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Gene Transposition Causing Natural Variation for Growth in Arabidopsis thaliana
Daniela Vlad,Fabrice Rappaport,Matthieu Simon,Olivier Loudet
PLOS Genetics , 2010, DOI: 10.1371/journal.pgen.1000945
Abstract: A major challenge in biology is to identify molecular polymorphisms responsible for variation in complex traits of evolutionary and agricultural interest. Using the advantages of Arabidopsis thaliana as a model species, we sought to identify new genes and genetic mechanisms underlying natural variation for shoot growth using quantitative genetic strategies. More quantitative trait loci (QTL) still need be resolved to draw a general picture as to how and where in the pathways adaptation is shaping natural variation and the type of molecular variation involved. Phenotypic variation for shoot growth in the Bur-0 × Col-0 recombinant inbred line set was decomposed into several QTLs. Nearly-isogenic lines generated from the residual heterozygosity segregating among lines revealed an even more complex picture, with major variation controlled by opposite linked loci and masked by the segregation bias due to the defective phenotype of SG3 (Shoot Growth-3), as well as epistasis with SG3i (SG3-interactor). Using principally a fine-mapping strategy, we have identified the underlying gene causing phenotypic variation at SG3: At4g30720 codes for a new chloroplast-located protein essential to ensure a correct electron flow through the photosynthetic chain and, hence, photosynthesis efficiency and normal growth. The SG3/SG3i interaction is the result of a structural polymorphism originating from the duplication of the gene followed by divergent paralogue's loss between parental accessions. Species-wide, our results illustrate the very dynamic rate of duplication/transposition, even over short periods of time, resulting in several divergent—but still functional—combinations of alleles fixed in different backgrounds. In predominantly selfing species like Arabidopsis, this variation remains hidden in wild populations but is potentially revealed when divergent individuals outcross. This work highlights the need for improved tools and algorithms to resolve structural variation polymorphisms using high-throughput sequencing, because it remains challenging to distinguish allelic from paralogous variation at this scale.
Allelic Heterogeneity and Trade-Off Shape Natural Variation for Response to Soil Micronutrient
Seifollah Poormohammad Kiani,Charlotte Trontin,Matthew Andreatta,Matthieu Simon,Thierry Robert,David E. Salt,Olivier Loudet
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1002814
Abstract: As sessile organisms, plants have to cope with diverse environmental constraints that may vary through time and space, eventually leading to changes in the phenotype of populations through fixation of adaptive genetic variation. To fully comprehend the mechanisms of evolution and make sense of the extensive genotypic diversity currently revealed by new sequencing technologies, we are challenged with identifying the molecular basis of such adaptive variation. Here, we have identified a new variant of a molybdenum (Mo) transporter, MOT1, which is causal for fitness changes under artificial conditions of both Mo-deficiency and Mo-toxicity and in which allelic variation among West-Asian populations is strictly correlated with the concentration of available Mo in native soils. In addition, this association is accompanied at different scales with patterns of polymorphisms that are not consistent with neutral evolution and show signs of diversifying selection. Resolving such a case of allelic heterogeneity helps explain species-wide phenotypic variation for Mo homeostasis and potentially reveals trade-off effects, a finding still rarely linked to fitness.
Natural Variation in Arabidopsis thaliana as a Tool for Highlighting Differential Drought Responses
Oumaya Bouchabke, Fengqi Chang, Matthieu Simon, Roger Voisin, Georges Pelletier, Mylène Durand-Tardif
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0001705
Abstract: To test whether natural variation in Arabidopsis could be used to dissect out the genetic basis of responses to drought stress, we characterised a number of accessions. Most of the accessions belong to a core collection that was shown to maximise the genetic diversity captured for a given number of individual accessions in Arabidopsis thaliana. We measured total leaf area (TLA), Electrolyte Leakage (EL), Relative Water Content (RWC), and Cut Rosette Water Loss (CRWL) in control and mild water deficit conditions. A Principal Component Analysis revealed which traits explain most of the variation and showed that some accessions behave differently compared to the others in drought conditions, these included Ita-0, Cvi-0 and Shahdara. This study relied on genetic variation found naturally within the species, in which populations are assumed to be adapted to their environment. Overall, Arabidopsis thaliana showed interesting phenotypic variations in response to mild water deficit that can be exploited to identify genes and alleles important for this complex trait.
