Éditeur(s) : HAL CCSD
Résumé : The concept of network provides a model for representing a wide variety of objects and systems, both natural and social, in which a set of homogeneous or heterogeneous entities interact. It is now widely used to describe various kinds of relational structures. However, if everyone has an idea of the concept of network, we often ignore the implications that these structures have in real world phenomena. This is for example the case of processes such as the spread of a rumor, the disease transmission, or even the emergence of subjects of common interest for a group of individuals, in which the relations maintained between individuals, and their nature, often prove to be the main factors determining the evolution of the phenomenon. This is the reason why the study of networks has become one of the emerging areas in the 21st century called the "Science of networks." In this thesis, we address three issues of the domain of the science of networks: the problem of diffusion in social networks, where we have addressed more particularly the impact of the network dynamics on the diffusion process, the problem of the analysis of social networks, in which we have proposed a solution to take full advantage of all information available on the network by combining information on both structure and node attributes and the central problem of the social data collection, for which we have focused on the particular case of the data collection in a wild environment.
Le concept de réseau offre un modèle de représentation pour une grande variété d'objets et de systèmes, aussi bien naturels que sociaux, dans lesquels un ensemble d'entités homogènes ou hétérogènes interagissent entre elles. Il est aujourd'hui employé couramment pour désigner divers types de structures relationnelles. Pourtant, si chacun a une idée plus ou moins précise de ce qu'est un réseau, nous ignorons encore souvent les implications qu'ont ces structures dans de nombreux phénomènes du monde qui nous entoure. C'est par exemple le cas de processus tels que la diffusion d'une rumeur, la transmission d'une maladie, ou même l'émergence de sujets d'intérêt commun à un groupe d'individus, dans lesquels les relations que maintiennent les individus entre eux et leur nature s'avèrent souvent être les principaux facteurs déterminants l'évolution du phénomène. C'est ainsi que l'étude des réseaux est devenue l'un des domaines émergents du 21e siècle appelé la "Science des réseaux". Dans ce mémoire, nous abordons trois problèmes de la science des réseaux: le problème de la diffusion dans les réseaux sociaux, où nous nous sommes intéressés plus particulièrement à l'impact de la dynamique du réseau sur le processus de diffusion, le problème de l'analyse des réseaux sociaux, dans lequel nous avons proposé une solution pour tirer parti de l'ensemble des informations disponibles en combinant les informations sur la structure du réseau et les attributs des noeuds et le problème central de la collecte de données sociales, où nous nous sommes intéressés au cas particulier de la collecte de données en milieux sauvages.
https://tel.archives-ouvertes.fr/tel-00830882

Droits : info:eu-repo/semantics/OpenAccess
tel-00830882
https://tel.archives-ouvertes.fr/tel-00830882
https://tel.archives-ouvertes.fr/tel-00830882/document
https://tel.archives-ouvertes.fr/tel-00830882/file/These_STATTNER_2012.pdf

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) : 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 Springer Verlag
Résumé : International audience
The actin cytoskeleton is a dynamic structure that provides an interactive platform for organelles and cellular components. It also serves as track for membranes and vesicles that move via myosin. The actin cytoskeleton of Symbiodinium is a well-organized reticular structure suggestive of multiple membrane interactions, very likely including those of the chloroplast. The Symbiodinium chloroplast membrane network is, in turn, a highly organized structure, suggestive of being under the control of an organizing network. We visualized the chloroplast membranes of cultured Symbiodinium sp. under various light conditions and observed changes dependent on illumination intensity. Since we suspected interaction between these two organelles, and we knew that the Symbiodinium actin cytoskeleton collapses upon treatment with either latrunculin B, an actin microfilament-disrupting agent, or butanedione monoxime, a myosin function inhibitor, we tested the Symbiodinium sp. oxygen evolution in their presence. Upon latrunculin B addition, the oxygen production decreased compared to non-treated cells; however, this was not observed after a 24 h latrunculin treatment. On the contrary, butanedione monoxime treatment caused a non-recoverable dysfunction of the chloroplast causing a severe loss in oxygen production even after long-term exposure. Using electron microscopy, we observed an alteration of the Symbiodinium sp. chloroplast distribution after latrunculin B treatment, with respect to untreated cells. Furthermore, a thorough disorganization of the chloroplast grana was observed after butanedione monoxime treatment. These data suggest that an actomyosin system would be important for chloroplast organization and distribution, and critical for normal photosynthetic function of Symbiodinium sp.
ISSN: 0166-8595

hal-01546164
https://hal.archives-ouvertes.fr/hal-01546164
DOI : 10.1007/s11120-015-0142-9

