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
We present a new set of brittle microtectonic measurements carried out in the Pliocene and Quaternary rocks outcropping in several key sectors of the western Betic and Rif orogen, the so-called Gibraltar orogenic arc. This data set, along with available earthquake focal mechanisms and borehole breakouts, allowed us to compile the Pliocene and Quaternary stress map of this area. This map provides new constraints for tectonic models and the present-day tectonic activity of the proposed active eastward subduction of oceanic lithosphere beneath the Gibraltar Arc and roll-back. The horizontal maximum compressive stress (S-Hmax) is NW-SE in the Betic Orogen and N-S/NNW-SSE in the southern Rif Cordillera. There is a significant consistency between S-Hmax and the displacement field deduced from GPS measurements with respect to the African plate: both appear to reflect the NW-SE convergence between the African and the European plates that is perturbed in the Rif. We propose that part of the eastern Rif behaves as a quasi-rigid block welded to the stable African plate. This block is bounded by important faults that localized most of the deformation disturbing the stress and surface displacement field. Pliocene to Quaternary N-S to NW-SE Africa-Europe plate convergence seem to be associated to the reorganization of the remnant Early Miocene subduction system in a continental-continental collision framework. Three-dimensional reconstruction of available seismic tomography plotted against the intermediate seismicity shows that only part of the old subduction system, whose orientation ranges from N20 degrees E to N100 degrees E, remains active: the portion ranging from N30 degrees E to N40 degrees E, orthogonal to the regional convergence. (C) 2011 Elsevier Ltd. All rights reserved.
ISSN: 0264-3707

hal-00671033
https://hal.archives-ouvertes.fr/hal-00671033
DOI : 10.1016/j.jog.2010.12.003

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Aim To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia.Location Two hundred and eighty-three c.1ha forest inventory plots from across Amazonia.Methods We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival.Results PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young- and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric.Main conclusions High ses.PDss and ses.MNTD reflect greater lineage diversity in communities. We suggest that high ses.PDss and ses.MNTD in western Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities.
ISSN: 1366-9516

hal-01557462
https://hal.univ-lorraine.fr/hal-01557462
DOI : 10.1111/ddi.12357

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few 'hyperdominant' species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region.
ISSN: 2041-1723

hal-01204225
https://hal.archives-ouvertes.fr/hal-01204225
DOI : 10.1038/ncomms7857
PRODINRA : 305614
PUBMED : 25919449

Éditeur(s) : Public Library Science
Résumé : Background: Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques - including site-based monitoring, genetic analyses, mark-recapture studies and telemetry - can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. Methodology/Principal Findings: To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine-to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs), for marine turtles globally. Conclusions/Significance: The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities. In addition, the RMU framework - including maps and supporting metadata - will be an iterative, user-driven tool made publicly available in an online application for comments, improvements, download and analysis.
Plos One (1932-6203) (Public Library Science), 2010-12 , Vol. 5 , N. 12 , P. -

Droits : 2010 Plos One
http://archimer.ifremer.fr/doc/00028/13926/11308.pdf
DOI:10.1371/journal.pone.0015465
http://archimer.ifremer.fr/doc/00028/13926/

Éditeur(s) : HAL CCSD Institute of Physics
Résumé : International audience
ISSN: 0957-4484

hal-01674723
https://hal-umontpellier.archives-ouvertes.fr/hal-01674723
DOI : 10.1088/1361-6528/aa9c07

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Large-scale conical and saucer-shaped sand injectites have been identified in the Upper Miocene sediments of the Lower Congo Basin. These structures are evidenced on the 3D high-resolution seismic data at about 600 ms TWT (two-way traveltime) beneath the seabed. The conical and saucer-shaped anomalies range from 20 to 80 m in height, 50 to 300 m in diameter, and 10 to 20 ms TWT in thickness. They are located within a sedimentary interval of about 100 m in thickness and are aligned over 20 km in dip direction (NE-SW), above the NW margin of an underlying Upper Miocene submarine fan. We have interpreted the conical and saucer-shaped anomalies as upward-emplaced sand injectites sourced from the Upper Miocene fan because of their discordant character, the postsedimentary uplifting of the sediments overlying the cones and saucer-shaped bodies, the alignment with the lateral fringe of the Upper Miocene submarine fan, and the geological context. Sand injection dates from the Miocene-Pliocene transition (approximately 5.3 Ma). The prerequisite overpressure to the sand injection process may be due to the buoyancy effect of hydrocarbons accumulated in the margins of the fan. Additionally, overpressure could have been enhanced by the lateral transfer of fluids operating in the inclined margins of the lobe. The short duration of sand injection and the presence of many sandstone intrusions suggested that the process of injection was triggered by an event, likely due to a nearby fault displacement related to diapiric movements. This is the first time that sand injectites of seismic scale have been described from the Lower Congo Basin. The localized nature of these injectites has led to a change in the migration path of fluids through the sedimentary cover. Consequently, the sand intrusions are both evidence and vectors of fluid migration within the basin fill.
ISSN: 1468-8115

