Éditeur(s) : Oxford Univ Press
Résumé : The impact of the fishing effort exerted by a vessel on a population depends on catchability, which depends on population accessibility and fishing power. The work investigated whether the variation in fishing power could be the result of the technical characteristics of a vessel and/or its gear or whether it is a reflection of inter-vessel differences not accounted for by the technical attributes. These inter-vessel differences could be indicative of a skipper/crew experience effect. To improve understanding of the relationships, landings per unit effort (lpue) from logbooks and technical information on vessels and gears (collected during interviews) were used to identify variables that explained variations in fishing power. The analysis was undertaken by applying a combination of generalized additive models and generalized linear models to data from several European fleets. The study highlights the fact that taking into account information that is not routinely collected, e. g. length of headline, weight of otter boards, or type of groundrope, will significantly improve the modelled relationships between lpue and the variables that measure relative fishing power. The magnitude of the skipper/crew experience effect was weaker than the technical effect of the vessel and/or its gear.
Ices Journal Of Marine Science (1054-3139) (Oxford Univ Press), 2011-11 , Vol. 68 , N. 10 , P. 2252-2263

Droits : 2011 International Council for the Exploration of the Sea. Published by Oxford University Press. All rights reserved.
http://archimer.ifremer.fr/doc/00049/16043/15172.pdf
DOI:10.1093/icesjms/fsr150
http://archimer.ifremer.fr/doc/00049/16043/

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
Résumé : International audience
Estrogens and progestins are widely used in combination in human medicine and both are present in aquatic environment. Despite the joint exposure of aquatic wildlife to estrogens and progestins, very little information is available on their combined effects. In the present study we investigated the effect of ethinylestradiol (EE2) and Levonorgestrel (LNG), alone and in mixtures, on the expression of the brain specific ER-regulated cyp19a1b gene. For that purpose, recently established zebrafish-derived tools were used: (i) an in vitro transient reporter gene assay in a human glial cell line (U251-MG) co-transfected with zebrafish estrogen receptors (zfERs) and the luciferase gene under the control of the zebrafish cyp19a1b gene promoter and (ii) an in vivo bioassay using a transgenic zebrafish expressing GFP under the control of the zebrafish cyp19a1b gene promoter (cyp19a1b-GFP). Concentration-response relationships for single chemicals were modeled and used to design the mixture experiments following a ray design. The results from mixture experiments were analyzed to predict joint effects according to concentration addition and statistical approaches were used to characterize the potential interactions between the components of the mixtures (synergism/antagonism). We confirmed that some progestins could elicit estrogenic effects in fish brain. In mixtures, EE2 and LNG exerted additive estrogenic effects both in vitro and in vivo, suggesting that some environmental progestin could exert effects that will add to those of environmental (xeno-)estrogens. Moreover, our zebrafish specific assays are valuable tools that could be used in risk assessment for both single chemicals and their mixtures. © 2016 Elsevier Inc.
Toxicology and Applied Pharmacology

hal-01367151
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367151
DOI : 10.1016/j.taap.2016.07.023
PUBMED : 27491593

Éditeur(s) : Academic Press Ltd- Elsevier Science Ltd
Résumé : Several empirical and theoretical studies have shown how the exploitation of food sources, the choice of resting sites or other types of collective decision-making in heterogeneous environments are facilitated and modulated by social interactions between conspecifics. It is well known that many pelagic fishes live in schools and that this form of gregarious behavior provides advantages in terms of food intake and predator avoidance efficiency. However, the influence of social behavior in the formation of aggregations by tuna under floating objects (FOBs) is poorly understood. In this work, we investigated the collective patterns generated by different theoretical models, which either include or exclude social interactions between conspecifics, in the presence of two aggregation sites. The resulting temporal dynamics and distributions of populations were compared to in situ observations of tuna behavior. Our work suggests that social interactions should be incorporated in aggregative behavior to reproduce the temporal patterns observed in the field at both the individual and the group level, challenging the common vision of tuna aggregations around FOBs. Our study argues for additional data to further demonstrate the role of social behavior in the dynamics of these fish aggregations. Understanding the interplay between environmental and social factors in the associative behavior of fish with FOBs is necessary to assess the consequences of the widespread deployment of artificial FOBs by fishermen.
Journal Of Theoretical Biology (0022-5193) (Academic Press Ltd- Elsevier Science Ltd), 2014-10 , Vol. 359 , P. 161-170

