Biochemistry, Biophysics, and Structural Biology Commons^™

Suppression Of Chronically Induced Breast Carcinogenesis And Role Of Mesenchymal Stem-Like Cells, Kusum Rathore

Doctoral Dissertations

Sporadic breast cancers are mainly attributable to long-term exposure to environmental factors, via a multi-year, multi-step, and multi-path process of tumorigenesis involving cumulative genetic and epigenetic alterations in the chronic carcinogenesis of breast cells from a non-cancerous stage to precancerous and cancerous stages. Epidemiologic and experimental studies have suggested that various dietary compounds like green tea and grape seed may be used as preventive agents for breast cancer control. In this research, I have developed a cellular model that mimics breast cell carcinogenesis chronically induced by cumulative exposures to low doses of environmental carcinogens. I used the chronic carcinogenesis model …

Development And Application Of Liquid Chromatography-Tandem Mass Spectrometry Methods To The Understanding Of Metabolism And Cell-Cell Signaling In Several Biological Systems, Jessica Renee Gooding

Doctoral Dissertations

Liquid chromatography tandem mass spectrometry has become a powerful tool for investigating biological systems. Herein we describe the development of both isotope dilution mass spectrometry methods and targeted metabolomics methods for the study of metabolic and cell-cell signaling applications.

A putative yeast enzyme was characterized by discovery metabolite profiling, kinetic flux profiling, transcriptomics and structural biology. These experiments demonstrated that the enzyme shb17 was a sedoheptulose bisphosphatase that provides a thermodynamically dedicated step towards riboneogenesis, leading to the redefinition of the canonical pentose phosphate pathway.

An extension of metabolic profiling and kinetic flux profiling methods was developed for a set …

Interaction Of A G Protein-Coupled Receptor (Ste2p) Of Saccharomyces Cerevisiae With Its Ligand And Its G-Protein Alpha Subunit, Li-Yin Huang

Doctoral Dissertations

The G protein-coupled receptor (GPCR) family is composed of hundreds of members and is expressed in eukaryotes. Each GPCR has seven transmembrane domains and is in charge of sensing changes from the environment, transducing signals, and activating a series of biological responses. The signal transduction pathway of the receptor starts from sensing outside signal and then activates G proteins. This signaling requires a tight control for activation without which impaired cellular function leads to pathology. We have used the pheromone alpha-factor receptor (Ste2p) of the yeast Saccharomyces cerevisiae as a model system to understand ligand binding, receptor activation, and G …

Getting Heavy: An Exploration Into The Effects Of D2o And High Hydrostatic Pressure On R67 Dihydrofolate Reductase, Mary Jane Timson

Masters Theses

Chromosomal dihydrofolate reductase (DHFR) enzymatically reduces dihydrofolate (DHF) to tetrahydrofolate (THF) using NADPH as a cofactor. R67 DHFR is an R-plasmid encoded enzyme that confers resistance to trimethoprim (TMP), an antibacterial drug. It shares no structural homology with TMP targeted, chromosomal DHFRs.

Previous osmolyte studies in our lab have indicated that DHF binding to R67 DHFR is accompanied by water uptake and NADPH binding is accompanied by water release. These data suggest that water plays a role in balancing the binding affinity. This may happen as R67 DHFR has a generalized binding surface and may need differential water effects to …

Nmr Structural Studies Of Endotoxin Receptor Cd14 In Complex With Gram-Negative And Gram-Positive Endotoxin, Seth Andrew Albright

Doctoral Dissertations

Endotoxin recognition by the innate immune receptor CD14 is a critical part of the innate immune system’s early detection and activation of the inflammatory response during microbial invasion. The differential recognition and high affinity binding of endotoxins from gram-negative and gram-positive bacteria is performed by the innate immune receptor CD14. Upon endotoxin binding, CD14 transfers the specific endotoxins to a Toll-like receptor signaling complex, which is responsible for initiating the intracellular signaling cascade. In the presence of overwhelming infection, the effects of CD14 lead to the over-activation of the inflammatory response, which results in the life threatening condition known as …

Examining The Roles Of Pstoc75 Potra Domains In Chloroplast Protein Import, Richard Franklin Simmerman

