Éditeur(s) : HAL CCSD Station Biologique
Résumé : International audience
From fish samplings (rotenone: 6 February 2002 & 13 May 2003; boxtraps: January 2008 to July 2009) in amangrove lagoon, the demographic structure, reproductive period and diet of Lophogobius cyprinoides were studied.Individual fish were measured (< 1 mm), weighed (± 0.01 g), and sexed by observing the urogenital papilla, sex-ratios andtotal length (TL)-standard length and length-mass relationships were calculated. Five individuals per size class (2 mm) wereused to study sexual maturity by macroscopic observation of gonad structure with a sexual maturity scale, and diet byqualitative and quantitative examination of digestive tract contents and calculation of the following indices: levels offullness and vacuity; occurrence, number, and point frequencies of various food items, and quality of nutrition. Growth isisometric and sexual dimorphism in favor of males (78 vs. 64 mm), demographic structure (18 ≤ TL ≤ 78 mm) and conditionevolved over time, with a distinct femininization of the population. Sexual inversion appeared from 46 mm onward, andtotal masculinization at 72 mm. Protogynous hermaphrodism is advantageous in a sedentary, subcryptobenthic species thatis reproductively active almost throughout the year. The species has an omnivorous diet specialized in copepods and plants
ISSN: 0007-9723

hal-00746079
https://hal.univ-antilles.fr/hal-00746079

Éditeur(s) : Society for General Microbiology
Résumé : A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a(T)) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0.1-50 MPa. Predominant cellular fatty acids were 16:1 omega7c, 15: 0 iso, 16: 0 and 13: 0 iso. The G + C content of the DNA was 44.9 mol%. On the basis of 16S rRNA gene sequences, strain LT13a(T) was shown to belong to the gamma-Proteobacteria, being closely related to Shewanella putrefaciens (98%), Shewanella oneidensis (97%) and Shewanella baltica (96 %). Levels of DNA homology between strain LT13a(T) and S. putrefaciens, S. oneidensis and S. baltica were < 20 %, indicating that strain LT13a(T) represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13a(T) constitutes a novel species of the genus Shewanella, Because of the deep origin of the strain, the name Shewanella profunda sp. nov. is proposed, with LT13a(T) (= DSM 15900(T)-JCM 12080(T)) as the type strain.
International journal of systematic and evolutionary microbiology (1466-5026) (Society for General Microbiology), 2004-11 , Vol. 54 , N. 6 , P. 1943-1949

Droits : 2004 International Union of Microbiological Societies
http://archimer.ifremer.fr/doc/2004/publication-590.pdf
DOI:10.1099/ijs.0.03007-0
http://archimer.ifremer.fr/doc/00000/590/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
This study aims to assess the evidence on adverse pregnancy outcome associated with living close to polluted industrial sites, and identify the strengths and weaknesses of published epidemiological studies. A systematic literature search has been performed on all epidemiological studies published in developed countries since 1990, on the association between residential proximity to industrial sites (hazardous waste sites, industrial facilities and landfill sites) and adverse pregnancy outcome (low birth weight, preterm birth, small for gestational age, intrauterine growth retardation, infant mortality, congenital malformation). Based on 41 papers, our review reveals an excess risk of reproductive morbidity. However, no studies show significant excess risk of mortality including fetal death, neonatal or infant mortality and stillbirth. All published studies tend to show an increased risk of congenital abnormalities, yet not all are statistically significant. All but two of these studies revealed an excess risk of low birth weight. Results for preterm birth, small for gestational age and intrauterine growth retardation show the same pattern. There is suggestive evidence from the post-1990 literature that residential proximity to polluted sites (including landfills, hazardous waste sites and industrial facilities) might contribute to adverse reproductive outcomes, especially congenital malformations and low birth weight—though not mortality. This body of evidence has limitations that impede the formulation of firm conclusions, and new, well-focused studies are called for. The review findings suggest that continued strengthening of rules governing industrial emissions as well as industrial waste management and improved land use planning are needed.
ISSN: 1476-072X

Droits : http://creativecommons.org/licenses/by/
hal-01547817
http://hal.upmc.fr/hal-01547817
http://hal.upmc.fr/hal-01547817/document
http://hal.upmc.fr/hal-01547817/file/s12942-017-0091-y.pdf
DOI : 10.1186/s12942-017-0091-y

