Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Both oedometric and plane-strain tests were performed with parallelepipedic samples made of synthetic granular, cohesive, frictional and dilatant rock analogue material GRAM2. For the first time parallel sets of fractures that have all the characteristics of natural joints were reproduced in the laboratory. The fractures are regularly spaced, normal to σ3, and have plumose morphology very similar to that of natural joints. These fractures can form at tensile stress σ3 much smaller in magnitude than the tensile strength of material and even at slightly compressive σ3. When mean stress σ exceeds a certain value, the fractures become oblique to σ1 (the obliquity increases with σ), forming networks of conjugate shear bands/fractures. These results of plane-strain experiments are in good agreement with those of better controlled conventional axisymmetric tests on a similar material in Chemenda et al. (2011b) and are closer to real geological situations. Both types of experiments are complementary. Their results lead to the conclusion that at least certain categories of natural fractures (including joints, and conjugate shear fractures/bands) were initiated as deformation localization bands. The band orientation is defined by the constitutive properties/parameters (notably the dilatancy factor) that are sensitive to σ.
ISSN: 0040-1951

hal-00795555
https://hal.archives-ouvertes.fr/hal-00795555
DOI : 10.1016/j.tecto.2011.11.021

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
While the effects of deforestation and habitat fragmentation on parasite prevalence or richness are well investigated, host-parasite networks are still understudied despite their importance in understanding the mechanisms of these major disturbances. Because fragmentation may negatively impact species occupancy, abundance and co-occurrence, we predict a link between spatiotemporal changes in habitat and the architecture of host-parasite networks. For this, we used an extensive data set on 16 rodent species and 29 helminth species from seven localities of South-East Asia. We analysed the effects of rapid deforestation on connectance and modularity of helminth-parasite networks. We estimated both the degree of fragmentation and the rate of deforestation through the development of land uses and their changes through the last 20 to 30years in order to take into account the dynamics of habitat fragmentation in our statistical analyses. We found that rapid fragmentation does not affect helminth species richness per se but impacts host-parasite interactions as the rodent-helminth network becomes less connected and more modular. Our results suggest that parasite sharing among host species may become more difficult to maintain with the increase of habitat disturbance.
ISSN: 0021-8790

hal-01355307
https://hal.archives-ouvertes.fr/hal-01355307
DOI : 10.1111/1365-2656.12368
IRD : fdi:010064927

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : no abstract
ISSN: 0256-2928

hal-01360229
https://hal.archives-ouvertes.fr/hal-01360229

Éditeur(s) : HAL CCSD Portland Press
Résumé : International audience
For cellular fitness and survival, gene expression levels need to be regulated in response to a wealth of cellular and environmental signals. TFs (transcription factors) execute a large part of this regulation by interacting with the basal transcription machinery at promoter regions. Archaea are characterized by a simplified eukaryote-like basal transcription machinery and bacteria-type TFs, which convert sequence information into a gene expression output according to cis-regulatory rules. In the present review, we discuss the current state of knowledge about these rules in archaeal systems, ranging from DNA-binding specificities and operator architecture to regulatory mechanisms.
ISSN: 0300-5127

hal-01542965
http://hal.upmc.fr/hal-01542965
DOI : 10.1042/BST20120312

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Networks of localized conjugate compactive shear bands with large dihedral angles (corresponding to so-called shear-enhanced compaction bands) were generated in 3-layer plane strain finite-difference models. The central layer has elastic–plastic properties with a small positive internal friction coefficient, negative dilatancy factor, and the hardening modulus reducing during the deformation. The two other layers are elastic. The spatial organization of the networks in the central layer, resulting from the elastic–plastic instability of the 3-layer system, was shown to be dependent on the contrast of the elastic stiffness of the layers and on the friction between them. When the stiffness E of the elastic layers and/or the friction are small, the networks are rather symmetric (the bands of both orientation families are distributed homogeneously within the layer). An increase in E at high friction, results in the clustering of the bands of one orientation along a layer segment which is followed by another segment filled with the bands of the other orientation. Different network types are characterized by different band spacing which is smaller in the clustered networks. The intensity of inelastic deformation and hence of porosity reduction within the bands are also smaller in this case. The obtained band networks are very similar to those in nature where the same variability of the network organization is observed. Available geological and mechanical data confirm the conclusions from the modeling about the origin of this variability.
ISSN: 0040-1951

hal-01116201
https://hal.archives-ouvertes.fr/hal-01116201
DOI : 10.1016/j.tecto.2014.01.021

