Thèse de doctorat--Sciences naturelles--Faculté des sciences de Paris, 1907. N°: 1265. / Notes bibliogr.

Thèse de doctorat--Sciences naturelles--Faculté des sciences de Paris, 1891. N°: 706.

Th. MS--Agronomie--Montpellier--CIHEAM, 1987. / Bibliogr. p. 84-89.

Thèse de doctorat--Sciences naturelles--Faculté des sciences de Paris, 1896. N°: 893.

L'alignement de séquences biologiques est une technique fondamentale en bioinformatique, et consiste à identifier des séries de caractères similaires (conservés) qui apparaissent dans le même ordre dans les deux séquences, et à inférer un ensemble de modifications (substitutions, insertions et suppressions) impliquées dans la transformation d'une séquence en l'autre. Cette technique permet de déduire, sur la base de la similarité de séquence, si deux ou plusieurs séquences biologiques sont potentiellement homologues, donc si elles partagent un ancêtre commun, permettant ainsi de mieux comprendre l'évolution des séquences. Cette thèse aborde les problèmes de comparaison de séquences dans deux cadres différents: la détection d'homologies et le séquençage à haut débit. L'objectif de ce travail est de développer des méthodes d'alignement qui peuvent apporter des solutions aux deux problèmes suivants: i) la détection d'homologies cachées entre des protéines par comparaison de séquences protéiques, lorsque la source de leur divergence sont les mutations qui changent le cadre de lecture, et ii) le mapping de reads SOLiD (séquences de di-nucléotides chevauchantes codés par des couleurs) sur un génome de référence. Dans les deux cas, la même idée générale est appliquée: comparer implicitement les séquences d'ADN pour la détection de changements qui se produisent à ce niveau, en manipulant, en pratique, d'autres représentations (séquences de protéines, séquences de codes di-nucléotides) qui fournissent des informations supplémentaires et qui aident à améliorer la recherche de similarités. Le but est de concevoir et d'appliquer des méthodes exactes et heuristiques d'alignement, ainsi que des systemes de scores, adaptés à ces scénarios. / Biological sequence alignment is a fundamental technique in bioinformatics, and consists of identifying series of similar (conserved) characters that appear in the same order in both sequences, and eventually deducing a set of modifications (substitutions, insertions and deletions) involved in the transformation of one sequence into the other. This technique allows one to infer, based on sequence similarity, if two or more biological sequences are potentially homologous, i.e. if they share a common ancestor, thus enabling the understanding of sequence evolution.This thesis addresses sequence comparison problems in two different contexts: homology detection and high throughput DNA sequencing. The goal of this work is to develop sensitive alignment methods that provide solutions to the following two problems: i) the detection of hidden protein homologies by protein sequence comparison, when the source of the divergence are frameshift mutations, and ii) mapping short SOLiD reads (sequences of overlapping di-nucleotides encoded as colors) to a reference genome. In both cases, the same general idea is applied: to implicitly compare DNA sequences for detecting changes occurring at this level, while manipulating, in practice, other representations (protein sequences, sequences of di-nucleotide codes) that provide additional information and thus help to improve the similarity search. The aim is to design and implement exact and heuristic alignment methods, along with scoring schemes, adapted to these scenarios.

With a view to design processes based on gas-solid reactiontowards the production of fine-grained novel alloys andintermetallics, studies of the reduction of the mixed oxides ofFe and Mo by hydrogen towards the production of Fe-Mo alloyshave been carried out in the present work. The route offersexcellent potentials toward the bulk production of nano-grainedmaterial of tailored-composition in bulk in a green processpath. As a case study, the reduction of the mixed oxides ofiron and molybdenum were carried out from the viewpoint ofmaterials processing, chemical reaction kinetics, as well asmechanical and structural properties. The reduction kinetics ofthin layer of fine oxide particles of Fe2MoO4 was studied usingthermogravimetric technique. This technique allowed determiningreduction parameters such as temperature of reduction as wellas the activation energies for the chemical reaction as therate-controlling step. The end products were analyzed by X-raydiffraction. The reduction product was found to be reduced topure, homogeneous Fe2Mo. In order to examine the upscaling ofthe process, production of the alloy in larger amounts wascarried out in a laboratory-scale fluidized reactor and theprocess parameters were optimized. It was found that, under theconditions of the experiments, the chemical reaction was therate-controlling step. TEM, SEM and X-ray analyses of thereaction product showed the presence of a monolithicintermetallic with micro- and nanocrystalline structure. Themechanical properties of this alloy were determined.Compositions of microcrystalline Fe-Mo alloys were varied byreducing mixtures of Fe2MoO4 with MoO2 or FeO with differentFe/Mo ratios. The products after the reduction consisted of twophases, viz. intermetallic FexMoy compound and metallic Fe orMo. XRD analyses revealed that the former had microcrystallinestructure while the latter were in crystalline form. This workshows that gas-solid reaction method, together with powdermetallurgy technique is a promising process route towards theproduction of novel metallic alloys such as Fe2Mo intermetallicwith micro- and nanocrystalline grains. <b>Key words</b>: nanoalloys, intermetallics, iron-molybdenumalloy, hydrogen reduction, thermogravimetry, fluidized bed,mechanical properties, structure