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Cell proliferation is a hallmark of cancer and depends on complex signaling networks that are chiefly supported by protein kinase activities. Therapeutic strategies have been used to target specific kinases but new methods are required to identify combined targets and improve treatment. Here, we propose a small interfering RNA genetic screen and an integrative approach to identify kinase networks involved in the proliferation of cancer cells. The functional siRNA screen of 714 kinases in HeLa cells identified 91 kinases implicated in the regulation of cell growth, most of them never being reported in previous whole-genome siRNA screens. Based on gene ontology annotations, we have further discriminated between two classes of kinases that, when suppressed, result in alterations of the mitotic index and provoke cell-cycle arrest. Extinguished kinases that lead to a low mitotic index mostly include kinases implicated in cytosolic signaling. In contrast, extinguished kinases that result in a high mitotic index mostly include kinases implicated in cell division. By mapping hit kinases in the PhosphPOINT phosphoprotein database, we generated scale-free networks consisting of 449 and 661 protein-protein interactions for kinases from low MI and high MI groups, respectively. Further analyses of the kinase interactomes revealed specific modules such as FER- and CRKL-containing modules that connect three members of the epidermal growth factor receptor (EGFR) family, suggesting a tight control of the mitogenic EGF-dependent pathway. Based on experimental studies, we confirm the involvement of these two kinases in the regulation of tumor cell growth. Based on a combined approach of large kinome-wide siRNA screens and ontology annotations, our study identifies for the first time two kinase groups differentially implicated in the control of cell proliferation. We further demonstrate that integrative analysis of the kinase interactome provides key information which can be used to facilitate or optimize target design for new therapeutic strategies. The complete list of protein-protein interactions from the two functional kinase groups will provide a useful database for future investigations.
ISSN: 1471-2164

hal-01118475
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118475
DOI : 10.1186/1471-2164-15-1169
PUBMED : 25540073

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Middle Atlas is a region where xenolith-bearing volcanism roughly coincides with the maximum of lithospheric thinning beneath continental Morocco. It is therefore a key area to study the mechanisms of lithospheric thinning and constrain the component of mantle buoyancy that is required to explain the Moroccan topography. Samples from the two main xenolith localities, the Bou Ibalghatene and Tafraoute maars, have been investigated for their mineralogy, microstructures, crystallographic preferred orientation, and whole-rock and mineral compositions. While Bou Ibalghatene belongs to the main Middle Atlas volcanic field, in the ‘tabular’ Middle Atlas, Tafraoute is situated about 45 km away, on the North Middle Atlas Fault that separates the ‘folded’ Middle Atlas, to the South-East, from the ‘tabular’ Middle Atlas, to the North-West. Both xenolith suites record infiltration of sub-lithospheric melts that are akin to the Middle Atlas volcanism but were differentiated to variable degrees as a result of interactions with lithospheric mantle. However, while the Bou Ibalghatene mantle was densely traversed by high melt fractions, mostly focused in melt conduits, the Tafraoute suite records heterogeneous infiltration of smaller melt fractions that migrated diffusively, by intergranular porous flow. As a consequence the lithospheric mantle beneath Bou Ibalghaten was strongly modified by melt–rock interactions in the Cenozoic whereas the Tafraoute mantle preserves the record of extensional lithospheric thinning, most likely related to Mesozoic rifting. The two xenolith suites illustrate distinct mechanisms of lithospheric thinning: extensional thinning in Tafraoute, where hydrous incongruent melting triggered by decompression probably played a key role in favouring strain localisation, vs. thermal erosion in Bou Ibalghatene, favoured and guided by a dense network of melt conduits. Our results lend support to the suggestion that lithospheric thinning beneath the Atlas mountains results from the combination of different mechanisms and occurred in a piecewise fashion at a short wavelength scale.
ISSN: 0040-1951

hal-01171756
https://hal.archives-ouvertes.fr/hal-01171756
DOI : 10.1016/j.tecto.2014.11.020

