Chemistry Theses and Dissertations

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https://hdl.handle.net/1794/2046

This collection contains some of the theses and dissertations produced by students in the University of Oregon Chemistry Graduate Program. Paper copies of these and other dissertations and theses are available through the UO Libraries.

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Browsing Chemistry Theses and Dissertations by Author "Bailey, Thomas"

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    Chromatin Regulation: How Nucleosomes Find their Positions and the Role of Chromatin Binding Proteins in Cellular Quiescence
    (University of Oregon, 2023-03-24) Bailey, Thomas; Selker, Eric
    Chromatin is made up of an organism’s DNA and DNA binding proteins inside of the nucleus. Nucleosomes are the fundamental unit of chromatin, consisting of a 147 base pair DNA sequence and a protein octamer comprised of 8 histone proteins, two copies of histone H2A, H2B, H3, and H4. Nucleosomes are used to regulate gene expression in both the positioning of the nucleosome along DNA, or the post-translational histone modifications. In the first chapter, we will demonstrate that the chromatin binding protein, Tup1 is essential for nucleosome positioning and H3K23 deacetylation, which is required for entry into cellular quiescence. In the next chapter, we will address how the chromatin remodeler complex, Isw2, precisely positions nucleosomes through direct interactions with transcription factors. In the next chapter, we present an optimized protocol for measuring nucleosome positioning. Finally, we will end on some preliminary data and discussion on the next steps in researching Tup1 and Isw2.This dissertation contains previously published co-authored material.
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    Development of Tools for Understanding Biological Sulfur Chemistry
    (University of Oregon, 2016-10-27) Bailey, Thomas; Pluth, Michael
    Hydrogen sulfide (H2S) is an important biomolecule for its role in mediating redox homeostasis and signaling biological processes. The study of biological sulfide is currently impeded by a lack of tools available that adequately address the questions currently facing the field. The most pressing of these questions are: how does H2S signal biological processes. To produce tools for studying H2S, chemiluminescent scaffolds were designed to study both H2S producing enzymes and directly measure free H2S. Additionally, small molecule organic persulfides were synthesized and characterized in order to study the properties and reactivity of H2S signaling species. By creating methods to directly measure biological H2S and creating model systems to investigate the active signaling species, the biological reactivity of H2S can be better understood. The luminescent methods for detecting H2S were developed in order to avoid photodecomposition inherent with fluorescent methods while still providing a spectroscopic readout for performing measurements in cells. D-cysteine concentrations can be measured using luciferin bioluminescence, and utilized to back out the H2S producing activity of DAO. Free H2S was measured using luminol derived chemiluminescence. The luminol scaffolds were studied in depth to determine what makes an H2S probe selective for H2S in order to inform the design of future H2S probes. Sulfide signaling processes were investigated using organic persulfide model systems. We found that under reducing conditions persulfides liberate free H2S, and that under basic conditions they decompose. The decomposition pathway is governed by substitution at the -carbon, which dictates the steric accessibility of the inner sulfur atom to act as an electrophile. Persulifdes do not react with acids, and are easily tagged by electrophiles to form disulfides. Persulfides are sufficiently reducing to generate NO from nitrite, facilitating cross-talk between multiple signaling species. This cross talk is mediated by formation of perthionitrite, which may function as an independent signaling species.