Éditeur(s) : HAL CCSD
Résumé : International audience
The Jaca basin is a thrust-sheet top basin transported southward andunderlain by basement and cover thrusts separated by a Triassic décollement.Basin-fill upper Cretaceous to lower Oligocene synorogenic sequencesrecord a southward depocenter migration, while growth stratadate a shift of deformation from the mid-Eocene in the N to the earlyMiocene in the S (S-Pyrenean front). However, the deep geometry andkinematic relationships between the cover and basement thrusts remainnon-consensual. We present a new structural and kinematic interpretationfor the eastern Jaca basin, based on subsurface structural maps andcross-sections constructed using industrial seismic reflection profiles.Raman Spectroscopy of Carbonaceous Material (RSCM), vitrinite reflectanceand apatite fission track (AFT) thermochronology data givefurther constraints for the restoration of the deformation and burialexhumationsequence. We define 3 main basement thrusts under thenorthern part of the basin, from N to S the Broto, Fiscal and Guargathrusts. The study also clarifies the deep structure of the cover thrustsand their links with these basement thrusts and those located more tothe north in the Axial Zone (AZ), which altogether define the timing ofthe basement thrust sequence as follows : the Lakoura-Eaux Chaudesthrust system (northern AZ) active up to the end Bartonian, the Gavarnie(central AZ) and Broto thrusts during the Priabonian-Rupelian andthe Fiscal and Guarga thrusts during the late Oligocene-early Miocene.AFT results in the basin fill and AZ date the exhumation of the basinto the late Oligocene-early Miocene, in relation to the Fiscal-Guargathrusting. AFT partial reset argues for a maximum burial < 6 km forthe base of the Eocene detrital sequence (Hecho Group turbidites). Bycontrast, RSCM and vitrinite thermometry at the same level indicatesTmax around 180°C, locally up to 240°C, attesting to a temperature anomalypossibly related to transient fluid circulation.
24 ème Réunion des sciences de la Terre 2014
Pau, France

insu-01080836
https://hal-insu.archives-ouvertes.fr/insu-01080836

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
The Tian Shan Mountains constitute central Asia's longest and highest mountain range. Understanding their Cenozoic uplift history thus bears on mountain building processes in general, and on how deformation has occurred under the influence of the India-Asia collision in particular. In order to help decipher the uplift history of the Tian Shan, we collected 970 samples for magnetostratigraphic analysis along a 4571-m-thick section at the Jingou River (Xinjiang Province, China). Stepwise alternating field and thermal demagnetization isolate a linear magnetization component that is interpreted as primary. From this component, a magnetostratigraphic column composed of 67 polarity chrons are correlated with the reference geomagnetic polarity timescale between ~1 Ma and ~23.6 Ma, with some uncertainty below ~21 Ma. This correlation places precise temporal control on the Neogene stratigraphy of the southern Junggar Basin and provides evidence for two significant stepwise increases in sediment accumulation rate at ~16–15 Ma and ~11–10 Ma. Rock magnetic parameters also undergo important changes at ~16–15 Ma and ~11–10 Ma that correlate with changes in sedimentary depositional environments. Together with previous work, we conclude that growth history of the modern Tian Shan Mountains includes two pulses of uplift and erosion at ~16–15 Ma and ~11–10 Ma. Middle to upper Tertiary rocks around the Tian Shan record very young (<~5 Ma) counterclockwise paleomagnetic rotations, on the order of 15° to 20°, which are interpreted as because of strain partitioning with a component of sinistral shear that localized rotations in the piedmont.
ISSN: 0278-7407

insu-00376345
https://hal-insu.archives-ouvertes.fr/insu-00376345
https://hal-insu.archives-ouvertes.fr/insu-00376345/document
https://hal-insu.archives-ouvertes.fr/insu-00376345/file/2007TC002137.pdf
DOI : 10.1029/2007TC002137