Biochemical, Transcriptional and Translational Evidences of the Phenol-meta-Degradation Pathway by the Hyperthermophilic Sulfolobus solfataricus 98/2
Alexia Comte, Pierre Christen, Sylvain Davidson, Matthieu Pophillat, Jean Lorquin, Richard Auria, Gwenola Simon, Laurence Casalot
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0082397
Abstract: Phenol is a widespread pollutant and a model molecule to study the biodegradation of monoaromatic compounds. After a first oxidation step leading to catechol in mesophilic and thermophilic microorganisms, two main routes have been identified depending on the cleavage of the aromatic ring: ortho involving a catechol 1,2 dioxygenase (C12D) and meta involving a catechol 2,3 dioxygenase (C23D). Our work aimed at elucidating the phenol-degradation pathway in the hyperthermophilic archaea Sulfolobus solfataricus 98/2. For this purpose, the strain was cultivated in a fermentor under different substrate and oxygenation conditions. Indeed, reducing dissolved-oxygen concentration allowed slowing down phenol catabolism (specific growth and phenol-consumption rates dropped 55% and 39%, respectively) and thus, evidencing intermediate accumulations in the broth. HPLC/Diode Array Detector and LC-MS analyses on culture samples at low dissolved-oxygen concentration (DOC = 0.06 mg.L?1) suggested, apart for catechol, the presence of 2-hydroxymuconic acid, 4-oxalocrotonate and 4-hydroxy-2-oxovalerate, three intermediates of the meta route. RT-PCR analysis on oxygenase-coding genes of S. solfataricus 98/2 showed that the gene coding for the C23D was expressed only on phenol. In 2D-DIGE/MALDI-TOF analysis, the C23D was found and identified only on phenol. This set of results allowed us concluding that S. solfataricus 98/2 degrade phenol through the meta route.
Production d'hydrogène par oxydation catalytique partielle du méthane Etude du mécanisme réactionnel
Matthieu Fleys,Yves Simon,Paul-Marie Marquaire,Fran?ois Lapicque
Physics , 2009,
Abstract: The partial oxidation of methane was investigated using a self-stirred reactor under a wide range of operating conditions. The recation mechanism was determined by comparing ecperimental results with the results of simulations made using the Chemkin-Surface software. The proposed mechanism includes 444 homogeneous reactions and 33 surface reactions.
Morphological Conservation in Human-Animal Hybrids in Science Fiction and Fantasy Settings: Is Our Imagination as Free as We Think It Is?  [PDF]
Matthieu J. Guitton
Advances in Anthropology (AA) , 2013, DOI: 10.4236/aa.2013.33021
Abstract:

The question of whether human imagination knows no boundaries or is, alternatively, constrained by conscious or unconscious cognitive templates is a key issue in defining human mind. We try here to address this extremely large question by focusing on one particular element of imaginary creations, the specific case of human-animal hybrids. Human-animal hybrids are common inhabitants of human imaginary spaces, being regularly encountered across numerous mythologies, as well as in modern popular culture. If human imagination was unconstrained, it would be expected that such hybrid creatures would display roughly half human and half animalistic features. Using several different popular science fiction and fantasy settings, we conducted an analysis of the morphological traits of human-animal hybrids, both anatomical and phenotypic. Surprisingly, we observed extremely high conservation of human morphological traits in human-animal hybrids, with a contrasting high use of phenotypic (“cosmetic”) alterations, and with highly stereotyped patterns of morphological alterations. While these alterations were independent of the setting considered, shape alterations were setting-dependent and used as a way to increase internal coherence. Finally, important gender differences were observed, as female human-animal hybrids retained significantly more human traits than males did, suggesting that conservation of female appearance may bear essential evolutionary importance. Taken together, these results demonstrate the existence of strong cognitive templates which frame and limit the expression of the capacity of human imagination, and unveil some of the psychological mechanisms which constrain the emergence of imaginary spaces.

Exact and approximate inference in graphical models: variable elimination and beyond
Nathalie Peyrard,Simon de Givry,Alain Franc,Stéphane Robin,Régis Sabbadin,Thomas Schiex,Matthieu Vignes
Computer Science , 2015,
Abstract: Probabilistic graphical models offer a powerful framework to account for the dependence structure between variables, which can be represented as a graph. The dependence between variables may render inference tasks such as computing normalizing constant, marginalization or optimization intractable. The objective of this paper is to review techniques exploiting the graph structure for exact inference borrowed from optimization and computer science. They are not yet standard in the statistician toolkit, and we specify under which conditions they are efficient in practice. They are built on the principle of variable elimination whose complexity is dictated in an intricate way by the order in which variables are eliminated in the graph. The so-called treewidth of the graph characterizes this algorithmic complexity: low-treewidth graphs can be processed efficiently. Algorithmic solutions derived from variable elimination and the notion of treewidth are illustrated on problems of treewidth computation and inference in challenging benchmarks from optimization competitions. We also review how efficient techniques for approximate inference such as loopy belief propagation and variational approaches can be linked to variable elimination and we illustrate them in the context of Expectation-Maximisation procedures for parameter estimation in coupled Hidden Markov Models.