Droits : 2014 Elsevier Ltd. All rights reserved.
http://archimer.ifremer.fr/doc/00195/30638/29091.pdf
DOI:10.1016/j.jtbi.2014.06.010
http://archimer.ifremer.fr/doc/00195/30638/

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
In this paper we investigate finite-frequency effects in crustal tomography. We developed an inversion procedure based on an exact numerical computation of the sensitivity kernels. In this approach we compute the 3D travel-time sensitivity kernels by using (1) graph theory and an additional bending to estimate accurately both rays and travel-times between source/receiver and diffraction points and (2) paraxial ray theory to estimate the amplitude along theses rays. We invert both the velocity and the hypocentre parameters, using these so-called banana-doughnut kernels and the LSQR iterative solver. We compare the ray-theoretical and the finite-frequency tomography to image the intermediate structures beneath the Gulf of Corinth (Greece), which has long been recognized as the most active continental rifting zone in the Mediterranean region. Our dataset consists of 451 local events with 9233 P- firstarrival times recorded in the western part of the Gulf (Aigion area) in the framework of the 3F-Corinth European project. Previous tomographic images showed a complex velocity crustal model and a low-dip surface that may accommodate the deformation. Accurate velocity models will help to better constrain the rifting process, which is still a subject of debate. The main results of this study show that finite-frequency tomography improves crustal tomographic images by providing better resolved images of the 3D complicated velocity structure. Because the kernels spread the information over a volume, finite-frequency tomography results in a sharpening of layer boundaries as we observed for the shallower part of the crust (down to 5 km depth) beneath the Gulf of Corinth.
ISSN: 0016-8025

insu-00354702
https://hal-insu.archives-ouvertes.fr/insu-00354702
DOI : 10.1111/j.1365-2478.2007.00683.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Development of hepatocellular carcinoma (HCC) is a complex and progressive disease that involves cycles of liver cell death, inflammation, and tissue regeneration/remodelling. Chemokines and chemokine receptors play numerous and integral roles in the disease progression of HCC. Here we investigated the novel chemokine receptor CXCR7/RDC1 in HCC progression, its two known ligands CXCL12 and CXCL11, as well as the other CXCL12 receptor, CXCR4. Our results show that in a cohort of 408 human HCCs, CXCR7 and CXCL11 were significantly higher in tumours compared to normal liver controls (5- and 10-fold, respectively). Immunohistochemical (IHC) staining on human HCC sections confirmed that both CXCL11 and CXCR7 were much higher in cancer tissues. Furthermore, IHC staining revealed that CXCR7 protein was only expressed in endothelial cells whereas CXCL11 exhibited a much broader tissue expression. At the cellular level we observed that in vitro, human microvascular endothelial cells (HMEC-1) up-regulated CXCR7 under hypoxic and acidic pH conditions, which are well known characteristics of the HCC tumour micro-environment. As for its ligand, we observed that IFNγ robustly induced CXCL11 in hepatic stellate cells, hepatocytes, and HMEC-1s. In addition, in the mouse Diethylnitrosamine model of hepatocarcinogenesis we observed a very strong induction of CXCR7 and CXCL11 transcripts, confirming that CXCR7/CXCL11 up-regulation is conserved between human and mice liver cancer. Altogether, our results strongly support the hypothesis that the CXCL11/CXCR7 pathway is involved HCC progression.
ISSN: 0959-8049

hal-00682463
https://hal.archives-ouvertes.fr/hal-00682463
DOI : 10.1016/j.ejca.2011.06.044
PUBMED : 21778049

