Browsing by Subject "Molecular"
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Item Growth of niobium oxide thin films by molecular beam epitaxy(2014-12) Hadamek, Tobias; Demkov, Alexander A.For this thesis niobium oxides (NbO [subscript x]) with the goal of obtaining phase pure epitaxial NbO₂ were grown under variable conditions by molecular beam epitaxy (MBE) on different substrates, mostly (111) oriented strontium titanate. The films were characterized by X-ray diffraction (XRD) and reflection high-energy electron diffraction (RHEED) and from that their epitaxial relationship to the substrate was determined. With X-ray photoelectron spectroscopy (XPS) the oxidation states and stoichiometry of the films were determined. Asymmetric NbO₂ Nb 3d core-level spectra are clearly seen for the first time in XPS. Additionally, the film thickness was measured by X-ray reflectivity (XRR). Judging from the XPS spectra and diffraction data the goal to grow epitaxial NbO₂ of high phase-purity was achieved.Item Immunosuppressive effects of PEG-fusion in peripheral nerve allografts(2021-03-08) Smith, Tyler Aaron; Bittner, George D.; Tucker, Haley O.; Sakiyama-Elbert, Shelly E.; Zakon, Harold; Poenie, MartinSurgical repair of ablation-type peripheral nerve injuries by using peripheral nerve allografts (PNAs) has been hindered for decades due to slow and ineffective axon regeneration from proximal nerve ends as well as immunological rejection of PNAs. We have developed a polyethylene glycol (PEG)-fusion repair protocol for sciatic PNAs in rats that results in maintenance of myelinated axons that do not degenerate, neuromuscular junction innervation, and significantly improved behavioral recovery, as compared to current nerve repair methods. These phenotypes are maintained for weeks postoperatively without using tissue-matching, decellularization, or immunosuppressive drugs. That is, PEG-fused PNAs are functionally tolerated by the host immune system. This dissertation presents work performed to characterize and investigate mechanisms underlying immunological responses to PNAs treated with PEG-fusion with the aim of understanding how and why PEG-fused allografts are not rejected by the host immune system in rat sciatic nerve injury models. Chapter 1 provides a review of the clinical significance of peripheral nerve injury, including: Biological processes of axonal degeneration and regeneration, current methods of nerve repair, immunological rejection of PNAs, concepts underlying PEG-fusion repair and current experimental results of PEG-fusion in rat PNAs, as well as the hypotheses and aims explored. Chapter 2 characterizes innate and adaptive immune responses to PEG-fused PNAs using primarily immunohistochemistry, electron microscopy, and quantitative reverse transcription PCR (RT-qPCR). Our results suggest that PEG-fused PNAs achieve immunotolerance via attenuated innate and adaptive immune responses. Chapter 3 examines via RNA sequencing the coding transcriptome of PEG-fused PNAs to determine which biological processes, protein families, pathways, and protein-protein interaction networks differentiate PEG-fused PNAs from negative control PNAs not treated with PEG with the goal of identifying potential mechanisms underlying immunotolerance. This work provides a critical molecular foundation for future studies investigating PEG-fusion-mediated immunosuppression in PNAs. Chapter 4 investigates whether treatment of PNAs with PEG alone without axonal fusion induces similar immunosuppressive effects. Our results suggest that PEG treatment alone does not prevent Wallerian degeneration or attenuation of innate and adaptive immune responses. Chapter 5 provides a summary of the dissertation work and describes future directions for research.Item Systematics and evolution of extinct and extant Pan-Alcidae (Aves, Charadriiformes) : combined phylogenetic analyses, divergence estimation, and paleoclimatic interactions(2011-08) Smith, Neil Adam; Clarke, Julia A.; Bell, Christopher J.; Cannatella, David C.; Rowe, Timothy B.; Sprinkle, JamesAlthough the ecological interactions and ethology of the wing-propelled diving seabirds known as the Alcidae (Aves, Charadriiformes) have been intensively studied, systematic studies of the clade have been overwhelmingly limited to extant taxa. Pan-Alcidae have the richest fossil record among Charadriiformes, with specimens representing more than 35 million years of evolutionary history. Morphometric and apomorphy-based taxonomic revision of previously named extinct pan-alcids along with description of new species of extinct pan-alcids facilitated refined estimates of species richness. Combined phylogenetic analyses of morphological and molecular sequence data including pan-alcid fossils elucidated the poorly understood evolutionary history of the clade. Divergence estimation analysis for Charadriiformes placed previously hypothesized episodes of pan-alcid radiation and extinction in context with proposed paleoclimatic drivers of alcid evolution.