Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Complex nongradual evolutionary processes such as gene remodeling are difficult to model, to visualize, and to investigate systematically. Despite these challenges, the creation of composite (or mosaic) genes by combination of genetic segments from unrelated gene families was established as an important adaptive phenomena in eukaryotic genomes. In contrast, almost no general studies have been conducted to quantify composite genes in viruses. Although viral genome mosaicism has been well-described, the extent of gene mosaicism and its rules of emergence remain largely unexplored. Applying methods from graph theory to inclusive similarity networks, and using data from more than 3,000 complete viral genomes, we provide the first demonstration that composite genes in viruses are 1) functionally biased, 2) involved in key aspects of the arm race between cells and viruses, and 3) can be classified into two distinct types of composite genes in all viral classes. Beyond the quantification of the widespread recombination of genes among different viruses of the same class, we also report a striking sharing of genetic information between viruses of different classes and with different nucleic acid types. This latter discovery provides novel evidence for the existence of a large and complex mobilome network, which appears partly bound by the sharing of genetic information and by the formation of composite genes between mobile entities with different genetic material. Considering that there are around 10E31 viruses on the planet, gene remodeling appears as a hugely significant way of generating and moving novel sequences between different kinds of organisms on Earth.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01324848
http://hal.upmc.fr/hal-01324848
http://hal.upmc.fr/hal-01324848/document
http://hal.upmc.fr/hal-01324848/file/Genome%20Biol%20Evol-2014-Jachiet-2195-205.pdf
DOI : 10.1093/gbe/evu168

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Upper mantle anisotropy beneath the African IRIS and Geoscope stations is investigated through the measurements of splitting of teleseismic shear waves such as SKS, SKKS and PKS phases. Seismic anisotropy data are interesting on their own as a measure of upper mantle active or frozen deformation beneath a given station, but each station is of potential interest since it can be used to retrieve source-side seismic anisotropy at remote sites if one is able to perform station-side anisotropy correction. We performed systematic investigations of teleseismic shear wave splitting at 15 stations from the IRIS and Geoscope global seismic networks, which are located on both the oceanic and the continental parts of the African plate. Anisotropy is generally well observed at continental stations. The patterns we present generally show much more complexity than the results previously published from smaller data sets. Despite this complexity, the splitting parameters generally appear in several places to contain a signature of the regional geodynamic setting (rift structures, Archaean craton, Pan-African belt), although a deeper source of anisotropy (asthenospheric) may be present. At the oceanic stations, anisotropy measurements are much more difficult to perform because the signal is generally of poor quality. MSEY, in the Seychelles (Indian ocean), is the exception and displays a clear correlation of the azimuth of the fast split shear wave with the trend of the absolute plate motion, as defined by hotspot tracks.
ISSN: 0956-540X

hal-01380389
https://hal.archives-ouvertes.fr/hal-01380389
https://hal.archives-ouvertes.fr/hal-01380389/document
https://hal.archives-ouvertes.fr/hal-01380389/file/Barruol_SKS_afric_GJI2001.pdf
DOI : 10.1046/j.0956-540x.2001.01481.x

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
The complexity and depth of the relationships between the three domains of life challenge the reliability of phylogenetic methods, encouraging the use of alternative analytical tools. We reconstructed a gene similarity network comprising the proteomes of 14 eukaryotes, 104 prokaryotes, 2,389 viruses and 1,044 plasmids. This network contains multiple signatures of the chimerical origin of Eukaryotes as a fusion of an archaebacterium and a eubacterium that could not have been observed using phylogenetic trees. A number of connected components (gene sets with stronger similarities than expected by chance) contain pairs of eukaryotic sequences exhibiting no direct detectable similarity. Instead, many eukaryotic sequences were indirectly connected through a ``eukaryote-archaebacterium-eubacterium-eukaryote'' similarity path. Furthermore, eukaryotic genes highly connected to prokaryotic genes from one domain tend not to be connected to genes from the other prokaryotic domain. Genes of archaebacterial and eubacterial ancestry tend to perform different functions and to act at different subcellular compartments, but in such an intertwined way that suggests an early rather than late integration of both gene repertoires. The archaebacterial repertoire has a similar size in all eukaryotic genomes whereas the number of eubacterium-derived genes is much more variable, suggesting a higher plasticity of this gene repertoire. Consequently, highly reduced eukaryotic genomes contain more genes of archaebacterial than eubacterial affinity. Connected componentswith prokaryotic and eukaryotic genes tend to include viral and plasmid genes, compatible with a role of gene mobility in the origin of Eukaryotes. Our analyses highlight the power of network approaches to study deep evolutionary events.
ISSN: 0027-8424

hal-01544798
https://hal.archives-ouvertes.fr/hal-01544798
DOI : 10.1073/pnas.1211371110

