Thesis (Ph. D.)--University of Wisconsin, 1967. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliography.

Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

xiv, 196 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / Establishing homologous (evolutionary) relationships among a set of genes allows us to hypothesize about their histories: how are they related, how have they changed over time, and are those changes the source of novel features? Likewise, aggregating related genes into larger, structurally conserved regions of the genome allows us to infer the evolutionary history of the genome itself: how have the chromosomes changed in number, gene content, and gene order over time? Establishing homology between genes is important for the construction of human disease models in other organisms, such as the zebrafish, by identifying and manipulating the zebrafish copies of genes involved in the human disease. To make such inferences, researchers compare the genomes of extant species. However, the dynamic nature of genomes, in gene content and chromosomal architecture, presents a major technical challenge to correctly identify homologous genes. This thesis presents a system to infer ancient homology between genes that takes into account a major but previously overlooked source of architectural change in genomes: whole-genome duplication. Additionally, the system integrates genomic conservation of synteny (gene order on chromosomes), providing a new source of evidence in homology assignment that complements existing methods. The work applied these algorithms to several genomes to infer the evolutionary history of genes, gene families, and chromosomes in several case studies and to study several unique architectural features of post-duplication genomes, such as Ohnologs gone missing. / Committee in charge: John Conery, Chairperson, Computer & Information Science; Virginia Lo, Member, Computer & Information Science; Arthur Farley, Member, Computer & Information Science; John Postlethwait, Member, Biology; William Cresko, Outside Member, Biology

Cette thèse s'intéresse au problème de calculer des résolutions projectives d'algèbres associatives. Notre point de départ est la résolution de Bardzell pour les algèbres monomiales. Étant donnée une algèbre, nous utilisons le principe de systèmes de réduction de Bergman pour lui associer des algèbres monomiales. Nous montrons que les différentielles de la résolution de Bardzell de ces algèbres peuvent se modifier pour obtenir des résolutions projectives de l'algèbre de départ. Par ailleurs, nous donnons un critère pour qu'un complexe provenant d'une modification de la résolution de Bardzell d'une algèbre monomiale associée soit exacte. Nous appliquons notre méthode à trois familles d'algèbres: les intersections complètes quantiques, les algèbres de Weyl généralisées quantiques, et les algèbres down-up. Dans le cas des algèbres down-up, nous utilisons la résolution obtenue pour calculer des invariants homologiques de ces algèbres. De cette façon nous montrons des propriétés de régularité et nous donnons une solution au problème de l'isomorphisme pour les algèbres down-up non-noethériennes. / This thesis is concerned with the problem of computing projective resolutions of associative algebras. Our starting point is Bardzell's resolution for monomial algebras. Given an associatve algebra, we use Bergman's principle of reduction systems to associate monomial algebras to it. We prove that the differentials in Bardzell's resolution of these monomial algebras can be modified to obtain projective resolutions of the original algebra. We also give sufficient conditions for a complex coming from a modification of Bardzell's resolution of an associated monomial algebra to be exact. We apply our method to three families of algebras: Quantum complete intersections, Quantum generalized Weyl algebras and down-up algebras. In the case of down-up algebras, we use the resolution obtained to compute homological invariants of these algebras. This way we prove regularity properties and we solve the isomorphism problem for non-noetherian down-up algebras.

