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  • Thesis


  • Authors: de los Rios, Stephanie Snyder (2006)

  • Biochemical and structural studies of Escherichia coli Lrp Transcriptional regulation of gene expression is an essential component for the life of any organism. For uropathogenic Escherichia coli, expression of the pa, genes, generating the structural and regulatory components of pap pili, has been seen to be correlated with the ability of these bacteria to colonize and infect the urinary tract. Transcription at the pap operon is regulated by a large number of proteins including the global regulator Lrp (leucine-responsive regulatory protein) and the ap-specific regulator PapI. Transcription activation is sensitive to the methylation states of the two GATC sequences contained within the pap promoter. We have been interested in studying specifically how these two regulators, Lrp and...

  • Thesis


  • Authors: Bergseid, Jacqueline (2006)

  • The product of the retinoblastoma gene (pRb) is a tumor suppressor protein that regulates cellular proliferation, apoptosis and differentiation of numerous tissues in mice. It contains multiple peptide-binding pockets through which it interacts with a host of cellular and viral proteins. The LxCxE-binding pocket of pRb has been highly conserved between pRb proteins from evolutionary distant species; however, the in vivo function of this binding pocket is unknown. The crystal structure of pRB bound to LxCxE peptide was used to design a single point mutation, N757F, which specifically inactivates interactions between pRB and LxCxE-containing proteins without affecting the pRB-E2F interaction. The N750F mutation (analogous to N757F in the human RB) was introduced into the mouse Rb-1 lo...

  • Thesis


  • Authors: Long, Wen (2006)

  • New Boussinesq-type equations are derived for surface water wave propagation and currents in relatively shallow water regions. The new equations are fully nonlinear and accurate to O(µ2), with µ the indicator of wave dispersion. 1-D and 2-D computer models (FUNWAVE1D2.0 and FUNWAVE2D2.0) are developed based on the new Boussinesq equations for wave current modeling. The new Boussinesq models are based on a staggered grid system. The FUNWAVE2D2.0 model is also based on generalized curvilinear coordinate to fit complex nearshore geometries. Wave breaking introduced undertow currents are included in the dependent reference velocities automatically. The new equations retain vertical vorticity generated by wave breaking and bottom friction to the second order of dispersion. Wetting and dr...

  • Thesis


  • Authors: Sabalka, Lucas Adam (2006)

  • Let r be a graph. The (unlabelled) configuration space UCnF of n points on r is the space of n-element subsets of P. The n-strand braid group of r, denoted BnF, is the fundamental group of UCnF. We apply a discrete version of Morse theory to the spaces UCH', for any n and any r, and provide a clear description of the critical cells in every case. As a result, we can calculate a presentation for the braid group of any tree, for any number of strands. We also give a simple proof of a theorem due to Christ: the space UCH' strong deformation retracts onto a CW complex of dimension at most k, where k is the number of vertices in r of degree at least 3 (and k is thus independent of n). We proceed to describe a presentation for the two-strand graph braid group B2P for any graph r, called ...

  • Thesis


  • Authors: Xie, Zhimin (2006)

  • We categorize American English phonemes into several groups: vowel, semi-vowel, nasal, whisper, fricative/affricative, closure/stop, silence and some special phonemes (/q/ and /dx/), among which five main groups (vowel, semi-vowel, nasal, fricative, stop) are further examined. Thereafter, we construct several detectors based on acoustic features for each phoneme group and compare them with HMM-based systems by testing on continuous speech data, TIMIT, and some data in unfavorable environments, like TIMIT with additive noise, and NTIMIT. To detect vowels, a compact vowel detector based only on two acoustic features, periodicity and energy, is implemented. It performs with 86.8% accuracy and 22.4% total error rate. Even under some adverse environments, it still works stably. To detec...

  • Thesis


  • Authors: Huang, Jin (2006)

  • Acid-gas removal is of great importance in many environmental or energy-related processes. Compared to current commercial technologies, membrane-based CO2 and H2S capture has the advantages of low energy consumption, low weight and space requirement, simplicity of installation / operation, and high process flexibility. However, the large-scale application of the membrane separation technology is limited by the relatively low transport properties. In this study, CO2 (H2S)-selective polymeric membranes with high permeability and high selectivity have been studied based on the facilitated transport mechanism. The membrane showed facilitated effect for both CO2 and H2S. A CO2 permeability of above 2000 Barrers, a CO2/H2 selectivity of greater than 40, and a CO2/N2 selectivity of greate...

  • Thesis


  • Authors: Cheng, Xuekun (2006)

  • C60 is a new form of carbon with unique properties due to its small size. Since it has been predicted that C60 will be manufactured by tons, there is no doubt that it will ultimately find their way to the environment. Because of the insolubility of C60 in water, one might expect that it would not enter groundwater in great quantities. However, "nC60" (water-stable C60 aggregates) can be formed in water by exchange of solvents, or simply by stirring, indicating that C60 might be readily available in groundwater. Therefore it is necessary to investigate the transport of C60 particles and their interactions with other environmental contaminants. The adsorption and desorption of naphthalene and 1,2-dichlorobenzene, two common organic contaminants, with nC60 in water was investigated an...

  • Thesis


  • Authors: Tijani, Jimoh (2006)

  • Hydroformylation of olefins is a versatile method and well-established industrial process for the production of aldehydes using transition metal complexes as homogeneous catalysts. Currently, worldwide production of aldehydes exceeded seven million tons/year. Rhodium (I) complexes are the most active and selective catalysts for hydroformylation reaction. For any industrial application of homogeneously catalyzed reaction, a complete recycling of the generally expensive catalyst should be guaranteed. A thermomorphic system is characterized by solvent pairs that reversibly changes from biphasic to monophasic and vice versa as a function of temperature. We have applied the thermomorphic approach to rhodium-catalyzed hydroformylation of higher olefins (C>6). The effect of CO/H2 pressure,...

  • Thesis


  • Authors: Schoenherr, Regine M. (2006)

  • Capillary electrophoresis-mass spectrometry (CE-MS) provides a powerful system that combines the speed and automation capabilities of CE with the detection and identification capabilities of MS. Integrating on-line enzymatic microreactor digestion with a CE-MS system reduces sample handling and allows fast digestions of small protein samples. In this thesis work, an on-line CE-microreactor-CE-MS-MS instrument is developed that can separate proteins in a first dimension, digest them inside a pepsin-immobilized microreactor, separate peptides in a second dimension, and detect the peptides with MS. The development begins from the MS end by coupling capillary free zone electrophoresis (CZE) to a linear ion trap mass spectrometer with a sheath flow interface, and works its way forward t...

  • Thesis


  • Authors: Mates-Muchin, Jonathan Todd (2006)

  • The impact of invasive insects threatens communities and ecosystems. In northeastern forests, the hemlock woolly adelgid (HWA; Adelgis tsugae Annand.) has influenced the decline of the eastern hemlock (Tsuga canadensis L. Can.). However, the effect of the HWA on community and ecosystem change has been understudied, especially across varying levels of hemlock mortality and dominance. To address community and ecosystem change, I measured the effects of hemlock mortality and dominance on forest community composition, net primary production (NPP), net N mineralization, and net N nitrification. Twenty-seven plots were established in three regional forests. Plots were categorized into hemlock-dominated, mixed, and hardwood-dominated stand-types based on hemlock relative importance. Nested...