The unveiling of small RNA (sRNA)-mediated gene regulatory pathways has profoundly shaped our understanding of the complexity of gene regulation. In eukaryotes, sRNAs have been found to control cellular metabolism, growth and differentiation, to maintain genome integrity, and to combat viruses and mobile genetic elements. To gain insight into the roles of small RNAs in apple and peach, we conducted sRNA-seq, computational analysis and molecular experiments to genome-widely characterize their microRNAs (miRNAs) and trans-acting siRNA (tasiRNA) pathways. We identified totally 75 miRNAs or families, including 23 conserved, 10 less-conserved and 42 apple-specific ones, and 118 miRNA target genes in apple. Two classical trans-acting siRNA (tasiRNA) pathways, miR390-TAS3 and miR828-TAS4, were characterized with similar but unique tasiRNA biogenesis profiles and target specificities. Importantly, miR159, miR828 and miR858 can collectively target up to 81 MYB genes potentially involved in diverse aspects of plant growth and development. In contrast to the location of the miR159 target site in a sequence-divergent region, the target sites of miR828 and miR858 are located in the region encoding the conserved R3 repeat domain of MYB proteins. 10 out of the 19 miR828-targeted MYBs undergo the biogenesis of various phased siRNA (phasiRNA), which potentially regulate diverse genes outside the MYB family. In peach, totally 94 miRNAs or families and 80 target genes were identified. Similar pathways of tasiRNA (miR828-TAS4 and miR390-TAS3) or phasiRNA (miR828-MYB-siRNA) processing were also characterized in peach. Taking advantage of reverse computation and public available deep-sequencing data, we demonstrated that the miRNA-TAS-PPR-siRNA pathway is a highly dynamic and widespread feature of eudicots. Nine eudicot plants, representing six different plant families, have evolved similar tasiRNA pathways to instigate phasiRNA production from PPR �genes, which are triggered by different 22-nt miRNAs, including miR7122, miR1509, and fve-PPRtri1/2 and through distinct mechanistic strategies, like miRNA direct-targeting or indirect-targeting through TAS-like genes, one-hit or two-hit, or even two layers of tasiRNA-TAS interactions. We found that the MIRNA genes of these miRNA triggers show great identity with the Arabidopsis MIR173, implying a common origin of this group of miRNAs (super-miR7122). Combined results from phylogenetic analyses and conservation extent profiling revealed that the super-miR7122 was potentially evolved from another miRNA superfamily (super-miR4376), which probably originated from the miR390. Additionally, the miR482/2118-NB-LRR-siRNA pathway was found to be conserved, but evolved with distinct features, in apple and peach. Taken together, widespread and complex miRNA and tasiRNA regulatory networks have been adapted in apple and peach. They add another crucial layer of regulation on gene activity and stability, and must exert essential functions in all aspects of plant life. / Ph. D.

No description available.

This report includes development of an already designed solar water heater. The product shall be constructed in a way that it will suit a manufacturing line in Kampala, Uganda. To find the most suitable design for each area a research was carried out which included study visits, interviews and background reading. It provided the following results: Regarding the attachment of in- and outgoing pipes from the water tank many methods were taken into consideration and it was found that the best and most suitable way for this case is to weld the fittings using a weld robot. Regarding the fitting of the acrylic, a suitable solution is to make a flange when vacuum forming the plastic casing to further support the design. This could also be used to waterproof the case by using a sealing material. A suggestion of using pre-molded PU-foam is also presented. Regarding the ability to open the case for maintenance, two solutions were recommended. Either the use of spire clips or having the clips integrated into the casing. Regarding the calculation of material usage when deep drawing the tank and collector, it is possible to do a reasonably accurate assumption. The complicated design in this product makes the estimation less accurate. It is recommended that test draws are done and often the machine producer has more precise numbers. Regarding the coloring of the collector; chemical coloration is not possible on a galvanized surface. The method used is painting, either with powder coating or with wet paint.