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Given a graph, its hyperbolicity is a measure of how close its distance distribution is to the one of a tree. This parameter has gained recent attention in the analysis of some graph algorithms and the classification of complex networks. We study on practical improvements for the computation of hyperbolicity in large graphs. Precisely, we investigate on relations between the hyperbolicity of a graph G and the hyperbolicity of its atoms, that are the subgraphs output by the clique-decomposition invented by Tarjan [51, 65]. We prove that the maximum hyperbolicity taken over the atoms is at most one unit off from the hyperbol-icity of G and the bound is sharp. We also give an algorithm to slightly modify the atoms, called the " substitution method " , which is at no extra cost than computing the clique-decomposition, and so that the maximum hyperbolicity taken over the resulting graphs is exactly the hyperbolicity of the input graph G. An experimental evaluation of our method for computing the hyperbolicity of a given graph from its atoms is provided for collaboration networks and biological networks. Finally, on a more theoretical side, we deduce from our results the first linear-time algorithm for computing the hyperbolicity of an outerplanar graph.
ISSN: 0304-3975

hal-01540756
https://hal.inria.fr/hal-01540756
https://hal.inria.fr/hal-01540756/document
https://hal.inria.fr/hal-01540756/file/CCDL-2017.pdf
DOI : 10.1016/j.tcs.2017.06.001

Éditeur(s) : HAL CCSD
Résumé : International audience
TRAMIL is a research program applied to the use of medicinal plants in the Caribbean, established in the 1980s. Significant uses of herbal remedies to address self limiting health problems are identified through participatory ethnopharmacological surveys and are the subject of scientific validation. The results are then disseminated to several audiences.While comprising an international scientific contribution to academic research, the TRAMIL network activities value the popular and local knowledge. This fertile relationship between local knowledge and scientific research draws answers to key challenges for Caribbean societies: improving the health of Caribbean populations first and foremost, but also indirectly developing economic prospects in various sectors (agriculture, industry, tourism, and health).The success of TRAMIL is based on a rigorous methodology and on a noteworthy informal network of collaborators invested at different levels of the program, locally and / or regionally. TRAMIL is one of the few trilingual networks that have been active for nearly forty years, well before the popularization of the Internet, in more than twenty Caribbean territories. It involves people and communities, health care professionals, researchers in many disciplines, and information and documentation professionals.This paper proposes to explore these new ways of working together and the accomplishments to which they give rise by presenting some concrete examples of the TRAMIL program in Puerto Rico and examining the program's website and the complex challenges faced by the stakeholders involved in its implementation.
TRAMIL es un programa de investigación aplicada a la medicina popular del Caribe, iniciado en la década de los ‘80. Su trabajo se basa en llevar a cabo encuestas etnofarmacológicas participativas para identificar usos significativos de remedios de plantas, que son objeto de la validación científica, para tratar problemas comunes de salud. La difusión de los resultados de validación de los remedios con uso significativo completa las líneas de acción de TRAMIL. Al tiempo que representan una contribución científica internacional para la investigación académica, las actividades de TRAMIL constituyen la valoración de los saberes populares y locales. Esta relación fecunda entre el conocimiento local y la investigación científica es una respuesta a desafíos fundamentales para las sociedades del Caribe: mejorar la salud de las poblaciones del Caribe directa y en primer lugar, pero también, indirectamente, desarrollar oportunidades económicas en varios sectores (agricultura, la industria, el turismo y la salud).El éxito de TRAMIL se basa en una metodología rigurosa y una importante red informal de colaboradores que participan en diversas funciones del programa, a nivel de país y regional. TRAMIL es una de las pocas redes totalmente trilingües, activa durante casi cuarenta años, mucho antes de la popularización del Internet, en más de una veintena de territorio caribeños. Asocia especialmente a comunidades, profesionales de la salud, investigadores en muchas disciplinas, y profesionales de la información y documentación.Este trabajo tiene como objetivos explorar las modalidades de cooperación y logros sin precedentes de TRAMIL, presentando algunos ejemplos concretos del programa en Puerto Rico y examinar el sitio Web del programa y la complejidad de los desafíos que han enfrentado los actores involucrados en su implementación.
TRAMIL est un programme de recherche appliquée à l’usage des plantes médicinales dans la Caraïbe, né dans les années 1980. Les usages significatifs des plantes pour répondre à des problèmes de santé sont recensés par des enquêtes ethnopharmacologiques participatives puis font l’objet de travaux scientifiques destinés à les valider. Les résultats sont ensuite diffusés auprès de larges publics.Tout en constituant un apport scientifique international à la recherche universitaire, les activités du réseau TRAMIL s’inscrivent dans la valorisation des savoirs locaux. Cette relation fertile entre savoirs locaux et recherche scientifique dessine des réponses à des défis essentiels pour les sociétés caribéennes : l’amélioration de la santé des populations caribéennes de façon directe et en premier lieu, mais également, de façon indirecte, le développement de perspectives économiques dans des secteurs divers (agriculture, industrie, tourisme, santé).Le succès de TRAMIL repose sur une méthodologie rigoureuse et sur un important réseau informel d’acteurs investis à différents niveaux du programme, sur le plan local et/ou pancaribéen. C’est l’un des rares réseaux entièrement trilingue, actifs depuis près de quarante ans (bien avant la popularisation d’internet), dans plus d’une vingtaine de territoire de la Caraïbe. Il associe notamment les populations, les professionnels de santé, les chercheurs dans de nombreuses disciplines, et les professionnels de l’information et de la documentation.La présente contribution propose d’explorer ces modalités de collaboration inédites et les réalisations auxquelles elles donnent lieu, en présentant quelques exemples concrets du programme TRAMIL à Porto Rico, puis en examinant le site internet du programme et les défis complexes auxquels il a confronté les acteurs impliqués dans sa réalisation.
ACURIL 2017
San Juan, Puerto Rico

