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Some ill. mounted / Bibliography: leaves 198-215 / xv, 215 leaves, [4] leaves of plates : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Physiology, 1985

Thesis (M. Ag. Sc.)--University of Adelaide, 1987. / Includes bibliographical references (leaves 213-223).

Chez la levure à bourgeon, l’établissement de domaines silencieux pour la transcription nécessite le recrutement du complexe SIR (Silencing Information Regulator).Mon travail de thèse s’est attaché à étudier une nouvelle voie d’établissement de la répression transcriptionnelle par les SIRs. Des travaux récents ont montré que la répétition en tandem de protéines fortement liées à l’ADN favorise la mise en silence d’un gène rapporteur voisin (Dubarry et al. 2011).En combinant des approches génétiques et moléculaires, j’ai pu montrer qu’un locus composé de 120 répétitions du site opérateur de l'opéron lactose (lacO) liées par la protéine LacI génère un stress chromatinien local et représente une source d'instabilité génomique. Cette instabilité étant limitée par la recombinaison homologue.Dans la seconde partie de ma thèse, j'ai étudié la dynamique d’établissement de la répression par les complexes lacO/LacI et montré que la répression transcriptionnelle et le recrutement du complexe SIR s'établissent sur plusieurs cycles cellulaires. En outre, mes résultats montrent que le complexe SIR stabilise les nucléosomes au niveau des complexes ADN / protéines de forte affinité.Enfin, deux cribles génétiques m’ont permis d’identifier les complexes HIR et LSM comme des facteurs impliqués dans l’hétérochromatinisation induite par les répétitions lacO/LacI. Les connaissances actuelles de ces complexes étant restreintes à la régulation de la transcription et au post-traitement des ARN messagers, d'autres études seront nécessaires pour disséquer le lien entre ces complexes et l'inhibition transcriptionnelle déclenchée par les complexes lacO /lacI. / Silent domains in budding yeast are formed by the recruitment and spreading of the Silent Information Regulator (SIR) complex.Previous studies showed that an array of tight protein-DNA complexes has the ability to trigger SIR dependent silencing of an ectopically placed EADE2I reporter (Dubarry et al. 2011). It was proposed that replication stress arising due to difficulties to replicate the array of tight protein-DNA complexes is the source of this phenomenon. In my work I have demonstrated that an array of 120 lacO repeats tightly bound by a LacI protein is a source of genomic instability. Investigating the genetic requirements for this event, I have demonstrated that homologous recombination pathways maintain the stability of the locus. My work is consistent with previous reports in fission yeast demonstrating that lacO/LacI is a chromatin stress site (Sofueva et al. 2011). As a second part of my PhD project, using an inducible system that I have developed, I followed the dynamics of establishment of silencing of an ectopically placed reporter gene. My results demonstrate that transcriptional silencing in this system takes many cell cycles to be established. Additionally, I have identified a novel role of the SIR proteins in stabilizing nucleosomes. In an attempt to elucidate the functional link between lacO/LacI and EADE2I silencing, I have performed two SGA (synthetic genetic array) screens. I have identified the HIR and LSM complexes involved into transcriptional regulation and mRNA processing respectively, as potential candidates. Further studies will elucidate the role of these factors on lacO/LacI induced silencing.

No description available.

The cell cycle of budding yeast is controlled by a complex chemically reacting network of a large group of species, including mRNAs and proteins. Many mathematical models have been proposed to unravel its molecular mechanism. However, it is hard for people with less training to visually interpret the dynamics from the simulation results of these models. In this thesis, we use the visualization toolkit D3 and jQuery to design a web-based interface and help users to visualize the cell cycle simulation results. It is essentially a website where the proliferation of the wild-type and mutant cells can be visualized as dynamical animation. With the help of this visualization tool, we can easily and intuitively see many key steps in the budding yeast cell cycle procedure, such as bud emergence, DNA synthesis, mitosis, cell division, and the current populations of species. / Master of Science / The cell cycle of budding yeast is controlled by a complex chemically reacting network. Many mathematical models have been proposed to unravel its molecular mechanism. However, it is hard to visually interpret the dynamics from the simulation results of these models. In this thesis, we use the visualization toolkit D3 and jQuery to design a web-based interface and help users to visualize the cell cycle simulation results. It is essentially a webpage where the proliferation of the wild-type and mutant cells can be visualized as dynamical animation.