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Exposure to solvents during pregnancy has long been suspected to increase the risk of congenital malformations. Glutathione S-transferases (GSTs) are enzymes essential for the detoxification of various chemicals. Our objective here was to assess whether GST polymorphisms might modify the association between maternal solvent exposure and the risk of birth defects. A prospective cohort included 3421 pregnant women in Brittany, France (2002-2006). Occupational exposure to solvents was assessed from a job-exposure matrix. Congenital malformations were diagnosed among livebirths, stillbirths, and medical pregnancy terminations. Using a nested case-control design, 32 babies with major birth defects were compared to 348 normal births for babies' cord blood genotypes (at GSTT1 and GSTM1) and maternal occupational solvent exposure. Logistic models were used to adjust for potential confounders. The risk of major defects increased significantly in women with solvent exposure (20% of controls and 34% of cases). Frequencies of the null genotype of both the GSTT1 and GSTM1 genes were similar among controls and cases. There was a significantly increased risk of birth defects in GSTM1 not-null cord-blood genotype in pregnancies exposed to solvents (odds ratio [OR], 1.0 for not-null, not-exposed; OR, 4.0 for not-null, exposed; 95% confidence interval [CI], 1.4-11.2; OR, 1.6 for null, not-exposed; 95% CI, 0.6-3.9; OR, 1.0 for null, exposed; 95% CI, 0.2-4.7; p = 0.05). This nested case-control study suggests that the child's GSTM1 genotype modifies the risk of major birth defects among offspring of solvent-exposed women. Replication and additional investigations are necessary to confirm and elucidate these findings.
ISSN: 1542-0752

hal-00875957
https://hal.archives-ouvertes.fr/hal-00875957
DOI : 10.1002/bdra.23018
PUBMED : 22570144

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We present archeointensity data carried out on pieces of incense burners from the ancient Maya city of Palenque, Chiapas, Mexico, covering much of the Mesoamerican Classic period, from A.D. 400 to A.D. 850. We worked on pieces from 24 incense burners encompassing the five Classic ceramic phases of Palenque: Motiepa (A.D. 400-500), Cascadas (A.D. 500-600), Otulum (A.D. 600-700), Murcielagos (A.D. 700-770), and Balunté (A.D. 770-850). All the samples come from highly elaborate, flanged pedestal of incense burners that are undoubtedly assigned to a ceramic phase by means of their iconographic, morphological and stylistic analyses. Archeointensity measurements were performed with the Thellier-Thellier's method on pre-selected samples by means of their magnetic properties. We obtained archeointensities of very good technical quality from 19 of 24 pieces, allowing the determination of a precise mean value for each ceramic phase, between View the MathML source29.1±0.9μT and View the MathML source32.5±1.2μT. The firing temperatures of ceramics were estimated with Mössbauer spectroscopy between 700 °C and 1000 °C. These values ensure that a full thermo-remanent magnetization was acquired during the original heating. Our results suggest a relative stability of the field intensity during more than 400 years in this area. The abundance of archeological material in Mesoamerica contrasts with the small amount of archeomagnetic data available that are, in addition, of uneven quality. Thus, it is not possible to establish a trend of intensity variations in Mesoamerica, even using the global databases and secular variation predictions from global models. In this context, our high technical quality data represent a strong constraint for the Mesoamerican secular variation curve during the first millennium AD. The corresponding Virtual Axial Dipole Moments (VADM) are substantially smaller than the ones predicted by the last global geomagnetic models CALS3k.4, suggesting the need for additional data to develop a regional model and a reference curve for Mesoamerica.
ISSN: 0012-821X

hal-00828696
https://hal.archives-ouvertes.fr/hal-00828696
DOI : 10.1016/j.epsl.2012.12.035