Tensions et coordinations entre les acteurs des sciences de la performance sportive
Matthieu Delalandre
SociologieS , 2012,
Abstract: Cet article part d’une étude qui questionne les conditions de production des savoirs scientifiques sur la performance sportive, en portant le regard sur les modes de coordination entre les chercheurs et les entra neurs avec qui ils collaborent. L’analyse d’un matériau empirique constitué d’entretiens et d’un corpus écrit nous a conduit à mettre en évidence trois régimes de scientificité, qui constituent à la fois des modes de coordination des chercheurs et des entra neurs et des formes particulières de production des savoirs. L’article met en lumière des tensions inhérentes à chacun de ces régimes et les solutions adoptées par les acteurs pour coopérer. Nous nous intéressons enfin aux contraintes que les chercheurs rencontrent pour passer d’un régime à l’autre. Tensions and coordinations between the actors of sports performance sciencesThis article is based on a study which examines how knowledge is produced in the field of sports performance, looking at the modes of coordination between researchers and the coaches with whom they collaborate. The analysis of empirical data made of interviews and texts leads us to show three scientific regimes, which are at the same time specific modes of coordination between scientists and coaches and particular forms of knowledge production. The paper sheds light on the tensions inherent in each regime and the solutions which the actors adopt in order to co-operate. Finally, we study the constraints scientists face when they go from one regime to another. Tensiones y coordinaciones entre los integrantes de las ciencias de la performance deportivaEste trabajo estudia las condiciones de producción del conocimiento científico respecto a la performance deportiva, destacando el modo de coordinación y colaboración entre investigadores y entrenadores. El análisis de un material empírico está constituido por entrevistas y por un corpus escrito que nos ha conducido a determinar tres regímenes de cientificidad, que constituyen a la vez diversos modos de coordinación entre investigadores y entrenadores; junto con formas particulares de producción del conocimiento. El artículo pone de manifiesto las tensiones inherentes en el seno de cada uno de estos regímenes, así como las soluciones adoptadas por sus integrantes para cooperar. Nos interesamos también por los obstáculos que encuentran los investigadores cuando desean pasar de un régimen a otro.
Panique dans le ciel intertextuel
Matthieu Letourneux
Strenae : Recherches sur les Livres et Objets Culturels de l'Enfance , 2012, DOI: 10.4000/strenae.537
Abstract: Lancée en 1953, la série des Bob Morane hérite des modèles narratifs du roman d’aventures coloniales et de ses reformulations anglo-saxonnes d’après-guerre dont elle investit massivement les stéréotypes ; mais elle se retrouve rapidement confrontée au processus de décolonisation qui condamne à terme les conventions sur lesquelles repose le genre investi par Henri Vernes. L’histoire de la série est donc celle d’un processus de réarticulation des codes d’un genre, celui du roman d’aventures coloniales, suivant des contraintes géopolitiques et un nouveau système architextuel dont elle illustre les mutations. Au croisement de problèmes historiques et esthétiques, cette série au long cours pose à la fois la question des pratiques de fictions sérielles et celle de la prise en compte par la littérature de jeunesse du phénomène de la décolonisation, mettant en évidence les tensions qui existent entre les logiques référentielles intertextuelles et la mise en scène de l’espace référentiel extratextuel. Si elle tend à privilégier les logiques sérielles, elle assimile l’évolution des représentations, mais de biais, par le détour des intertextes et des imaginaires romanesques. Dès lors, le discours sur le monde ne peut être saisi que médiatement, comme réalité sous-jacente au jeu des imaginaires intertextuels, quand ceux-ci tendent à pérenniser les héritages du genre, comme autant de couches archéologiques du récit. Procéder à cette archéologie de l’ uvre sérielle, décomposer les couches narratives et les imaginaires successifs dont elle est le résultat, déterminer la fa on dont l’auteur les organise en un discours propre, c’est à la fois révéler la part des idéologies dont le récit est le produit, et échapper à une lecture trop monologique d’une uvre qui est aussi la manifestation en un discours auctorial unique d’une multitude de voix.
Hiroki Azuma, Génération Otaku : les enfants de la post-modernité
Matthieu Letourneux
Strenae : Recherches sur les Livres et Objets Culturels de l'Enfance , 2010,
Abstract: Dirigée par Charles Pépin, la collection Haute Tension s’est spécialisée dans la publication d’essais philosophiques en prise avec l’actualité. C’est un de ces sujets de société qu’évoque l’ouvrage d’Hiroki Azuma, Génération Otaku, renvoyant à cet ensemble d’adolescents et d’adultes japonais, consommant massivement des productions de la culture de masse – jeux vidéo, séries animées, bandes dessinées, figurines et produits dérivés. Si son travail ne porte pas directement sur la culture de ...
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