Éditeur(s) : HAL CCSD Wiley
Résumé : absent
ISSN: 1354-1013

hal-01204212
https://hal.archives-ouvertes.fr/hal-01204212
PRODINRA : 261473
PUBMED : 23996917

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 Elsevier
Résumé : International audience
The Ukrainian shield hosts two Palaeoproterozoic anorthosite-mangerite-charnockite-granite (AMCG) complexes (the Korosten and Korsun-Novomyrhorod complexes) that intruded Palaeoproterozoic continental crust in north-western and central parts of the shield, respectively. We report results of U-Pb zircon and baddeleyite dating of 16 samples from the Korosten plutonic complex (KPC), and 6 samples from the Korsun-Novomyrhorod plutonic complex (KNPC). Fifteen zircon samples from both complexes were also analysed for Hf isotopes. These new, together with previously published data indicate that the formation of the KPC started at c. 1815 Ma and continued until 1743 Ma with two main phases of magma emplacement at 1800–1780 and 1770–1758 Ma. Each of the main phases of magmatic activity included both basic and silicic members. The emplacement history of the KNPC is different from that of the KPC. The vast majority of the KNPC basic and silicic rocks were emplaced between c. 1757 and 1750 Ma; the youngest stages of the complex are represented by monzonites and syenites that were formed between 1748 and 1744 Ma. Both Ukrainian AMCG complexes are closely associated in space and time with mantle-derived mafic and ultramafic dykes. The Hf isotope ratios in the zircons indicate a predominantly crustal source for the initial melts with some input of juvenile Hf from mantle-derived tholeiite melts.The preferred model for the formation of the Ukrainian AMCG complexes involves the emplacement of large volumes of hot mantle-derived tholeiitic magma into the lower crust. This resulted in partial melting of mafic lower-crustal material, mixing of lower crustal and tholeiitic melts, and formation of ferromonzodioritic magmas. Further fractional crystallization of the ferromonzodioritic melts produced the spectrum of basic rocks in the AMCG complexes. Emplacement of the ferromonzodioritic and tholeiitic melts into the middle crust and their partial crystallization caused abundant melting of the ambient crust and formation of the large volumes of granitic rocks present in the complexes.
ISSN: 0301-9268

hal-01622715
https://hal.archives-ouvertes.fr/hal-01622715
DOI : 10.1016/j.precamres.2017.02.009

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Grey (Halichoerus grypus) and harbour seals (Phoca vitulina) are sympatric seal species, but they display distinct strategies of habitat use and connectivity between haulout sites. The distribution patterns and variations in relative abundance of both species were investigated along the French coast of the English Channel, at the southern limit of their range where seal numbers are increasing. Regular censuses conducted at all main haulout sites in mainland France showed significant seasonal variations at most sites, with more harbour seals counted during summer (breeding and moulting seasons), and more grey seals during summer only in the eastern English Channel. Trends in maximum haulout numbers at haulout sites showed a significant increase over the last five years, ranging from 9.7 to 30.9% per year for harbour seals, and from 5.8% (in the western English Channel) to 49.2% (in the eastern English Channel) per year for grey seals. These rates of increase in grey seal numbers are not linked to local pup production and most probably result from seal movements from the southwest British Isles and the North Sea, respectively. Aerial surveys conducted across the English Channel showed that most seal observations at sea were concentrated in the north-eastern English Channel. Telemetry showed that the 28 harbour seals tracked remained highly coastal, within a radius of 100 km from their haulout sites, and did not move to other known colonies. Grey seals moved much greater distances, reaching up to 1200 km from their capture site. More than half of the 45 grey seals tracked crossed the English Channel, especially during the breeding season, moving to known colonies in the southwest British Isles and the North Sea. Combining individual tracks and long-term surveys of the seal populations allowed a better understanding of the dynamics of these populations and their connectivity at a larger regional scale. The findings provide direct information for the management of grey and harbour seals within the frame of the Marine Strategy Framework Directive, and highlight focus areas where potential interactions between the two species should be monitored.
ISSN: 0967-0645

hal-01509674
https://hal.archives-ouvertes.fr/hal-01509674
DOI : 10.1016/j.dsr2.2017.04.004