Éditeur(s) : HAL CCSD
Résumé : Transposable elements play a major role in the evolution of eukaryotic genomes. Knowing the distribution of transposable elements between different species within the same taxon is essential to study their dynamics and to better understand their role in the evolution of species. Given their abundance, species diversity and living environment, crustaceans are an excellent model for studying comparative genomics of retrotransposons. It is notably in the squat lobsters that the GalEa clade of Superfamily Copia was defined. We studied the distribution of two well-known LTR retrotransposons superfamilies: Gypsy and Copia, in crustaceans. By combining PCRs with degenerate primers and in silico analysis, we identified 35 families of Copia retrotransposons and 46 families of Gypsy retrotransposons in 15 and 18 species of crustaceans (mainly Malacostraca: crabs, shrimp, krill ...). These elements have different distribution and diversity in crustaceans. Gypsy elements appear relatively commonly and diverse in all species. Conversely, the Copia elements seem rare, and consequently more difficult to detect, and are largely dominated by the elements of the clade GalEa. These results suggest two different dynamic strategies for retrotransposons Gypsy (the Red Queen theory) and retrotransposons GalEa (‘domino days spreading’ branching process). In addition, GalEa elements present a great evolutionary success being widely distributed in many branches of metazoans. They are also present in certain red algae and we have also detected them in Fungi. Taking advantage of the large amount of available genomic data, we have studied the distribution of GalEa elements of Fungi, in order to compare it with the results obtained in crustaceans. In fact, they appear only in a large phylum of Ascomycetes, in Pezizomycotina, and they form a monophyletic group within the GalEa. Finally, in the Fungi, the GalEa elements are not majority among Copia retrotransposons. We have therefore initiated a new study in molluscs, to define if the results obtained in crustaceans are a feature of GalEa elements, Malacostraca or metazoans.
Les éléments transposables jouent un rôle majeur dans l’évolution des génomes eucaryotes. La connaissance de la distribution des éléments transposables entre différentes espèces au sein d’un même taxon est une condition essentielle pour étudier leur dynamique et mieux comprendre leur rôle dans l'évolution des espèces. Compte tenu de leur abondance, de leur diversité spécifique et de milieu de vie, les crustacés sont un excellent modèle pour étudier la génomique comparative des rétrotransposons. C’est notamment chez les Galathées qu’a été défini le clade GalEa des éléments de la superfamille des Copia. Nous avons étudié la distribution de deux superfamilles de rétrotransposons à LTR bien connus: les Gypsy et les Copia, au sein des crustacés. En combinant des PCRs avec amorces dégénérées et des analyses in silico, nous avons identifié 35 familles de rétrotransposons Copia et 46 familles de rétrotransposons Gypsy dans respectivement 15 et 18 espèces de crustacés (principalement des malacostracés : crabes, crevettes, krill...). Ces éléments présentent une distribution et une diversité différentes au sein des crustacés. Les éléments Gypsy apparaissent relativement fréquents et diversifiés dans toutes les espèces. A l’inverse, les éléments Copia semblent rares, donc difficilement détectables, et sont largement dominés par les éléments du clade GalEa. Ces résultats suggèrent deux stratégies différentes de dynamique pour les rétrotransposons Gypsy (théorie de la Reine Rouge) et les rétrotransposons GalEa (‘domino days spreading’ branching process). De plus, les éléments GalEa présentent un grand succès évolutif en étant largement distribués dans de nombreuses branches de métazoaires. Ils sont aussi présents chez quelques algues rouges et nous en avons également détecté chez des Fungi. Profitant des nombreuses données génomiques disponibles, nous avons donc étudié la distribution des éléments GalEa de Fungi, dans le but de comparer celle-ci aux résultats obtenus chez les crustacés. En fait, ils n’apparaissent qu’au sein d’un grand embranchement d’ascomycètes, les Pezizomycotina, et ils forment un groupe monophylétique au sein des GalEa. Enfin, chez les Fungi, les éléments GalEa ne sont pas majoritaire parmi les rétrotransposons Copia. Nous avons donc initié une nouvelle étude chez les mollusques, afin de définir si les résultats obtenus chez les crustacés sont une caractéristique des éléments GalEa, des malacostracés ou des métazoaires.
https://tel.archives-ouvertes.fr/tel-01132413

NNT : 2015PA066017
tel-01132413
https://tel.archives-ouvertes.fr/tel-01132413
https://tel.archives-ouvertes.fr/tel-01132413/document
https://tel.archives-ouvertes.fr/tel-01132413/file/these_archivage_2600252o.pdf

Éditeur(s) : HAL CCSD Wiley-Blackwell Wiley
Résumé : International audience
Rhodamine 123 is a fluorescent cationic dye commonly used as a mitochondrial probe and known or suspected to be transported by certain drug membrane transporters. The present study was designed to characterize the putative interactions of rhodamine 123 with human organic cation transporter (OCT) 1 and OCT2. Intracellular uptake of the dye was demonstrated to be enhanced in both hOCT1- and hOCT2-overexpressing HEK293 cells when compared with control HEK293 cells. This increase of rhodamine 123 influxes was found to be a saturable carrier-mediated process, with low K(m) values (K(m) = 0.54 μm and K(m ) = 0.61 μm for transport of the dye in hOCT1- and hOCT2-positive HEK293 cells, respectively). Known inhibitors of hOCT1 and hOCT2 activities such as verapamil, amitriptyline, prazosin, and quinine were next demonstrated to decrease rhodamine 123 accumulation in hOCT1- and hOCT2-overexpressing HEK293 cells. In addition, the dye was found to inhibit hOCT1- and hOCT2-mediated uptake of tetraethylammonium (TEA), a model substrate for both hOCT1 and hOCT2; rhodamine 123 appeared nevertheless to be a more potent inhibitor of hOCT1-mediated TEA transport (IC(50) = 0.37 μm) than of that mediated by hOCT2 (IC(50 ) = 61.5 μm). Taken together, these data demonstrate that rhodamine 123 is a high-affinity substrate for both hOCT1 and hOCT2. This dye may be therefore useful for fluorimetrically investigating cellular hOCT1 or hOCT2 activity, knowing, however, that other factors potentially contributing to cellular accumulation of rhodamine 123, including mitochondrial membrane potential or expression of the efflux transporter P-glycoprotein, have also to be considered.
ISSN: 0767-3981

