Thesis (Ph. D.)--Illinois State University, 1991. / Title from title page screen, viewed January 5, 2006. Dissertation Committee: Radheshyam K. Jayaswal, Brian J. Wilkinson (co-chairs), Herman E. Brockman, Anthony J. Otsuka, Hou Tak Cheung. Includes bibliographical references (leaves 117-129) and abstract. Also available in print.

Thesis (M.S.)--Ball State University, 2009. / Title from PDF t.p. (viewed on Apr. 15, 2010). Includes bibliographical references (p. 53-65).

Thesis (Ph. D.)--Illinois State University, 1998. / Title from title page screen, viewed July 17, 2006. Dissertation Committee: Radheshyam K. Jayaswal (chair), Herman E. Brockman, Brian J. Wilkinson, Anthony J. Otsuka, Alan J. Katz. Includes bibliographical references and abstract. Also available in print.

Thesis (M.S.)--Ohio University, August, 2003. / Title from PDF t.p. Includes bibliographical references (leaves 114-117)

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (p. 257-268).

Thesis (M.S.)--University of Missouri-Columbia, 2004. / Typescript. Vita. Includes bibliographical references (leaves 63-65). Also available on the Internet.

Thesis (M.Sc.)--York University, 2005. Graduate Programme in Mathematics and Statistics. / Typescript. Includes bibliographical references (leaves 201-205). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://gateway.proquest.com/openurl?url%5Fver=Z39.88-2004&res%5Fdat=xri:pqdiss &rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:MR11838

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The complete nucleotide sequence of the region encoding the DHCDH function of the pDK1 lower operon was determined. DNA analysis has shown the presence of two open reading frames, one gene consisting of 777 nucleotides encoding a polypeptide of 27.85 kDa and another gene of 303 nucleotides encoding a polypeptide of 11.13 kDa. The results of enzymatic expression studies suggest that DHCDH activity is associated only with xy1L. However although the addition of xy1T cell-free extracts to xy1L cell-free extracts does not produce an increase in DHCDH activity, subclones carrying both xy1L and xy1T exhibit 300- 400% more DHCDH activity than subclones carrying only xy1L.

The study of cell physiology and functional genomics has seen an explosion of interest stemming from the development and commercialization of DNA sequencing technologies that allow upwards of several billion molecules to be probed simultaneously. However, of the three most abundant biomolecules in the cell—DNA, RNA, and protein—the dynamic and ever-changing quantities of RNA and proteins in a cell dictate much of the phenotypic variation observed from tissue-to-tissue, organ-to-organ, and cell-to-cell. Though much work has been done to measure RNA quantities in cells, and even to model their temporal dynamics from a single time-point measurement, the focus of this thesis will be on the development of methods to measure proteins within cells to draw conclusions about their physiological implications for the larger organism. In the outlined work, we couple protein measurements to DNA readouts that allow us to leverage commercial sequencing platforms to determine phenotypic outcomes through different methodologies. This thesis will proceed in two parts. Chapter 2 highlights the development of our method (Quantum Barcoding 2; QBC2) which uses DNA-barcoded antibodies to simultaneously quantify the expression of dozens of proteins on single cells. We demonstrate through head-to-head comparisons between our method and the traditional diagnostic gold standard of flow cytometry that we can accurately distinguish cell types and readily capture rare phenotypes that are otherwise too costly or labor intensive to probe using traditional methods. Chapter 3 discusses a deep mutational scanning (DMS) study conceived and developed during the COVID-19 pandemic, which reveals a detailed understanding of the 3CL protease of the SARS-CoV-2 virus, one of the critical components of the virus replication machinery. This technique is similarly applied to DNAJB6 to evaluate its ability to function as a chaperone protein. By leveraging comprehensive mutagenesis with methods of probing gene function en masse, we were able to evaluate the fitness effect of all amino acid substitutions within the 3CL protease and a large portion of DNAJB6, giving us valuable insight into their mechanisms of action. As a whole, this thesis presents a multi-faceted view of how new tools can be developed to measure protein expression and function, with the potential to generalize to other currently unexplored modalities.