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Intraguild predation (IGP) is a type of biological interaction involving the killing and consuming of competing species that exploit similar and often limited resources. This phenomenon is widespread among a great variety of taxonomic groups and has already been reported for mosquito (Diptera: Culicidae) larvae. Moreover, the larvae of certain mosquito species of the tribe Sabethini have evolved modified mouthparts ending in rigid apical structures signaling their capacity to be effective intraguild predators. We assumed that IGP confers a selective advantage under severe competitive conditions by both providing an immediate energetic gain and reducing potential competition. Because potential competition is likely to increase with decreasing habitat size, we hypothesized that the proportion of species with modified mouthparts would increase in smaller aquatic habitats. We tested this hypothesis by examining the mosquito species naturally associated with phytotelmata of decreasing sizes in French Guiana. We show that the degree of specialization in mosquito-phytotelm associations is high, suggesting a long coevolutive process. Indeed, short-term interaction experiments confirmed that species with modified mouthparts are able to prey upon similarly-sized intraguild prey and are, thus, effective intraguild predators. In addition, these species are larger and associated with smaller phytotelmata than those with typical mouthparts. Moreover, below a certain threshold of phytotelm size, only species with modified mouthparts were present. These results show that IGP confers a selective advantage under severe competitive conditions and results from the coadaptation of mosquito species to their specific phytotelm habitat. The presence of functionally analogous structures in different mosquito genera also implies that IGP has emerged from convergent evolution in small phytotelmata.
ISSN: 0269-7653

hal-01603304
https://hal.archives-ouvertes.fr/hal-01603304
DOI : 10.1007/s10682-016-9862-3
PRODINRA : 405771

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

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

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Motivation: Gene fusion is an important evolutionary process. It can yield valuable information to infer the interactions and functions of proteins. Fused genes have been identified as non-transitive patterns of similarity in triplets of genes. To be computationally tractable, this approach usually imposes an a priori distinction between a dataset in which fused genes are searched for, and a dataset that may have provided genetic material for fusion. This reduces the `genetic space' in which fusion can be discovered, as only a subset of triplets of genes is investigated. Moreover, this approach may have a high-false-positive rate, and it does not identify gene families descending from a common fusion event. Results: We represent similarities between sequences as a network. This leads to an efficient formulation of previous methods of fused gene identification, which we implemented in the Python program FusedTriplets. Furthermore, we propose a new characterization of families of fused genes, as clique minimal separators of the sequence similarity network. This well-studied graph topology provides a robust and fast method of detection, well suited for automatic analyses of big datasets. We implemented this method in the C++ program MosaicFinder, which additionally uses local alignments to discard false-positive candidates and indicates potential fusion points. The grouping into families will help distinguish sequencing or prediction errors from real biological fusions, and it will yield additional insight into the function and history of fused genes.
ISSN: 1367-4803

hal-01544795
https://hal.archives-ouvertes.fr/hal-01544795
DOI : 10.1093/bioinformatics/btt049

Éditeur(s) : HAL CCSD IGI Global
Résumé : International audience
The social behavior of individuals is an important factor of the transmission and the evolution of many diseases. As such, epidemic studies have attempted to integrate social aspects in dissemination modeling. Since the pioneering works of Klovdahl on AIDS in 1985, epidemiological investigations and interventions increasingly focus on social networks. Significant factors of the transmission and outbreak of many infectious diseases are the structure and nature of human interactions. Network-based modeling approaches have found various applications in epidemiology as a simple yet efficient way to represent the complexity of human relationships implicated in dissemination processes. However, most results have been obtained by considering social networks as steady stage structures. Evolving networks have not been explored. The objective is first to give an overview of network-based modeling attempts in epidemiology to analyze and understand the dissemination processes with an emphasis on dynamic networks. The authors approach is designed to understand the impact of social links dynamics on epidemic spread. The authors present the results obtained by combining network evolution patterns (link creation and deletion) and a typical epidemic model. The speed of link dynamics and the infection time strongly influence the occurrence and value of the epidemic peak.
ISSN: 1947-8186

hal-00700105
https://hal.archives-ouvertes.fr/hal-00700105
DOI : 10.4018/jismd.2012070103