hal-00963594
https://hal.archives-ouvertes.fr/hal-00963594
DOI : 10.1111/gfl.12057

Éditeur(s) : Public Library Science
Résumé : Where conservation resources are limited and conservation targets are diverse, robust yet flexible priority-setting frameworks are vital. Priority-setting is especially important for geographically widespread species with distinct populations subject to multiple threats that operate on different spatial and temporal scales. Marine turtles are widely distributed and exhibit intra-specific variations in population sizes and trends, as well as reproduction and morphology. However, current global extinction risk assessment frameworks do not assess conservation status of spatially and biologically distinct marine turtle Regional Management Units (RMUs), and thus do not capture variations in population trends, impacts of threats, or necessary conservation actions across individual populations. To address this issue, we developed a new assessment framework that allowed us to evaluate, compare and organize marine turtle RMUs according to status and threats criteria. Because conservation priorities can vary widely (i.e. from avoiding imminent extinction to maintaining long-term monitoring efforts) we developed a "conservation priorities portfolio" system using categories of paired risk and threats scores for all RMUs (n = 58). We performed these assessments and rankings globally, by species, by ocean basin, and by recognized geopolitical bodies to identify patterns in risk, threats, and data gaps at different scales. This process resulted in characterization of risk and threats to all marine turtle RMUs, including identification of the world's 11 most endangered marine turtle RMUs based on highest risk and threats scores. This system also highlighted important gaps in available information that is crucial for accurate conservation assessments. Overall, this priority-setting framework can provide guidance for research and conservation priorities at multiple relevant scales, and should serve as a model for conservation status assessments and priority-setting for widespread, long-lived taxa.
Plos One (1932-6203) (Public Library Science), 2011-09 , Vol. 6 , N. 9 , P. 1-14

Droits : 2011 Wallace et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License
http://archimer.ifremer.fr/doc/00050/16097/13573.pdf
DOI:10.1371/journal.pone.0024510
http://archimer.ifremer.fr/doc/00050/16097/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Miradouro da Lua cliffs, which are 60 km south of Luanda, record the building and uplift of the late Neogene Palaeo-Cuanza delta. The detailed study of the sedimentary architecture and stacking pattern permitted separation of the pile into five depositional units bounded by erosional surfaces and characterised by separate facies associations (genetic sequences = units in this paper). At the base of the series, aeolian deposits (Unit 1) mark the development of a possible coastal desert during the late Miocene aridification. The major Pliocene sea-level rise (Transgressive Systems Tract) led to the drowning of the continental platform into a discrete shoreface-foreshore sequence (Unit 2), followed by an expanded deltaic sequence (Unit 3) that represents the main outcrop of the area. The sedimentary fabric of this prograding wedge during the Highstand Systems Tract reveals laterally stacked pluri-hectometic mouth bars built by the abrupt switching of a bird-foot delta during the Pliocene highstand. The clinoforms are deeply incised by submarine gullies filled both by periodic river-driven turbidite and tidal currents (Unit 4) during the coeval growing of the delta. The topset of the prograding wedge and associated gullies infill is truncated by an overall erosional unconformity that marks the widespread development of an extensive braid-delta system (Unit 5) during the lower Pleistocene sea-level drop (Lowstand Systems Tract). The last 6 m of the Braid-delta unit is overprinted by a ferallitic profile, forming the surface of the plateau and indicating long-term subaerial exposure and weathering processes consistent with the maximum warming of the middle to late Pleistocene interglacial periods. The successive abrupt shifts of the depositional systems through the sedimentary pile indicate a high-amplitude sea level amplified by major coastal uplifts and the reorganisation of the fluvial network. In this context, the palaeo-Cuanza prograding wedge signals the westward tilting and 60 m total uplift of the coastal plain during the Pliocene. A new uplift pulse by differential tilt and slope increase is deduced from the widespread development of the braid-delta complex during the early Pleistocene. The last tectonic event corresponds to the 80- to 100-m uplift and ferallitic paedogenesis during the middle to late Pleistocene interglacial stages.
ISSN: 0899-5362

hal-01053716
https://hal.archives-ouvertes.fr/hal-01053716
DOI : 10.1016/j.jafrearsci.2014.01.013

