Éditeur(s) : HAL CCSD
Résumé : Carbon and Oxygen isotope profiles from a well-dated carbonate section spanning the Sinemurian time on the Caussenard High (southeast France) are compared to sedimentological data and the results from sequence stratigraphy analysis, in order to discuss the origin of isotopic variations in a shallow-marine carbonate succession. The sedimentological study has enabled the identification of four types of depositional environments (peritidal, lagoonal, sand shoal, outer-shelf) that formed meter-scale cycles. The latter are arranged in two third-order cycles whose boundaries correspond to distinct δ13C and δ18O negative peaks (at the end of the Hettangian time and during Middle Sinemurian). The origin of the isotopic signals is discussed and several hypothesis are envisaged: sea water ageing, early meteoric diagenesis. Isotopic curves observed here seems to be related to early meteoric diagenesis linked to variations of third-order sea-level cycles rather than environmental factors (temperature, salinity).
Swiss Journal of Geosciences

hal-00406603
https://hal.archives-ouvertes.fr/hal-00406603
DOI : 10.1007/s00015-007-1206-4

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
ISSN: 1754-6834

hal-01592860
http://hal.upmc.fr/hal-01592860
http://hal.upmc.fr/hal-01592860/document
http://hal.upmc.fr/hal-01592860/file/s13068-017-0897-7.pdf

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Random walk (RW) methods are recurring Monte Carlo methods used to modelconvective and diffusive transport in complex heterogeneous media. Many applications canbe found, including fluid mechanic, hydrology and chemical reactors modeling. These methodsare easy to implement, very versatile and flexible enough to become appealing for manyapplications because they generally overlook or deeply simplify the building of explicit complexmeshes required by deterministic methods. RWprovides a good physical understandingof the interactions between the space scales of heterogeneities and the transport phenomenaunder consideration. In addition, they can result in efficient upscaling methods, especiallyin the context of flow and transport in fractured media. In the present study, we review theapplications of RW to several situations that cope with diverse spatial scales and differentinsights into upscaling problems. The advantages and downsides of RW are also discussed,thus providing a few avenues for further works and applications.
ISSN: 0169-3913

insu-01308060
https://hal-insu.archives-ouvertes.fr/insu-01308060
DOI : 10.1007/s11242-016-0693-z

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
During the last decade, the interaction of deep processes in the lithosphere and mantle with surface processes (erosion, climate, sea-level, subsidence, glacio-isostatic readjustment) has been the subject of heated discussion. The use of a multidisciplinary approach linking geology, geophysics, geodesy, modelling, and geotechnology has led to the awareness of coupled deep and surface processes. Deep earth dynamics (topography, erosion, tectonics) are strongly connected to natural hazards such as earthquakes, landslides, and tsunamis; sedimentary mass transfers have important consequences on isostatic movements and on georesources, geothermal energy repartitions. The ability to read and understand the link between deep Earth dynamics and surface processes has therefore important societal impacts. Ground-truthing at carefully-selected sites of investigation is imperative to better understand these connections.Due to its youth (<30 Ma) and its subsidence history, the almost land-locked Gulf of Lion–Sardinia continental margins system provides a unique record of sedimentary deposition from the Miocene to present. Due to its high subsidence rate, palaeoclimatic variations, tectonic events and vertical evolution are all recorded here at very high resolution. The late Miocene isolation and desiccation of the Mediterranean, the youngest and most catastrophic event, the Messinian Salinity Crisis (MSC), induced drastic changes in marine environments: widespread deposition of evaporite (gypsum, anhydrite and halite) in the central basin, and intense subaerial erosion along its periphery. These extraordinary mass transfers from land to sea induced strong isostatic re-adjustments that are archived in the sedimentary record and represent a window to the lithospheric rheology and the deep processes.The GOLD (Gulf of Lion Drilling) project, proposes to explore this unique sedimentary record as well as the nature of the deep crustal structure, providing valuable information about the mechanisms underlying vertical motions in basins and their margins.
ISSN: 0264-8172

insu-01197393
https://hal-insu.archives-ouvertes.fr/insu-01197393
https://hal-insu.archives-ouvertes.fr/insu-01197393/document
https://hal-insu.archives-ouvertes.fr/insu-01197393/file/Rabineau%20et%20al.-final-MPG2014_REVISED-FINAL-No-Marked_FINAL%2BFigures.pdf
DOI : 10.1016/j.marpetgeo.2015.03.018