inserm-00872840
http://www.hal.inserm.fr/inserm-00872840
DOI : 10.1111/j.1472-8206.2012.01071.x
PUBMED : 22913740

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
The spatio‐temporal dynamics of disease spread provide an area of acute scientific interest but substantial analytic challenges. Analytic approaches need to draw from current knowledge of disease systems yet be flexible enough to provide targeted inference without restrictive assumptions. We explore this balance in detail with respect to the observed pattern of spread of sugarcane yellow leaf virus, the causal agent of yellow leaf disease. This disease affects cultivated sugarcane plants and spreads via an aphid vector (Melanaphis sacchari). The system is of considerable economic interest, but presents several analytic complications. First, the plants begin as well separated individuals that grow into large plants with overlapping leaf canopies enabling increased vector access between neighbouring plants. The overlap between neighbouring plants first occurs within rows and then extends between rows, presenting another interesting spatial component to consider when modelling the propagation of infection. Second, the vector initially flies between plants but at some point sheds wings and shifts to walking between plants. We are particularly interested in how these two features of the system and their interrelation may impact the spatial spread of disease over time. In addition, we also explore the impact of potential immigration of infected vectors from outside of the study area. We treat our observed cane field as a spatial grid with regular spacing between rows and smaller spacing within rows. Our data consist of observed disease status of each of 1643 plants at each of six time points. We provide descriptive summaries of the temporal evolution of spatial pattern in infection, then propose hierarchical models to describe the pattern and capture the influence of the ecological and environmental factors listed above.
ISSN: 0143-9782

hal-00684235
https://hal.archives-ouvertes.fr/hal-00684235

Éditeur(s) : HAL CCSD National Institute of Environmental Health Sciences
Résumé : International audience
Safe drinking water is essential for well-being. Although microbiological contamination remains the largest cause of water-related morbidity and mortality globally, chemicals in water supplies may also cause disease, and evidence of the human health consequences is limited or lacking for many of them. We aimed to summarize the state of knowledge, identify gaps in understanding, and provide recommendations for epidemiological research relating to chemicals occurring in drinking water. Assessing exposure and the health consequences of chemicals in drinking water is challenging. Exposures are typically at low concentrations, measurements in water are frequently insufficient, chemicals are present in mixtures, exposure periods are usually long, multiple exposure routes may be involved, and valid biomarkers reflecting the relevant exposure period are scarce. In addition, the magnitude of the relative risks tends to be small. Research should include well-designed epidemiological studies covering regions with contrasting contaminant levels and sufficient sample size; comprehensive evaluation of contaminant occurrence in combination with bioassays integrating the effect of complex mixtures; sufficient numbers of measurements in water to evaluate geographical and temporal variability; detailed information on personal habits resulting in exposure (e.g., ingestion, showering, swimming, diet); collection of biological samples to measure relevant biomarkers; and advanced statistical models to estimate exposure and relative risks, considering methods to address measurement error. Last, the incorporation of molecular markers of early biological effects and genetic susceptibility is essential to understand the mechanisms of action. There is a particular knowledge gap and need to evaluate human exposure and the risks of a wide range of emerging contaminants.
ISSN: 0091-6765

hal-01118530
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118530
PUBMED : 24380896
DOI : 10.1289/ehp.1206229
PUBMEDCENTRAL : PMC3948022