hal-01629021
https://hal.univ-antilles.fr/hal-01629021

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The tree model and tree-based methods have played a major, fruitful role in evolutionary studies. However, with the increasing realization of the quantitative and qualitative importance of reticulate evolutionary processes, affecting all levels of biological organization, complementary network-based models and methods are now flourishing, inviting evolutionary biology to experience a network-thinking era. We show how relatively recent comers in this field of study, that is, sequence-similarity networks, genome networks, and gene families–genomes bipartite graphs, already allow for a significantly enhanced usage of molecular datasets in comparative studies. Analyses of these networks provide tools for tackling a multitude of complex phenomena, including the evolution of gene transfer, composite genes and genomes, evolutionary transitions, and holobionts.
ISSN: 0966-842X

Droits : http://creativecommons.org/licenses/by-nc-nd/
hal-01300043
http://hal.upmc.fr/hal-01300043
http://hal.upmc.fr/hal-01300043/document
http://hal.upmc.fr/hal-01300043/file/Network-Thinking.pdf
DOI : 10.1016/j.tim.2015.12.003

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper proposes a new knowledge discovery method called FLMin to discover frequent patterns in a social network. The algorithm works without previous knowledge on the network and exploits both the structure and the attributes of nodes to extract regularities called Frequent Links. Unlike traditional works in this area that solely exploit structural regularities of the network, the originality of FLMin is its ability to gather these two kinds of information in the search for patterns. In this paper, we detail the method proposed for extracting frequent links and discuss its complexity and its flexibility. The efficiency of our solution is evaluated by conducting qualitative and quantitative studies for understanding how behaves FLMin according to different parameters.
Networked Digital Technologies
Dubai, United Arab Emirates

hal-00768431
https://hal.archives-ouvertes.fr/hal-00768431
DOI : 10.1007/978-3-642-30567-2_38

Éditeur(s) : Université de Bretagne Occidentale
Résumé : Archaea are micro-organisms present in all ecosystems, but are majoritary present in extremophilic environments. Hyperthermophilic Archaea, as Pyrococcus abyssi, are permanently exposed at temperature which can increase the rate of spontaneous DNA damage. It is probable that hyperthermophilic Archaea possess efficient molecular mechanism to duplicate, maintain and stabilize their genomes. The aim of this project was to investigate the interaction network involved in the process of DNA replication and DNA repair. The methodological approach consists in the coupling of pull-down with mass spectrometry identification of interacting partners. A preliminary interaction network was identified that was composed of new proteins as well as unsuspected interactions between known components of DNA replication machinery. The main results consist in: (1) the nuclease Pab2263, which interacts with PCNA, is a novel player in DNA metabolism. (2) PCNA is likely part of a macrocomplex with the ubiquitary proteins Mre11 and Rad50 suggesting a role of this complex in the repair of double strand break in connection with a replication fork. (3) Fen1 and DNA primase interact physically and can collaborate in vitro to resolve intermediate step of the base excision repair pathway. These results enhance our understanding of DNA repair process in Archaea.
Les Archaea sont des micro-organismes rencontrés dans tous les écosystèmes, mais qui apparaissent comme majoritaires dans les environnements dits extrêmes. Les archaea hyperthermophiles, comme Pyrococcus abyssi sont en permanence exposées à des températures qui peuvent augmenter le taux de dommages de l'ADN, pourtant, le taux de mutations spontanés chez ces micro-organismes est similaire à celui des espèces modèles mésophiles. Il est ainsi probable que les hyperthermophiles possèdent des systèmes particulièrement efficaces pour dupliquer, maintenir et stabiliser leur génome. L'objectif de ce projet était d'explorer le réseau d'interaction impliqué dans les processus de réplication et de réparation de l'ADN. L'approche méthodologique mise en oeuvre a consisté à coupler la capture de partenaires d'interaction par pull-down avec leur identification par spectrométrie de masse. J'ai pu ainsi mettre en évidence, au sein l'extrait cellulaire de P. abyssi, un réseau préliminaire reliant des protéines de la maintenance génomique. Nous avons non seulement mis en évidence de nouvelles protéines impliquées probablement dans des mécanismes de réparation, mais également des nouvelles interactions non suspectées entre des composants déjà caractérisés. Les principaux résultats sont les suivants : (1) La nucléase Pab2263, partenaire du PCNA, est un nouvel acteur du métabolisme de l'ADN. (2) Le PCNA forme un macrocomplexe avec les protéines ubiquitaires Mre11 et Rad50 suggérant un rôle de ce complexe dans la réparation des cassures double brin de l'ADN lors de la réplication. (3) Les protéines Fen1 et l'ADN primase interagissent physiquement et peuvent collaborer in vitro pour résoudre une étape intermédiaire de la voie de réparation par excision de base. Ces résultats enrichissent notre compréhension des processus de réparation de l'ADN chez les archées.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2008/these-3722.pdf
http://archimer.ifremer.fr/doc/00000/3722/