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
After Jurassic rifting, numerous carbonate platforms (i.e., the Orizaba, Cordoba and Golden Lane-Tuxpan platforms) developed during the Lower and Middle Cretaceous episode of thermal subsidence along the western passive margin of the Gulf of Mexico, with intervening basinal domains (i.e., the Tampico-Misantla, Zongolica, Veracruz and Deep Gulf of Mexico - DGM - basins).;During the Late Cretaceous-Paleocene, the east-verging Sierra Madre Oriental thrust belt developed, resulting in tectonic uplift and unroofing of the allochthonous units (i.e. tectonic units made up of former Orizaba and Cordoba platforms and Zongolica Basin series). This new topography provided also an important source of clastics to feed the adjacent foredeep, where coeval tectonic loading accounted for the bending of the foreland lithosphere. However, shallow water facies or even emersion persisted until the Eocene in the forebulge area (at the present location of the Golden Lane), preventing locally the clastics to reach the DGM. This topographic barrier was ultimately bypassed by the clastics only during the Oligocene and Neogene, once (1) the prograding clastic wedge had exceeded accommodation, and (2) the long lasting thermal subsidence of the passive margin could overpass the effect of the bending and force the former bulge to sink.;Numerous paleo-thermo-meters (Tmax, Ro), paleo-thermo-barometers (fluid inclusions), PVT and coupled forward kinematic and thermal modeling have been used to calibrate and date the progressive unroofing of the thrust belt. Coupled tectonic and sedimentologic modeling was applied in the foreland to predict the distribution of sand versus shale ratios in the Oligocene to Plio-Quaternary clastic sedimentary wedge of the passive margin, where gravitational gliding of post-Eocene series occurred during the Neogene along major listric faults.;Mantle dynamics are advocated as the main process accounting for post-orogenic uplift and regional tilting of the basement, which initiated a massive transfer of sediments from the Cordillera towards the Gulf of Mexico, from Oligocene onward, resulting in a destabilization and gravitational collapse of the western slope of the Gulf of Mexico in Neogene times.
ISSN: 0040-1951

hal-00445248
https://hal.archives-ouvertes.fr/hal-00445248
DOI : 10.1016/j.tecto.2009.04.012

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background : Trichoderma reesei is the main industrial source of cellulases and hemicellulases required for the hydrolysis of biomass to simple sugars, which can then be used in the production of biofuels and biorefineries. The highly productive strains in use today were generated by classical mutagenesis. As byproducts of this procedure, mutants were generated that turned out to be unable to produce cellulases. In order to identify the mutations responsible for this inability, we sequenced the genome of one of these strains, QM9136, and compared it to that of its progenitor T. reesei QM6a.Results : In QM9136, we detected a surprisingly low number of mutagenic events in the promoter and coding regions of genes, i.e. only eight indels and six single nucleotide variants. One of these indels led to a frame-shift in the Zn2Cys6 transcription factor XYR1, the general regulator of cellulase and xylanase expression, and resulted in its C-terminal truncation by 140 amino acids. Retransformation of strain QM9136 with the wild-type xyr1 allele fully recovered the ability to produce cellulases, and is thus the reason for the cellulase-negative phenotype. Introduction of an engineered xyr1 allele containing the truncating point mutation into the moderate producer T. reesei QM9414 rendered this strain also cellulase-negative. The correspondingly truncated XYR1 protein was still able to enter the nucleus, but failed to be expressed over the basal constitutive level.Conclusion : The missing 140 C-terminal amino acids of XYR1 are therefore responsible for its previously observed auto-regulation which is essential for cellulases to be expressed. Our data present a working example of the use of genome sequencing leading to a functional explanation of the QM9136 cellulase-negative phenotype.
ISSN: 1471-2164

Droits : http://creativecommons.org/licenses/by/
hal-01149671
http://hal.upmc.fr/hal-01149671
http://hal.upmc.fr/hal-01149671/document
http://hal.upmc.fr/hal-01149671/file/Lichius_2015_Genome_sequencing.pdf
DOI : 10.1186/s12864-015-1526-0

