pour les écosystèmes, (ii) la gestion des ressources par des populations locales ou traditionnelles ou (iii) la mise en place d’une gestion forestière durable sur des terres publiques. Nous nous plaçons dans une posture comparative entre la Guyane (France) et l’Amapá (Brésil), territoires partageant une frontière commune, principalement matérialisée par le fleuve Oyapock. La comparaison internationale entre ces deux régions présentant une couverture exceptionnelle en espaces protégés, dans des conditions écologiques et géographiques relativement similaires, nous permet d’observer l’influence du contexte historique et sociopolitique sur les modes de prise en charge de la gestion de l’environnement par les aires protégées. Nous nous sommes basés sur une approche constructiviste, appuyée sur une production de données principalement qualitatives (entretiens semi-directifs, analyse de documents, observation participante…). Nous avons ainsi procédé à une déconstruction critique des dispositifs « aires protégées », permettant de mettre en lisibilité les enjeux environnementaux qu’ils portent, et d’analyser l’efficacité environnementale des stratégies mises en œuvre. Cette analyse s’est articulée autour d’une lecture à la fois diachronique et multiscalaire des processus de gestion.Nous montrons que la mise en place des espaces protégés de Guyane et d’Amapá a été portée par des coalitions d’acteurs structurées autour de doctrines de gestion, c’est à dire de conceptions partagées des conditions de mise en œuvre d’une « bonne gestion environnementale ». Les dispositifs créés ont hérité des ressources stratégiques d’action et de la légitimité de ces coalitions. Les coalitions porteuses de la création des espaces protégés en Amapá sont fortement articulées aux mouvements sociaux et environnementaux plus généraux de l’Amazonie brésilienne, notamment pour les revendications socio-environnementales émergeant à la sortie de la période dictatoriale. En Guyane française, les espaces naturels protégés sont principalement la résultante de compromis entre d’une part une volonté d’exemplarité de l’action de la France en Amazonie, et d’autre part une recherche de minimisation des conflits avec les acteurs politiques locaux.
Nowadays, natural protected areas are one of the main public policies implemented at the international level in order to prevent the destruction of ecosystems. During the last decades, they became very numerous, and mobilized more and more diversified modes of action. However, natural ecosystems continue to deteriorate, and the effectiveness of protected areas is often questioned. The aim of this thesis was to analyse the factors influencing the effectiveness of protected areas in a context of Amazonian ecosystems that are still well preserved. We observed the implementation of environmental management arrangement (protected areas) that are based on various doctrines: (i) the strong limitation of all harmful human activities through legislation; (ii) the management of resources by local or traditional populations; and (iii) the implementation of sustainable forest management on public lands. We adopted a comparative approach between Guyana (France) and Amapá (Brazil), territories that share a common border, mainly identifiable by the Oyapock River. These two territories present quite similar ecological and geographical conditions, and both have an exceptional coverage of protected areas. Therefore this international comparison allowed us to observe the influence of the historical and socio-political context on the implementation of protected areas. We used a constructivist approach, mainly based on qualitative data (semi-structured interviews, document analysis, participant observation...). We effected a critical deconstruction of "protected areas" management arrangements in order to make their environmental objectives intelligible, and we analysed the environmental effectiveness of the strategies implemented. This analysis was based on a diachronic and multiscalar lecture of management processes. We show that the establishment of protected areas in Guiana and Amapá was led by coalitions of actors structured around management doctrines, i.e. shared conceptions of "good environmental management". Management arrangements created inherited the strategic resources of action and the legitimacy of these coalitions. In Amapá, coalitions were strongly articulated with wider social and environmental movements of the Brazilian Amazon, especially in the case of socio-environmental claims rising at the end of the dictatorship. In French Guiana, the natural protected areas are mainly the result of compromise between the French willingness to serve as an example in the Amazon region, and the minimisation of conflicts with local politicians.

http://www.theses.fr/2014AGUY0744/document

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Key message Molecular markers were used for paternity recovery in a maritime pine (Pinus pinasterAit.) polycross trial, facilitating forward selection. Different breeding strategies for seed orchard establishment were evaluated by comparing genetic gains and diversity. This work opens up new perspectives in maritime pine breeding.Context Polycross mating designs are widely used in forest tree breeding to evaluate parental breeding values for backward selection. Alternatively, polycross progeny trials may be used to select the best trees on the basis of individual breeding values and molecular pedigree analysis.Aims This study aimed to test such a forward selection strategy for the maritime pine breeding program.Methods In a maritime pine polycross trial, progeny with higher breeding values for growth and stem straightness was first preselected with or without relatedness constraints. After paternity recovery, the preselected trees were ranked on the basis of their breeding values, estimated from the recovered full pedigree. Finally, the best candidates were selected with three different strategies (forward, backward, mixed) and three levels of coancestry constraints to establish a virtual clonal seed orchard.Results Complete pedigrees were successfully recovered for most of the preselected trees. There was no major difference in expected genetic gains between the two preselection strategies which differed for relatedness constraints. Genetic gains were slightly higher for forward selection than for classical backward selection.Conclusion This seminal study opens up new perspectives for using forward selection within the French maritime pine breeding program.
ISSN: 1932-6203

hal-01601804
https://hal.archives-ouvertes.fr/hal-01601804
DOI : 10.1371/journal.pone.0049990
PRODINRA : 391860