Ma thèse vise à caractériser l’évolution dynamique et l’organisation des génomes des différentes espèces du blé (genres Triticum et Aegilops) en relation avec la prolifération des éléments transposables (TEs) dans leur génome (>80%), les polyploïdisations récurrentes ainsi que la syntenie avec d’autres espèces de la famille des Poaceae. En constituant des sets de séquences génomiques représentatives et en étudiant la variabilité entre des haplotypes des génomes du blé, j’ai caractérisé la dynamique et la prolifération différentielle des TEs qui est la résultante de l’équilibre entre leurs insertions et aussi leurs éliminations actives. Le taux moyen de remplacement de l’espace TEs, mesurant les différences de séquences dues aux insertions et aux délétions entre deux haplotypes, a été ainsi estimé à 86% par million d’années (Ma) et dépasse celles bien documentées du maïs. Les insertions des TEs mais aussi leurs éliminations par recombinaisons illégitimes de l’ADN (pouvant atteindre plusieurs dizaines de kb) ainsi que les recombinaisons génétiques entre haplotypes divergents représentent les principaux mécanismes à la base des changements rapides de l’espace TEs. Sur une échelle d’évolution plus longue (60 Ma), j’ai analysé la conservation des gènes et l’évolution du locus (Ha) entre différentes espèces des Poaceae. J’ai pu ainsi préciser l’émergence du caractère grain tendre et des gènes Ha, comme nouveaux membres de la famille des gènes de Prolamine, dans l’ancêtre commun des Pooideae (blé et Brachypodium, de la tribu des Triticeae et des Brachypodieae) et des Ehrhartoideae (riz), après leur divergence des Panicoideae (maïs, sorgho). / My PhD aims to characterize dynamic evolution and organization of wheat genomes from différent species (Triticum and Aegilops genera) in relation to transposable element (TE) proliferation in their genomes (>80%), polyploidizations and synteny with other Poaceae species. By constituting and comparing representative genomic sequences and analyzing haplotype variability of the wheat genomes, I have characterized dynamics and differential proliferation of TEs, as resulting from the combinations of their insertions and deletions. Mean replacement rate of the TE space, which measures sequence differences due to insertion and removal of TEs between two haplotypes, was estimated to 86% per one million year (My). This is more important than the well-documented haplotype variability found in maize. It was observed that TE insertions and DNA elimination by illegitimate recombination (implicating several ‘tens’ of kb) as well as homologous recombination between divergent haplotypes represent the main molecular basis for rapid change of the TE space. At a longer evolutionary scale (60 My), I have compared gene conservation at the Ha locus region between different Poaceae species. The comparative genome analysis and evolutionary comparison with genes encoding grain reserve proteins of grasses suggest that an ancestral Ha-like gene emerged, as a new member of the Prolamin gene family, in a common ancestor of the Pooideae (wheat and Brachypodium from the Triticeae and Brachypodieae tribes) and Ehrhartoideae (rice), between 60 and 50 My, after their divergence from Panicoideae (Sorghum).

The subject of this study is the influence which Dutch has had on Papiamentu. The first chapter deals with the history of the Benedenwindse Eilanden of the Netherlands Antilles in order to explain the reason for the "mixed" nature of the language. The second chapter is devoted to the influence which the various component parts of the population have had or may have had on the language. It further shows how Papiamentu developed from a pidgin into a Creole and subsequently into an independent language. This growth is demonstrated by statements from writers on the language. The third chapter concerns in particular the Dutch element in Papiamentu. After a short description of the various categories in which Dutch influence is apparent, an analysis is made of the presence of words and expressions from those categories in Ora Solo Baha, a collection of children's stories by Pierre Antoine Lauffer. In this analysis attention is given to the lexicon as well as to syntactic caiques. Words and expressions have been explained not only on the basis of present-day Dutch, but, as far as possible, also in the light of their occurrence in earlier forms of Dutch, the seventeenth-century language, or in the West Frisian and Zealandic dialects, as well as in colloquial Dutch. / Arts, Faculty of / French, Hispanic, and Italian Studies, Department of / Graduate

Bibliography: pages 51-54. / The microstructure of different types of industrially produced heating elements was examined and an x-ray diffraction method was devised to determine the relative amounts of α- and β-silicon carbide present in these materials. It was confirmed that the α- to β-silicon carbide transformation occurs during heat treatment, because of the influence of the nitrogen atmosphere in the furnace. The fabrication parameters important in the manufacture of heating elements were investigated. Porous sintered silicon carbide samples were made using different proportions of grit sizes and various firing schedules. Both resistivity and crushing strength were determined. It was found that the resistivity is dependent upon degree of sintering (indicated by crushing strength) as well as the packing density of the porous body.