Éditeur(s) : HAL CCSD
Résumé : poster
International audience
Locations for earthquake recorded in the Lesser Antilles subduction zone are processed separately by regional observatories, NEIC and ISC. There is no earthquake location catalog available compiling all available phase arrival data. We propose a new best complete earthquake catalog by merging all available phase arrival data for better constrains on earthquake locations. ISC provides the phase arrival data of 29243 earthquakes (magnitude range from 1.4 to 6.4) recorded by PRSN (Porto Rico), SRC (British West Indies), and from FUNVISIS (Venezuela). We add phases data from IPGP observatories for 68718 earthquakes from magnitudes 0.1 to 7.5 (OVSG, Guadeloupe, recorded 53226 earthquakes since 1981, and OVSM, Martinique, recorded 29931 earthquakes since 1972). IPGP also provides the accelerometer waveform data of the GIS-RAP network. We achieved automatic picking on the GIS-RAP data using the Component Energy Correlation Method. The CECM provides high precision phase detection, a realistic estimation of picking error and realistic weights that can be used with manual pick weights. The CECM add an average of 3 P-waves and 2 S-waves arrivals to 3846 earthquakes recorded by the GIS-RAP network since 2002. The final catalog contains 84979 earthquakes between 1972 and 2013, 24528 of which we compiled additional data. We achieve earthquake location using NonLinLoc, regional P and S waves data and a set of one dimensional velocity models. We produce improved locations for 22974 earthquakes (better residuals, on equal or larger arrival dataset) and improved duration magnitudes for 6258 earthquakes (using duration data and improved locations). A subset of best constrained 15626 hypocenters (with more than 8 phases and an average RMS of 0.48_0.77s) could be used for structural analysis and earthquake local tomography. Relative locations are to be applied in order to image active faulting. We aim to understand coupling in the seismogenic zone as well as triggering mechanisms of intermediate depth seismicity like fluid migration beneath the volcanic arc.
Geophysical Research Abstracts
Vienne, Austria

hal-01059207
https://hal-brgm.archives-ouvertes.fr/hal-01059207

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
TIF1γ (Transcriptional Intermediary Factor 1 γ) has been implicated in Smad-dependent signaling by Transforming Growth Factor beta (TGF-β). Paradoxically, TIF1γ functions both as a transcriptional repressor or as an alternative transcription factor that promotes TGF-β signaling. Using ordinary differential-equation models, we have investigated the effect of TIF1γ on the dynamics of TGF-β signaling. An integrative model that includes the formation of transient TIF1γ-Smad2-Smad4 ternary complexes is the only one that can account for TGF-β signaling compatible with the different observations reported for TIF1γ. In addition, our model predicts that varying TIF1γ/Smad4 ratios play a critical role in the modulation of the transcriptional signal induced by TGF-β, especially for short stimulation times that mediate higher threshold responses. Chromatin immunoprecipitation analyses and quantification of the expression of TGF-β target genes as a function TIF1γ/Smad4 ratios fully validate this hypothesis. Our integrative model, which successfully unifies the seemingly opposite roles of TIF1γ, also reveals how changing TIF1γ/Smad4 ratios affect the cellular response to stimulation by TGF-β, accounting for a highly graded determination of cell fate.
ISSN: 1932-6203

hal-00851483
https://hal.archives-ouvertes.fr/hal-00851483
https://hal.archives-ouvertes.fr/hal-00851483/document
https://hal.archives-ouvertes.fr/hal-00851483/file/pone.0033761.pdf
DOI : 10.1371/journal.pone.0033761

Éditeur(s) : HAL CCSD
Résumé : International audience
Despite their dynamic nature, certain chromatin marks must be maintained over the long term. This is particulary true for histone 3 lysine 9 (H3K9) trimethylation, that is involved in the maintenance of healthy differentiated cellular states by preventing inappropriate gene expression, and has been recently identified as the most efficient barrier to cellular reprogramming in nuclear transfer experiments. We propose that the capacity of the enzymes SUV39H1/2 to rebind to a minor fraction of their products, either directly or via HP1α/β, contributes to the solidity of this mark through (i) a positive feedback involved in its establishment by the mutual enforcement of H3K9me3 and SUV39H1/2 and then (ii) a negative feedback sufficient to strongly stabilize H3K9me3 heterochromatin in post-mitotic cells by generating local enzyme concentrations capable of counteracting transient bursts of demethylation. This model does not require direct molecular interactions with adjacent nucleosomes and is favoured by a series of additional mechanisms including (i) the protection of chromatin-bound SUV39H1/2 from the turnovers of soluble proteins, which can explain the uncoupling between the cellular contents in SUV39H1 mRNA and protein; (ii) the cooperative dependence on the local density of the H3K9me3 of HP1α/β-dependent heterochomatin condensation and, dispensably (iii) restricted enzyme exchanges with chromocenters confining the reactive bursts of SUV39H1/2 in heterochromatin. This mechanism illustrates how seemingly static epigenetic states can be firmly maintained by dynamic and reversible modifications. © 2016 Elsevier B.V.
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