Masters Theses

During chloroplast formation via endosymbiosis most of the plastid genome was transferred to the host nuclear genome. Genomic and proteomic analysis suggests that >95% of the original plastid proteome is now encoded in the nucleus, and these now cytosolically fabricated proteins require a post-translational transport pathway back into the organelle. This process is not well understood, yet it has been shown to involve translocons at the outer and inner envelope of the chloroplast membranes (TOC & TIC). These translocons interact with a cleavable N-terminal extension of between 20 and 100 residues on chloroplast-bound precursor proteins known as the transit-peptide. Precursor …

Non-Thermal Plasma Inactivation Of Bacillus Amyloliquefaciens Spores, Yaohua Huang

Masters Theses

Bacterial spores have remarkable resistance to a variety of harsh conditions, causing spoilage in food industry and becoming the primary bacterial agent in biowarfare and bioterrorism. In this study, inactivation mechanisms of Bacillus amyloliquefaciens (BA) spores by non-thermal plasma (NTP) were investigated by using Fourier-transform infrared spectroscopy (FTIR) as a major tool to exam spores after NTP treatment. Chemometric techniques, such as multivariate classification models based on soft independent modeling of Class Analogy (SIMCA) and Principal Component Analysis (PCA), were employed to identify functional group changes in FTIR spectra. The IR absorbance bands correlated to dipicolinic acid (DPA) decreased after …

A Time-And-Space Parallelized Algorithm For The Cable Equation, Chuan Li

Doctoral Dissertations

Electrical propagation in excitable tissue, such as nerve fibers and heart muscle, is described by a nonlinear diffusion-reaction parabolic partial differential equation for the transmembrane voltage $V(x,t)$, known as the cable equation. This equation involves a highly nonlinear source term, representing the total ionic current across the membrane, governed by a Hodgkin-Huxley type ionic model, and requires the solution of a system of ordinary differential equations. Thus, the model consists of a PDE (in 1-, 2- or 3-dimensions) coupled to a system of ODEs, and it is very expensive to solve, especially in 2 and 3 dimensions.

In order to …

Protein Engineering For The Enhanced Photo-Production Of Hydrogen By Cyanobacterial Photosystem I, Ifeyinwa Jane Iwuchukwu

Doctoral Dissertations

Photosystem I (PSI) from plants, algae, and cyanobacteria can mediate H2 evolution in vivo and in vitro. A simple, self-platinization procedure that permits stable PSI-mediated H2 evolution in vitro has been developed. The H2 evolution capabilities of PSI from Thermosynechococcus elongatus have been characterized. This organism utilizes cytochrome c6 (cyt c6) as the e- donor to P700. Using a solution-based, self-organized platinization of the PSI nanoparticles, this study demonstrates a sodium ascorbate-cyt-PSI-Pt-H2 electron transport and proton reduction system that yields light-dependent H2. The system was thermostable with H2 evolution increasing up to 55°C. In addition, stability studies have shown the …

Microscopy Techniques For Investigating Interactions In Microbial Systems, Amanda Nicole Edwards

Doctoral Dissertations

Biological interactions occur on multiple length scales, ranging from molecular to population wide interactions. This work describes the study of two specific areas of biological interactions in microbial systems: intracellular protein-protein interactions and cell-to-cell interactions. The implementation of optical and atomic force microscopy and the methodologies developed during this study proved to be invaluable tools for investigating these systems.

Identifying and characterizing protein interactions are fundamental steps toward understanding complex cellular networks. We have developed a unique methodology which combines an imaging-based protein interaction assay with a fluorescence recovery after photobleaching technique (FRAP). Protein interactions are readily detected by co-localization …

Deciphering Substrate Promiscuity By Aminoglycoside Resistance Enzymes Via A Biophysical Characterization And Dynamics Of The Aminoglycoside Acetyltransferase-(3)-Iiib And The Aminoglycoside Phosphotransferase-(3′)-Iiia, Adrianne Lee Norris

Doctoral Dissertations

Aminoglycoside antibiotics are losing their bactericidal efficacy due to the spread of enzymes that catalyze a covalent modification to them. A common property of many of these aminoglycoside modifying enzymes (AGMEs) is the capacity to modify multiple diverse aminoglycosides thus conferring resistance to these drugs among several pathogenic bacterial species. To gain a better understanding of the protein-antibiotic interactions responsible for resistance and the promiscuous nature of AGMEs, a variety of biophysical techniques including nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC), steady state kinetics, intrinsic tryptophan fluorescence, and computational modeling are employed in this work. Results and discussion presented …