Submitted to the faculty of Indiana University in partial fulfillment of the requirements for the degree Master of Science in the School of Informatics, December 2004 / The process of generating RNA message from a gene is termed "transcription," and is performed by aptly named "transcription factors." These transcription factors can function singly or in conjunction with other factors to regulate gene expression, and thereby control, at one level, the amount of protein product which a gene can produce. This transcriptional regulation can have profound biological effects. Identification of the DNA sequences bound by transcription factors (regulatory elements) is a challenge as these sequences can be very short and may be located large distances from the target gene. Also, many current approaches for discovering regulatory elements in genomic DNA are limited to those sequences previously identified as consensus sequences for transcription factors. We have developed a novel tool, ReguLocator, for the identification of putative regulatory element. It uses the Smith-Waterman algorithm to identify short, conserved DNA sequences (ranked by p-value) derived from 2 large DNA sequences of interest. No weighting is applied for spatial alignment. Although speed must be improved to make use of ReguLocator practical, initial comparisons to similar tools provide promising results, and may open the door to better regulatory element identification.

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The modern world has forgotten a crucial part of what historically has been a beautiful experience in our homes: its connection to the planet. This thesis proposes a mix-use building that acts as an instrument to connect the users with the planet while maintaining contemporary standards of living. I believe that human beings have an innate tendency to connect with nature. The building design will have a passive aspect that is experiential and the active aspect that is functional. The spaces come alive through design by translating the planets four elements as a part of the daily lives of the users, activating the Fifth element, the Spirit. Connecting with nature on a fundamental level will enhance the inhabitants experience and create a connection with the planet through the spaces we inhabit. / Master of Architecture

High levels of primary sequence conservation are observed in many noncoding regions of eukaryotic genomes. These conserved noncoding elements (CNEs) have shown to be robust indicators of functionally constrained elements. Nevertheless, the function of only a small fraction of such CNEs is known and their role in genome biology remains largely a mystery. Comparative genomics analysis in model organisms can shed light on CNE function and evolution of noncoding DNA in general. Recently, it has been reported that short CNEs in the Drosophila genome are typically very AT-rich but have unusually high levels of GC content in a much larger (~500 bp) window around them. To understand whether these "side effects" are dependent on their CNE definition or are a more general feature of the Drosophila genome, we analysed base composition of CNEs from two different CNE detection methods. We found side effects are real, but are restricted to a subset of CNEs in the genome. An alternative hypothesis to explain the existence of CNEs is the mutational cold spot hypothesis. Previous work using SNPs was shown evidence that CNEs are not mutational cold spots. Here, non-reference transposable elements (TEs) were used to test cold spot hypothesis. A significant reduction in levels of non-reference TEs was found in intronic and intergenic CNEs compared to the expected number of insertions. TEs in intergenic CNEs were also found at lower allele frequencies than TEs in intergenic spacers. Furthermore, we used simulation to explore the effects of insertion/deletion (indel) evolution on noncoding DNA sequences with and without constrained noncoding elements. We assessed several indel-capable simulators to test expected outcomes with no selectively constrained elements. Simulations with constrained elements show that sequences grow in length even when the deletion rate is exactly the same as the insertion rate. This result can be interpreted as being due to purifying selection on CNEs acting to remove an excess of deletion over insertions. Together, the results presented here provide insights into the evolution of noncoding DNA in one of the most important model organisms.

The Pieman River catchment has seen continuous mining of economic deposits of gold, silver, lead, copper, zinc and tin since the 1870’s. Tributaries of this river which receive mining effluent, either directly or from acid mine drainage (AMID), have total metal concentrations considerably above background levels and are of regulatory concern. The lower Pieman River is however classified as a State Reserve in which recreational fishing and tourism are the major activities. It is therefore important that water entering the lower Pieman River from upstream hydroelectric impoundments is of high quality. Metals in natural waters exist in a variety of dissolved, colloidal and particulate forms. The bioavailability and hence toxicity of heavy metal pollutants is very dependant on their physico form. Knowledge of the speciation of a metal in natural aquatic environments is therefore necessary for understanding its geochemical behaviour and biological availability. Complexation of metal ions by natural ligands in aquatic systems is believed to play a significant role in controlling their chemical speciation. This study has investigated temporal and spatial variation in complexation of metal ions in the Pieman River. The influence of pH, temperature, organic matter, salinity, ionic strength and time has been investigated in a series of field studies and in laboratory-based experiments which simulated natural and anthropogenic disturbances. Labile metals were measured using two techniques in various freshwater and estuarine environments. Diffusive gradients in thin-films (DGT) allowed in situ measurement of solution speciation whilst differential pulse anodic stripping voltammetry (DPASV) was used to measure labile metal species in water samples collected from the catchment. Organic complexation was found to be a significant regulating mechanism for copper speciation and the copper-binding ligand concentration usually exceeded the total copper concentration in the river water. Complexation was highly dependent on pH and at the river-seawater interface was also regulated by salinity, probably as a result of competitive complexation by major ions in seawater (eg. Ca 2+ ions). Zinc complexation was also evident, however total zinc concentrations in the water column often far exceeded the potential binding capacity of available ligands. In addition to organic complexation, Zn speciation may also be associated with adsorption by flocculated or resuspended colloidal Mn and/or Fe oxyhydroxides. Metal ion complexation and hence speciation was found to be highly variable within the Pieman River catchment. This presents major difficulties for environmental managers, as it is therefore not possible to make catchment-wide assumptions about the bioavailability of these metals. These results emphasise the importance of site-specific sampling protocols and speciation testing, ideally incorporating continuous, in situ monitoring.