hal-01467548
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01467548
DOI : 10.1016/j.bbagrm.2016.11.006
PUBMED : 27876670

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
The hydraulic and electrical properties of pyroclastic rocks have been investigated in laboratory on a representative sampling of Montagne Pelée (Martinique, France) deposits with renewed interest in geophysical applications. This sampling covers all the lithologic units of this volcano: lava dome and lava flows, pumices from ash-and-pumice fall and flow deposits, lava blocks from block-and-ash flow and Peléean “nuées ardentes” deposits, scoriae from scoria flow deposits. The connected porosity varies over a wide range from 3 to 62%. The unconnected porosity is important only on pumices where it can reach 15%. The permeability covers more than 5 orders of magnitude, ranging from 10−16 to 35 × 10−12 m2. The higher values are obtained on lava blocks and the scoriae, even if these rocks are less porous than the pumices. The formation factor ranges from 7 to 1139. The transport properties of these rocks are slightly correlated with porosity. This indicates that these properties are not only controlled by the connected porosity. To connect the transport properties to the textural characteristics of the pore network of pyroclastic rocks, different models, based on geometrical considerations or percolation theory, were tested. The pore access radius distribution and the tortuosity control the transport properties of pyroclastic rocks. Consequently, the models (electric and hydraulic) based on the concept of percolation (e.g., the models of Katz and Thompson), apply better than the equivalent channel model of Kozeny-Carman. In addition, the difference in transport properties observed on lava blocks and pumices confirms that the mechanisms of degassing and vesiculation are different for these two types of rock.
ISSN: 2169-9313

hal-00310237
https://hal.archives-ouvertes.fr/hal-00310237
DOI : 10.1029/2006JB004385, 2007

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

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

Éditeur(s) : HAL CCSD
Résumé : International audience
Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various intermediate forms which can be reshuffled by minor modifications of physico-chemical conditions or amino-acid sequences. To bypass this complexity, the multifaceted phenomenon of fibril formation is reduced here to its most elementary principles defined for a linear prototype of fibril. Selected generic features, including nucleation, elongation, and conformational recruitment, are modeled using minimalist hypotheses and tools, by separating equilibrium from kinetic aspects and in vitro from in vivo conditions. These reductionist approaches allow to bring out known and new rudiments, including the kinetic and equilibrium effects of nucleation, the dual influence of elongation on nucleation, the kinetic limitations on nucleation and fibril numbers, and the accumulation of complexes in vivo by rescue from degradation. Overlooked aspects of these processes are also pointed: the exponential distribution of fibril lengths can be recovered using various models because it is attributable to randomness only. It is also suggested that the same term "critical concentration" is used for different things, involved in either nucleation or elongation
Journal of Chemical Physics

hal-01263103
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01263103
DOI : 10.1063/1.4940149
PUBMED : 26801045

Éditeur(s) : HAL CCSD Springer Verlag
Résumé :  
A closed depression is defined as a geomorphologic element where a sediment depository is encircled by hillslopes. Despite the fact that closed depressions are often the only stagnant water points in many European landscapes, few ecological researches on their plant assemblages have been done. The main goal of this study was to give first results of the environmental factors responsible for the vegetation composition, richness and rarity in the closed depressions of the Lorraine biogeographical district (Belgium, France and grand-duche de Luxembourg). We surveyed for plant presence 85 forest and 77 grassland closed depressions. For each site, wetland area, local environmental factors and regional connectivities registered. For each species, the Ellenberg values were compiled. To investigate the main source of variation in species composition and in species richness (including richness in rare species), Non-metric Multidimensional Scaling analyses and Generalized Linear Models were respectively used. Species pools in forest (forest and preforest species) and in grassland (bog plants, pioneers, helophytes) were quite different. In both landscapes, a gradient from plants typical of basic high-productive soils to plants typical of acid low-productive soils reflects a shared successional gradient. The accumulation of organic matter allowed the establishment of Sphagnum spp., which slowly acidified the soil and thus acted as ecosystem engineers for the arrival of bog plants. Moreover, the species composition was additionally driven by the plant light tolerance in forests and by the plant water requirements in grasslands. Mechanisms of species accumulation (increase in species richness) were different in forests and in grasslands: respectively related to the plant light tolerance and to the wetland area. At the regional level, the averaged soil productivity was negatively related to the richness in rare species. Indeed, perennial highly-competitive plants such as Glyceria spp., Iris pseudacorus or Urtica dioica impeded the establishment of smaller and rarer species. At the habitat level, isolated closed depressions (due to either low connectivity or low grazing pressure) have more habitat rare species, giving evidences of dispersal limitation in plant assemblages of closed depressions.
ISSN: 0960-3115