Éditeur(s) : HAL CCSD
Résumé : 1 p.
For groundwater issues (potential leakages in waste repository, aquifer management ...), the development of modeling techniques is far ahead of the actual knowledge of aquifers. This raises two fundamental issues: 1) which and how much data are necessary to make predictions accurate enough for aquifer management issues; 2) which models remain relevant to describe the heterogeneity and complexity of geological systems. The French observatory H+ was created in 2002 with the twofold motivation of acquiring a large database for validating models of heterogeneous aquifers, and of surveying groundwater quality evolution in the context of environmental changes. H+ is a network of 4 sites (Ploemeur, Brittany, France; HES Poitiers, France; Cadarache, France; Campos, Mallorca, Spain) with different geological, climatic, and economic contexts. All of them are characterized by a highly heterogeneous structure (fractured crystalline basement for Ploemeur, karstified and fractured limestone for Poitiers, Cadarache and Mallorca), which is far to be taken into account by basic models. Ploemeur is exploited as a tap-water plant for a medium-size coastal city (15,000 inhabitants) for 20 years. Each site is developed for long term investigation and monitoring. They involves a dense network of boreholes, detailed geological and geophysical surveys, periodic campaigns and/or permanent measurements of groundwater flow, water chemistry, geophysical signals (including ground motions), climatic parameter, etc. Several large-scale flow experiments are scheduled per year to investigate the aquifer structure with combined geophysical, hydrogeological, and geochemical instruments. All this information is recorded in a database that has been developed to improve the sustainability and quality of data, and to be used as a collaborative tool for both site researchers and modelers. This project lasts now for 5 years. It is a short time to collect the amount of information necessary to apprehend the complexity of aquifers; but it is already enough to obtain a few important scientific results about the very nature of the flow heterogeneity, the origin and residence time of water elements, the kinetic of geochemical processes, etc. We have also developed new methods to investigate aquifers (in-situ flow measurements, flow experiment designs, groundwater dating, versatile in-situ probes, etc.). This experience aiming at building up long term knowledge appears extremely useful to address critical issues related to groundwater aquifers: the structure and occurrence of productive aquifer in crystalline basement, the assessment of aquifer protection area in the context of highly heterogeneous flow, the biochemical reactivity processes, the long term evolution of both water quantity and quality in the context of significant environmental changes, for instance.
AGU, Fall Meeting 2008
San Francisco, United States