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Random walk (RW) or Continuous Time Random Walk (CTRW) are recurring Monte Carlo methods used to model convective and diffusive transport in complex heterogeneous media. Many applications can be found, including fluid mechanic, hydrology, and chemical reactors modeling. These methods are easy to implement, very versatile and flexible enough to become appealing for many applications because they generally overlook of deeply simplify the building of explicit complex meshes required by deterministic methods. RW and CTRW provide a good physical understanding of the interactions between the space scales of het-erogeneities and the transport phenomena under consideration. In addition, they can result in efficient up-scaling methods, especially in context of flow and transport in fractured media. In the present study, we review the applications of RW or CTRW for several situations coping with various spatial scales, and different insights into up-scaling applications. RW and CTRW advantages and downsides are also discussed, thus providing a few avenues for further works and applications.
ISSN: 0169-3913

hal-01449131
https://hal.archives-ouvertes.fr/hal-01449131
https://hal.archives-ouvertes.fr/hal-01449131/document
https://hal.archives-ouvertes.fr/hal-01449131/file/0025972-02.pdf
DOI : 10.1007/s11242-016-0693-z

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour. Results: We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance. Conclusions: This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.
ISSN: 1754-6834

Droits : http://creativecommons.org/licenses/by/
hal-01112360
http://hal.upmc.fr/hal-01112360
http://hal.upmc.fr/hal-01112360/document
http://hal.upmc.fr/hal-01112360/file/Poggi-Parodi_2014_Kinetic.pdf
DOI : 10.1186/s13068-014-0173-z

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This paper focuses on the analyses of the clastic sedimentary infill of the Coastal Plain of Eastern Mexico, which initiated synchronously with the Laramide orogeny in the vicinity of the Golden Lane. Results of these analyses are used as boundary conditions for calibrating/interpreting seismic profiles across more distal depocenters in the offshore of the Gulf of Mexico, from the sea shore and continental slope in the west to the abyssal plain in the east. The objective of the study is to better predict the reservoir distribution in the Deep offshore Basin of the Gulf of Mexico (DBGM), in order to explore for petroleum. The Coastal Plain is underlain by three morpho-tectonic domains: the tectonic front of the Sierra Madre Orientale (SMO), the Chicontepec deep water flexural basin, and the Tuxpan Platform (also known as the Golden Lane). Each domain is characterized by a distinct, dominantly siliciclastic Cenozoic lithostratigraphy. After a Jurassic rifting episode, followed by thermal subsidence, the oceanic basin and its western passive margin were deformed during the Upper Cretaceous and Paleogene, by far field stresses associated with the Cordilleran-Laramide Orogeny. Starting in the Late Cretaceous-Early Paleogene and during the Early Eocene, the tectonic load associated with the Laramide Orogen (Sierra Madre Oriental, SMO) caused flexural subsidence of the foreland located under the Coastal Plain. During this period, a massive transfer of siliciclastic sediments occurred from the Laramide foothills into the adjacent foreland. Sediments were eroded of the Sierra Madre tectonic wedge. Loading by these sediments pushed source units associated with the former passive margin down ward. The first syn-tectonic sediments of the Laramide orogeny were turbiditic silt layers in submarine fans which record also numerous collapse episodes and gravity slides. During the Late Eocene and Oligocene, the flexural subsidence stopped in the hinterland, whereas the subsidence of the passive margin resumed. This resulted in a change in the overall sedimentary architecture of the basin. Paleo-highs and reefs facies of the Golden Lane were flooded. Clastics by-passed the reefs and progradational clastic stratification formed as sediment moved towards the DBGM in the east. The final depositional environment of the continental platform/Coastal Plain became deltaic, marked by a succession of sand bars, levees and channels systems. From Miocene times onward, a system of gravitational listric faults developed near the platform to slope transition, resulting in a coeval compressional system at the transition between the slope and the abyssal plain. This system is driven by sediments charge. Because the sedimentation rate is larger than the subsidence, a large amount of clastics and slumped sediments are deposited in hangingwall basins.
ISSN: 0264-8172

hal-00424586
https://hal.archives-ouvertes.fr/hal-00424586
DOI : 10.1016/j.marpetgeo.2008.03.009