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
1. Our understanding of the contribution of interspecific interactions to functional diversity in nature lags behind our knowledge of spatial and temporal patterns. Although two-species mutualisms are found in all types of ecosystems, the study of their ecological influences on other community members has mostly been limited to third species, while their influence on entire communities remains largely unexplored. 2. We hypothesized that mutualistic interactions between two respective ant species and an epiphyte mediate the biological traits composition of entire invertebrate communities that use the same host plant, thereby affecting food webs and functional diversity at the community level. 3. Aechmea mertensii (Bromeliaceae) is both a phytotelm ('plant-held water') and an ant-garden epiphyte. We sampled 111 bromeliads (111 aquatic invertebrate communities) associated with either the ant Pachycondyla goeldii or Camponotus femoratus. The relationships between ants, bromeliads and invertebrate abundance data were examined using a redundancy analysis. Biological traits information for invertebrates was structured using a fuzzy-coding technique, and a co-inertia analysis between traits and abundance data was used to interpret functional differences in bromeliad ecosystems. 4. The vegetative traits of A. mertensii depended on seed dispersion by C. femoratus and P. goeldii along a gradient of local conditions. The ant partner selected sets of invertebrates with traits that were best adapted to the bromeliads' morphology, and so the composition of the biological traits of invertebrate phytotelm communities depends on the identity of the ant partner. Biological traits suggest a bottom-up control of community structure in C. fenaoratus-associated phytotelmata and a greater structuring role for predatory invertebrates in P. goeldii-associated plants. 5. This study presents new information showing that two-species mutualisms affect the functional diversity of a much wider range of organisms. Most biological systems form complex networks where nodes (e.g. species) are more or less closely linked to each other, either directly or indirectly, through intermediate nodes. Our observations provide community-level information about biological interactions and functional diversity, and perspectives for further observations intended to examine whether large-scale changes in interacting species/community structure over broad geographical and anthropogenic gradients affect ecosystem functions.
Functional Ecology

hal-01096909
https://hal-agroparistech.archives-ouvertes.fr/hal-01096909
DOI : 10.1111/j.1365-2435-2011.01863.x

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Glioblastoma (GB), the most frequent primary tumor of the central nervous system, remains one of the most lethal human cancers despite intensive researches. Current paradigm in the study of GB has been focused on inter-patient variability and on trying to isolate new classification elements or prognostic factors. Here, using ICPL, a technique for protein relative quantification by mass spectrometry, we investigated protein expression between the four regions of GB on clinically relevant biopsies from 5 patients. We identified 584 non-redundant proteins and 31 proteins were found to be up-regulated in the tumor region compared to the peri-tumoral brain tissue, among which, 24 proteins belong to an interaction network linked to 4 biological processes. The core of this network is mainly constituted of interactions between beta-actin (ACTB) with heat shock proteins (HSP90AA1, HSPA8) and 14-3-3 proteins (YWHAZ, YWHAG, YWHAB). A cluster of three isoforms of the sodium pump α-subunit (ATP1A1, ATP1A2, ATP1A3) was also identified outside this network. The differential expression observed for ACTB and 14-3-3γ was further validated by western blot and/or immunohistochemistry. Our study confirms the identity of previously proposed molecular targets, highlights several functional processes altered in GB such as energy metabolism and synaptic transmission and could thus provide added value to new therapeutic trails.
ISSN: 1874-3919

hal-00877756
https://hal.archives-ouvertes.fr/hal-00877756
DOI : 10.1016/j.jprot.2012.04.034
PUBMED : 22575386