insu-00375980
https://hal-insu.archives-ouvertes.fr/insu-00375980

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
Résumé : Indigenous territories comprise extensive areas of tropical forest and hold significant social and conservation value. Today, they are subject to various constraints and opportunities, and face many territorial transformations. These transformations are complex and multifaceted. They involve the adoption of new production and consumption modes, the modification of forms of social organisation and identity and territorial claims. However, the links between these on-going processes are still poorly understood, and make difficult to appreciate the adaptation dynamics of indigenous common natural resources management. This thesis is particularly concerned with the territorial dynamics of the Wayãpi and Teko indigenous people of the municipality of Camopi in French Guiana. It integrates methods that include land use analysis using remotely sensed data, socio-economic and agricultural systems analysis at the household scale, and empirical analysis on the influence of identity claims, kinship networks, and conservation policies. It shows that despite the residential settlement around local towns, the growth of cash income from wage labour and welfare, associated with strong kinship networks, allows the revival of mobility and the diversification of indigenous territorialities. Environmental policies implemented on the territory involve processes of identity and territorial claims and motivate the construction of a collective project of endogenous local development. A comparative approach with the situation of the wayãpi people living in Brazil and evolving in a completely different institutional, socio-economic and environmental context shows similar dynamics. Indigenous peoples of these two sites adopt "multi-local" land use systems, allowing them to extend their territory occupation and taking part of a broader dynamic of territorial and identity affirmation. They articulate forest and local town environments. This multi-local land use system can be interpreted as a new form of environmental governance, which overcomes the access difficulties to natural resources around local towns and ensures their sovereignty over the territory.
Les territoires amérindiens couvrent de vastes étendues de forêts tropicales et possèdent une forte valeur sociale et environnementale. Soumis à des contraintes et opportunités variées, ils sont de nos jours le siège de nombreuses transformations territoriales. Ces transformations sont complexes et multiformes. Elles impliquent l'adoption de nouveaux modes de production et de consommation, le réajustement des formes d'organisation sociale et des dynamiques de réaffirmation identitaire et territoriale. Or les liens entre tous ces processus sont encore mal compris, et rendent délicate la compréhension des dynamiques d'adaptation des systèmes amérindiens de gestion des ressources communes. Cette thèse s'intéresse particulièrement aux dynamiques territoriales des Amérindiens wayãpi et teko de la commune de Camopi en Guyane française. Elle intègre des données sur l'occupation du sol obtenues par télédétection, des données socio-économiques et productives à l'échelle des ménages et des données qualitatives sur les processus identitaires, les réseaux de parenté, les politiques de conservation et la gouvernance du territoire. Elle montre que malgré la sédentarisation de l'habitat autour des bourgs locaux, la croissance des revenus monétaires issus des emplois salariés et des aides sociales, combinée avec le maintien de réseaux de parenté et d'entraide, permet une redynamisation des systèmes de mobilité et une diversification des territorialités amérindiennes. De plus, les politiques environnementales mises en place sur le territoire impliquent des processus de territorialisation et de revendications identitaires et motivent la construction collective d'un projet de développement local endogène. Une approche comparative avec la situation des Amérindiens wayãpi vivant au Brésil et évoluant dans un contexte socio-économique, institutionnel et environnemental bien différent montre des dynamiques similaires. Les Amérindiens de ces deux pays adoptent des systèmes d'exploitation du territoire multi-locaux, leur permettant d'étendre leur occupation du territoire et s'inscrivant dans une dynamique de réaffirmation identitaire et territoriale. Ils articulent ainsi les espaces de la forêt et des bourgs. Cette forme d'exploitation multi-locale du territoire peut être interprétée comme une nouvelle forme de gouvernance environnementale, qui leur permet de contourner les difficultés d'accès aux ressources naturelles autour des bourgs et d'affirmer leur souveraineté sur le territoire.
https://tel.archives-ouvertes.fr/tel-00831619

tel-00831619
https://tel.archives-ouvertes.fr/tel-00831619
https://tel.archives-ouvertes.fr/tel-00831619/document
https://tel.archives-ouvertes.fr/tel-00831619/file/These_TRITSCH_mai2013_vf.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) : ESA Publication
Résumé : Satellite remote sensing has emerged as an essential and necessary observing system to acquire global information about the state of the ocean. Complemented with in situ observing networks, the ultimate goals are to be able to make accurate estimates of selected key sets of geophysical variables, with the intention of either making operational predictions across time and spatial boundaries, or advancing fundamental knowledge through development of empirical relationships and theoretical models. For satellite oceanography, improvements are then constantly being sought in our understandings of the geophysical processes, the sensor physics, the electromagnetic and microwave properties and interactions at the complex air-sea interface. Challenges appear as unlimited as the variety of sea surface dynamics and boundary layer meteorological conditions with their broad range of spatial and temporal scales across the globe. To face these challenges, numerous efforts took places over the passed decade to build an ever-increasing quality, quantity, duration and integration of ocean observations. In parallel, simulation capabilities largely improved. All these efforts are then all critically calling for improved methodologies to better structure the wealth of information that is made readily accessible. This latter aspect is a very demanding new component for future multidisciplinary scientific research. Major innovations to consolidate sensor data repositories, to automate tailored queries, to extract, reveal and quantify relationships will then closely associate computer science developments and applied statistics with comprehensive theoretical and experimental thematic studies.
Proceedings of OceanObs'09: Sustained Ocean Observations and Information for Society (ESA Publication), 2010

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00029/14046/11241.pdf
DOI:10.5270/OceanObs09.pp.12
http://archimer.ifremer.fr/doc/00029/14046/