Éditeur(s) : HAL CCSD Société géologique de France
Résumé : International audience
The central part of the Gulf of Lions shoreline is characterized by many coastal wetlands that resulted from the interaction between a process of shoreline regularization by migrations of littoral barriers and a slow filling of the back-barrier areas by the riverine and marine inputs. Analyses of Late-Holocene deposits with a very high-resolution multi-proxy study of two sediment cores, allow us to reconstruct the evolution of this coastal system. Two main Holocene sediment units are identified overlying a Pliocene carbonate continental formation. The lower unit consists of sandy and pebbly marine sediments deposited around 7800 B.P., during the final stand of the last sea level rise. Just above, the upper unit displays lagoonal grey clay silts with shells and some intercalated layers of silty sands related to paleostorm events. The age model was established from radiocarbon dating, for the oldest part of the core. Over the last century, sedimentation rates were calculated using the CFCS Pb-210 model, together with Cs-137 data. Radiocarbon data show an increase in he accumulation rate from the base to the top of cores. Marine sand units related to the last transgressive deposit allow to refine the curve of Holocene post-glacial sea level rise. Sedimentological and faunal analyses associated with chronological data provide a means for reconstructing the Late-Holocene paleoenvironments along this part of the coast and suggest that the final closure of the coastal lagoon by the sandy barrier occurred at around 730 +/- 120 yr cal B.P. The beginning of this closure, together with the progradation of the coastal plain, could be responsible for the decline in economic activity of the Lattara harbour during the Roman period.
La partie centrale du littoral du golfe du Lion est caractérisée par de nombreuses lagunes qui résultent de l'interaction entre un processus de régularisation du trait de côte par migration de barrières littorales et d'un lent remplissage des zones situées en arrière des barrières par des apports continentaux et marins. Les analyses des dépôts tardi-holocènes avec une étude multi-traceurs à très haute résolution de deux carottes sédimentaires nous permettent de reconstruire l'évolution de ce système côtier. Deux unités sédimentaires holocènes sont identifiées recouvrant une formation pliocène carbonatée. L'unité inférieure est constituée de sables et de galets d'origine marine déposés vers 7800 B.P., durant les stades ultimes de la dernière remontée marine. Audessus, l'unité supérieure montre des dépôts d'argile et de silt gris coquilliers d'origine lagunaire, dans lesquels sont intercalés des niveaux de sable silteux révélant la présence d'événements de tempêtes. Le modèle d'âge est établi à partir de dates radiocarbones pour les parties les plus anciennes des archives sédimentaires, tandis que pour le dernier siècle, les taux de sédimentation sont calculés en utilisant le modèle CFCS pour le 210Pb, associé aux données de 137Cs. Les données 14C montrent une augmentation du taux d'accumulation depuis la base jusqu'en surface des carottes. Les unités de sables marins liées aux dépôts de la dernière transgression marine permettent de préciser la courbe post-glaciaire de remontée du niveau marin. Les analyses sédimentologiques et faunistiques associées aux données chronologiques fournissent une méthode permettant de reconstituer les paléoenvironnements littoraux tardi-holocènes dans la zone d'étude et suggèrent que la fermeture finale de ces lagunes par le cordon sableux survient autour de 730 ± 120 ans cal B.P. Le début de cette fermeture, associée à la une progradation deltaïque, pourrait être responsable du déclin des activités économiques du port de Lattara durant la période Romaine.
EISSN: 1777-5817

halshs-00740923
https://halshs.archives-ouvertes.fr/halshs-00740923
DOI : 10.2113/gssgfbull.181.1.27

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The western margin of the Gulf of Mexico (Veracruz State, Mexico) displays an extensive Neogene gravitational system, whereby the Neogene siliciclastic sediments are detached from underlying Mesozoic carbonates along decollement surface in Oligocene underpressured clays. Rapidly subsiding half-grabens develop above the footwall associated with major listric faults, whereas mini-basins develop in the deepest parts of the slope, in conjunction with the growth of west-verging compressional features. Between the high-angle normal faults in the west and the thrust anticlines in the east, a wide roll-over structure has grown progressively, resulting in a major topographic break in the morphology of the slope profile. Coupled forward kinematic modelling (Thrustpack) and stratigraphic modelling (Dionisos), calibrated against seismic profiles and two key nearshore wells, have been applied to representative regional transects across the margin, in order to quantify the vertical (subsidence) and horizontal (gravitational) deformations, and to discuss the impact of various key parameters on the distribution of debris flow depositions. These simulations are compared with data from distant ODP wells and discussed in the scope of current exploration strategies in both the US and Mexican portions of the Gulf of Mexico basin.
ISSN: 0040-1951

hal-00424595
https://hal.archives-ouvertes.fr/hal-00424595
DOI : 10.1016/j.tecto.2008.06.017