Éditeur(s) : HAL CCSD Springer-Verlag
Résumé : The Chile-Argentina Patagonian Cordillera is a natural laboratory to study the interactions between oceanic and continental lithosphere during the subduction of an active spreading ridge beneath a continent. Subduction of the South Chile spreading ridge, which separates the Nazca plate from the Antarctic plate, started around 15–14 Ma at the southern tip of Patagonia. Presently, the southernmost segment of the Chile Ridge enters the Peru-Chile trench at 46°S, at the site of the Chile Triple Junction (CTJ). We review the main events which occurred on land in the CTJ region (46–47°S), related with processes of ridge subduction. We summarize tectonic, sedimentary, and magmatic features in a 30 Ma-to Present chronological table. A preridge subduction stage, from 30 to 15 Ma, is characterized by the onset and growth of Patagonian relief and by a shift from marine to continental detrital sedimentation in the foreland at 20–22 Ma. The change from pre-ridge subduction to ridge subduction is marked on land by a transition from calc-alkaline to alkaline volcanism, at 14–12 Ma, and by the onset of eruption of very large fl ood basalt provinces (future volcanic plateaus) following rapid erosion of the eastern foreland belt. Post-plateau basaltic volcanism (<4 Ma) is coeval with a period of tectonic and morphological rejuvenation during which the eastern foreland of the Cordillera has been affected by extensional/transtensional tectonics. We place these events in the framework of a tectonomagmatic model involving the opening of slab windows due to both slab tear and ridge axis subduction.
Subduction Zone Geodynamics

hal-00421053
https://hal.archives-ouvertes.fr/hal-00421053
DOI : 10.1007/978-3-540-87974-9_12

Éditeur(s) : Elsevier
Résumé : The gametogenic cycle and the reproductive effort of the blacklip pearl oyster, Pinctada margaritifera, cultivated in Takapoto lagoon were studied for a 1-year period (March 1997-April 1998) by bimonthly observations of gonadal sections, dry tissue weights and gonadal index in a population of pearl oyster composed of three age-groups. pearl oysters attained sexual maturity in the end of their first year (height approximate to 40 mm), implying that P. margaritifera is a late-maturing species in comparison with other Pteriidae. This species was also confirmed to be a marked protandrous successive hermaphrodite in culture, with 100 % of males at first maturity and 75 % in older pearl oyster (height > 120 mm). The general pattern of gametogenic activity, fairly synchronous in both sexes, was comparable with that of other tropical bivalves: reproduction occurs continuously throughout the year with a maximal activity during the warm season (November-May). No resting period was observed. Quantitative growth data showed that P. margaritifera exhibits an annual synchronised polymodal spawning pattern, with two spawning peaks in age-group I (height approximate to 70 mm) and five in age-groups II (height approximate to 100 mm) and III (height approximate to 120 mm). Spawning was sometimes incomplete, nevertheless a clear relationship between gamete production (P-R, g) and size (height H, mm) was obtained: P-R = 5.26 x 10(-7) H-2.91 (R-2 = 0.99, p < 0.05). Estimation of P-R was used to calculate the annual reproductive effort in P. margaritifera. Reproductive effort (%) was similar to those calculated for temperate species and showed a progressive increase with the age of pearl oyster, from 7 % in age-group I to 38 % in age-group III. This study showed that, in a fairly stable tropical environment such as the Takapoto lagoon, P. margaritifera is a multiple spawner, which uses an opportunistic reproductive strategy, allowing investment all year around, of any surplus energy into gamete production. Surplus energy is ensured by the high pumping rates developed by this non-symbiotic bivalve to succeed in low seston conditions. (C) 2000 Ifremer/Cnrs/Inra/Ird/Cemagref/Editions scientifiques et medicales Elsevier SAS.
Le cycle et l'effort de reproduction de l'huître perlière à lèvres noires, Pinctada margaritifera, cultivée dans le lagon de Takapoto, ont été étudiés sur une période annuelle (de mars 1997 à avril 1998), par un suivi bimensuel des stades de maturation et des indices gonadiques, sur une population en élevage composée de trois groupes d'âge (1, 2 et 3 ans). Cette étude a confirmé que P. margaritifera est une espèce qui se reproduit tardivement par rapport aux autres Ptériidés (elle atteint sa maturité sexuelle à la fin de sa première année, pour une hauteur approximative de 40 mm). Par ailleurs, elle présente, en élevage, une protandrie marquée (100 % de mâles à première maturité, 75 % pour des huîtres âgées de trois ans). Le schéma général de sa gamétogenèse, relativement synchrone dans les deux sexes, est comparable à celui des autres bivalves tropicaux : la reproduction est quasiment continue (aucune période de repos sexuel) avec une activité accrue en saison chaude (de novembre à mai). L'analyse des variations du poids de la gonade suggère l'existence de deux pics d'émission de gamètes chez les huîtres de un an et cinq pics chez les huîtres de 2 et 3 ans (cycle de reproduction de type polymodal). Bien que ces émissions de gamètes soient parfois incomplètes, une relation entre la production de gamètes (PR, en g) et la taille de l'huître perlière (hauteur, H, en mm) a été établie : PR = 5,26 x 10-7 H2,91 (R2 = 0,99, p < 0,05). Ces résultats ont permis de calculer l'effort de reproduction de P. margaritifera à Takapoto et sur un bilan annuel : il augmente avec l'âge de l'huître perlière de 7 % pour le groupe d'âge I à 38% pour le groupe d'âge III. Ces valeurs annuelles sont similaires à celles calculées chez les bivalves de milieux tempérés. Cette étude a donc montré que, dans un environnement tropical assez stable tel que celui du lagon de Takapoto, P. margaritifera présente une reproduction continue, avec plusieurs pics d'émission de gamètes par an. Cette stratégie « opportuniste » permet l'investissement, de tout surplus d'énergie en production de gamètes, tout au long de l'année. Malgré la faible concentration du milieu en nourriture, ces surplus d'énergie sont assurés par les fortes capacités de filtration développées par cette espèce tropicale non-symbiotique.
Aquatic Living Resources (0990-7440) (Elsevier), 2000 , Vol. 13 , N. 1 , P. 37-48