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
DNA sequencing technology is becoming more accessible to a variety of researchers as costs continue to decline. As researchers begin to sequence novel transcriptomes, most of these data sets lack a reference genome and will have to rely on de novo assemblers. Making comparisons across assemblies can be difficult: each program has its strengths and weaknesses, and no tool exists to comparatively evaluate these data sets. We developed software in R, called Sequence Comparative Analysis using Networks (SCAN), to perform statistical comparisons between distinct assemblies. SCAN uses a reference data set to identify the most accurate de novo assembly and the ``good'' transcripts in the user's data. We tested SCAN on three publicly available transcriptomes, each assembled using three assembly programs. Moreover, we sequenced the transcriptome of the oomycete Achlya hypogyna and compared de novo assemblies from Velvet, ABySS, and the CLC Genomics Workbench assembly algorithms. One thousand one hundred twenty-eight of the CLC transcripts were statistically similar to the reference, compared with 49 of the Velvet transcripts and 937 of the ABySS transcripts. SCAN's strength is providing statistical support for transcript assemblies in a biological context. However, SCAN is designed to compare distinct node sets in networks, therefore it can also easily be extended to perform statistical comparisons on any network graph regardless of what the nodes represent.
ISSN: 0737-4038

hal-01544800
https://hal.archives-ouvertes.fr/hal-01544800
DOI : 10.1093/molbev/mst087

Éditeur(s) : HAL CCSD
Résumé : International audience
The Corinth Rift is the most seismically active zone in Europe. Since the year 2000, the Corinth Rift Laboratory (CRL, http://crlab.eu) consisting in a multidisciplinary natural observatory, aims at understanding the mechanics of faulting and earthquake nucleation in the Rift. Recent studies have improved our view about fault geometry and mechanics within CRL but there is still a critical need for a better knowledge of the structure at depth.In this project, we aim to analyze the complete seismological database (13 years of recordings) of CRL by using recently developed methodologies of structural imaging in order to determine, with high resolution, the local 3D structure and the earthquake locations. We perform an iterative joint determination of 3D velocity model and earthquake coordinates. P and S velocity models are estimated through a first arrival traveltime tomography by using the adjoint state method proposed by Taillandier et al. (2009). It consists in the minimization of the cost function between observed and theoretical arrival times,which is achieved by estimating the gradient of the cost function. Earthquake locations are also estimated with a linearized inversion approach by computing the gradient of the misfit function. Iterations are repeated until the cost function no longer decreases. We present preliminary results consisting in: (1) the adjustment of a 1D velocity model that is used as initial model of the 3D tomography and (2) a first attempt of the joint determination of 3D velocity model and earthquake locations.We also perform a preliminary receiver function analysis of teleseismic data recorded by the broadband stations of the CRL network. The multiscale approach (Gesret et. al., 2010) analysis of teleseismic P to S converted waves allows to analyze the signal toward the higher frequencies and thus to characterize the structure at depth with a high resolution. Our multiscale approach should give us reliable depth of interfaces beneath seismometers in the CRL area. In this first attempt, we adjust the 1D velocity model that produces a synthetic RF as similar as possible to the stack of observed RF for a subset of data. The identified interfaces could then be compared with heterogeneities imaged by the tomography.
AGU Fall Meeting
San Fransico, United States