Éditeur(s) : HAL CCSD Annual Reviews
Résumé : International audience
The record of the continental lithosphere is patchy and incomplete; no known rock is older than 4.02 Ga, and less than 5% of the rocks preserved are older than 3 Ga. In addition, there is no recognizable mantle lithosphere from before 3 Ga. We infer that there was lithosphere before 3 Ga and that ∼3 Ga marks the stabilization of blocks of continental lithosphere that have since survived. This was linked to plate tectonics emerging as the dominant tectonic regime in response to thermal cooling, the development of a more rigid lithosphere, and the recycling of water, which may in turn have facilitated plate tectonics. A number of models, using different approaches, suggest that at 3 Ga the volume of continental crust was ∼70% of its present-day volume and that this may be a minimum value. The continental crust before 3 Ga was on average more mafic than that generated subsequently, and this pre-3 Ga mafic new crust had fractionated Lu/Hf and Sm/Nd ratios as inferred for the sources of tonalite-trondhjemite-granodiorite and later granites. The more intermediate composition of new crust generated since 3 Ga is indicated by its higher Rb/Sr ratios. This change in composition was associated with an increase in crustal thickness, which resulted in more emergent crust available for weathering and erosion. This in turn led to an increase in the Sr isotope ratios of seawater and in the drawdown of CO2. Since 3 Ga, the preserved record of the continental crust is marked by global cycles of peaks and troughs of U-Pb crystallization ages, with the peaks of ages appearing to match periods of supercontinent assembly. There is increasing evidence that the peaks of ages represent enhanced preservation of magmatic rocks in periods leading up to and including continental collision in the assembly of supercontinents. These are times of increased crustal growth because more of the crust that is generated is retained within the crust. The rates of generation of continental crust and mantle lithosphere may have remained relatively constant at least since 3 Ga, yet the rates of destruction of continental crust have changed with time. Only relatively small volumes of rock are preserved from before 3 Ga, and so it remains difficult to establish which of these are representative of global processes and the extent to which the rock record before 3 Ga is distorted by particular biases.
ISSN: 0084-6597

hal-01622692
https://hal.archives-ouvertes.fr/hal-01622692
DOI : 10.1146/annurev-earth-063016-020525

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
ISSN: 0305-1048

hal-01146849
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146849
DOI : 10.1093/nar/gkv350
PUBMED : 25897122

Éditeur(s) : HAL CCSD Royal Society, The
Résumé : International audience
To forecast marine disease outbreaks as oceans warm requires new environmental surveillance tools. We describe an iterative process for developing these tools that combines research, development and deployment for suitable systems. The first step is to identify candidate host–pathogen systems. The 24 candidate systems we identified include sponges, corals, oysters, crustaceans, sea stars, fishes and sea grasses (among others). To illustrate the other steps, we present a case study of epizootic shell disease (ESD) in the American lobster. Increasing prevalence of ESD is a contributing factor to lobster fishery collapse in southern New England (SNE), raising concerns that disease prevalence will increase in the northern Gulf of Maine under climate change. The lowest maximum bottom temperature associated with ESD prevalence in SNE is 128C. Our seasonal outlook for 2015 and long-term projections show bottom temperatures greater than or equal to 128C may occur in this and coming years in the coastal bays of Maine. The tools presented will allow managers to target efforts to monitor the effects of ESD on fishery sustainability and will be iteratively refined. The approach and case example highlight that temperature-based surveillance tools can inform research, monitoring and management of emerging and continuing marine disease threats.
ISSN: 0080-4622

Droits : http://creativecommons.org/licenses/by/
hal-01282834
https://hal-univ-perp.archives-ouvertes.fr/hal-01282834
https://hal-univ-perp.archives-ouvertes.fr/hal-01282834/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01282834/file/20150208.full.pdf
DOI : 10.1098/rstb.2015.0208

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Losses of corals worldwide emphasize the need to understand what drives reef decline. Stressors such as overfishing and nutrient pollution may reduce resilience of coral reefs by increasing coral–algal competition and reducing coral recruitment, growth and survivorship. Such effects may themselves develop via several mechanisms, including disruption of coral microbiomes. Here we report the results of a 3-year field experiment simulating overfishing and nutrient pollution. These stressors increase turf and macroalgal cover, destabilizing microbiomes, elevating putative pathogen loads, increasing disease more than twofold and increasing mortality up to eightfold. Above-average temperatures exacerbate these effects, further disrupting microbiomes of unhealthy corals and concentrating 80% of mortality in the warmest seasons. Surprisingly, nutrients also increase bacterial opportunism and mortality in corals bitten by parrotfish, turning normal trophic interactions deadly for corals. Thus, overfishing and nutrient pollution impact reefs down to microbial scales, killing corals by sensitizing them to predation, above-average temperatures and bacterial opportunism.
ISSN: 2041-1723