Droits : 2000 Ifremer/Cnrs/Inra/Ird/Cemagref/Éditions scientifiques et médicales Elsevier SAS
http://archimer.ifremer.fr/doc/2000/publication-1391.pdf
DOI:10.1016/S0990-7440(00)00135-2
http://archimer.ifremer.fr/doc/00000/1391/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Despite decades of petrological and geochemical studies, the nature and setting of obducted ophiolites remain controversial: the influence of supra-subduction zone environments on pre-existing oceanic lithosphere is yet to assess, and the processes leading to subduction/obduction initiation are still poorly constrained. Our study documents successive influx of slab-derived fluids and progressive strain localization within the upper mantle in a supra-subduction environment during the first few My of the subduction history. We focus on strongly sheared mafic amphibolites intruding peridotites near the mantle–crust transition of the New Caledonia obducted ophiolite and ~ 50 to 100 m above the basal thrust contact of the ophiolite. These m- to hm-long and several m-thick shear bands are interpreted as inherited small-scale intrusions of mafic melts, probably dikes or sills, which were derived from a moderately refractory mantle source refertilized by supra-subduction zone fluids. 40Ar/39Ar age constraints on pargasite at ca. 90 Ma suggest that they could be inherited from the former Pacific west-dipping subduction.Secondary deformation of these mafic intrusions is intimately associated to three major stages of fluid infiltration: (1) the first stage of deformation and metasomatism is marked by syn-kinematic growth of Ca-amphibole (at 700–800 °C and 3–5 kbar) with a distinctive supra-subduction zone signature, and controlled later channelization of aqueous fluids. 40Ar/39Ar dating on magnesio-hornblende indicates that this deformation episode occurred at ca. 55 Ma, coincident with east-dipping subduction initiation; (2) the main metasomatic stage, characterized by the development of a phlogopite-rich matrix wrapping peridotites and amphibolite boudins, points to the percolation of alkali-rich aqueous fluids at still high temperature (650–750 °C); (3) the last, low temperature (< 600 °C) metasomatic stage results in the formation of deformed veinlets containing talc, chlorite and serpentine.
ISSN: 0024-4937

hal-01306664
https://hal.archives-ouvertes.fr/hal-01306664
https://hal.archives-ouvertes.fr/hal-01306664/document
https://hal.archives-ouvertes.fr/hal-01306664/file/Soret_2016_Strain_localization.pdf
DOI : 10.1016/j.lithos.2015.11.022