L'expression des gènes mitochondriaux est grande partie dirigée par des protéines codées dans le noyau et importées dans l'organite depuis le cytosol. Diverses études ont montré que les protéines de la famille PentatricoPeptide Repeat (PPR) jouent un rôle prépondérant et varié dans ce phénomène. Au cours de ma thèse, j'ai déterminé la fonction de deux nouvelles protéines PPR chez Arabidopsis thaliana, nommées MTSF1 (pour Mitochondrial Stability Factor 1) et PPR24. Chacune de ces protéines est impliquée dans l'expression d'un ARNm mitochondrial codant une sous-unité du complexe I de la chaine respiratoire. J'ai montré que la protéine MTSF1 était requise pour stabiliser l'ARN mitochondrial nad4. Le site de liaison de MTSF1 a été déterminé et il correspond aux vingt derniers nucléotides de l'ARN nad4. Nous pensons donc qu'en s'associant à l'extrémité 3' terminale de cet ARN, la protéine MTSF1 bloque la progression d'exoribonucléases 3'-5' et stabilise ainsi l'ARN nad4 in vivo. L'étude de la protéine PPR24 nous a conduit à observer qu'elle était essentielle à la traduction de l'ARNm mitochondrial nad7. J'ai pu démontrer que la protéine NAD7 n'était pas synthétisée chez les mutants ppr24 et que cela était associé à l'absence de ribosomes sur l'ARNm nad7. J'ai aussi montré que la protéine PPR24 pouvait se lier spécifiquement à une courte région située au milieu de la 5' UTR de l'ARN nad7. La modélisation de la 5' UTR de cet ARN indique que ce site de liaison se situerait à la base d'une structure en tige-boucle pouvant diminuer fortement l'accessibilité au codon initiateur de la traduction de l'ARN nad7. Il est donc possible que la fixation de la protéine PPR24 puisse déstabiliser cette structure en tige-boucle et permettre aux ribosomes mitochondriaux d'accéder plus facilement au codon AUG. L'ensemble de ces études a permis d'apporter des informations essentielles sur la fonction et le mode d'action des protéines PPR dans l'expression génétique mitochondriale chez les plantes.

[pt] Esta pesquisa aborda o processo de fraturamento hidráulico ou processo de propagação de fraturas em rocha através da injeção de um fluido sob pressão, o que gera fissuras no material que se propagam de acordo com a quantidade de fluido injetado. Esta técnica leva a um incremento da transmissividade hidráulica da rocha e, como consequência, ocorre um incremento da produção de óleo. Diversos trabalhos analíticos e numéricos têm sido propostos para estudar o mecanismo de fratura, geralmente baseados em meios contínuos ou através da utilização de elementos de interface em uma trajetória de propagação conhecida. Neste trabalho, a propagação de uma fratura é simulada utilizando o modelo potencial PPR[72] através da sua implementação extrínseca. Assim, os elementos coesivos de interface são inseridos na malha de elementos finitos de forma adapativa para capturar o processo de fraturamento. A pressão do fluido é simulada utilizando o modelo de lattice-Boltzmann[84]. Através de um processo interativo, os contornos da fratura, computados utilizando o método dos elementos finitos, são transferidos para o modelo de lattice-Boltzmann como uma condição de contorno. Assim, a força que o fluido exerce nestes contornos, gerada pela injeção do fluido, pode ser calculada. Estas forças são utilizadas no modelo de elementos finitos como uma força externa aplicada nas faces da fratura. A nova posição das faces da fratura é calculada e transferida novamente para o modelo de lattice-Boltzmann como condição de contorno. Este processo interativo fluido-estrutura permite modelar o processo de fraturamento hidráulico em trajetórias de propagação irregulares. / [en] This research addresses hydraulic fracturing or hydro-fracking, i.e. fracture propagation process in rocks through the injection of a fluid under pressure, which generates cracks in the rock that propagate according to the amount of fluid injected. This technique leads to an increase of the hydraulic transmissivity of the rock mass and, consequently, improves oil production. Several analytical and numerical models have been proposed to study this fracture mechanism, generally based in continuum mechanics or using interface elements through a known propagation path. In this work, the crack propagation is simulated using the PPR potential-based cohesive zone model[72] by means of an extrinsic implementation. Thus, interface cohesive elements are adaptively inserted in the mesh to capture the softening fracture process. The fluid pressure is simulated using the lattice Boltzmann model[84] through an iterative procedure. The boundaries of the crack, computed using the finite element method, are transferred to the lattice Bolztmann model as boundary conditions, where the fluid pressure (or fluid forces) applied on these boundaries, caused by the fluid injected, can be calculated. These forces are then used in the finite element model as external forces applied on the faces of the crack. The new position of the crack faces is then calculated and transferred to the lattice-Boltzmann model to update the boundary conditions. This feedback-loop for fluid-structure interaction allows modeling of hydraulic fracturing processes for irregular path propagation.