hal-01417184
https://hal-mines-paristech.archives-ouvertes.fr/hal-01417184

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Numerous field studies highlighted the capacities of marine sponges to bioaccumulate trace elements and assessed their potential as biomonitors of the marine environment. Experimental works demonstrated that dissolved metals and radionuclides can be taken up directly by sponge tissues but, to the best of our knowledge, little is known on the contribution of the dietary pathway through the consumption of contaminated bacteria considered as one of the trophic source in sponge diet. Objectives of this work are to study trophic transfer of radiotracers 110mAg, 241Am, 109Cd, 57Co, 134Cs, 54Mn and 65Zn from the marine bacteria Pseudomonas stutzeri to the Mediterranean sponges Aplysina cavernicola and Ircinia oros. P. stutzeri efficiently bioaccumulated trace elements in our culture experimental conditions with CF comprised between 105 and 107 after 48 hours of growth in radiolabeled medium. When fed with these radiolabelled bacteria, A. cavernicola took up around 60% of radiotracers accumulated in trophic source except 134Cs for which only 8% has been transferred from bacteria to sponge. Contrasting to this, I. oros retained only 7% of 110mAg, 109Cd and 65Zn counted in bacteria, but retained 2-fold longer accumulated metals in its tissues. The sponge inter-specific differences of accumulation and depuration following a trophic exposure are discussed with respect to the structure and the clearance capacities of each species.
ISSN: 0045-6535

hal-01217273
https://hal.archives-ouvertes.fr/hal-01217273
https://hal.archives-ouvertes.fr/hal-01217273/document
https://hal.archives-ouvertes.fr/hal-01217273/file/Pub%20Bacteria%20CHEM_HAL.pdf
DOI : 10.1016/j.chemosphere.2015.10.046

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Cnidarian-dinoflagellate symbiosis mainly relies on nutrient recycling, thus providing both partners with a competitive advantage in nutrient-poor waters. Essential processes related to lipid metabolism can be influenced by various factors, including hyperthermal stress. This can affect the lipid content and distribution in both partners, while contributing to symbiosis disruption and bleaching. In order to gain further insight into the role and distribution of lipids in the cnidarian metabolism, we investigated the lipid composition of the sea anemone Anemonia viridis and its photosynthetic dinoflagellate endosymbionts (Symbiodinium). We compared the lipid content and fatty acid profiles of the host cellular layers, non-symbiotic epidermal and symbiont-containing gastrodermal cells, and those of Symbiodinium, in a mass spectrometry-based assessment. Lipids were more concentrated in Symbiodinium cells, and the lipid class distribution was dominated by polar lipids in all tissues. The fatty acid distribution between host cell layers and Symbiodinium cells suggested potential lipid transfers between the partners. The lipid composition and distribution was modified during short-term hyperthermal stress, mainly in Symbiodinium cells and gastrodermis. Exposure to elevated temperature rapidly caused a decrease in polar lipid C18 unsaturated fatty acids and a strong and rapid decrease in the abundance of polar lipid fatty acids relative to sterols. These lipid indicators could therefore be used as sensitive biomarkers to assess the physiology of symbiotic cnidarians, especially the effect of thermal stress at the onset of cnidarian bleaching. Overall, the findings of this study provide some insight on key lipids that may regulate maintenance of the symbiotic interaction.
ISSN: 1095-6433

hal-01546160
https://hal.archives-ouvertes.fr/hal-01546160
DOI : 10.1016/j.cbpa.2015.10.017