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
The yeast Candida glabrata has become the second cause of systemic candidemia in humans. However, relatively few genome-wide studies have been conducted in this organism and our knowledge of its transcriptional regulatory network is quite limited. In the present work, we combined genome-wide chromatin immunoprecipitation (ChIP-seq), transcriptome analyses, and DNA binding motif predictions to describe the regulatory interactions of the seven Yap (Yeast AP1) transcription factors of C. glabrata. We described a transcriptional network containing 255 regulatory interactions and 309 potential target genes. We predicted with high confidence the preferred DNA binding sites for 5 of the 7 CgYaps and showed a strong conservation of the Yap DNA binding properties between S. cerevisiae and C. glabrata. We provided reliable functional annotation for 3 of the 7 Yaps and identified for Yap1 and Yap5 a core regulon which is conserved in S. cerevisiae, C. glabrata, and C. albicans. We uncovered new roles for CgYap7 in the regulation of iron-sulfur cluster biogenesis, for CgYap1 in the regulation of heme biosynthesis and for CgYap5 in the repression of GRX4 in response to iron starvation. These transcription factors define an interconnected transcriptional network at the crossroads between redox homeostasis, oxygen consumption, and iron metabolism.
ISSN: 1664-302X

Droits : http://creativecommons.org/licenses/by/
hal-01323791
http://hal.upmc.fr/hal-01323791
http://hal.upmc.fr/hal-01323791/document
http://hal.upmc.fr/hal-01323791/file/fmicb-07-00645.pdf
DOI : 10.3389/fmicb.2016.00645

Éditeur(s) : HAL CCSD
Résumé : International audience
The SOX8 and SOX9 transcription factors are involved in, among others, sex differentiation, male gonad development and adult maintenance of spermatogenesis. Sox8(-/-) mice lacking Sox9 in Sertoli cells fail to form testis cords and cannot establish spermatogenesis. Although genetic and histological data show an important role for these transcription factors in regulating spermatogenesis, it is not clear which genes depend upon them at a genome-wide level. To identify transcripts that respond to the absence of Sox8 in all cells and Sox9 in Sertoli cells we measured mRNA concentrations in testicular samples from mice at 0, 6 and 18 days post-partum. In total, 621 and 629 transcripts were found at decreased or increased levels, respectively, at different time points in the mutant as compared to the control samples. These mRNAs were categorized as preferentially expressed in Sertoli cells or germ cells using data obtained with male and female gonad samples and enriched testicular cell populations. Five candidate genes were validated at the protein level. Furthermore, we identified putative direct SOX8 and SOX9 target genes by integrating predicted SOX-binding sites present in potential regulatory regions upstream of the transcription start site. Finally, we used protein network data to gain insight into the effects on regulatory interactions that occur when Sox8 and Sox9 are absent in developing Sertoli cells. The integration of testicular samples with enriched Sertoli cells, germ cells and female gonads enabled us to broadly distinguish transcripts directly affected in Sertoli cells from others that respond to secondary events in testicular cell types. Thus, combined RNA profiling signals, motif predictions and network data identified putative SOX8/SOX9 target genes in Sertoli cells and yielded insight into regulatory interactions that depend upon these transcription factors. In addition, our results will facilitate the interpretation of genome-wide in vivo SOX8 and SOX9 DNA binding data.
Andrology

hal-00877013
https://hal.archives-ouvertes.fr/hal-00877013
DOI : 10.1111/j.2047-2927.2012.00049.x
PUBMED : 23315995