Droits : http://creativecommons.org/licenses/by/
hal-01340547
https://hal-univ-perp.archives-ouvertes.fr/hal-01340547
https://hal-univ-perp.archives-ouvertes.fr/hal-01340547/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01340547/file/ncomms11833.pdf
DOI : 10.1038/ncomms11833

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
Coral reef fisheries support the development of local and national economies and are the basis of important cultural practices and worldviews. Transitioning economies, human development, and environmental stress can harm this livelihood. Here we focus on a transitioning social-ecological system as a case study (Moorea, French Polynesia). We review fishing practices and three decades of effort and landing estimates with the broader goal of informing management. Fishery activities in Moorea are quite challenging to quantify because of the diversity of gears used, the lack of centralized access points or markets, the high participation rates of the population in the fishery, and the overlapping cultural and economic motivations to catch fish. Compounding this challenging diversity, we lack a basic understanding of the complex interplay between the cultural, subsistence, and commercial use of Moorea's reefs. In Moorea, we found an order of magnitude gap between estimates of fishery yield produced by catch monitoring methods (2 t km −2 ∼ year −1) and estimates produced using consumption or participatory socioeconomic consumer surveys (∼24 t km −2 year −1). Several lines of evidence suggest reef resources may be overexploited and stakeholders have a diversity of opinions as to whether trends in the stocks are a cause for concern. The reefs, however, remain ecologically resilient. The relative health of the reef is striking given the socioeconomic context. Moorea has a relatively high population density, a modern economic system linked into global flows of trade and travel, and the fishery has little remaining traditional or customary management. Other islands in the Pacific in similar contexts in Polynesia such as Hawaii, that continue to develop economically, may have small-scale fisheries that increasingly resemble Moorea. Therefore, understanding Moorea's reef fisheries may provide insight into their future.
ISSN: 2296-7745

Droits : http://creativecommons.org/licenses/by/
hal-01325804
https://hal-univ-perp.archives-ouvertes.fr/hal-01325804
https://hal-univ-perp.archives-ouvertes.fr/hal-01325804/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01325804/file/fmars-03-00070.pdf
DOI : 10.3389/fmars.2016.00070

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 Elsevier
Résumé : International audience
Sedimentary rocks and detrital minerals sample large areas of the continental crust, and they are increasingly seen as a reliable archive for its global evolution. This study presents two approaches to model the growth of the continental crust through the sedimentary archive. The first builds on the variations in U-Pb, Hf and O isotopes in global databases of detrital zircons. We show that uncertainty in the Hf isotope composition of the mantle reservoir from which new crust separated, in the 176Lu/177Hf ratio of that new crust, and in the contribution in the databases of zircons that experienced ancient Pb loss(es), adds some uncertainty to the individual Hf model ages, but not to the overall shape of the calculated continental growth curves. The second approach is based on the variation of Nd isotopes in 645 worldwide fine-grained continental sedimentary rocks with different deposition ages, which requires a correction of the bias induced by preferential erosion of younger rocks through an erosion parameter referred to as K. This dimensionless parameter relates the proportions of younger to older source rocks in the sediment, to the proportions of younger to older source rocks present in the crust from which the sediment was derived. We suggest that a Hadean/Archaean value of K = 1 (i.e., no preferential erosion), and that post-Archaean values of K = 4–6, may be reasonable for the global Earth system. Models built on the detrital zircon and the fine-grained sediment records independently suggest that at least 65% of the present volume of continental crust was established by 3 Ga. The continental crust has been generated continuously, but with a marked decrease in the growth rate at ~ 3 Ga. The period from > 4 Ga to ~ 3 Ga is characterised by relatively high net rates of continental growth (2.9–3.4 km3 yr− 1 on average), which are similar to the rates at which new crust is generated (and destroyed) at the present time. Net growth rates are much lower since 3 Ga (0.6–0.9 km3 yr− 1 on average), which can be attributed to higher rates of destruction of continental crust. The change in slope in the continental growth curve at ~ 3 Ga is taken to indicate a global change in the way bulk crust was generated and preserved, and this change has been linked to the onset of subduction-driven plate tectonics. At least 100% of the present volume of the continental crust has been destroyed and recycled back into the mantle since ~ 3 Ga, and this time marks a transition in the average composition of new continental crust. Continental crust generated before 3 Ga was on average mafic, dense, relatively thin (< 20 km) and therefore different from the calc-alkaline andesitic crust that dominates the continental record today. Continental crust that formed after 3 Ga gradually became more intermediate in composition, buoyant and thicker. The increase in crustal thickness is accompanied by increasing rates of crustal reworking and increasing input of sediment to the ocean. These changes may have been accommodated by a change in lithospheric strength at around 3 Ga, as it became strong enough to support high-relief crust. This time period therefore indicates when significant volumes of continental crust started to become emergent and were available for erosion and weathering, thus impacting on the composition of the atmosphere and the oceans.
ISSN: 0037-0738