Éditeur(s) : HAL CCSD Réseau « Développement durable et territoires fragiles »
Résumé : The Green and Blue infrastructure (Trame verte et bleue –TVB) is a new conservation policy tool based on the notions of ecological network and corridor. The introduction of this new instrument through the French Grenelle environment commitments brings about some change in the spatial strategy of the conservation policy. Beyond the identification of priority conservation areas, ecological planning of all the territory is concerned. The TVB’s implementation process establishes the connection of multi and nested decisional and action levels. It thus creates specific situations of complexity and uncertainty that require innovation and perpetual change of governance. The study of the Auvergne region case through the adaptive governance analytical framework highlights the potential fruitful role of Regional nature parks in such dynamics of change and learning. Mots-clés : aménagement durable des territoires, biodiversité, réseau écologique, corridor écologique, gouvernance adaptative, socio-écosystème, trame verte et bleue Keywords : Sustainable landplaning, Biodiversity, Ecological network, Adaptive governance, socio-ecosystem
La Trame verte et bleue (TVB), nouveau dispositif d’action publique visant à enrayer la perte de biodiversité traduit un renouvellement des référentiels de justification des politiques de conservation et de leur stratégie territoriale. Il s’agit d’intégrer la planification écologique dans l’aménagement de l’ensemble du territoire. Le processus de territorialisation de la TVB met en rapport de multiples niveaux de décision et d’action imbriqués. Il crée de ce fait des configurations inédites de complexité et d’incertitude et implique des innovations en termes de gouvernance que le cadre analytique de la gouvernance adaptative permet d’appréhender. En nous appuyant sur l’exemple du Parc Naturel Régional des Volcans d’Auvergne, nous analysons le rôle que ces institutions sont susceptibles de jouer dans ces dynamiques de changement et d’apprentissage socio-technique et politique qui conditionnent une mise en œuvre effective de la TVB.
ISSN: 1772-9971

hal-01195370
https://hal.archives-ouvertes.fr/hal-01195370
DOI : 10.4000/developpementdurable.9675
PRODINRA : 269288

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Mammalian spermatogenesis, which takes place in complex testicular structures called seminiferous tubules, is a highly specialized process controlled by the integration of juxtacrine, paracrine and endocrine information. Within the seminiferous tubules, the germ cells and Sertoli cells are surrounded by testicular fluid (TF), which probably contains most of the secreted proteins involved in crosstalk between these cells. It has already been established that germ cells can modulate somatic Sertoli cell function through the secretion of diffusible factors. We studied the germ cell secretome, which was previously considered inaccessible, by analyzing the TF collected by microsurgery in an "integrative omics" strategy combining proteomics, transcriptomics, genomics and interactomics data. This approach identified a set of proteins preferentially secreted by Sertoli cells or germ cells. An interaction network analysis revealed complex, interlaced cell-cell dialog between the secretome and membranome of seminiferous cells, mediated via the TF. We then focused on germ cell-secreted candidate proteins, and we identified several potential interacting partners located on the surface of Sertoli cells. Two interactions, APOH/CDC42 and APP/NGFR, were validated in situ, in a proximity ligation assay (PLA). Our results provide new insight into the crosstalk between germ cells and Sertoli cells occurring during spermatogenesis. Our findings also demonstrate that this "integrative omics" strategy is powerful enough for data mining and highlighting meaningful cell-cell communication events between different types of cells in a complex tissue, via a biological fluid. This integrative strategy could be applied more widely, to gain access to secretomes that have proved difficult to study whilst avoiding the limitations of in vitro culture.
ISSN: 1932-6203

hal-01129957
https://hal.archives-ouvertes.fr/hal-01129957
https://hal.archives-ouvertes.fr/hal-01129957/document
https://hal.archives-ouvertes.fr/hal-01129957/file/2014_FChalmel_PlosOne_%7B1236BFCE-4830-400D-B816-4B6651311900%7D.pdf
DOI : 10.1371/journal.pone.0104418

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
The regulatory mechanisms involved in the acquisition of thermal tolerance are unknown in insects. Reversible phosphorylation is a widespread post-translational modification that can rapidly alter proteins function(s). Here, we conducted a large-scale comparative screening of phosphorylation networks in adult Drosophila flies that were cold-acclimated versus control. Using a modified SIMAC method followed by a multiple MS analysis strategy, we identified a large collection of phosphopeptides (about 1600) and phosphoproteins (about 500) in both groups, with good enrichment efficacy (80%). The saturation curves from the four biological replicates revealed that the phosphoproteome was rather well covered under our experimental conditions. Acclimation evoked a strong phosphoproteomic signal characterized by large sets of unique and differential phosphoproteins. These were involved in several major GO superclusters of which cytoskeleton organization, positive regulation of transport, cell cycle, and RNA processing were particularly enriched. Data suggest that phosphoproteomic changes in response to acclimation were mainly localized within cytoskeletal network, and particularly within microtubule associated complexes. This study opens up novel research avenues for exploring the complex regulatory networks that lead to acquired thermal tolerance.
ISSN: 2045-2322

hal-01532256
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01532256
DOI : 10.1038/s41598-017-01974-z
PUBMED : 28490779