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Primary hepatocyte cultures are now considered as convenient models for in vitro analyzing liver drug transport. However, if primary human and rat hepatocytes have been well-characterized with respect to drug transporter expression and regulation, much less is known for primary mouse hepatocytes. The present study was therefore designed to gain insights about this point. The profile of sinusoidal and canalicular drug transporter mRNA expression in short time (4h)-cultured mouse hepatocytes was found to be highly correlated with that of freshly isolated hepatocytes; by contrast, those of counterparts cultured for a longer time (until 4days) either in monolayer configurations on plastic or collagen or in sandwich configuration with matrigel were profoundly altered: uptake drug transporters such as Oct1, Oatps and Oat2 were thus down-regulated, whereas most of efflux transporters such as Mdr1a/b, Mrp3, Mrp4 and Bcrp were induced. Moreover, short time-cultured hepatocytes exhibited the highest levels of sinusoidal influx transporter activities. Transporter-mediated drug secretion into canalicular networks was however only observed in sandwich-cultured hepatocytes. Mouse hepatocytes cultured either in monolayer or sandwich configurations were finally shown to exhibit up-regulation of referent transporters in response to exposure to prototypical activators of the drug sensing receptors pregnane X receptor, aryl hydrocarbon receptor or constitutive androstane receptor. Taken together, these data demonstrate the feasibility of using primary mouse hepatocytes for investigating potential interactions of xenobiotics with hepatic transporter activity or regulation, provided that adequate culture conditions are retained.
ISSN: 0928-0987

inserm-00823243
http://www.hal.inserm.fr/inserm-00823243
DOI : 10.1016/j.ejps.2013.01.013
PUBMED : 23396053

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Evolution involves interplay between natural selection and developmental constraints(1-3). This is seen, for example, when digits are lost from the limbs during evolution(1,3,4). Extant archosaurs (crocodiles and birds) show several instances of digit loss(3,5,6) under different selective regimes, and show limbs with one, two, three, four or the ancestral number of five digits. The `lost' digits sometimes persist for millions of years as developmental vestiges(7-10). Here we examine digit loss in the Nile crocodile and five birds, using markers of three successive stages of digit development. In two independent lineages under different selection, wing digit I and all its markers disappear. In contrast, hindlimb digit V persists in all species sampled, both as cartilage, and as Sox9-expressing precartilage domains, 250 million years after the adult digit disappeared. There is therefore a mismatch between evolution of the embryonic and adult phenotypes. All limbs, regardless of digit number, showed similar expression of sonic hedgehog (Shh). Even in the one-fingered emu wing, expression of posterior genes Hoxd11 and Hoxd12 was conserved, whereas expression of anterior genes Gli3 and Alx4 was not. We suggest that the persistence of digit V in the embryo may reflect constraints, particularly the conserved posterior gene networks associated with the zone of polarizing activity (ZPA(11)). The more rapid and complete disappearance of digit I may reflect its ZPA-independent specification, and hence, weaker developmental constraints. Interacting with these constraints are selection pressures for limb functions such as flying and perching. This model may help to explain the diverse patterns of digit loss in tetrapods. Our study may also help to understand how selection on adults leads to changes in development.
ISSN: 0028-0836

hal-01545485
https://hal.archives-ouvertes.fr/hal-01545485
DOI : 10.1038/nature12336

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
We studied the patterns, rates and evolution of fluvial terraces and fault system during the building process of an intracontinental transpressional mountain in the Gobi-Altay (Mongolia). By analyzing incisions and offsets of fluvial terraces and alluvial fans, we show that the massif has grown by outward migration of thrust faults through time. On the northern flank, the present bounding thrust fault began its activity ~600 ka ago, while a more internal sub-parallel fault was still active until ~200-100 ka. Vertical offset of an alluvial fan abandoned ~100 ka ago allows an estimate of 0.1 mm/yr Upper Pleistocene - Holocene uplift rate. The morphology of the catchment-piedmont system strongly suggests a periodical formation of the alluvial surfaces, controlled by the climatic pulses, at the beginning of the wet interglacial periods. The abandonment of the alluvial terraces lags by several thousand years the abandonment of the alluvial fans, showing a diachronous incision propagating upstream. The incision rate deduced from the different elevations of straths exceeds of one order of magnitude the rock uplift rate. This excess is mostly due to ongoing drainage network growth at the core of the massif, and incision due to alluvial apron entrenchment near the outlet. This implies that fluvial response is mainly controlled by drainage growth, interaction with piedmont and cyclic climatic variations, rather than by rock uplift.
ISSN: 0278-7407

hal-00323558
https://hal.archives-ouvertes.fr/hal-00323558
https://hal.archives-ouvertes.fr/hal-00323558v2/document
https://hal.archives-ouvertes.fr/hal-00323558/file/Vassallo2007.pdf
DOI : 10.1029/2006TC002081

