Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We explore the use of seismic noise produced by rivers to monitor the bed load transport in the case of a low-discharge braided river in the French Alps: the "torrent de St Pierre". For this purpose, we deployed two dedicated seismic networks during summers 2007 and 2008, for which the characteristics of the recorded continuous signal are similar despite changes in the sensor locations. For dry weather conditions, only melting of nearby glaciers controls the supply of water to the stream. In these conditions, the river hydrology and the seismic energy in the 2-80 Hz frequency band both follow a diurnal fluctuation similar to the thermal amplitude. In contrast during rainfall episodes, the temperature variation fails to explain the hydrodynamic changes. Dense cloud covers reduce glacier melting and the recorded seismic energy denotes bursts of high-frequency seismic noise well correlated with water level data. Comparisons between the recorded seismic signals and the collected hydrological and sediment load data indicate that a frequency band of 3-9 Hz best explains the water level changes and thus the seismic waves coming from the flow turbulence. These analyses also reveal the presence of a seismic noise threshold that might be linked to the water shear stress exerted by the flowing water. Using the seismic energy in this frequency band as a proxy of the fluvial shear stress, the seismic-hydrologic relationship may be sensitive to variations in bed load transport. The spectral content of the seismic energy shows patterns consistent with the mobilization of sediment particles. From the interpretations of the seismic wave attenuation of river sources, we finally propose that stations at a distance from the stream less than 50 m are able to record most sediment particles. Farther stations are still useful during extreme events when largest grain sizes are mobilized. More generally this study demonstrates the feasibility of using the river seismic signal to survey bed load transport in various river types from small braided mountain rivers like the "torrent de St Pierre" to the large entrenched Himalayan rivers.
ISSN: 0022-1694

hal-00644789
https://hal.archives-ouvertes.fr/hal-00644789
DOI : 10.1016/j.jhydrol.2011.07.014

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
Résumé : International audience
Geodynamics and Environment in East Asia Symposium (GEEA Meeting)
Hualien, Taiwan

insu-01119754
https://hal-insu.archives-ouvertes.fr/insu-01119754

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : International audience
ISSN: 0168-1923

hal-01086595
https://hal-agroparistech.archives-ouvertes.fr/hal-01086595
DOI : 10.1016/j.agrformet.2009.06.020

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 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
Résumé : International audience
Extreme rainfall events can trigger numerous landslides in mountainous areas and a prolonged increase of river sediment load. The resulting mass transfer at the Earth surface in turn induces stress changes at depth, which could be sufficient to trigger shallow earthquakes. The 2009 Morakot typhoon represents a good case study as it delivered 3 m of precipitation in 3 days and caused some of the most intense erosion ever recorded. Analysis of seismicity time-series before and after the Morakot typhoon reveals a systematic increase of shallow (i.e. 0-15 km of depth) earthquake frequency in the vicinity of the areas displaying a high spatial density of landslides. This step-like increase in frequency lasts for at least 2-3 years and does not follow an Omori-type aftershock sequence. Rather, it is associated to a step change of the Gutenberg-Richter b-value of the earthquake catalog. Both changes occurred in mountainous areas of southwest Taiwan, where typhoon Morakot caused extensive landsliding. These spatial and temporal correlations strongly suggest a causal relationship between the Morakot-triggered landslides and the increase of earthquake frequency and their associated b-value. We propose that the progressive removal of landslide materials from the steep mountain landscape by river sediment transport acts as an approximately constant increase of the stress rate with respect to pre-typhoon conditions, and that this in turn causes a step-wise increase in earthquake frequency. To test this hypothesis, we investigate the response of a rate-and-state fault to stress changes using a 2-D continuum elasto-dynamic model. Consistent with the results of Ader et al. (2013), our preliminary results show a step-like increase of earthquake frequency in response to a step-like decrease of the fault normal stress. We also investigate the sensitivity of the amplitude and time-scale of the earthquake frequency increase to the amplitude of the normal stress change and to rheological parameters. Our study offers new insights on the potential influence of extreme erosional events on the short-time scale dynamics of faults and earthquakes.
American Geophysical Union Fall Meeting 2016
San Francisco, United States

insu-01416987
https://hal-insu.archives-ouvertes.fr/insu-01416987

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The investigation of deformation rates on a mountain piedmont can provide key information for improving our understanding of the overall dynamics of a mountain range. Here, we estimate the shortening rate absorbed by a Quaternary emergent detachment fold on the southeastern piedmont of the Tianshan (China). Our work is primarily based on new 10Be cosmogenic exposure dating of deformed alluvial surfaces. The method we have developed combines depth profiling with sampling of surface cobbles, thereby allowing exposure time, erosion rate and inheritance to be simultaneously constrained. The exposure ages of the uppermost uplifted alluvial surfaces are around 140±17 ka140±17 ka, 130±9 ka130±9 ka and 47±9 ka47±9 ka, from west to east. A terrace lying below the 140 ka surface is dated at 65±5 ka65±5 ka. The ages of the uplifted and folded alluvial surfaces were then combined with estimates of shortening obtained using two distinct methods: (1) the excess area method, where sedimentation rates, extracted from magnetostratigraphic studies, are used to determine the amount of sedimentation after the abandonment of the river; and (2) a folding model derived from sandbox experiments. The late Pleistocene shortening rates are shown to be between 0.4±0.1 mm/yr0.4±0.1 mm/yr and 0.8±0.5 mm/yr0.8±0.5 mm/yr on the western part of the fold and 2.1±0.4 mm/yr2.1±0.4 mm/yr along its central part. The central part of the frontal Yakeng anticline therefore accommodates up to 25% of the total shortening currently absorbed across the whole Eastern Tianshan range (8 mm/yr). However, this situation seems to have prevailed for only the last 150 ka, as the shortening rate absorbed by this nascent fold was previously ten times slower. While the initiation of folding of the Yakeng anticline can be traced back to 5.5 Ma ago, the basinward migration of the active deformation front onto the Yakeng fold is a relatively recent phenomenon and appears to be diachronous from west to east, probably in relation to the tectonic activity of the folds in the hinterland.
ISSN: 0012-821X

