http://hdl.handle.net/2374.OX/4080 2013-05-18T22:43:49Z http://hdl.handle.net/2374.OX/107961 Characterization of Genomic MidRange Inhomogeneity Bechtel, Jason M. Genomes encode many signals at multiple levels. They must therefore manifest inhomogeneity in their nucleotide composition. Inhomogeneity is identifiable from the shortrange where neighboring nucleotides influence the choice of base at a site, to the longrange, commonly known as isochores, where a particular base composition can span millions of nucleotides. This work explores the mostly overlooked phenomenon of genomic midrange inhomogeneity (MRI). MRI is defined as an interdependence between nucleotide choice and base composition over a distance of 301000 base pairs. Through the investigation of thousands of human genes, the results presented herein establish the existence of MRI throughout mammalian genomes, establish a link with strong local secondary structures and characterize the properties of MRI. A public computational resource has been created to support further study of genomic MRI. 2009-04-10T08:21:25Z http://hdl.handle.net/2374.OX/107960 Identification and Functional Characterization of Adipogenesis-related Genes Wu, Yu This dissertation is focused on identification and characterization of novel genes in adipogenesis from different angles. Wdnm1-like was identified as a novel 6.8 kDa adipokine secreted by adipocytes. Wdnm1-like is a differentiation-dependent gene in white and brown adipogenesis. TNFα treatment of 3T3-L1 adipocytes increases Wdnm1-like transcript level 2.4-fold and this can be attenuated by pretreatment with the p38 MAP kinase inhibitor SB203580. Ectopic overexpression of Wdnm1-like in HT1080 fibrosarcoma cells markedly increases active MMP-2 level. TSC-36 was identified as a preadipocyte gene that is highly expressed in 3T3-L1 preadipocytes and downregulated to nearly undetectable levels in 3T3-L1 adipocytes. TSC-36 is therefore a preadipokine secreted by preadipocytes. PPARγ and KLF15 downregulate TSC-36 promoter activities. TSC-36 transcript and protein levels are increased in 3T3-L1 adipocytes after TNFα treatment. In 3T3-L1 preadipocytes, TSC-36 expression is downregulated by 5-azacytidine. In a study to identify genes distinctly expressed in specific WAT depots and which may impart depot-dependent physiological functions, Boc transcript demonstrated a 12-fold enrichment in EP adipocytes. Expression of transcript for the Boc binding partner, Cdon was also assessed in adipose tissue and cell fractions thereof. We also identified a dramatic enrichment in SC adipocytes vs. EP adipocytes and in SC WAT vs. EP WAT for transcript(s) for the major urinary proteins (Mups). We established and characterized mBAP-9 which is derived from interscapular BAT of C57BL/6 mice as a new brown preadipocyte cell line. 10 adipocyte differentiation-dependent genes that are upregulated 4-fold or greater during mBAP-9 adipogenesis were identified. Two of these encoding putative hydrolases, Cmbl and Atabh were further studied. Tmem182 is a novel predicted transmembrane protein found to exhibit 45-fold upregulation in mBAP-9 adipogenesis. Further characterization of Tmem182 transcript expression revealed that Tmem182 transcript is markedly upregulated in various in vitro models of white adipogenesis. Moreover, Tmem182 transcript is also upregulated ~770-fold during the C2C12 cells myogenesis, which suggests Tmem182 may function in intracellular pathways important in both adipogenesis and myogenesis. In summary, this dissertation reveals novel genes distinctly expressed in adipocyte, preadipocyte or in specific WAT depots and also demonstrates mBAP-9 as a new brown preadipocyte cell line. This work will contribute to define a more complete picture of adipogenesis. 2009-04-10T08:21:12Z http://hdl.handle.net/2374.OX/107959 Design and Set Up of a System for Testing HEPA Filter Efficiency Smigielski, Ken Alan High efficiency particulate air (HEPA) filters by definition have an air particle removal efficiency of ≥ 99.97%. Installation of a HEPA filter, however, introduces variables that can compromise the filter’s efficiency. The main objective of this research project was to set up a “filter testing unit” to evaluate HEPA filter efficiency in relation to specific filter handling and installation variables. A closed system “HEPA filter testing unit” was assembled consisting of a fan, industrial damper, two ducts, and filter housing. The concentrations of a challenge aerosol up-stream and down-stream were used to calculate the filters capture efficiency. Eight filters were evaluated based on filter characteristics, particle capture efficiency, and consistency of proper installation. The results of this study indicated that any damage to the filter or flaw in the handling and installation process can compromise the performance of the HEPA filter significantly. 2009-04-10T08:21:00Z http://hdl.handle.net/2374.OX/107958 Development and Implementation of a GafChromic EBT In-Vivo Personal Dosimetry System Bugno, Jacob R. RadioChromic EBT film was used to create an in-vivo dosimetry system. General properties of chromic film were investigated. Statistical analysis of previous diode doses was used to create dose ranges encompassing 95% of clinical applications. Calibration curves were generated for 6 MV, 10 MV, 18 MV, 6 MeV, 9 MeV, and 12 MeV energies and fitted to polynomial equations of the third power. Calibration equations were used to create clinical dose calculation forms. Statistical analysis was performed to measure dose reproducibility and error. Skin doses and Dmax doses were measured and compared against accepted values. Dmax measurements were shown to have an average percent error of 4.47%. Skin measurements had average percent errors of 5.67% for 6 MV, 3.40% for 18 MV, 2.18% for 6 MeV, and 5.86% for 12 MeV. Film handling, storage, and scanning instructions were created to make the dosimetry system user friendly with reproducible outcomes. 2009-04-10T08:20:47Z