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Upper-mantle flow beneath the South Pacific is investigated by analysing shear wave splitting parameters at eight permanent long-period and broad-band seismic stations and 10 broad-band stations deployed in French Polynesia from 2001 to 2005 in the framework of the Polynesian Lithosphere and Upper Mantle Experiment (PLUME). Despite the small number of eventsand the rather poor backazimuthal coverage due to the geographical distribution of the natural seismicity, upper-mantle seismic anisotropy has been detected at all stations except at Tahiti where two permanent stations with 15 yr of data show an apparent isotropy. The median value of fast polarization azimuths (N67.5°W) is parallel to the present Pacific absolute platemotion direction in French Polynesia (APM: N67°W). This suggests that the observed SKS fast polarization directions result mainly from olivine crystal preferred orientations produced by deformation in the sublithospheric mantle due to viscous entrainment by the moving Pacific Plate and preserved in the lithosphere as the plate cools. However, analysis of individualmeasurements highlights variations of splitting parameters with event backazimuth that imply an actual upper-mantle structure more complex than a single anisotropic layer with horizontal fast axis. A forward approach shows that a two-layer structure of anisotropy beneath French Polynesia better explains the splitting observations than a single anisotropic layer. Second ordervariations in the measurements may also indicate the presence of small-scale lateral heterogeneities. The influence of plumes or fracture zones within the studied area does not appear to dominate the large-scale anisotropy pattern but may explain these second-order splitting variations across the network.
ISSN: 0956-540X

hal-01249275
https://hal.archives-ouvertes.fr/hal-01249275
https://hal.archives-ouvertes.fr/hal-01249275/document
https://hal.archives-ouvertes.fr/hal-01249275/file/GJI2007SKS.pdf
DOI : 10.1111/j.1365-246X.2007.03475.x

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Clin Microbiol Infect 2012; 18 (Suppl. 4): 4043 Abstract In order to study complex microbial communities and their associated mobile genetic elements, such as the human gut microbiome, evolutionists could explore their genetic diversity with shared sequence networks. In particular, the detection of remarkable structures in gene networks of the gut microbiome could serve to identify important functions within the community, and would ease comparison of data sets from microbiomes of various sources (human, ape, mouse etc.) in a single analysis.
ISSN: 1198-743X

hal-01544804
https://hal.archives-ouvertes.fr/hal-01544804
DOI : 10.1111/j.1469-0691.2012.03856.x

