Thesis (Ph. D.)--University of Oregon, 2003. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 205-212). Also available for download via the World Wide Web; free to University of Oregon users.

Reverse transcription of HIV-1 genome involves multiple nucleic acids structural rearrangements chaperoned by nucleocapsid protein (NC). One such critical step is that the DNA transactivation response element (TAR) anneals to it complementary RNA region on the genome. It has been challenging to investigate mechanistic details on the annealing process because of the involvement of heterogeneous sets of protein/nucleic acid complexes. Here, we use single-molecule spectroscopy to study the NC induced melting of nucleic acid structure and the annealing activity of different regions along TAR structure. We find that NC induced secondary fluctuations are limited to the terminal stems, and the mechanism for the fluctuations is complex. By employing complementary targeted oligomers, we kinetically trap and investigate stable states of the putative nucleation complexes for the annealing process. This single molecule spectroscopy method directly probes kinetic reversibility and the chaperone role of NC at various stages along the reaction sequence. The new results lead to detailed understanding of NC chaperoned reverse-annealing and the partially annealed conformational sub-states. Argininamide, because of its specific binding to the loop regions of TAR, was studied on its specific inhibition to strand transfer. The loopmediated annealing is found to be more potentially inhibited than stem-mediated one.

The quality of machinery liquids plays a critical role in ensuring safe and cost-effective operation of engines. Especially in the aviation industry, there is a great need for real-time and online monitoring of the purity, lubricity and age of machinery fluids. In this work, two optical techniques, excitation-emission matrix spectroscopy (EEMS) and cavity ring-down spectroscopy (CRDS), are used for monitoring of degradation and contamination of aero-turbine lubricants and jet fuels using optical fiber probes. We implement EEMS combined with a modified fiber probe design to characterize lubricant quality through the characteristic fluorescence of antioxidant additives. Multi-way analysis procedures, such as parallel factor analysis, are applied to correlate spectral features to antioxidant concentration, oxidative stability, and lubricant age. The spectroscopic data are then correlated to commonly used, off-line parameters such as the induction time and the breakdown number. It is shown that the decrease in fluorescence intensities of antioxidants coincides with the decomposition of the oil base stock. The induction times of synthetic jet turbine oil degraded at 150ºC, 195ºC and 215ºC are found to be at about 10,000, 3,500 and 400 min respectively. Simple kinetic models are developed that are capable of describing antioxidant reactions as pseudo first-order processes. We also demonstrate that with fluorescence detection it is possible to determine the concentration of oil contamination in jet fuel from about 10 to 1000 ppmv. In addition, a fiber-loop cavity ring-down spectrometer has been developed to quantitatively identify oil contamination of jet fuel by measuring optical absorption in the UV region. CRDS is a very sensitive, path-enhanced absorption technique that may be used for trace-species measurements in gas and liquids. The absorption measurements on samples with small volumes are characterized by measuring the concentration of turbine oil in jet fuel from 100 000 ppmv to a limit of detection of 400 ppmv. In summary, the obtained results permit us to specify the life time of lubrication oil and to determine the contamination of jet fuel with turbine oil qualitatively and quantitatively. In a simple optical configuration the fiber-coupled EEM and CRD methods permit in situ sampling of the machinery fluids. / Thesis (Ph.D, Chemistry) -- Queen's University, 2014-04-25 13:24:37.761

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Wyoming, 2005. / Title from PDF title page (viewed on Feb. 22, 2008). Includes bibliographical references (p. 110-118).

Thesis (M.S.)--University of Missouri-Columbia, 2007. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on January 11, 2008) Includes bibliographical references.

Thesis (Ph.D.). / Written for the Dept. of Chemistry. Title from title page of PDF (viewed 2008/07/23). Includes bibliographical references.

Thesis (Ph. D.)--University of Nevada, Reno, 2008. / "May 2008." Includes bibliographical references. Online version available on the World Wide Web.

Thesis (Ph. D.)--University of Canterbury, 2007. / Typescript (photocopy). Includes bibliographical references (leaves 170-182). Also available via the World Wide Web.