<p>With a view to design processes based on gas-solid reactiontowards the production of fine-grained novel alloys andintermetallics, studies of the reduction of the mixed oxides ofFe and Mo by hydrogen towards the production of Fe-Mo alloyshave been carried out in the present work. The route offersexcellent potentials toward the bulk production of nano-grainedmaterial of tailored-composition in bulk in a green processpath. As a case study, the reduction of the mixed oxides ofiron and molybdenum were carried out from the viewpoint ofmaterials processing, chemical reaction kinetics, as well asmechanical and structural properties. The reduction kinetics ofthin layer of fine oxide particles of Fe2MoO4 was studied usingthermogravimetric technique. This technique allowed determiningreduction parameters such as temperature of reduction as wellas the activation energies for the chemical reaction as therate-controlling step. The end products were analyzed by X-raydiffraction. The reduction product was found to be reduced topure, homogeneous Fe2Mo. In order to examine the upscaling ofthe process, production of the alloy in larger amounts wascarried out in a laboratory-scale fluidized reactor and theprocess parameters were optimized. It was found that, under theconditions of the experiments, the chemical reaction was therate-controlling step. TEM, SEM and X-ray analyses of thereaction product showed the presence of a monolithicintermetallic with micro- and nanocrystalline structure. Themechanical properties of this alloy were determined.Compositions of microcrystalline Fe-Mo alloys were varied byreducing mixtures of Fe2MoO4 with MoO2 or FeO with differentFe/Mo ratios. The products after the reduction consisted of twophases, viz. intermetallic FexMoy compound and metallic Fe orMo. XRD analyses revealed that the former had microcrystallinestructure while the latter were in crystalline form. This workshows that gas-solid reaction method, together with powdermetallurgy technique is a promising process route towards theproduction of novel metallic alloys such as Fe2Mo intermetallicwith micro- and nanocrystalline grains.</p><p><b>Key words</b>: nanoalloys, intermetallics, iron-molybdenumalloy, hydrogen reduction, thermogravimetry, fluidized bed,mechanical properties, structure</p>

Reproduction de : Thèse de doctorat : Agrosystèmes, écosystèmes et environnement : Toulouse, INPT : 2008. / Titre provenant de l'écran-titre. Bibliogr. 253 réf.

Pendant la maturation des graines, la germination, tolérance à la dessication et longévité sont acquises de manière séquentielle. La maturation s’achève par la dessication qui amène l’embryon à l’état de quiescence. La maturité des graines à la récolte est le premier facteur qui in¿ uence la longévité et l’établissement de la culture lors du semis. On ne comprend pas comment la longévité est installée pendant la maturation et comment un séchage prématuré in¿ uence la longévité et la reprise des activités cellulaires pendant l’imbibition. L’objectif de la thèse était de répondre à ces questions en comparant les transcriptomes de graines immatures et matures de soja et Medicago truncatula pendant la dessication et l’imbibition. Les graines immatures furent récoltées après le remplissage avant la dessiccation, lorsque la longévité n’est pas encore acquise.Chez le soja, la comparaison des transcriptomes des graines immatures et matures montre que le séchage forcé n’est pas identique à la dessication in planta qui se caractérise par la synthèse de protéines chaperones. Plus de 89% des gènes différentiellement exprimés après 18 h d’imbibition présentent des pro¿ ls d’expression identiques dans les graines immatures et matures, en accord avec la germination comparable de celles-ci. L’analyse des transcrits dont la teneur augmente uniquement pendant l’imbibition des graines mature suggère la mise en place de mécanismes de réparation. La comparaison de ces données avec Medicago montre que l’imbibition des graines matures se caractérise par une sur-représentation des gènes liés au / During seed maturation, germination, desiccation tolerance and longevity are acquired sequentially. Seed maturation is terminated by a desiccation phase that brings the embryo to a quiescent state. Seed maturity at harvest in¿ uences seed longevity and crop establishment. After harvest, seeds are usually dried to water content compatible with long term storage and post-harvest treatments. However, there is a lack of understanding of how seed longevity is acquired during seed maturation and how premature drying impacts longevity and resumption of cellular activities during imbibition. This was addressed here by comparing transcriptome changes associated with maturation drying and imbibition of seeds of soybean and Medicago truncatula, harvested at an immature stage and mature dry stage.The immature stage corresponded to end of seed ¿ lling when longevity was not acquired while other vigor traits were acquired. Transcriptome characterization in soybean revealed that enforced drying was not similar to maturation drying in planta, which stimulated degradation of chlorophyll and synthesis of protective chaperones. Eighty-nine % of the differentially expressed genes during a 18h-imbibition period showed a similar pattern between immature and mature seeds, consistent with a comparable germination between stages. An analysis of the 147 transcripts that increased during imbibition of mature seeds but not in immature seeds suggested an activation of processes associated with shoot meristem development and DNA repair. These data were compared with imbibing immature and mature seeds

Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques.<br />Elles se basent sur un principe de filtrage du texte qui permet de localiser les régions potentiellement similaires.<br />Dans cette thèse, nous proposons de nouvelles définitions de filtres pour la recherche de similarités sur les séquences génomiques et des algorithmes associés pour mesurer leurs caractéristiques.<br /> Plus précisément, nous avons étudié le modèle des graines espacées, et proposé un algorithme d'évaluation de l'efficacité des graines sur des similarités d'une classe particulière (similarités dites homogènes). Nous avons également développé un algorithme général pour la mesure de l'efficacité des graines, ainsi qu'un nouveau modèle de graine appelé graine sous-ensemble, extension du modèle des graines espacées. Enfin nous donnons, dans le cadre du filtrage sans perte, une extension à l'aide de graines multiples, que nous analysons et appliquons au problème de la conception d'oligonucléotides.<br /> Nous avons réalisé et donnons accès à des outils pour la conception des filtres, ainsi que pour la recherche de similarités.