Éditeur(s) : HAL CCSD
Résumé : In coastal carbonate aquifers submitted to a saline intrusion, water - rock interactions processes at the interface between freshwater and saltwater are a cause for heterogeneities development within the porous media. The dissolutions and precipitations induced by the mixing zone play a major role in the transport properties of the reservoir and so in the long term evolution of the saltwater intrusion. The characterization and the in situ observation of a current saline intrusion in the Llucmajor carbonate platform at the experimental site of Ses Sitjoles (South-Easth of Mallorca Island, Spain), allowed to study the temporal evolution of the saltwater intrusion and the biogeochemical processes active in the mixing zone. The influence of microstructure, characterized using X-Ray microtomography, on the petrophysical and flow properties was investigated in laboratory and flow-through experiments were also conducted to study the modifications of the microstructures when submitted to water - rock interactions processes. The mixing zone at the Ses Sitjoles site appears as quite thick and not very sensitive to climate and anthropic stress and is proved to be the locus of active microbiological activity. Laboratory studies highlight a strong control of the microporosity on transport processes and of pCO2 on water - rock interactions. The percolation experiments of slightly reactive waters reveal calcite dissolution together with a decrease in permeability due to a rearrangement of micro-grains within the microporous network.
Les processus d'interactions fluide-roche à l'interface eau douce-eau salée, dans les aquifères carbonatés côtiers soumis à une intrusion saline, sont une des causes du développement d'hétérogénéités dans la structure du milieu poreux. Les dissolutions et/ou précipitations engendrées par la présence de cette zone de mélange jouent un rôle déterminant pour les propriétés de transport du réservoir et donc l'évolution à long terme de l'intrusion d'eau salée. En prenant l'exemple de la plateforme carbonatée de Llucmajor au niveau du site expérimental de Ses Sitjoles (Sud-Est de Majorque, Espagne), un travail de caractérisation et d'observation in situ à moyen terme de l'intrusion saline actuelle de ce réservoir permet de décrire son évolution temporelle et les processus biogéochimiques actifs dans la zone de mélange. L'influence de la microstructure du milieu poreux, caractérisée par microtomographie RX, sur les propriétés pétrophysiques et hydrodynamiques est étudiée en laboratoire et des expériences de percolations d'eaux réactives (mélanges eau douce - eau salée et eau pure chargée en CO2) sont réalisées afin d'étudier les modifications de ces microstructures lorsqu'elles sont soumises à des interactions eau - roche. La zone de mélange eau douce - eau salée rencontrée au niveau du site de Ses Sitjoles est large et peu sensible aux contraintes extérieures (climatologiques et anthropiques) et constitue un lieu d'activité microbiologique particulièrement actif. En laboratoire, on observe un fort contrôle des phénomènes de transport par la microporosité et des processus d'interactions eau - roche par la pCO2. Dans le cas d'une percolation de fluides moyennement réactifs, les expériences mettent en évidence une dissolution de calcite accompagnée par une diminution de la perméabilité, liée à un réarrangement des micro-grains à l'intérieur du réseau microporeux.
https://tel.archives-ouvertes.fr/tel-00767152

tel-00767152
https://tel.archives-ouvertes.fr/tel-00767152
https://tel.archives-ouvertes.fr/tel-00767152/document
https://tel.archives-ouvertes.fr/tel-00767152/file/thesegaring.pdf