Éditeur(s) : HAL CCSD Histochemical Society
Résumé : International audience
The galectin-4 protein is mostly expressed in the digestive tract and is associated with lipid raft stabilization, protein apical trafficking, wound healing, and inflammation. While most mammalian species, including humans, have a single Lgals4 gene, some mice have two paralogues: Lgals4 and Lgals6. So far, their significant similarities have hindered the analysis of their respective expression and function. We took advantage of two antibodies that discriminate between the galectin-4 and galectin-6 proteins to document their patterns of expression in the normal and the dextran sodium sulfate (DSS)-damaged digestive tract in the mouse. In the normal digestive tract, their pattern of expression from tongue to colon is quite similar, which suggests functional redundancy. However, the presence of galectin-4, but not galectin-6, in the lamina propria of the DSS-damaged colon, its association with luminal colonic bacteria, and differences in subcellular localization of these proteins suggest that they also have distinct roles in the normal and the damaged mouse digestive tract. Our results provide a rare example of ancestral and derived functions evolving after tandem gene duplication.
ISSN: 0022-1554

hal-01544764
https://hal.archives-ouvertes.fr/hal-01544764
DOI : 10.1369/0022155413478612

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Absolute earthquake hypocenter locations have been determined in the area offshore eastern Taiwan, at the Southernmost Ryukyu subduction zone. Location process is run within a 3D velocity model by combining the Taiwanese and neighboring Japanese networks and using the 3D MAXI technique. The study focuses on the most active seismic cluster in the Taiwan region that occurs in the forearc domain offshore eastern Taiwan. Earthquakes distribute mainly along 2 active planes. The first one aligns along the subduction interface and the second one, shallower affects the overriding margin. Focal mechanisms within the shallow group indicate that nodal planes are either compatible with high-angle back-thrusts or low-angle thrusts. The active seismic deformation exclusively indicates reverse faulting revealing that the forearc basement undergoes trench-perpendicular strong compression. By integrating the seismological image into the regional context, we favor the hypothesis in which the dense seismicity occurring offshore marks the activity of en-échelon high-angle reverse faults accommodating the uplift of a broken piece of Ryukyu Arc basement, called Hoping Basement Rise. The uplift is inferred to be caused by the subduction of an oceanic relief, either exotic block, seamount or oceanic crust sliver. Our favored solution satisfies the narrowness of epicenter's cluster along the Hoping Canyon, and the observation of high-angle active faults on seismic lines crossing the area. Furthermore, this solution is compatible with the active uplift of the Hoping Rise demonstrated from morphological and sedimentological data. We do not exclude the branching of the high-angle reverse faults system onto a splay fault connected with the subduction interface but further investigations are needed to map precisely the 3D distribution of active faults that break the margin.
ISSN: 0040-1951

hal-00407726
https://hal.archives-ouvertes.fr/hal-00407726
DOI : 10.1016/j.tecto.2007.11.018

Éditeur(s) : HAL CCSD Centers for Disease Control and Prevention
Résumé : International audience
ISSN: 1080-6040

hal-01447667
https://hal.archives-ouvertes.fr/hal-01447667
DOI : 10.3201/eid2210.160052

Éditeur(s) : HAL CCSD
Résumé : International audience
Geophysical Research Abstracts
Wien, Austria

hal-00417298
https://hal.archives-ouvertes.fr/hal-00417298

Éditeur(s) : HAL CCSD
Résumé : International audience
Rhyme patterns in Old Chinese poems are important for the reconstruction of Old Chinese pronunciation, as they provide evidence for groups of words which formerly had similar pronunciation. Rhyme patterns can also be used to test Old Chinese reconstruction systems for consistency and plausibility, as reconstruction systems should minimize the conflict with attested rhyme patterns. Here, we build on the idea that rhyming in Old Chinese followed the principle of vowel purity, a tendency to disallow rhymes of words with different vowels, to develop a quantitative test for reconstruction systems of Old Chinese. The test is illustrated by comparing seven different Old Chinese reconstruction systems and by showing that, although the systems differ regarding their degree of vowel purity, the principle seems to hold for Old Chinese rhyme data.
Lingua Sinica

Droits : http://creativecommons.org/licenses/by/
hal-01555483
http://hal.upmc.fr/hal-01555483
http://hal.upmc.fr/hal-01555483/document
http://hal.upmc.fr/hal-01555483/file/10.1186_s40655-017-0021-8.pdf
DOI : 10.1186/s40655-017-0021-8

