Biochemistry, Biophysics, and Structural Biology Commons^™

Lipid Dependence In Ras-Driven Tumors, Darin Salloum

Dissertations, Theses, and Capstone Projects

Over past decade, metabolic alterations in cancer cells have received a substantial amount of interest. It had been established that cancer cells undergo a significant amount of metabolic alterations, and some of these alterations are similar to those in normal highly proliferative cells. However, it is becoming more apparent that many of the metabolic alterations are specific to particular oncogenic signaling pathways. Although altered metabolic machinery makes cancer cells more efficient at promoting growth when nutrients are supplied at the sufficient amounts, the dependency of cancer cells on particular metabolic reprogramming deems cancer cells susceptible to disruptions within metabolic network. …

Metabolic Checkpoints In Cancer Cell Cycle, Mahesh Saqcena

Dissertations, Theses, and Capstone Projects

Growth factors (GFs) as well as nutrient sufficiency regulate cell division in metazoans. The vast majority of mutations that contribute to cancer are in genes that regulate progression through the G1 phase of the cell cycle. A key regulatory site in G1 is the growth factor-dependent Restriction Point (R), where cells get permissive signals to divide. In the absence of GF instructions, cells enter the quiescent G0 state. Despite fundamental differences between GF signaling and nutrient sensing, they both have been confusingly referred to as R and therefore by definition considered to be a singular event in G1. Autonomy from …

An Experimental Investigation Into The Mechanisms Of Bacterial Evolution, Zhenmao Wan

Dissertations, Theses, and Capstone Projects

This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium Escherichia coli through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in E. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation …

Identification And Characterization Of Protein Phopshatases Regulating The Sma/Mab Pathway In C. Elegans, Sheng Xiong

Dissertations, Theses, and Capstone Projects

TGF-beta signaling is a conserved signaling pathway among eukaryotes, which controls various normal cellular responses from cell proliferation to cell death. The mutations in its components are found in developmental disorders and cancer. Therefore, this signaling pathway is extensively investigated so that new therapeutic targets could be discovered and novel drugs could be developed. Previous studies suggested the involvement of phosphatases in regulation of TGF-beta signaling, but these studies were performed in cell culture rather than intact organisms. C. elegans is a tractable organism in which to study signaling in vivo. In C. elegans, growth is controled by a conserved …

Boronic Acids As Penicillinase Inhibitors, Juan F. Barquero

Dissertations, Theses, and Capstone Projects

β-lactamases are enzymes produced by bacteria resistant to antibiotics. A common feature on beta lactam antibiotics is the beta-lactam ring. β-lactamases hydrolyze the β-lactam ring leaving the antibiotic inoperative. The advent of bacteria that are resistant to β-lactams has impelled researchers to find inhibitors for β-lactamases that mimic the lactam ring but do not get hydrolyzed. One group of these new antibiotics is the aryl boronic acids. The main reason the boronic acids have been chosen as potential drugs is their lack of toxicity and their easy excretion in the urine. One of the most important structural features of these …

The Role Of Mdm2 In Estrogen-Mediated Breast Cancer Cell Proliferation, Angelika Brekman

Dissertations, Theses, and Capstone Projects

Estrogen signaling is important in breast cancer development and progression. Mdm2, a negative regulator of the p53 tumor suppressor, is often over-expressed in estrogen receptor positive breast cancers. To study the role of Mdm2 in the estrogen-mediated breast cancer cell proliferation, we examined the effect of estrogen on the p53-Mdm2 pathway in estrogen receptor positive and p53 wild-type MCF-7 breast cancer cells. Estrogen-mediated increase in cell proliferation correlated with increased Mdm2, but no concomitant decrease in the p53 protein level. Blocking Mdm2 expression with inducible shRNA inhibited estrogen-mediated cell proliferation and colony formation in soft agar. Mdm2 knockdown in the …

Involvement Of Inflammation In Tau Pathology And Mechanisms That Drive Neurodegeneration In Alzheimer's Disease, Lisette T. Arnaud

Dissertations, Theses, and Capstone Projects

Two of the hallmarks of neurodegenerative disorders, such as Alzheimer's disease (AD), are (1) the appearance of proteinaceous deposits in inclusion bodies containing aggregates of ubiquitinated proteins and (2) activated microglia and astrocytes surrounding the diseased neurons. In Alzheimer's disease, the intracellular inclusion bodies are known as neurofibrilary tangles (NFT). The mechanisms leading to inclusion body formation and their role in the progression of neurodegeneration are still largely unknown.

Many of the proteins that accumulate in inclusion bodies depend on the ubiquitin/proteasome pathway (UPP) for their degradation. This pathway is responsible for the bulk (∼80%) of intracellular protein degradation. Because …

Pldb, A Putative Phospholipase D Homologue, Mediates Quorum Sensing In Dictyostelium Discoideum Development, Yi Chen

Dissertations, Theses, and Capstone Projects

Quorum sensing, the ability to measure the local cell density, is required for animal cells to achieve proper cell growth, differentiation and development. However, because of the genetic intractability of mammalian cells, we study quorum sensing in the genetically pliable unicellular eukaryote Dictyostelium discoideum. D. discoideum cells live as individual cells under vegetative conditions. Starvation sets off development to a multicellular organism. But cells won't develop unless enough cells are under starvation conditions. Approximately 10⁵ cells are needed to form a fruiting body, the final stage of the development. When starved, cells are able to calculate the concentration …

I. Comparison Of Translesion Bypass Of Guanine–N2 Monoadducts Of Mitomycin C And Guanine-N7 Monoadducts Of 2,7-Diaminomitosene By T7 Exo-, Klenow Exo-, Eta And Klenow Exo+ Dna Polymerases. Ii. Structure-Based Design, Synthesis, Structure-Conformation And Structure-Activity Relationships Studies Of D-Phe-Pro-D-Arg-P1’-Conh2 Tetrapeptides With Inhibitory Activity For Thrombin., Cristina C. Clement

Dissertations, Theses, and Capstone Projects

The guanine (G)-N² DNA monoadduct of mitomycin C (MC), a cytotoxic anticancer drug, inhibits translesion bypass by DNA polymerases. 2,7-Diaminomitosene (2,7-DAM) is the major metabolite of MC in tumor cells, generated by the reduction of MC. 2,7-DAM alkylates DNA in the cell in situ, forming an adduct at the N7 position of 2'-deoxyguanosine (2,7-DAM-dG) and is noncytotoxic. In part I of this study we tested a potential correlation between the lack of cytotoxicity of 2,7-DAM and the relative ease of bypass of this adduct as compared with the MC adduct. 24-mer and 27-mer templates, adducted at a single …

Aspects Of Mitochondrial Oxidative Metabolism, Leslie Kushner

Dissertations, Theses, and Capstone Projects

The effects of metabolic intermediates and coenzymes on the activities of fatty acyl-CoA synthetase and carnitine palmitoyltransferase (CPT) in rat heart mitochondria were studied. ADP and palmitoyl-l-carnitine were weak inhibitors of fatty acyl-CoA synthetase. CPT A was inhibited 59.3% by 100 (mu)M succinyl-CoA. However, succinate thiokinase activity in rat heart cytosol was too low to maintain a succinyl-CoA concentration sufficient to affect the activity of CPT A. There was no indication that fatty acid oxidation in rat heart mitochondria is controlled via the regulation of either CPT A or fatty acyl-CoA synthetase.

The dependence of the oxidation of unsaturated fatty …