Éditeur(s) : HAL CCSD Wiley
Résumé :  
Positive aboveground biomass trends have been reported from old-growth forests across the Amazon basin and hypothesized to reflect a large-scale response to exterior forcing. The result could, however, be an artefact due to a sampling bias induced by the nature of forest growth dynamics. Here, we characterize statistically the disturbance process in Amazon old-growth forests as recorded in 135 forest plots of the RAINFOR network up to 2006, and other independent research programmes, and explore the consequences of sampling artefacts using a data-based stochastic simulator. Over the observed range of annual aboveground biomass losses, standard statistical tests show that the distribution of biomass losses through mortality follow an exponential or near-identical Weibull probability distribution and not a power law as assumed by others. The simulator was parameterized using both an exponential disturbance probability distribution as well as a mixed exponential-power law distribution to account for potential large-scale blowdown events. In both cases, sampling biases turn out to be too small to explain the gains detected by the extended RAINFOR plot network. This result lends further support to the notion that currently observed biomass gains for intact forests across the Amazon are actually occurring over large scales at the current time, presumably as a response to climate change.
ISSN: 1354-1013

hal-01032162
https://hal.archives-ouvertes.fr/hal-01032162
DOI : 10.1111/j.1365-2486.2009.01891.x

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
We analyse the fluid flow regime within sediments on the Eastern levee of the modern Mississippi Canyon using 3D seismic data and downhole logging data acquired at Sites U1322 and U1324 during the 2005 Integrated Ocean Drilling Program (IODP) Expedition 308 in the Gulf of Mexico. Sulphate and methane concentrations in pore water show that sulphate-methane transition zone, at 74 and 94 m below seafloor, are amongst the deepest ever found in a sedimentary basin. This is in part due to a basinward fluid flow in a buried turbiditic channel (Blue Unit, 1000 mbsf), which separates sedimentary compartments located below and above this unit, preventing normal upward methane flux to the seafloor. Overpressure in the lower compartment leads to episodic and focused fluid migration through deep conduits that bypass the upper compartment, forming mud volcanoes at the seabed. This may also favour seawater circulation and we interpret the deep sulphate-methane transition zones as a result of high downward sulphate fluxes coming from seawater that are about 5-10 times above those measured in other basins. The results show that geochemical reactions within shallow sediments are dominated by seawater downwelling in the Mars-Ursa basin, compared to other basins in which the upward fluid flux is controlling methane-related reactions. This has implications for the occurrence of gas hydrates in the subsurface and is evidence of the active connection between buried sediments and the water column.
ISSN: 1468-8115

hal-00590501
https://hal.archives-ouvertes.fr/hal-00590501
DOI : 10.1111/j.1468-8123.2010.00304.x

Éditeur(s) : HAL CCSD
Résumé : Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades, with a substantial fraction of this sink probably located in the tropics, particularly in the Amazon. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale, and is contrary to expectations based on models.
ISSN: 1476-4687

hal-01204223
https://hal.archives-ouvertes.fr/hal-01204223
DOI : 10.1038/nature14283
PRODINRA : 294797
PUBMED : 25788097

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Clin Microbiol Infect 2012; 18 (Suppl. 4): 4043 Abstract In order to study complex microbial communities and their associated mobile genetic elements, such as the human gut microbiome, evolutionists could explore their genetic diversity with shared sequence networks. In particular, the detection of remarkable structures in gene networks of the gut microbiome could serve to identify important functions within the community, and would ease comparison of data sets from microbiomes of various sources (human, ape, mouse etc.) in a single analysis.
ISSN: 1198-743X

hal-01544804
https://hal.archives-ouvertes.fr/hal-01544804
DOI : 10.1111/j.1469-0691.2012.03856.x

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 Oxford University Press (OUP)
Résumé : International audience
Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as ``public goods,'' subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define `` family resemblances'' to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.
ISSN: 0737-4038

hal-01544794
https://hal.archives-ouvertes.fr/hal-01544794
DOI : 10.1093/molbev/mst228