Éditeur(s) : Elsevier Science Bv
Résumé : The breakup of Pangea and onset of growth of the Pacific plate led to several paleoenvironmental feedbacks, which radically affected paleoclimate and ocean chemistry during the Jurassic. Overall, this period was characterized by intense volcanic degassing from large igneous provinces and circum-Panthalassan arcs, new oceanic circulation patterns, and changes in heat and humidity transports affecting continental weathering. Few studies, however, have attempted to unravel the global interactions linking these processes over the long-term. In this paper, we address this question by documenting the global changes in continental drainage and surface oceanic circulation for the whole Jurassic period. For this purpose, we present 53 new neodymium isotope values (εNd(t)) measured on well-dated fossil fish teeth, ichthyosaur bones, phosphatized nodules, phosphatized ooids, and clastic sediments from Europe, western Russia, and North America. Combined with an extensive compilation of published εNd(t) data, our results show that the continental sources of Nd were very heterogeneous across the world. Volcanic inputs from a Jurassic equivalent of the modern Pacific Ring of Fire contributed to radiogenic εNd(t) values (− 4 ε-units) in the Panthalassa Ocean. For the Tethyan Ocean, the average surface seawater signal was less radiogenic in the equatorial region (− 6.3), and gradually lower toward the epicontinental peri-Tethyan (− 7.4), western Russian (− 7.4) and Euro-Boreal seas (− 8.6). Different Nd sources contributed to this disparity, with radiogenic Nd influxes from westward Panthalassan currents or juvenile volcanic arcs in open oceanic domains, and substantial unradiogenic inputs from old Laurasian and Gondwanan shields for the NW Tethyan platforms. Overall, the εNd(t) values of Euro-Boreal, peri-Tethyan, and western Russian waters varied quite similarly through time, in response to regional changes in oceanic circulation, paleoclimate, continental drainage, and volcanism. Three positive shifts in εNd(t) values occurred successively in these epicontinental seas during the Pliensbachian, in the Aalenian-Bathonian interval, and in the mid-Oxfordian. The first and third events are interpreted as regional incursions of warm surface radiogenic currents from low latitudes. The Aalenian-Bathonian shift seems linked to volcanic outbursts in the NW Tethys and/or circulation of deep currents resulting from extensional events in the Hispanic Corridor and reduced influences of boreal currents crossing the Viking Corridor. In contrast, the εNd(t) signals decreased and remained very low (< − 8) during the global warming events of the Toarcian and Late Oxfordian - Early Tithonian intervals. In these greenhouse contexts, a latitudinal expansion of humid belts could have extended the drainage pathways toward boreal Nd sources of Precambrian age and increased the supply of very unradiogenic crustal-derived inputs to seawater. Finally, a brief negative εNd(t) excursion recorded in parallel with regional drops in seawater temperature suggests that southward circulation of cold unradiogenic Arctic waters occurred in the NW Tethys in the Callovian - Early Oxfordian. All these results show that changes in surface oceanic circulation resulting from the Pangean breakup could have regionally impacted the evolution of seawater temperatures in the NW Tethys.
Gondwana Research (1342-937X) (Elsevier Science Bv), 2015-06 , Vol. 27 , N. 4 , P. 1599-1615

Droits : 2014 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved
http://archimer.ifremer.fr/doc/00179/29015/27443.pdf
DOI:10.1016/j.gr.2014.02.006
http://archimer.ifremer.fr/doc/00179/29015/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Abstract View references (38)Silicalite-1 (S-1) and ZSM-5 membranes prepared by secondary growth on tubular ceramic supports were tested using a pervaporation set up for the desalination of aqueous solutions containing NaCl in concentrations corresponding to brackish (0.3-1wt%), sea (3.5wt%) and brine (7.5-15wt%) water. ZSM-5 membranes delivered higher water fluxes when compared with S-1 membranes due to enhanced hydrophilicity of the Al-rich zeolite structure leading to fluxes as high as 11.5kgm -2h -1 for 0.3wt% NaCl feed solutions at 75°C. At higher salt concentration the water flux decreased alongside with the salt rejection rate, however the hydrophilic ZMS-5 membrane became more susceptible to performance loss, particularly at high temperatures. Detailed stability experiments carried out for up to 560h showed the dissolution of both S-1 and ZSM-5 top layers. This was attributed to the combined effects of ion exchange and water dissolution mechanisms. Interesting though, the MFI structure zeolite was still observed on the XRD patterns whilst EDX depth profile showed the presence of silica up to 30μm depth into the support. These results suggest the formation/infiltration of a compact amorphous phase in the substrate, derived from the aggregation of the dissolved silicate species and possibly together with the arrangement of MFI nano-slabs during the desalination tests. Despite generating lower water fluxes, the S-1 membrane exhibited relatively high robustness under the long term testing conditions which included temperature cycling, delivering salt rejections from initial >99% to <80% at the end of the testing period (560h). © 2012 Elsevier B.V.
ISSN: 0376-7388

hal-01683201
https://hal.univ-antilles.fr/hal-01683201
DOI : 10.1016/j.memsci.2012.05.074