Éditeur(s) : HAL CCSD
Résumé : contient des versions PDF d'articles scientifiques (versions éditeur)
Spectrins are actin binding proteins that constitute the main components of membrane skeletons, the protein network located under the plasma membrane. Erythroid or non erythroid (in this case, they are called fodrins), spectrins play an important structural function in the membrane as demonstrated in the red blood cell. Spectrins are composed of two long α and β chains, associated in tetramers (αβ)2, forming the long flexible filaments of the network. Both chains are composed of repeating units which are folded in a triple helical arrangement (A, B and C helices), except for segment α10 which corresponds to a Src Homology 3 domain (SH3). The head-to-head interaction between dimers implies the N-terminal end of α chain and the C-terminal end of β chain. A model was proposed for the tetramerization site of spectrin : the two A and B helices of the last repeat of α chain interact with the C helix of the β chain in order to constitute a triple-helical structure similar to the repeats along the remainder of spectrin molecule. This model was first inferred from the relationship between the severity of the spectrin self-association defect and the location of the underlying mutations found in hereditary elliptocytosis (HE). Using recombinant peptides we defined the region, on both chains, which was sufficient and necessary to generate a fully functional tetramerization site. Producing peptides carrying a βHE mutation, we reproduced the tetramerization defect as observed in red blood cells of patients.
Finally, the presence of an SH3 domain probably gives to spectrins new functions which are different from the stability of the membrane. After contesting the existence of interaction between the fodrin SH3 domain and the α subunit of epithelial sodium channel sensitive to amiloride, we searched for partners of this domain, by screening a rat kidney library with the yeast two-hybrid system. We identified severals proteins implicated in the actin polymerization asoociated with motility or cell differenciation, suggesting that SH3 domain could play a part in this process.
Les spectrines, protéines liant l'actine, sont des constituants majeurs du squelette membranaire, réseau multiprotéique localisé sous la membrane plasmique. Érythroïdes ou non érythroïdes (dans ce cas, on les appelle fodrines), les spectrines ont un rôle structural important dans la membrane comme cela a déjà été démontré, pour la spectrine, dans le globule rouge. Elles sont constituées de deux longues chaînes a et ß associées côte à côte en tétramères (aß)2 qui forment les longs filaments du réseau. Chacune des chaînes est composée par la répétition de segments homologues, 22 pour a et 17 pour ß. Ces segments sont constitués de trois hélices a (hélices A, B et C) repliées sur elles-mêmes. Cette succession de structures trihélicoïdales est parfois interrompue par un domaine particulier comme le domaine SH3 (Src Homology 3) présent au milieu de la chaîne a. Les tétramères (aß)2 de spectrine constituent les filaments du squelette membranaire. L'interaction tête-à-tête de deux dimères aß implique les extrémités NH2 de la chaîne a et COOH de la chaîne ß. D'une part la sévérité du défaut d'auto-association et la localisation des mutations associées à celui-ci et d'autre part, les séquences en acides aminés des extrémités impliquées dans le site d'auto-association ont permis de proposer un modèle : la première hélice C isolée de la chaîne a pourrait s'associer aux deux dernières hélices A et B de la chaîne ß pour reconstituer une unité conformationnelle trihélicoïdale semblable à celles observées le long de la molécule. Un défaut dans la formation du tétramère est le support moléculaire le plus fréquemment observé dans les elliptocytoses héréditaires (HE). À l'aide de peptides recombinants, nous avons défini, sur les deux chaînes, les régions nécessaires et suffisantes possédant les caractéristiques pleinement fonctionnelles du site de tétramérisation. Nous avons ensuite, par mutagenèse dirigée, reproduit le lien entre la présence de mutations HE localisées dans les hélices A ou B et le défaut d'auto-association observé dans les globules rouges de patients HE. La présence d'un domaine SH3 localisé au milieu de la chaîne a confère probablement aux spectrine des fonctions autres que le maintien et la stabilité de la membrane. Les SH3, petits domaines protéiques, participent aux interactions protéine/protéine. Le seul partenaire connu du domaine SH3 de la fodrine était la sous-unité a du canal sodium sensible à l'amiloride (ENaC) mais la fonction de ce complexe n'était pas encore caractérisée. À l'aide de différentes méthodes, nous avons remis en cause l'interaction directe entre ENaC et le SH3 de la fodrine. La fonction de ce domaine SH3 étant liée à la nature de son ligand, nous avons donc recherché les partenaires putatifs du domaine SH3 de la fodrine par la technique du double-hybride. 29 partenaires ont été identifiés, regroupés en 19 familles et 10 clones isolés. La spécificité des interactions a été étudiée à la fois par double-hybride, à l'aide de mutants du domaine SH3 de la fodrine produits par mutagenèse dirigée. Les interactions vis-à-vis d'autres domaines SH3 (spectrine ou une protéine de levure non relatée Scd2) ont été également analysées. Enfin, la spécificité de certains partenaires a été confirmée par des études d'interactions in vitro. Deux des protéines les plus spécifiques du domaine SH3 de la fodrine sont des protéines tyrosine-phosphatase PTP. La première est l'isoforme A de PTP de faible poids moléculaire (LMPTPA) mais l'interaction n'a pas été confirmée in vitro. La deuxième, TD14, est une nouvelle PTP dont la seule fonction connue est d'inhiber la formation des foyers tumoraux des cellules surexprimant l'oncogène Ha-ras. Ces PTP pourraient soit déphosphoryler la fodrine, soit être recrutées sous la membrane pour déphosphoryler une autre cible. Nous avons également identifié trois partenaires (N-WASP, Evl et une protéine de la famille des formines) suggérant que les domaines SH3 des spectrines pourraient être impliqués dans les processus de polymérisation de l'actine liés à la mobilité ou la différenciation cellulaire. Mot clés : spectrine, fodrine, tétramérisation, SH3, double-hybride, polymérisation de l'actine
https://tel.archives-ouvertes.fr/tel-00284819

Droits : info:eu-repo/semantics/OpenAccess
tel-00284819
https://tel.archives-ouvertes.fr/tel-00284819
https://tel.archives-ouvertes.fr/tel-00284819/document
https://tel.archives-ouvertes.fr/tel-00284819/file/Nicolas_1999_-_These.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Recently it has become clear that exposure to xenobiotics may result in various forms of cell death; not only passive cell deaths like necrosis, or programmed cell deaths such as apoptosis, but also regulated necrosis, autophagy, senescence, or mitotic catastrophe. Complex cell signaling networks influence the processing of cell death. Furthermore, recent research has revealed early complex molecular interactions between organelles prior to the final triggering of cell death. The plasma membrane may play an important role in the early cell death signaling events. Regarding this latter aspect, drugs and environmental pollutants have been reported to affect plasma membrane characteristics which may further affect cell fate. Changes in membrane fluidity or in composition and function of specialized membrane microdomains (plasma membrane remodeling) have been proven to be involved in the regulation of many important physiological signaling pathways, including cell death. Furthermore, it has been suggested that a crosstalk between chemical-induced cellular membrane effects and other organelles may be of vital importance to explain the final outcome of chemical exposure. Here, we review the effects of plasma membrane remodeling on cell survival and cell death; we describe how the cell signaling pathways activated by changes in plasma membrane characteristics may influence cell fate. Since plasma membrane function plays an important role in the regulation of a number of cellular responses, it has been implicated in the development or progress of several diseases. A better knowledge of the effects of various chemicals on plasma membrane remodeling may be important for understanding the pathogenesis of major diseases, and may assist in developing new therapeutic strategies.
ISSN: 0300-483X

inserm-00818916
http://www.hal.inserm.fr/inserm-00818916
DOI : 10.1016/j.tox.2012.12.014
PUBMED : 23287390