Les protéines PentatricoPeptide-Repeats (PPR) représentent la plus grande famille de protéines de liaison à l’ARN connue. Elles sont caractérisées par la présence de motifs répétés en tandem d’environ 35 résidus ayant une structure hélice-tour-hélice. Depuis les premières études sur l’organisme modèle Arabidopsis thaliana, les protéines PPR ont aussi été découvertes chez d’autres espèces non-plantes, incluant les levures et l’humain. Cependant, la détection des protéines PPR en dehors des plantes est compliquée par le fait que les outils de recherche sont tous conçus pour les protéines de plantes. Récemment, une étude réalisée chez les levures a rapporté une méthode itérative semi-automatisée d’identification de PPR utilisant des profils Hidden Markov Models (HMM). Inspirés par cette approche, nous visons ici à développer une méthode complètement automatisée plus généralisable et sensible qui ne dépend pas du protéome de départ. Comme preuve de concept, nous avons choisi une espèce non reliée aux plantes possédant le plus grand nombre de protéines PPR en-dehors des plantes – le protiste marin unicellulaire Diplonema papillatum. Il s’agit d’un modèle émergent ayant reçu beaucoup d’intérêt pour l’excentricité de l’expression de son génome mitochondrial, pour lequel il a été suggéré que les protéines PPR jouent un rôle clé. Nous avons ici développé une approche itérative pour identifier et cataloguer les protéines PPR chez D. papillatum. Les fonctionnalités particulières de notre algorithme incluent l’inspection des intervalles de 30 à 40 résidus entre les motifs classiques déjà identifiés et l’utilisation des structures secondaires caractéristiques des motifs PPR pour valider les motifs candidats nouvellement identifiés. Au final, nous avons identifié près de 800 motifs PPR chez D.papillatum, dont plusieurs motifs « déviants » identifiés dans les espaces entre les motifs. La validation expérimentale des motifs candidats les plus prometteurs est en attente. / PentatricoPeptide-Repeat (PPR) proteins represent the largest family of RNA-binding proteins known. They are defined by containing tandemly arranged, ~35-residue long motifs assuming a helix-turn-helix structure, which are referred to as PPR motifs. Since the seminal studies undertaken in the model organism Arabidopsis, a few PPR proteins have been also discovered outside plants, including yeast and human. However, the detection of PPR proteins in non-plant eukaryotes is complicated by the fact that current search tools are tailored toward plants. Recently, a semi-automated method has been reported for identifying PPR motifs in yeast using iterative searches with profile Hidden Markov models (HMMs). Inspired by this work, we aimed to develop a fully automated, sensitive approach that can be used for detecting PPR proteins in any species, when using the corresponding proteome as input. For a proof of concept, we used a species that contains the largest number of PPR genes outside the plant kingdom –the unicellular protist Diplonema papillatum. This emerging model system has garnered much interest for the eccentricities of its mitochondrial gene expression, in which PPR proteins are posited to play a key role. Here, we have developed an iterative HMM-search method that comprehensively catalogues and classifies PPR motifs in D. papillatum. Particular features of our algorithm are that it inspects closely 30 to 40 residue-long intervals between readily identified (classical) motifs, makes use of the characteristic secondary structure of PPR motifs to validate newly detected candidate motifs. In total, we have identified around 800 PPR motifs in D. papillatum. Including several deviant candidates detected in ”gaps”. High ranking representatives of both classical and deviant motifs await experimental validation.

Approved for public release, distribution is unlimited / This thesis examines the process by which enlisted goal shares are generated by Commander, Navy Recruiting Command (CNRC) and assigned to Navy Regional recruiting commands. Through use of an econometric goaling and forecasting model employed by CNRC and a less complicated weighting system used by Regions, goal shares are generated using factors believed to accurately predict future recruiting success. The factors used in the new contract prediction model include local economic conditions, population demographics, and recruiting resources. This thesis evaluates these factors to obtain a clear understanding of how each affects the establishment of goal shares. The various levels within the recruiting organization are analyzed, to include a discussion on how each of these levels prioritizes assigned goals, specifically accessions and new contract objectives, and the reasons why these priorities differ across levels within the organization. The thesis analyzes the role of past production data and Production per Recruiter (PPR) in establishing goal. Recruiter incentives and potential impacts of these incentives on the attainment of quality contracts are also discussed. Finally, the accuracy of CNRC forecasts is evaluated and recommendations are made to help ensure the continued success of these forecasts well into the future. This thesis finds CNRC's goaling forecasts to be quite accurate; however, with more precise data for a few specific variables within the goaling model, it is believed the accuracy of forecasts could be improved. Additionally, this thesis finds that due to current recruiter incentives, recruiters may not be motivated to contract the best possible candidates for enlistment at all times. / Lieutenant, United States Navy

