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  • Thesis

  • Fixed-film anaerobic digestion: Mechanisms of pathogen reduction and impacts on virus adsorption to soil

    • Authors: Davis, Johnny A. (2006)

  • Anaerobic digesters have been used for treatment of various wastewaters. Systems are usually operated at mesophilic (35°C) temperatures and long hydraulic retention times (HRTs) (> 20 days). Pathogen reduction during anaerobic digestion is mainly correlated with operating temperature and HRT. Higher temperatures and longer HRTs result in increased rates of pathogen decimation. Previous studies show that a novel fixed-film anaerobic digester, operated at a low HRT (< 3 days) and ambient temperature (< 28°C) treating flushed dairy manure wastewater, achieved significant reductions of indicator and pathogenic bacteria. Thus, we sought to determine factors that contributed to indicator and pathogenic bacteria reduction during operation at a low HRT and ambient temperature. The presen...
  • Thesis

  • Functional roles of the human cytomegalovirus IE2 86 kDa protein in HCMV-infected cells

    • Authors: White, Elizabeth A. (2006)

  • The human cytomegalovirus (HCMV) IE2 86 kDa protein is an essential viral regulatory factor that has been shown in transient transfection and in vitro assays to transactivate early viral promoters and to interact with many viral and celular proteins. To understand the functions provided by this protein in the HCMV-infected cel, we have constructed and characterized a family of recombinant viruses containing changes to the IE2 gene and other parts of the HCMV major immediate early (IE) region. The study of these HCMV mutants has alowed us to confirm that several of the predicted functions of IE2 86 are relevant in the virus-infected cel and has identified new functions for the protein. Introducing smal deletions into the C-terminus of IE2 86 resulted in viruses that do not support ...
  • Thesis

  • Game-theoretic approaches for complex systems optimization

    • Authors: Cheng, Shih-Fen (2006)

  • A complex system is an artificial system that cannot be modeled analytically or optimized in an effective manner, usually because it possesses the following properties: (1) the system can only be modeled as a simulation, (2) the size of the problem is untenable, so that even if the system could be modeled analytically, it would be impractical to solve it exactly, (3) necessary information required for problem solving is distributed in nature. This thesis presents methods for modeling and optimizing systems with the above challenging properties. We first discuss the important modeling decision of whether to include stochasticity. By employing a real-world case study, we show that a standard numerical procedure can indeed help us make this decision. Next, we use the challenging probl...
  • Thesis

  • Identification of secondary and tertiary motifs in DNA sequences through naive Bayesian text classification

    • Authors: Villalobos, Rodney V. (2006)

  • Faced with uncertain data and an unpredictable return on computational tool investment, researchers are opting for laboratory studies over in silico (computer based) studies. This study addressed the lack of efficiency in identifying motifs (biologically significant amino sequences) in deoxyribonucleic acid (DNA) sequences via naive Bayesian text classification. DNA is a nucleic acid that carries genetic information in cells. A naive Bayesian text classifier is a machine-learning tool that uses automated means of determining metadata and has been used to identify e-mail worms, viruses, and spam. This quantitative study utilized a naive Bayesian text classification algorithm as the primary data collection technique. The data were analyzed using the independent t test and the chi-squa...
  • Thesis

  • Imidazoline receptors in insulin signaling and metabolic regulation

    • Authors: Sun, Zheng (2006)

  • The I1-imidazoline receptor is a novel target of drug development for hypertension and insulin resistance. This thesis focused on the molecular basis for I1-imidazoline binding and cell signaling and the mechanisms linking this signaling protein to regulation glucose metabolism. IRAS is a gene candidate for the I1-imidazoline receptor. To investigate the possibility that IRAS is the I1-imidazoline receptor, antisense oligo-nucleotides directly against the initiation site of IRAS sequence were designed and transfected into PC12 cells. Antisense transfection for 48h reduced specific imidazoline radioligand binding to plasma membrane fractions by about 50%, with parallel drops in IRAS protein expression as detected by Western blot. Furthermore, transfection with antisense caused functi...
  • Thesis

  • Interactions of N-alkyl-2-pyrrolidinone surfactants with DMPC bilayers

    • Authors: Kopkalli, Yasemin (2006)

  • There is great interest in identifying and characterizing new surfactants with predictable solubilization and reconstitution characteristics for use in membrane research. Among them, Triton X-100 and octyl glucoside (OG) are the best-studied surfactants. However, no physical data is available characterizing the interactions of two non-ionic pyrrolidinone surfactants, N-(2-ethylhexyl)-2-pyrrolidinone (C2,6P) and N-octyl-2-pyrrolidinone (C8P), with lipid bilayers. In the present study, their physical effects on dimyristoylphosphatidylcholine small unilamellar vesicles (DMPC SUVs) above the lipid phase transition temperature are described using surface tension, fluorescence spectroscopy, and isothermal titration calorimetry (ITC) methodologies. Surface tension methods show significant...
  • Thesis

  • Intercellular adhesion and pathfinding molecule T-cadherin in the development of the nervous system

    • Authors: VanSteenhouse, Harper C. (2006)

  • Adult animals exhibit an amazing array of behaviors controlled by an exquisitely complex nervous system. Axon pathfinding is an essential component to the development of a fully functioning nervous system. Axon pathfinding cues are molecules in the tissue surrounding growing axons that instruct directionality of axonal outgrowth leading to their proper trajectory from cell body to target. Cell adhesion molecules are one class of proteins that function as contact attractant or repellent pathfinding cues. This dissertation examines the contribution to axon pathfinding of T-cadherin, a member of the cadherin family of adhesion molecules. Both in vitro and in vivo, T-cadherin is found to be a contact repellant pathfinding cue. Not only is T-cadherin a cue in the environment, it signals...
  • Thesis

  • Laboratory pull-out testing study on soil nails in compacted completely decomposed granite fill

    • Authors: Su, Li-Jun (2006)

  • Soil nailing is a technique for stabilizing soil slopes and excavations by installing a large number of closely spaced passive inclusions into the in-situ soil mass. The soil nailing technique has been increasingly used worldwide since its origination in the early 1970's because of its technical and economical advantages. In Hong Kong, soil nailing has been commonly used to stabilize new cut and sub-standard existing slopes since the late 1980's. The interface shear strength between a soil nail and the surrounding soil is a key parameter for design and stability assessment of the soil nailing system. However, in current practice in Hong Kong, this parameter is generally assumed to be the same as the shear strength of the soil and verified by field pull-out tests in the construction ...
  • Thesis

  • Liquefaction mitigation in silty soils using stone columns supplemented with wick drains

    • Authors: Shenthan, Thevachandran (2006)

  • Vibro replacement stone columns are in use to mitigate liquefaction hazards in sandy soils for almost three decades. There are three mechanisms that help reduce liquefaction potential of a sandy soil improved using stone columns. During stone column installation sandy soils densify due to installation vibration. Further, the stiffness of the composite improved soil increases leading to a reduction in cyclic shear stress induced on the soil surrounding the stone columns during earthquakes. In addition, pore pressures generated in the soil during earthquakes are quickly dissipated through the highly permeable stone columns. These combined mechanisms reduce the liquefaction potential of the improved soil. Sandy soil sites improved using stone columns have performed well during earthqua...