Chemical Tools To Characterize Membrane-Protein Binding Interactions Using Synthetic Lipid Probes, Meng Meng Rowland

Doctoral Dissertations

Signaling lipids such as diacylglycerol (DAG) and the phosphatidylinositol polyphosphates (PIP_ns) play crucial roles in numerous cellular pathways. However, characterization of their activities is hindered by the complexity of associated signaling pathways and of the membrane environment. To address this issue, we have developed lipid probes that are effective for characterizing biological events using different applications, including activity-based probing (PIP_ns and DAG) and microarray analysis (PIP_ns). The activity-based probes have been applied to label receptor targets in multiple cancer cell proteomes through photocrosslinking followed by click reactions. The probes were found to label several …

Adaptation And Stochasticity Of Natural Complex Systems, Roy David Dar

Doctoral Dissertations

The methods that fueled the microscale revolution (top-down design/fabrication, combined with application of forces large enough to overpower stochasticity) constitute an approach that will not scale down to nanoscale systems. In contrast, in nanotechnology, we strive to embrace nature’s quite different paradigms to create functional systems, such as self-assembly to create structures, exploiting stochasticity, rather than overwhelming it, in order to create deterministic, yet highly adaptable, behavior. Nature’s approach, through billions of years of evolutionary development, has achieved self-assembling, self-duplicating, self-healing, adaptive systems. Compared to microprocessors, nature’s approach has achieved eight orders of magnitude higher memory density and three orders …

Design And Synthesis Of Metabolically Stabilized Lipid Probes For The Investigation Of Protein–Lipid Binding Interactions, Ashdeep Kaur Rajpal

Masters Theses

Protein–lipid binding interactions play crucial roles in various physiological and pathological processes, making it very important to study these interactions at the molecular level. However, investigation of these interactions is complicated by several issues, including the inherent complexity of membranes as well as the diverse mechanisms by which proteins interact with the membrane surfaces. As a result, many of these interactions remain poorly characterized. Synthetic probes are useful tools employed for studying protein–lipid binding interactions. This thesis will detail the design and synthesis of metabolically stabilized analogues of various signaling lipids, which mimic the natural species and are not easily …

Pollen Myosins And The Specific Role Of Xij, Whitnee Michelle Ferari

Chancellor’s Honors Program Projects

No abstract provided.

The Effects Of Bisphenol A On Adipose Tissue Development, Metabolism, And Endocrine Function And The Role It May Play In The Development Of Obesity, Brantley Nelson Wyatt

Masters Theses

While diet and sedentary lifestyle remain important factors in the development of obesity, recent findings have shown the possible involvement of environmental obesogens, chemicals that can disrupt homeostatic energy balance and increase adiposity. Bisphenol A (BPA) is a compound used in the manufacturing of plastics as a hardening agent and is ubiquitous in the environment due to its widespread use. BPA has been shown to be an endocrine disruptor through its ability to mimic estrogen, which is now known to play important roles in adipose tissue growth and metabolism. In fact, a small but compelling number of studies have shown …

Understanding The Thermodynamics Of Enzyme-Antibiotic Interactions With Aminoglycoside Phosphotransferase-3’-Iiia, Michele K. Miller

Chancellor’s Honors Program Projects

No abstract provided.

Recombinant Production Of Vitronectin And Insights Into Its Structure And Role In Fibrinolysis, Cameron T. Landers

Chancellor’s Honors Program Projects

No abstract provided.

Neurogenetic Studies On The Role Of Diap1 In Neuronal Programmed Cell Death In Drosophila, Faith V. Creekmore, Ritika Sehgal, Jae H. Park

Chancellor’s Honors Program Projects

No abstract provided.

Spatial And Temporal Characterization Of Extracellular Proteases In The Scn, The Mammalian Circadian Clock, Alicia N. Mcclintock

Chancellor’s Honors Program Projects

No abstract provided.

Stress Effects On Myosin Mutant Root Length In Arabidopsis Thaliana, Brett A. George

Chancellor’s Honors Program Projects

No abstract provided.