hal-01622696
https://hal.archives-ouvertes.fr/hal-01622696
DOI : 10.1016/j.sedgeo.2017.06.001

Éditeur(s) : HAL CCSD Wiley
Résumé : The intensification of the hydrological cycle, with an observed and modeled increase in drought incidence and severity, underscores the need to quantify drought effects on carbon cycling and the terrestrial sink. FLUXNET, a global network of eddy covariance towers, provides dense data streams of meteorological data, and through flux partitioning and gap filling algorithms, estimates of net ecosystem productivity (FNEP), gross ecosystem productivity (P), and ecosystem respiration (R). We analyzed the functional relationship of these three carbon fluxes relative to evaporative fraction (EF), an index of drought and site water status, using monthly data records from 238 micrometeorological tower sites distributed globally across 11 biomes. The analysis was based on relative anomalies of both EF and carbon fluxes and focused on drought episodes by biome and climatic season. Globally P was ≈50% more sensitive to a drought event than R. Network-wide drought-induced decreases in carbon flux averaged −16.6 and −9.3 g C m−2 month−1 for P and R, i.e., drought events induced a net decline in the terrestrial sink. However, in evergreen forests and wetlands drought was coincident with an increase in P or R during parts of the growing season. The most robust relationships between carbon flux and EF occurred during climatic spring for FNEP and in climatic summer for P and R. Upscaling flux sensitivities to a global map showed that spatial patterns for all three carbon fluxes were linked to the distribution of croplands. Agricultural areas exhibited the highest sensitivity whereas the tropical region had minimal sensitivity to drought. Combining gridded flux sensitivities with their uncertainties and the spatial grid of FLUXNET revealed that a more robust quantification of carbon flux response to drought requires additional towers in all biomes of Africa and Asia as well as in the cropland, shrubland, savannah, and wetland biomes globally.
ISSN: 1354-1013

hal-01032076
https://hal.archives-ouvertes.fr/hal-01032076
DOI : 10.1111/j.1365-2486.2009.01991.x

Éditeur(s) : HAL CCSD
Résumé : International audience
Indic scripts are among few scripts in the world that have had continuous development for more than two millennia. The modern forms of the scripts are the result of infinitesimal changes in handwriting being accumulated over centuries. They present us with a unique opportunity to understand various changes occurring in handwriting behavior. We have taken four major Indic scripts in six different stages of evolution and extracted features quantifying their handwriting behavior. We have derived these features by applying the principles of handwriting production and gesture analysis on a paleographic data set. We present various trends and behaviors that occurred during script development and discuss our interpretation of the results in terms of evolution of handwriting behavior. We then briefly discuss the detailed analyses that will be performed on the dataset in the future. We also consider the applications of these results in digital paleography and handwriting-driven systems.
17th Biennial Conference of the International Graphonomics Society
Pointe-à-Pitre, Guadeloupe

hal-01165770
https://hal.univ-antilles.fr/hal-01165770
https://hal.univ-antilles.fr/hal-01165770/document
https://hal.univ-antilles.fr/hal-01165770/file/IGS_2015_submission_8.pdf