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Before attaining the mantle wedge, where they trigger partial melting, volatiles released from dehydration reactions in the slab have to migrate across a relatively cold (<750 degrees C), peridotite-layer above the incoming slab. In order to unravel the mechanisms allowing for this initial stage of fluid transport, we performed a detailed field and microstructural study of metamorphic prograde peridotites in the Cerro del Almirez ultramafic massif (Betic Cordillera, Spain), where evidences of one of the most important dehydration reactions in subduction zones, the high-pressure antigorite breakdown (P = 1.6-1.9 GPa and T approximate to 680 degrees C), can be mapped in the field. This reaction led to arborescent growth of centimeter-size olivine and orthopyroxene, producing a chlorite-harzburgite with a spinifex-like texture. Microstructural observations and crystal preferred (CPO) mapping show no evidences of solid-state deformation during the prograde growth of olivine and orthopyroxene at the expenses of antigorite. However, a few tens to a hundred meters away from the reaction front, the metamorphic texture is partially obliterated by grain-size reduction in roughly planar conjugate zones, a few mm to meters wide. Grain size reduction zones (GSRZ) are characterized by (1) sharp contacts with undeformed spinifex-like texture domains, (2) important reduction of the olivine grain size (60-250 mu m), (3) olivine color change from brownish to colorless, (4) decrease in the modal amount of orthopyroxene, and (5) at the mm- to cm-scale, irregular shapes and abrupt terminations. Field and microstructural observations exclude that relative displacement took place across these GSRZ. Changes in modal composition imply reactions with fluids undersaturated in silica. Analysis of olivine crystal-preferred orientations (CPO) in GSRZ shows patterns similar, but more dispersed, than those in neighboring spinifex-like domains. It also reveals mm- to cm-scale discrete domains with rather homogeneous crystallographic orientations suggesting inheritance from the preexisting spinifex-like olivines in the host peridotite. Misorientation angles between neighboring grains in the GSRZ show peaks at similar to 5-10 degrees and similar to 20 degrees, but rotations are not crystallographically controlled. Based on these observations, we rule out the formation of the GSRZ by dynamic recrystallization during dislocation creep and propose that they record brittle deformation (microcraking) of the spinifex-like chlorite-harzburgite, probably induced by hydrofracturing at high pressure and relative low temperature conditions (680-710 degrees C). High-pressure hydrofracturing can, thus, be invoked as an efficient mechanism for fluid flow across the cold top-slab mantle layer, hence allowing the slab-derived fluids to ingress in the wedge.
ISSN: 0012-821X

hal-00534035
https://hal.archives-ouvertes.fr/hal-00534035
DOI : 10.1016/j.epsl.2010.06.029

Éditeur(s) : HAL CCSD
Résumé : International audience
The study of complex biological processes requires to forgo simplified models for extensive ones. Yet, these models' size and complexity place them beyond understanding. Their analysis requires new methods for identifying general patterns. The Transforming Growth Factor TGF-β is a multifunctional cytokine that regulates mammalian cell development , differentiation, and homeostasis. Depending on the context, it can play the antagonistic roles of growth inhibitor or of tumor promoter. Its context-dependent pleiotropic nature is associated with complex sig-naling pathways. The most comprehensive model of TGF-β-dependent signaling is composed of 15,934 chains of reactions (trajectories) linking TGF-β to at least one of its 159 target genes. Identifying functional patterns in such a network requires new automated methods. This article presents a framework for identifying groups of similar trajec-tories composed of the same molecules using an exhaustive and without prior assumptions approach. First, the trajectories were clustered using the Relevant Set Correlation model, a shared nearest-neighbors clustering method. Five groups of trajectories were identified. Second, for each cluster the over-represented molecules were determined by scoring the frequency of each molecule implicated in trajectories. Third, Gene set enrichment analysis on the clusters of trajectories revealed some specific TGF-β-dependent biological processes, with different clusters associated to the antagonists roles of TGF-β. This confirms that our approach yields biologically-relevant results. We developed a web interface that facilitates graph visualization and analysis. Our clustering-based method is suitable for identifying families of functionally-similar trajectories in the TGF-β signaling network. It can be generalized to explore any large-scale biological pathways.
CMSB 2017 - 15th International Conference on Computational Methods in Systems Biology
Darmstadt, France