Masters of Science / The three-dimensional structures of proteins are important in understanding their function and interaction with ligands and other proteins. In this work, the structures of two proteins, ImuA’ from mycobacterium tuberculosis and GH9 C1 cellulase from a metagenomic library, were analysed using structural biological and modelling techniques. The gene encoding ImuA’ was amplified by two-step PCR, cloned, and expressed in E. coli. The recombinant ImuA’ produced was found to be largely insoluble. The insoluble protein was successfully solubilized in 8M urea but refolding the protein to its native structure was unsuccessful. By homology modelling, a 3D model of ImuA’ was obtained from a partly homologous protein RecA. In comparison to RecA, ImuA’ appears to lack some loop amino acids critical for DNA binding. Hence ImuA’ is postulated to not bind DNA. The second protein, GH9 C1 cellulase, was produced in E. coli. The protein was purified by chromatographic techniques and crystallized in a precipitant to protein ratio of 1:2 by hanging and sitting drop crystallization methods. The reservoir solution was made up of 15-30% (w/v) PEG 3350, 200 mM salt and 100 mM Tris-HCL pH 7.5-8.5. The protein crystals only diffracted x-rays to 4 å resolution which could not be used to obtain a crystal structure of the protein. The diffraction data, however, showed the crystal to be monoclinic with space group P2. Homology modelling revealed GH9 C1 cellulase to be a two domain protein with a smaller N-terminal Ig-like domain and a larger catalytic domain.The catalytic domain retains two ca2+ binding sites, which potentially stabilize the active site conformation and increase thermostability of the protein. Overall GH9 C1 cellulase is structurally similar to other GH9 cellulases, suggesting that its catalytic mechanism may be conserved.

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Thesis advisor: Michelle M. Meyer / Non-coding RNA (ncRNA) perform vital functions in cells, but the impact of diversity across structure and function of homologous motifs has yet to be fully investigated. One reason for this is that the standard phylogenetic analysis used to address these questions in proteins cannot easily be applied to ncRNA due to their inherent characteristics. Compared to proteins, ncRNA have shorter sequence lengths, lower sequence conservation, and secondary structures that need to be incorporated into the analysis. This has necessitated an effort to develop methodology for investigating the evolutionary and functional relationship between sets of ncRNA. In this pursuit, I studied closely related riboswitches. Riboswitches are structured ncRNA found in bacterial mRNA that regulate gene expressions using their two major components: the aptamer and the expression platform. The aptamer of a riboswitch is able to bind a specific small molecule (ligand), and the bound/unbound state of the aptamer influences conformational changes in the expressions platform that can lead to increased or decreased downstream gene expression. Utilizing sequence and structural similarity metrics combined with graph clustering and de novo community detection algorithms I have determined a methodology for investigating the functional and evolutionary relationship between closely related riboswitches, and other ncRNA by extension, that are found across a range of diverse phyla. / Thesis (PhD) — Boston College, 2021. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

The simplicial homology global optimisation (SHGO) algorithm is a general purpose global optimisation algorithm based on applications of simplicial integral homology and combinatorial topology. SHGO approximates the homology groups of a complex built on a hypersurface homeomorphic to a complex on the objective function. This provides both approximations of locally convex subdomains in the search space through Sperner's lemma (Sperner, 1928) and a useful visual tool for characterising and e ciently solving higher dimensional black and grey box optimisation problems. This complex is built up using sampling points within the feasible search space as vertices. The algorithm is specialised in nding all the local minima of an objective function with expensive function evaluations e ciently which is especially suitable to applications such as energy landscape exploration. SHGO was initially developed as an improvement on the topographical global optimisation (TGO) method rst proposed by T orn (1986; 1990; 1992). It is proven that the SHGO algorithm will always outperform TGO on function evaluations if the objective function is Lipschitz smooth. In this dissertation SHGO is applied to non-convex problems with linear and box constraints with bounds placed on the variables. Numerical experiments on linearly constrained test problems show that SHGO gives competitive results compared to TGO and the recently developed Lc-DISIMPL algorithm (Paulavi cius and Zilinskas, 2016) as well as the PSwarm and DIRECT-L1 algorithms. Furthermore SHGO is compared with the TGO, basinhopping (BH) and di erential evolution (DE) global optimisation algorithms over a large selection of black-box problems with bounds placed on the variables from the SciPy (Jones, Oliphant, Peterson, et al., 2001{) benchmarking test suite. A Python implementation of the SHGO and TGO algorithms published under a MIT license can be found from https://bitbucket.org/upiamcompthermo/shgo/. / Dissertation (MEng)--University of Pretoria, 2017. / Chemical Engineering / MEng / Unrestricted

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mathematics, 1980 / Vita. / Bibliography: leaves 50-51. / by Jeanne Duflot. / Ph. D. / Ph. D. Massachusetts Institute of Technology, Department of Mathematics

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