hal-01306997
https://hal.archives-ouvertes.fr/hal-01306997
DOI : 10.1016/j.epsl.2015.11.041

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
: Estradiol signaling is ideally suited for analyzing molecular and functional linkages between the different layers of information directing transcriptional regulations: DNA sequence, chromatin modifications and the spatial organization of the genome. Hence, estrogen receptor (ER) can bind at a distance from its target genes and engages timely and spatially coordinated processes to regulate their expression. In the context of the coordinated regulations of co-linear genes, identifying which ER binding sites (ERBSs) regulate a given gene still remains a challenging question. Here, we investigated the coordination of such regulatory events at a 2 Mb genomic locus containing the estrogen-sensitive TFF cluster of genes in breast cancer cells. We demonstrated that this locus exhibits a hormone and cohesin-dependent reduction in the plasticity of its three-dimensional organization that allows multiple ERBSs to be dynamically brought to the vicinity of estrogen-sensitive genes. Additionally, by using triplex forming oligonucleotides, we could precisely document the functional links between ER engagement at given ERBSs and the regulation of particular genes. Hence, our data evidence a formerly suggested cooperation of enhancers towards gene regulations, and also show that redundancy between ERBSs can occur.
ISSN: 0270-7306

hal-00984591
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00984591
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00984591/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00984591/file/Mol._Cell._Biol.-2014-Quintin-MCB.00918-13.pdf
DOI : 10.1128/MCB.00918-13

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : We present a regional surface waveform tomography of the Pacific upper mantle, obtained using an automated multimode surface waveform inversion technique on fundamental and higher mode Rayleigh waves, to constrain the VSV structure down to ∼400 km depth. We have improved on previous implementations of this technique by robustly accounting for the effects of uncertainties in earthquake source parameters in the tomographic inversion. We have furthermore improved path coverage in the South Pacific region by including Rayleigh wave observations from the French Polynesian Pacific Lithosphere and Upper Mantle Experiment deployment. This improvement has led to imaging of vertical low-velocity structures associated with hotspots within the South Pacific Super-Swell region. We have produced an age-dependent averagecross-sectionforthePacificOceanlithosphereandfoundthattheincreaseinVSV with age is broadly compatible with a half-space cooling model of oceanic lithosphere formation. We cannot confirm evidence for a Pacific-wide reheating event. Our synthetic tests show that detailed interpretation of average VSV trends across the Pacific Ocean may be misleading unless lateral resolution and amplitude recovery are uniform across the region, a condition that is difficult to achieve in such a large oceanic basin with current seismic stations.
ISSN: 0956-540X

hal-00105949
https://hal.archives-ouvertes.fr/hal-00105949
https://hal.archives-ouvertes.fr/hal-00105949/document
https://hal.archives-ouvertes.fr/hal-00105949/file/Maggi_Pacif_tomo_GJI2006.pdf
DOI : 10.1111/j.1365-246X.2006.03037.x

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
The 856 A.D. Qumis earthquake (M7.9) is the most destructive earthquake to have occurred in Iran, killing more than 200,000 people and destroying the cities of Damghan and the old Parthian capital of Shahr-i Qumis (Hecatompylos). This study combines evidence of historical seismicity with observations of the geomorphology and paleoseismology to provide the first detailed description of active faulting in the Damghan region of the east Alborz mountains, Iran. Regional left-lateral shear is accommodated on the Astaneh, Damghan, and North Damghan faults. Quaternary alluvial fans have been displaced along the Astaneh fault, with 15–20 m stream offsets recording the cumulative displacement over the last two to five earthquakes. A paleoseismology study from a single trench along a 5–10 km segment of the Astaneh fault reveals a rupture prior to 1300 A.D. and significantly later than 600 B.C. Despite the limitations of a single trench in documenting the spatial and temporal evolution of the fault over the late Quaternary, we are nevertheless able to bracket the last event to a time period consistent with the 856 A.D. earthquake. Two older earthquakes were also identified during the Holocene occurring between 600 B.C. and 4600 B.C. and between 4600 B.C. and 9600 B.C. The location of our trench within a bend on the Astaneh fault, which could act as a barrier to rupture propagation, means the three earthquakes recovered from our trench over the Holocene may represent a minimum. Further trenching will reveal how the Astaneh fault ruptures over repeated earthquakes and, consequently, the magnitude and extent of slip during the 856 A.D. earthquake.
ISSN: 0148-0227

hal-00551330
https://hal.archives-ouvertes.fr/hal-00551330
https://hal.archives-ouvertes.fr/hal-00551330v2/document
https://hal.archives-ouvertes.fr/hal-00551330/file/Hollingsworth2010.pdf
DOI : 10.1029/2009JB007185