hal-01559249
https://hal.archives-ouvertes.fr/hal-01559249
https://hal.archives-ouvertes.fr/hal-01559249/document
https://hal.archives-ouvertes.fr/hal-01559249/file/JeanCoquet_CMSB.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
GenMol (TM) code is used to simulate Atomic Force Microscopy (AFM) tests at a kaolinite/brine/kaolinite contact, the confined fluid in sub-nanometre interspaces being in equilibrium with an external multi-species solution. The attraction/repulsion effort, i.e. the derivative versus the interspace aperture h of the interaction energy between both kaolinite faces, is computed versus the variable composition of the confined fluid (see for the method Part I of this work). Two external solutions are tested. Solution Si is a neutral brine (pH=7.5) leading to a possible attraction for apertures lower than 7 angstrom. Solution S2 is an acidified brine (pH=3.2) leading to repulsion whatever may be the aperture h. These two AFM simulations prove the existence of a critical pH value (3.2 < pH(crit) < 7.5) of the external solution, below which the acidification of a natural brine in a CO2 confinement inhibits adhesion between kaolinite aggregates.
ISSN: 0022-0248

hal-00544678
https://hal.archives-ouvertes.fr/hal-00544678
DOI : 10.1016/j.jcrysgro.2010.08.012

Éditeur(s) : HAL CCSD
Résumé : International audience
The extraction of knowledge from social networks is an area that has experienced significant growth in recent years. Indeed, thanks to the improvement of storage and calculation capacities, and the heterogeneity of data that can currently be extracted, much effort has been made to go beyond traditional knowledge, by proposing new kinds of patterns that take into account the context. However, while many works were interested in designing new patterns of knowledge or in optimizing existing approaches, few studies have been focused in merging patterns and on the useful knowledge emerging from such fusions. In this work, we focus on two network clustering approaches, able to extract two distinct kinds of patterns, and we seek to understand both the intersections that can exist between them and the knowledge that emerges from their fusion. The first is the classical nodes clustering approach that consists in searching for communities into a network. The second is the search for frequent conceptual links, a new link clustering approach that aims identifying frequent links between groups of nodes sharing common attributes. We propose a set of original measures that aim to evaluate the amount of shared information between these patterns when they are extracted from a same network. These measures are applied to three datasets and demonstrate the interest in simultaneously considering several sources of knowledge.
Advances in Knowledge Discovery and Management (AKDM)

hal-01514227
https://hal.archives-ouvertes.fr/hal-01514227
DOI : 10.1007/978-3-319-45763-5_13

Éditeur(s) : HAL CCSD
Résumé : Cell signaling contains the whole biological mecanisms allowing the response of a cell to its microenvironnement in an adapted way. Many extremely intertwinned biological reactions are involved in a network that behaves as a complex system. The understanding of cell response requires the development of data acquisition technics and methods to formalize data into models. This point is the main drive of this thesis. We present here two approaches in order to analyse different granularities of cell signaling. In the first one, we used differential model to study the role of a new component of TGF-β canonical pathway. In the second one, we explored the combinatorial complexity of cell signaling, developing a discrete formalism based on guarded transitions. In this approach, we interpreted the whole database Pathway Interaction Database into a single unified model of signal transduction. Simulation and analysis methods, such as reachability and invariance research, have been developed. The interests are presented through an application on cell cycle regulation by cell signaling, and a global analysis on the regulation of genes compared to experimental data.
La signalisation cellulaire regroupe l'ensemble des mécanismes biologiques permettant à une cellule de répondre de façon adaptée à son microenvironnement. Pour ce faire, de nombreuses réactions biologiques entrent en jeux avec un important enchevêtrement, créant ainsi un réseau dont le comportement s'apparente à un système complexe. Le compréhension de la réponse cellulaire à une stimulation passe par le développement conjoint des techniques d'acquisition de données, et des méthodes permettant de formaliser ces données dans un modèle. C'est sur ce dernier point que s'inscrivent les travaux exposés dans cette thèse. Nous présentons ici deux approches visant à répondre à des questions de natures différentes sur la signalisation cellulaire. Dans la première nous utilisons un modèle différentiel pour étudier le rôle d'un nouvel interactant dans la voie canonique du TGF-beta. Dans la seconde nous avons exploré la combinatoire de la signalisation cellulaire en développant un formalisme discret basé sur les transitions gardées. Cette approche regroupe l'interprétation de la base de données Pathway Interaction Database dans un unique modèle dynamique de propagation du signal. Des méthodes de simulations et d'analyses inspirées des techniques de vérification de modèles telles que l'atteignabilité et l'invariance ont été développées. En outre, nous avons étudié la régulation du cycle cellulaire en réponse à la signalisation, ainsi que la régulation des gènes de notre modèle en comparaison avec des données d'expressions.
https://tel.archives-ouvertes.fr/tel-00926487