Ce travail consacré aux risques dans les territoires touristiques de montagne propose une analyse de l'action de gestion dans la complexité de sa mise en œuvre. Pour ce faire cette recherche s'inscrit dans une approche endogène du risque, en questionnant l'offre de gestion, c'est-à-dire la réponse au problème collectif qu'il constitue. En prenant plus particulièrement appui sur la question du risque d'avalanches dans différentes communes supports de station de sports d'hiver de l'arc alpin français, deux axes d'analyse complémentaires sont proposés. Le premier vise la description des modalités pratiques de l'action publique relative au risque dans les territoires touristiques. Le second propose de se pencher sur certains facteurs actifs de vulnérabilité liés aux modalités de gestion observées. <br />En matière de risque d'avalanches, la vulnérabilité désigne classiquement les éléments passifs exposés aux phénomènes : espaces urbanisés, infrastructures routières, domaines skiables. Toutefois dans une acception active, la vulnérabilité peut aussi couvrir un champ d'analyse plus large, lorsqu'elle permet de questionner les logiques et dynamiques de gestion dans leurs contextes territoriaux de mise en œuvre. Cette gestion se structure autour de dispositifs multiples à l'échelle locale qui impliquent différentes sphères d'acteurs : locales / nationales, publiques / privées, politiques, techniques, civiles, économiques,...<br /><br />L'analyse des scènes de risques propose une description comparée des modalités d'engagement des acteurs dans l'action structurée autour des grands cadres d'action que sont le PPR ou le PIDA. Pour ce faire une analyse empirique est menée sur 7 communes supports de station de sports d'hiver, situées dans l'arc alpin français. Sur chacun des sites, les conditions particulières de mise en œuvre de ces dispositifs sont caractérisées et mises en parallèle. L'attention est portée sur la réalité des pratiques et diversité des situations de gestion auxquelles les protagonistes de l'action sont confrontés pour un même dispositif de gestion. Par ailleurs, en complément des cadres d'action classiques, existent d'autres formes de réponse collective au risque. Il s'agit d'initiatives, de politiques, de dispositifs préventifs portés par les acteurs territoriaux qui expriment parfois une autre vision du risque et de la réponse à lui apporter.<br /><br />Parallèlement à ces analyses centrées sur les modalités de gestion, un questionnement sur la vulnérabilité même de certaines modalités de gestion dans ces territoires est proposé. La fragilité, mais aussi les limites relatives au pilotage de certains dispositifs sont ainsi considérées. Il s'agit ici de replacer la question du risque au centre du débat politique et collectif de ces territoires. Nous pointons ainsi le poids de la dimension technique dans les pratiques de gestion, occultant parfois la question du sens de l'action. Nous pointons également à cette occasion l'accentuation de certains décalages et décrochements au sein de l'action de gestion, entre les acteurs en responsabilité ou bénéficiaires des dispositifs et ceux en charge de les mettre en œuvre.

This paper deals with medical data extraction from electronic patient record (EPR) system. Most of the medical data are stored in patient record systems, and data that are much valuable for medical research. If a researcher wants to extract medical information today, it has to be done manually because the data are stored in unstructured textual format in a system created by hospital staff. There is no way of extracting data in structure way. This paper is going to introduce an information extraction application for EPR system that allows the researcher to set up a study with inclusion and parameters for extraction for retrospective surveys in a webuser-interface environment. Inclusion is what the researcher would like to study (a defined category or criteria) and parameters specify the characteristics of inclusion the criteria. Result of this application provides an extracted clinical data that is used for retrospective surveys, downloadable to an MS-Excel file.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第23045号 / 理博第4722号 / 新制||理||1677(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 鹿内 利治, 准教授 竹中 瑞樹, 教授 松下 智直 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM