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Les racines ont deux grands rôles. Le premier est le prélèvement de l’eau et des éléments nutritifs et le second est l’ancrage dans le sol. Identifier les gènes responsables de la mise en place des tissus et de l'architecture du système racinaire est donc essentiel pour pouvoir améliorer les variétés de riz soumises à des stress abiotiques de plus en plus fréquents et nombreux du fait du changement climatique. Au cours de cette thèse, j'ai réalisé une analyse fonctionnelle du gène DEFECTIVE IN OUTER CELL LAYER SPECIFICATION (DOCS1) qui appartient à la famille des récepteurs kinases à répétitions riches en leucine (LRR-RLK). Ces protéines sont composées de deux domaines principaux: un domaine extra-cytoplasmique composé de répétitions LRR et un domaine kinase intra-cytoplasmique. Un mutant de ce gène, nommé c68, possède une mutation non-sens dans le domaine kinase. Les plantes mutantes c68 présentent plusieurs phénotypes: une sensibilité accrue à l'aluminium, une réduction du nombre et de la taille des poils absorbants dans les racines, et des couches d’exoderme/épiderme d’identité mêlée. Le premier chapitre de la thèse porte sur l’étude conjointe de lignées knock-out CRISPRs du gène DOCS1 et de c68. Nos résultats ont montré que les mutants c68 et CRISPRs présentaient les mêmes phénotypes : sensibilité à l’aluminium, défauts des poils absorbants et tissus externes d’identité mixte. Ces résultats suggéraient que chez le mutant c68, soit la protéine DOCS1 n'était pas fonctionnelle, soit elle n'était pas traduite. Nos analyses phénotypiques ont aussi révélé que tous les mutants présentaient des défauts de réponse à la gravité à différents stades de développement. A 3 jours, un retard de réponse à la gravité était observé pendant la première heure après gravistimulation. Les plantules mutantes présentaient aussi des défauts de localisation d’un transporteur d’auxine. A 40 jours, nous avons observé que l'angle du cône racinaire des plantes mutantes était plus ouvert que celui des plantes sauvages. Deux gènes liés à l’auxine et plusieurs QTLs ont déjà été identifiés comme participant à ce phénotype chez le riz. Dans la suite de notre étude, nous avons donc cherché à identifier de nouveaux QTLs et gènes impliqués dans ce phénotype morphologique par étude d'association pan-génomique dans deux panels Indica et Japonica. Toutes les accessions de l'écotype bulu d'Indonésie et trois japonicas tempérés d'Asie du Sud présentaient un angle du cône racinaire très ouvert. En utilisant un modèle mixte associé à une technique de ré-échantillonnage, 55 QTLs ont été détectés. L'analyse des gènes sous-jacents ou voisin (+/- 50kb) a identifié 539 gènes, dont 6 LRR-RLK, 5 gènes liés à l’auxine et 5 gènes avec une fonction validée dans le développement ou l'architecture racinaire. Une approche complémentaire par cartographie génétique classique est proposée pour identifier les gènes en cause dans la ou les mutations à angle du cône racinaire très ouvert. Des perspectives de poursuite du travail effectué sont aussi présentées afin de déterminer si le phénotype affectant l'angle du cône racinaire induit par les mutations du gène DOCS1 ou des nouveaux gènes identifiés est lié à des perturbations des flux d’auxine. / Roots have two major roles. The first one is to uptake water and nutrients and the second one is to anchor plants into the ground. Identifying the genes responsible for the establishment of tissues and architecture of the root system is essential to improve rice varieties subject to increasingly frequent and numerous abiotic stresses due to climate change. During my PhD, I undertook a functional analysis of the DEFECTIVE IN OUTER CELL LAYER SPECIFICATION (DOCS1) gene which belongs to the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family. These proteins are composed of two main domains: an extra-cytoplasmic domain containing LRR repeats and a cytoplasmic kinase domain. A mutant of this gene, named c68, carries a nonsense mutation in the kinase domain. The c68 mutant plants show several phenotypes: increased sensitivity to aluminum, reduced number and size of root hairs, and layers of external tissues with exodermis/epidermis mixed identity. The first chapter of the thesis focuses on the joint study of knockout CRISPRs lines of the DOCS1 gene and c68. Our results showed that the c68 and CRISPRs mutants displayed the same phenotypes: sensitivity to aluminum, defects in root hairs and mixed identity of external tissues. These results suggested that in the c68 mutant, either the DOCS1 protein was not functional, or the protein was not translated. Our phenotypic analyses also showed that all mutants exhibited impaired gravity responses at different development stages. At 3 days, a delay of response to gravity was observed during the first hour after gravistimulation. Mutant seedlings also had defects in an auxin transporter localization. At 40 days, we observed that the root cone angle of mutant plants was more open than that of wild-type plants. Two genes associated with auxin and several QTLs have been identified as contributing to this phenotype in rice. In the rest of our study, we therefore tried to identify new QTLs and genes involved in this morphological phenotype by a genome-wide association study in two Indica and Japonica panels. All accessions of the bulu ecotype from Indonesia and three South Asian temperate japonica had a very open root cone angle. Using a mixed model associated with a resampling technique, 55 QTLs were detected. The analysis of the underlying or neighbor (+/- 50kb) genes identified 539 genes, including 6 LRR-RLK, 5 genes related to auxin and 5 genes with a function validated in root development or architecture. A complementary approach by classical genetic mapping is proposed to identify genes involved in the mutation(s) involved in very open root cone angle. Prospective research lines are also presented to determine if the root cone angle phenotype , induced by DOCS1 or by newly identified genes, is linked with disruption of auxin fluxes.

Das stetig wachsende Datenaufkommen - die weltweite Datenmenge verdoppelt sich alle zwei Jahre - ist eine wesentliche Herausforderung für den Menschen in allen Bereichen des beruflichen und privaten Alltags. Um trotzdem relevante Informationen zu identifizieren und auch zu verstehen, nehmen Techniken und Anwendungen zur InfoVis einen immer größeren Stellenwert ein. Leider hat sich die Vision der "InfoVis for and by the masses" aufgrund des notwendigen Daten-, Visualisierungs- und Programmierwissens noch nicht durchgesetzt. Zudem sind heutige InfoVis-Softwareanbieter mit dem Problem konfrontiert, verschiedenste Kontexte, wie Nutzergruppen oder Hard- und Softwareplattformen, unterstützen zu müssen. Ein möglicher Lösungsansatz für dieses Problem ist das Paradigma der kompositen Webanwendungen. Auf deren Basis können Daten und UI-Widgets je nach Anwendungsfall teils automatisch kombiniert werden. Dies erhöht die Wiederverwendbarkeit und spart Zeit sowie Entwicklungskosten. Unter Zuhilfenahme von (semantischen) Modellen ist es zudem möglich, eine komposite RIA an die vorliegende Situation zu adaptieren. Um dem Endanwender Zugang zu den kompositen RIA zu verschaffen, mangelt es jedoch an einem Integrationsprozess, der den speziellen Anforderungen der InfoVis gerecht wird. Diese Dissertation stellt deshalb neue Konzepte für einen ganzheitlichen Semantik-gestützten InfoVis-Prozess vor, der bspw. die Endnutzer-gerechte Filterung großer Datensätze, die kontextsensitive Auswahl von InfoVis-Komponenten, die Nutzerunterstützung bei der Exploration und Interpretation der Daten sowie die Gewinnung und Wiederverwendung von Visualisierungswissen adressiert. Zur Unterstützung des InfoVis-Prozesses werden weiterhin Konzepte für eine formale Wissensbasis mit Domänenwissen vorgeschlagen. Die modulare, mit W3C-Standards prototypisch realisierte Visualisierungsontologie definiert u.a. Konzepte und Relationen zu Daten, graphischen Vokabular, menschlicher Aktivität sowie veränderliches Faktenwissen. Ein weiterer, wesentlicher Beitrag der Arbeit liegt in der Architekturkonzeption für modellbasierte, komposite RIA für die InfoVis-Domäne, womit ein neues Anwendungsfeld des Software-Paradigmas erschlossen wird. Damit steht nun erstmals für eine komposite, webbasierte InfoVis-Lösung ein ganzheitliches Architekturkonzept zur Verfügung, das die Ausführbarkeit der Anwendungen in der heute existierenden, heterogenen Landschaft der (mobilen) Endgeräte gewährleisten kann. Durch die Implementierung entscheidender Architekturkonzepte sowie einer beispielhaften InfoVis-Anwendung für semantische Daten wurde die Tragfähigkeit der geschaffenen Konzepte nachgewiesen. Anhand einer Vielzahl von formativen sowie einer summativen Nutzerstudien konnte validiert werden, dass sich aus den neuen Konzepten Vorteile für den Endanwender bei der Erstellung einer InfoVis ergeben.

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Doctor of Philosophy / Department of Physics / Hongxing Jiang / InGaN based, blue and green light emitting diodes (LEDs) have been successfully produced over the past decade. But the progress of these LEDs is often limited by the fundamental problems of InGaN such as differences in lattice constants, thermal expansion coefficients and physical properties between InN and GaN. This difficulty could be addressed by studying pure InN and In[subscript]xGa[subscript]1-xN alloys. In this context Ga-rich In[subscript]xGa[subscript]1-xN (x≤ 0.4) epilayers were grown by metal organic chemical vapor deposition (MOCVD). X-ray diffraction (XRD) measurements showed In[subscript]xGa[subscript]1-xN films with x= 0.37 had single phase. Phase separation occurred for x ~ 0.4. To understand the issue of phase separation in Ga-rich In[subscript]xGa[subscript]1-xN, studies on growth of pure InN and In-rich In[subscript]xGa[subscript]1-xN alloys were carried out. InN and In-rich In[subscript]xGa[subscript]1-xN (x~0.97- 0.40) epilayers were grown on AlN/Al[subscript]2O[subscript]3 templates. A Hall mobility of 1400 cm[superscript]2/Vs with a carrier concentration of 7x1018cm[superscript]-3 was observed for InN epilayers grown on AlN templates. Photoluminescence (PL)emission spectra revealed a band to band emission peak at ~0.75 eV for InN. This peak shifted to 1.15 eV when In content was varied from 1.0 to 0.63 in In-rich In[subscript]xGa[subscript]1-xN epilayers. After growth parameter optimization of In- rich In[subscript]xGa[subscript]1-xN alloys with (x= 0.97-0.40) were successfully grown without phase separation. Effects of Mg doping on the PL properties of InN epilayers grown on GaN/Al[subscript]2O[subscript]3 templates were investigated. An emission line at ~ 0.76 eV, which was absent in undoped InN epilayers and was about 60 meV below the band edge emission peak at ~ 0.82 eV, was observed to be the dominant emission in Mg-doped InN epilayers. PL peak position and the temperature dependent emission intensity corroborated each other and suggested that Mg acceptor level in InN is about 60 meV above the valance band maximum. Strain effects on the emission properties of InGaN/GaN multiple quantum wells (MQWs) were studied using a single blue LED wafer possessing a continuous variation in compressive strain. EL emission peak position of LEDs varies linearly with the biaxial strain; a coefficient of 19 meV/GPa, characterizes the relationship between the band gap energy and biaxial stress of In[subscript]0.2Ga[subscript]0.8N/GaN MQWs.

Master of Science / Department of Chemical Engineering / James H. Edgar / Pure boron exists in two main polymorphs, the common β-rhombohedral boron and the relatively rare α-rhombohedral boron. α-rhombohedral boron (α-B) possesses several extraordinary properties: self-healing from radiation damage and a high hole mobility. In addition, the [superscript]10B isotope has a large thermal neutron capture cross section. Such properties make it an excellent candidate for novel electronic device, such as direct energy conversion devices (alphacells and betacells) and neutron detectors. However, research on the properties and applications of α-B has been limited due to the difficulty to produce high quality α-B crystals of significant size. The preparation of α-rhombohedral boron is challenging for several reasons: first, α-rhombohedral boron has a low thermodynamic stability; it is only stable below 1100°C, at higher temperature β-rhombohedral boron is the stable polymorph. In addition, at elevated temperatures, boron is highly reactive, which make it is difficult to produce pure boron crystals. The primary goal of this research was to produce high quality α-B crystals of significant size. The main focus of this study was to explore the feasibility of producing α-B from a copper flux. Copper is a promising solvent for α-B crystal growth: the eutectic temperature of copper-boron is low, 996°C, and the phase diagram of copper-boron is relatively simple, and there are not many intermediate boride-copper compounds. In addition, copper is easily removed from crystals by etching with concentrated nitric acid. Last but not least, copper is less expensive than other metal solvents such as platinum. Boron crystal growth from a platinum solvent and vapor-liquid-solid growth by chemical vapor deposition were also performed for comparison. A series of crystals were grown over a range of initial boron concentrations (9.9 to 27.7 mole %) and cooling rates. Small irregular-shaped black crystals (>100μm) and well-faceted red crystals in various shapes, as large as 500 microns were produced. The crystals were characterized by optical microscopy, scanning electron microscopy, energy dispersive spectroscopy, x-ray diffraction analysis, and Raman spectroscopy. The correlation between experiment results and experimental parameters (source materials, the purity of growth atmosphere, and crucible materials, etc.) are reported. Suggestions about further investigation for α-B crystal growth are proposed.

No description available.

HIV-NC is a multifunctional protein which plays an important role in almost every step of the retroviral life cycle. NC is essential in catalyzing stand transfers of HIV-1 reverse transcription, including the annealing of the transactivation response element (TAR) of the viral genome to the complementary TAR DNA in minus-strong-stop DNA. In this dissertation, the research starts with focus on elucidating the reaction mechanism of NC-facilitated TAR DNA/RNA annealing using single molecule spectroscopy (SMS) approaches. The results indicate that nucleation of TAR DNA/RNA annealing occurs in an encounter complex form in which one or two DNA/RNA strands in the partially open “Y” form associated with multiple NC molecules. This encounter complex leads to annealing through the 3’/5’ termini, namely “zipper” pathway and the annealing through the hairpin loop region, namely “kissing” pathway. By employing target oligonucleotides for specific TAR regions, we directly probed kinetic reversibility and the chaperone role of NC. Concentration-dependence of NC chaperoned melting and annealing of TAR hairpins was investigated and the results further support the proposed reaction mechanism. Additionally, we used a single-stranded DNA (ssDNA) as model to study ssDNA conformational change upon NC binding. Here we present observation of NC binding to d(TG)n and d(T)n, including NC effect on flexibility and conformation of these oligonucleotides chains. Our results reveal that the rigidity of ssDNA chain is dramatically reduced through interaction with NC. Meanwhile the results of NC dissociation experiments indicate the interaction of NC/ssDNA is complex and heterogeneous. Finally, we used SMS in vitro to systematically compare and contrast the RNA/protein interactions for the zinc-finger-binding-motif protein (NC) and the arginine-rich-binding-motif (ARM) protein (Tat) encoded by HIV-1. Tat and NC use different RNA binding motifs to recognize and interact with RNA hairpin, giving rise to very different changes in the RNA secondary structure upon protein binding. Competition experiments show that the presence of Tat can effectively inhibit the NC binding-induced local melting of TAR RNA hairpins. These results indicate that Tat specifically binds and stabilizes the TAR RNA hairpin structure, which likely inhibits the local melting of the hairpin induced by NC. / text

In 2012, the Austin Independent School District implemented a ten-year Creative Learning Initiative to develop every school in the district into an arts rich school. However, research on arts richness presents varied descriptions of what an arts rich school looks like and lacks student voices. This MFA Thesis documents an applied project utilizing an arts based research process to explore student beliefs about the value of the arts and arts richness at the middle school level. In the document, I analyze student beliefs about the value of the arts through modified grounded theory from a data set including a performance, a playscript, group discussions, surveys, and my personal field notes and reflections. I find that the students share a similar understanding with published research of overall categories describing arts richness, including quantity of arts opportunities, quality of artistic and educational programs, and school climate. They deepen the perspective researchers present on school climate in arts rich schools, offering specific ways in which the arts invite a positive school climate. I conclude the document with reflections on defining arts richness, the arts based research process, and areas for further consideration as schools move toward creative learning for the 21st century. / text

G-quadruplexes, characterized by stacked G-tetrad rings held together by Hoogsteen hydrogen bonds, have been visualized in human cells and implicated in transcriptional and translational control, telomere maintenance and disease. RHA Helicase associated with AU-rich element (RHAU), a DEAH-box helicase, is a major G-quadruplex resolvase in human cell lysates. It binds G-quadruplexes through the RHAU specific motif in its N-terminus. In order to investigate the recognition of G-quadruplexes by helicases, the binding between the N-terminal construct of RHAU, RHAU53-105, and the DNA analog of the quadruplex formed by the 5’ terminus of human telomerase RNA component, hTR1-20, was investigated in a comprehensive biophysical approach followed by crystallization screening. RHAU53-105, hTR1-20 DNA and their complexes were analysed by gel electrophoresis, UV-visible spectroscopy, spectropolarimetry, dynamic light scattering and small angle X-ray scattering (SAXS). The findings reveal that hTR1-20 DNA, separated in two conformations by size exclusion chromatography in the presence of potassium cations, assumes a disk-like parallel G-quadruplex secondary structure in solution. Far-UV circular dichroism spectra and SAXS demonstrate that RHAU53-105 assumes an extended (Dmax = 7.8 nm , rG = 2.1 (±0.2) nm) and ordered conformation in solution. The analysis confirms the binding between RHAU53-105 and each conformation of the hTR1-20 DNA quadruplex. Circular dichroism spectra indicate the retention of quadruplex secondary structure in both RHAU53-105•hTR1-20 DNAc1 and RHAU53-105•hTR1-20 DNAc2 complexes. This analysis provides some insight into the interaction between G-quadruplexes and the N-terminal domain of RHAU and identifies 0.2 M sodium formate, 20 % (w/v) polyethylene glycol 3350 and 1.5 M sodium chloride, 10 % (v/v) ethanol as preliminary conditions for crystallization of the complex of RHAU53-105 and hTR1-20 DNAc2. / October 2014