Droits : info:eu-repo/semantics/OpenAccess
tel-00926487
https://tel.archives-ouvertes.fr/tel-00926487
https://tel.archives-ouvertes.fr/tel-00926487/document
https://tel.archives-ouvertes.fr/tel-00926487/file/AndrieuxThese.pdf

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: The TGF-β transforming growth factor is the most pleiotropic cytokine controlling a broad range of cellular responses that include proliferation, differentiation and apoptosis. The context-dependent multifunctional nature of TGF-β is associated with complex signaling pathways. Differential models describe the dynamics of the TGF-β canonical pathway, but modeling the non-canonical networks constitutes a major challenge. Here, we propose a qualitative approach to explore all TGF-β-dependent signaling pathways. RESULTS: Using a new formalism, CADBIOM, which is based on guarded transitions and includes temporal parameters, we have built the first discrete model of TGF-β signaling networks by automatically integrating the 137 human signaling maps from the Pathway Interaction Database into a single unified dynamic model. Temporal property-checking analyses of 15934 trajectories that regulate 145 TGF-β target genes reveal the association of specific pathways with distinct biological processes. We identify 31 different combinations of TGF-β with other extracellular stimuli involved in non-canonical TGF-β pathways that regulate specific gene networks. Extensive analysis of gene expression data further demonstrates that genes sharing CADBIOM trajectories tend to be co-regulated. CONCLUSIONS: As applied here to TGF-β signaling, CADBIOM allows, for the first time, a full integration of highly complex signaling pathways into dynamic models that permit to explore cell responses to complex microenvironment stimuli.
ISSN: 1752-0509

inserm-00978313
http://www.hal.inserm.fr/inserm-00978313
http://www.hal.inserm.fr/inserm-00978313/document
http://www.hal.inserm.fr/inserm-00978313/file/1752-0509-8-30.pdf
DOI : 10.1186/1752-0509-8-30

Éditeur(s) : HAL CCSD
Résumé : International audience
Energy is a critical enabler. In tropical countries, access to modern electricity is vital to reducing poverty and improving health, increasing productivity and promoting economic growth. However, the International Energy Agency reported in 2015 more than 1.2 billion people still did not have access to electricity in 2013, around 80% of them live in developing and tropical countries. Then, the same agency report also in 2016 around 6.5 million premature deaths each year can be attributed to air pollution. Therefore, it is time to support appropriate renewable energy developments, particularly the river hydrokinetic developments seems to be a better solution in tropics because of large and powerful rivers in these areas.In French Guiana, 35% of the inland populations are still not connected to the electrical grid (Région Guyane, 2012). This could be ascribed to the fact that extending grid wires hundreds of kilometers through difficult terrain and thick jungles just to serve a small remote village is economically unviable initiative (Ajan et al., 2003; Anyi et al., 2010). As an alternative, French Guiana and most of the tropical countries resort to diesel-powered generators which requires significant imports of expensive fuel, difficult to bring into remote areas (Région Guyane, 2012).This works proposes guidelines to estimate river hydrokinetic fluxes in the vicinity of remote communities in tropics. The method is applied to identify and characterise potential sites along an important reach of the Maroni river in French Guiana. First, a novel method to carry out river terrain elevation model is presented and some results about the Maroni river are reported. It begins from how to conduct ADCP survey, which corrections on them should be made and ends up by interpolating bathymetry over curvilinear profiles which handle the flow lines. That approach involves how mutli-source data (sparse ADCP-cross profiles, incomplete LiDAR tiles and hydroligic data) are merged and combined to estimate local cross section shape, maximum water depth and carry out cross profile in ungauged sites.This is followed by a deep characterisation about time-evolution of hydrokinetic fluxes field in the areas of interest by implementation of a full 2D hydrodynamic model (TELEMAC2D) over an important reach of the Maroni river. To optimise computational cost, river sections outside the areas of interest are modelled as a porous media where only the flows variables up and down stream must fulfil the field data.
CAS
Deshaies, Guadeloupe

hal-01514240
https://hal.archives-ouvertes.fr/hal-01514240