Éditeur(s) : HAL CCSD Nakanishi Printing Co
Résumé : International audience
In Vibrio cholerae, the etiological agent of cholera, most of the virulence genes are located in two pathogenicity islands, named TCP (Toxin-Co-regulated Pilus) and CTX (Cholera ToXins). For each V. cholerae pathogenicity gene, we retrieved every primer published since 1990 and every known allele in order to perform a complete in silico survey and assess the quality of the PCR primers used for amplification of these genes. Primers with a melting temperature in the range 55-60 degrees C against any target sequence were considered valid. Our survey clearly revealed that two thirds of the published primers are not able to properly detect every genetic variant of the target genes. Moreover, the quality of primers did not improve with time. Their lifetime, i.e. the number of times they were cited in the literature, is also not a factor allowing the selection of valid primers. We were able to improve some primers or design new primers for the few cases where no valid primer was found. In conclusion, many published primers should be avoided or improved for use in molecular detection tests, in order to improve and perfect specificity and coverage. This study suggests that bioinformatic analyses are important to validate the choice of primers.
ISSN: 1342-6311

hal-01546178
https://hal.archives-ouvertes.fr/hal-01546178
DOI : 10.1264/jsme2.ME11317

Éditeur(s) : HAL CCSD Magnolia Press
Résumé : International audience
The species belonging to the trechine genus Adriaphaenops Noesske, 1928 are studied. As a result, seven currently known and five newly described species are recognized. Morphological characters of the habitus (especially the shape of head and pronotum) as well as male genitalia are widely used to delimit the species. The following new species are described: A. albanicus sp. nov. (Albania, Shkoder, Boga, Thate Mts.), A. jasminkoi sp. nov. (Bosnia & Hercegovina, Nevesinje, Novakova pecina cave), A. mlejneki sp. nov. (Montenegro, Gornje Stravce, Kucke planine Mts.), A. njegosiensis sp. nov. (Montenegro, Cetinje, Cetinjska pecina cave) and A. rumijaensis sp. nov. (Montenegro, Virpazar, Rumija Mts.). Lectotype for A. stirni (Pretner, 1959) is designated. Data on the distribution and ecology of new taxa, complemented with descriptions of the type localities are provided. Key to the identification of all twelve Adriaphaenops species, as well as a key of all hitherto known aphaenopsoid Trechini genera from Dinarides are also given.
ISSN: 1175-5326

hal-01544473
https://hal.archives-ouvertes.fr/hal-01544473
DOI : 10.11646/zootaxa.4205.6.1

Éditeur(s) : HAL CCSD
Résumé : International audience
The subterranean environment is often described as “extreme” and food poor. Laboratory experiments have shown that blind Mexican tetra Astyanax mexicanus (De Filippi, 1853) cavefish are better at finding food in the dark than surface fish. Several morphological and behavioural attributes that could foster this obvious adaptive response to cave environments have been described. Nonetheless, it is currently unknown what young cavefish actually eat in their natural cave environment. Our results from the Pachón cave in México during the dry and rainy season show that fry are efficient predators in their natural cave environment. Their primary food item is aquatic crustaceans. The guts of post-larval, pre-juvenile stage individuals (n=9) contained an average of 17.9 water fleas (Cladocera), copepods, ostracods, and isopods. Thus, the fry in this cave are well-fed. The Pachón cave environment does not appear to be “food poor” for juvenile cavefish. Food regimes change between post-larval and adult stages to become more dependent on partially decomposed material, guano, or detritus from the mud. We discuss the data with regards to our current developmental and genetic understanding of cavefish morphological and behavioural evolution, particularly regarding its enhanced Vibration Attraction Behaviour (VAB).
Subterranean Biology

hal-01432027
https://hal.archives-ouvertes.fr/hal-01432027
DOI : 10.3897/subtbiol.21.11046