Résumé : Les graphes définis à partir de structures algébriques possèdent d’excellentes propriétés de symétries particulièrement intéressantes. L’exemple le plus flagrant est la notion de graphe de Cayley qui s’est révélée très riche non seulement du point de vue théorique mais aussi pratique par ses applications à de nombreux domaines incluant l’architecture des réseaux ou les machines parallèles. Néanmoins, la régularité des graphes de Cayley se révèle parfois être une limite étant donné qu’ils sont toujours sommet-transitifs et donc en particulier non pertinents pour générer des réseaux semiréguliers.Cette observation a motivé, en 2005, la définition d’une nouvelle classe de graphes définis à partir d’un groupe, appelés G-graphes. Ils possèdent aussi de nombreuses propriétés de régularité mais de manière moins restrictive.Cette thèse propose un nouveau regard sur cette classe de graphes par une approche plutôt orientée recherche opérationnelle alors que la grande majorité des études précédentes est dominée par des approches essentiellement algébriques. Nous-nous sommes alors intéressés à plusieurs questions :— La caractérisation des G-graphes : nous proposons des améliorations par rapport aux précédents résultats.— Identifier des classes de graphes comme des G-graphes grâce à des isomorphismes ou en utilisant le théorème de caractérisation.— Etudier la structure et les propriétés de ces graphes, en particulier pour de possibles applications aux réseaux : colorations semi-régulières, symétries et robustesse.— Une approche algorithmique pour la reconnaissance de cette classe avec notamment un premier exemple de cas polynomial lorsque le groupe est abélien.
Interactions between graph theory and group theory have already led to interesting results for both domains. Graphs defined from algebraic groups have highly symmetrical structure giving birth to interesting properties. The most famous example is Cayley graphs, which revealed to be particularly interesting both from a theoretical and a practical point of view due to their applications in several domains including network architecture or parallel machines. Nevertheless, the regularity of Cayley graphs is also a limit as they are always vertex-transitive and therefore not relevant to generate semi-regular networks. This observation motivated the definition, in 2005, of a new family of graphs defined from a group, called G-graphs. They also have many regular properties but are less restrictive. These graphs are in particular semi-regular k-partite, with a chromatic number k directly given in the group representation and they can be either transitive or not.This thesis proposes a new insight into this class of graphs using an approach based on operational research while most of previous studies have been so far dominated by algebraic approaches. Then, the thesis addresses different kind of questions:— Characterizing G-graphs: we propose improvements of previous results.— Identifying some classes of graphs as G-graphs through isomorphism or using the characterization theorem.— Studying the structure and properties of these graphs, in particular for possible applications to networks: semi-regular coloring, symmetries and robustness.— Algorithmic approach for recognizing this class with a first example of polynomial case when the group is abelian.

http://www.theses.fr/2014AGUY0787/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We studied the deformation in a partially molten mantle through detailed petrostructural analysis of plagioclase lherzolites from the northwestern part of the central Lanzo massif. These peridotites display a pervasive anastomosed network of millimetre to centimetre-scale plagioclase-rich bands, which grades locally into a planar layering marked by an intercalation of plagioclase-rich and olivine-rich layers up to tens of centimetres wide. Both the anastomosed and the planar layering are subparallel to the deformation fabric, characterized by a foliation defined by the shape-preferred orientation of olivine and by crystal preferred orientation (CPO) of olivine, orthopyroxene, and clinopyroxene. This parallelism, the coexistence of microstructural evidence for melt-rock reactions and for deformation by dislocation creep, and the predominance of axial-[010] olivine CPO patterns, characterized by [010] axes clustered normal to the layering, indicate that deformation and the reactive melt percolation that formed the layering were coeval. Strong heterogeneity in mineral composition in the planar layering domains, with Fe-enrichment in olivine and spinel and highly variable Ti content in spinel in cm-scale plagioclase-rich bands, implies that the latter interacted with higher melt volumes. High Ti contents in pyroxenes and spinel in the anastomosed layering domains point to changes in melt composition, hinting to less effective melt transport. We propose therefore that the planar layering records melt segregation in layers parallel to the shear plane, whereas the anastomosed layering results from melt alignment along grain boundaries subparallel to the shear plane, without segregation. Finite strain in the different layers cannot be quantified, but comparison of the present observations with data from experiments and from other mantle outcrops displaying shear-controlled melt organization suggests that the transition from the anastomosed to the planar layering might record an increase in finite strain, that is, strain localization associated with variations in the instantaneous melt fraction.
ISSN: 0040-1951

hal-01053509
https://hal.archives-ouvertes.fr/hal-01053509
DOI : 10.1016/j.tecto.2014.01.007