The red-cockaded woodpecker (Picoides borealis) is a federally endangered species. As such, populations need to be increased in order to achieve recovery goals outlined by the U.S. Fish and Wildlife Service. My thesis is composed of two chapters that represent opposite sides of this issue. The first chapter investigates whether military training activity negatively affects red-cockaded woodpeckers. Military installations in the southeastern United States contain several of the largest remaining red-cockaded woodpecker populations. Six of the 15 installations harboring these birds are designated primary core populations; thus, population increases on these sites are critical to recovery of the species. However, restrictions on military training activity associated with red-cockaded woodpecker protection are a cause of concern on military installations that sometimes constrains management for population growth. Current restrictions are based on assumptions of potential impacts rather than scientific evidence, so we evaluated two different restriction regimes to test for training activity effects. The second chapter concerns how to induce populations to grow more rapidly through natural processes. As a cooperative breeder, red-cockaded woodpeckers preferentially compete for existing breeding positions and queue in the form of helping or floating to obtain a breeding vacancy, rather than create new territories. I used 20 years of demographic data collected as part of a long-term monitoring study of red-cockaded woodpeckers to investigate mechanisms that stimulate territory creation in this cooperatively breeding species. / Master of Science

Large-scale changes are common in genomes, and are often associated with pathological disorders. In the work presented in this dissertation, I provide insights into how inverted repeat sequences in budding yeast fuse during replication. Fusion leads to the formation of dicentric chromosomes, a translocation, and other chromosomal rearrangements.Using extensive genetics and some molecular analyses, I demonstrate that dicentric chromosomes are key intermediates in genome instability of a specific chromosome in budding yeast. I provide three pieces of evidence that is consistent with this conclusion. First, I detect a recombination fusion junction that is diagnostic of a dicentric chromosome (using a PCR technique). Second, I show a strong correlation between the amount of the dicentric fragment and the frequency of instability of the entire chromosome. Third, I demonstrate that a mutant known to stabilize dicentric chromosomes suppress instability. Based on these observations, I conclude that dicentric chromosomes are intermediates in causing genome instability in this system.Next, we demonstrate that fusion of inverted repeats is general. Both endogenous and synthetic nearby inverted repeats can fuse. Using genetics, I also show that many DNA repair and checkpoint pathways suppress fusion of nearby inverted repeats and genome instability. Based on our analysis, we propose a novel mechanism for fusion of inverted repeats that we term `faulty template switching.'Lastly, I discuss two genes that are necessary for fusion of nearby inverted repeats. I identified a mutant of the Exonuclease 1 (Exo1) and a mutant of anaphase inhibitor securin (Pds1) that suppress nearby inverted repeat fusion and genome instability. Studies of Exo1 and Pds1 provide us with insights into the molecular mechanisms of fusion.Our finding that nearby inverted repeats can fuse to form dicentric chromosomes that lead to genome instability may have great implications. The generality of this fusion reaction raises the possibility that dicentric chromosomes formed by inverted repeats can lead to genome instability in mammalian cells, and thereby contribute to a cancer phenotype.

Numerous wild bigtooth maple (Acer grandidentatum Nutt.) specimens in northern Utah have potential for use in landscapes, but improvements in selection and propagation need to be developed before these specimens can be introduced to the green industry. Criteria-based evaluations centered on aesthetics, function, and fall color were performed to objectively select superior bigtooth maple specimens. Out of 56 trees initially selected for red fall color, six were selected for propagation based on all three criteria. Five of the six selected trees yielded viable bud take via chip budding. Optimum time for chip budding propagation was determined by four experiments. Coppiced seedling rootstocks were used with the "return budding" of excised buds as scions to parent stock (2006) and grafting buds from wild trees as scions (2007 and 2009). A fourth experiment examined chip budding of wild scions on 2-year-old, containerized, seedling rootstocks. The general time period identified as the optimum time for budding bigtooth maple was July through mid-August. Propagation by cuttings was also explored as an alternative production method among bigtooth maple selections. Softwood cuttings were taken from six selections of wild bigtooth maples grafted on seedling rootstocks growing in a coppiced stool bed environment. Open-ended, black, velour, drawstring bags were placed over the end of pruned shoots at bud swell to initiate etiolation of the cuttings. The bags were left in place during shoot elongation to insure etiolation of the shoot base. Cuttings were harvested after 3 to 4 weeks, wounded, dipped in auxin, and placed on heating mats under an intermittent mist system. Rooting was evaluated on the cuttings after four weeks. Results showed the effects of etiolation to significantly increase the percentage of rooted cuttings and the number of roots per cutting.

<p>By using AR/ARX-models on data generated by a nonlinear differential equation system representing a model for the cell-cycle control system in budding yeast, the interactions among proteins and thereby also to some extent the genes, are sought. A method consisting of graphical analysis of differences between estimates from two local linear models seems to make it possible to separate a set of linear equations from the nonlinear system. By comparing the properties of the estimations in the linear equations a set of approximate equations corresponding well to the real ones are found. </p><p>A NARX model is tested on the same system to see whether it is possible to find the dependencies in one of the nonlinear differential equations. This approach did, for the choice of model, not work.</p>