Éditeur(s) : HAL CCSD SAGE Publications (UK and US)
Résumé : International audience
Genetic approaches have shown that several genes could modify caries susceptibility; AmelogeninX (AMELX) has been repeatedly designated. Here, we hypothesized that AMELX mutations resulting in discrete changes of enamel microstructure may be found in children with a severe caries phenotype. In parallel, possible AMELX mutations that could explain resistance to caries may be found in caries-free patients. In this study, coding exons of AMELX and exon-intron boundaries were sequenced in 399 individuals with extensive caries (250) or caries-free (149) individuals from nine French hospital groups. No mutation responsible for a direct change of amelogenin function was identified. Seven single-nucleotide polymorphisms (SNPs) were found, 3 presenting a high allele frequency, and 1 being detected for the first time. Three SNPs were located in coding regions, 2 of them being non-synonymous. Both evolutionary and statistical analyses showed that none of these SNPs was associated with caries susceptibility, suggesting that AMELX is not a gene candidate in our studied population.
ISSN: 0022-0345

hal-01545481
https://hal.archives-ouvertes.fr/hal-01545481
DOI : 10.1177/0022034513482941

Éditeur(s) : HAL CCSD Humana Press
Résumé : International audience
The sodium-proton exchanger 1 (NHE-1) is a membrane transporter that exchanges Na(+) for H(+) ion across the membrane of eukaryotic cells. It is cooperatively activated by intracellular protons, and this allosteric regulation is modulated by the biophysical properties of the plasma membrane and related lipid environment. Consequently, NHE-1 is a mechanosensitive transporter that responds to osmotic pressure, and changes in membrane composition. The purpose of this study was to develop the relationship between membrane surface tension, and the allosteric balance of a mechanosensitive transporter such as NHE-1. In eukaryotes, the asymmetric composition of membrane leaflets results in a difference in surface tensions that is involved in the creation of a reservoir of intracellular vesicles and membrane buds contributing to buffer mechanical constraints. Therefore, we took this phenomenon into account in this study and developed a set of relations between the mean surface tension, membrane asymmetry, fluid phase endocytosis and the allosteric equilibrium constant of the transporter. We then used the experimental data published on the effects of osmotic pressure and membrane modification on the NHE-1 allosteric constant to fit these equations. We show here that NHE-1 mechanosensitivity is more based on its high sensitivity towards the asymmetry between the bilayer leaflets compared to mean global membrane tension. This compliance to membrane asymmetry is physiologically relevant as with their slower transport rates than ion channels, transporters cannot respond as high pressure-high conductance fast-gating emergency valves.
ISSN: 1085-9195

inserm-00871709
http://www.hal.inserm.fr/inserm-00871709
http://www.hal.inserm.fr/inserm-00871709/document
http://www.hal.inserm.fr/inserm-00871709/file/art_3A10.1007_2Fs12013-012-9340-7.pdf
DOI : 10.1007/s12013-012-9340-7

Éditeur(s) : HAL CCSD Magnolia Press
Résumé : International audience
Hydroporus galloprovincialis sp. n. is described from Jouques, north-east of Aix-en-Provence in south-eastern France (Provence). The new species belongs to the Hydroporus memnonius-group, within which it is the only ascertained normandi-complex species of the French fauna. The habitat (small springs) and morphological features of the species suggest a semi-subterranean life style. It can be separated from the other species of the complex notably by its more elongated and parallel-sided habitus, by its wider pronotum and flatter dorsal surface, and furthermore differs from H. normandi Regimbart, 1903 by a different shape of the gonocoxa. Illustrations are provided for other described normandi-complex species and subspecies for comparison. Analyses of partial cox1 sequences indicate that the three sampled H. normandi-complex species (H. galloprovincialis sp. n., H. normandi and H. lluci Fery, 1999) diverged recently; their relationships are unresolved. H. galloprovincialis sp. n. is for the moment the only species of the genus Hydroporus Clairville, 1806 endemic to continental France.
ISSN: 1175-5326

hal-01544484
https://hal.archives-ouvertes.fr/hal-01544484
DOI : 10.11646/zootaxa.3652.4.4