hal-01032125
https://hal.archives-ouvertes.fr/hal-01032125
DOI : 10.1007/s10531-007-9227-x

Éditeur(s) : HAL CCSD
Résumé : International audience
The purpose of our study is to model a geothermal reservoir. When geothermal reservoir are assumed to be composed of pure water, the transfer of mass and energy is classically described by two balance equations: mass balance equation and the energy balance equation. In addition to those equations, fluid velocity ist classically given by the Darcy law while thermodynamic properties, inferred from theoretical or empirical equations of state, are used to close the mathematical system. Once this system is closed, there exist different solutions. The first one is to solve for pressure and temperature with a variable switch to saturation in the two-phase region (e.g. TOUGH2). The second one is to solve for pressure and enthalpy to increase stability of phase transition between single and two-phase states (e.g. Hydrotherm). We adopted the second option and chose te use a splitting method to get rid of the complexity of coupling equations and a finite volume method for the spatial discretization. Selecting object-oriented languages, we developed a multi-language framework, combining Python, Fortran and a C++ implementation of IAPWS (from the freesteam project) including the supercritical equations, in porous media velocity is given by Darcy law and to close the system physical properties are determined by the IAPWS-IF97 thermodynamic formulation. We resolve the equations in pressure and enthalpy instead of pressure and temperature in order to increase stability and to handle easier the passage from a single-phase to a two-phase system. We solve the system by using a splitting method - to get rid of the complexity of coupling equations - and a finite volume method. We offer some freedom to users thanks to the implementation of several methods like explicit or implicit Euler, Runge-Kutta or BDF2 for time solvers or GMRES and BICGSTAB for the linear solver. We can handle several boundary conditions like no-flow - describing a boundary which can not exchange matter with the exterior - or like a mixed-therm condition - a Dirichlet condition to the pressure and a Dirichlet or an outflow condition to the temperature in order to describe a recharge or a discharge zone - ... We're developing a multi-language framework, combining Python, Fortran and the C++ implementation of IAPWS (from the freesteam project). All these languages are object-oriented. We've applied this simulation model to the dogger in Paris, France, to several one-dimensional systems and a two-dimensional one made by Coumou with the CSMP++ platform. The dogger is a reservoir exploited to produce heat by pumping water at 70 and reinjecting it in the reservoir at 40. In the one-dimensional systems we wanted to observe the process of heat transfer from a higher temperature boundary to a smaller one in a high-energy domain. The last simulation shows the natural convection of water in a fault. For every simulation we compared the solutions we found with an other code (TOUGH2 or CSMP++) and they agreed. The next step will be to model the geothermal plant in Guadeloupe, West Indies. It's the only place in France - and in the West Indies so far - producing electricity with the earth power. The temperature can reach up to 1000 and the pressure range is around a few hundreds MPa. In some surface zones we can see two-phase water at atmospheric pressure. In the 1980s Bouillante was a laboratory for France. Since 1995 Bouillante has given 30GWh electricity a year to the Guadeloupeans.
PROCEEDINGS, Thirty-Ninth Workshop on Geothermal Reservoir Engineering
Stanford, United States

Droits : info:eu-repo/semantics/OpenAccess
hal-00944133
https://hal-brgm.archives-ouvertes.fr/hal-00944133
https://hal-brgm.archives-ouvertes.fr/hal-00944133/document
https://hal-brgm.archives-ouvertes.fr/hal-00944133/file/Copol.pdf