Biochemistry, Biophysics, and Structural Biology Commons^™

Development Of Peripheral Innervation In The Frog Xenopus Laevis, Mitali A. Gandhi

Theses and Dissertations

The skin in Xenopus laevis is innervated by two different sets of mechanosensory neurons at different times during development. Rohon Beard (RB) neurons start differentiating during gastrulation, innervate the embryonic skin and mediate sensory function during hatching. Dorsal Root Ganglion (DRG) neurons start differentiating after neural crest migration, innervate adult epidermal targets and mediate mechanosensory function during larval and adult stages and eventually replace RB neurons. The change in sensory neurons occurs during the transformation of skin, sensory structures, and behavior from their embryonic to their larval forms. We hypothesized that developmental changes in either the sensory end organs or …

Characterizing Populations Of Non-Coding Rnas In Karenia Brevis At Different Times Of The Diel Cycle, Scott Boyd Anglin

Master's Theses

Karenia brevis is a mixotrophic, marine dinoflagellate found in the Gulf of Mexico that generates periodic, if not annual, harmful algal blooms (also known as “red tides”) in certain coastal areas. In an effort to better understand the biology of this organism, a functional genomics project has been initiated. As part of that project, it has been determined that a significant number of natural antisense transcripts (NATs) as well as double-stranded RNA (dsRNA) molecules exist within the transcriptome of K. brevis. I hypothesize that the non-coding NATs, similar to microRNAs (miRNAs) in other organisms play a role in regulating …

Testing Predicted Specificity Determinants In The Dihydrofolate Reductase Enzyme Family, Seema J. Patel

Theses, Dissertations and Culminating Projects

Dihydrofolate Reductase (DHFR) is an essential enzyme for most organisms, ranging from bacteria to humans. DHFR has essential functions in DNA biosynthesis and cell replication; as a result, cell growth can be inhibited by the inhibition of DHFR. Evaluating the use of well-known DHFR inhibitors is becoming essential in treating infections in the developing world as DHFR is a known target of antibacterial and antiparasitic drugs. Understanding determinants of DHFR inhibitor specificity in terms of amino acid sequence and structure will allow repurposing or designing of new compounds that selectively target DHFR from the pathogenic organism of interest over the …

Mechanism Of The Hydroxylation Reactions Catalyzed By 4-Hydroxyphenylpyruvate Dioxygenase And Hydroxymandelate Synthase, Dhara D. Shah

Theses and Dissertations

4-Hydroxyphenylpyruvate dioxygenase (HPPD) and Hydroxymandelate synthase (HMS) carry out highly similar complex dioxygenation reactions using the substrates, 4-hydroxyphenylpyruvate (HPP) and dioxygen. HPPD catalyzes decarboxylation, aromatic hydroxylation and substituent migration (NIH shift) in a single catalytic cycle to form homogentisate (HG), whereas HMS catalyzes decarboxylation and aliphatic hydroxylation to give hydroxymandelate (HMA). Wild-type HPPD, HPPD variants and HMS variants produce both native and non-native products. Based on this observation, we have employed a product analysis method with HPP deuterium substitutions (ring or benzylic) that reveal kinetic isotope effects from intermediate partitioning ratios. In this study we offer evidence for the 1) …

Angiomotin Is A Novel Cadherin-11 Interacting Protein That Mediates Migration In Prostate Cancer Cells, Angelica Ortiz

Dissertations & Theses (Open Access)

Prostate cancer (PCa), the second leading cause of cancer-related deaths among men in the United States, has the proclivity to metastasize to bone resulting in sclerotic lesions. These cancer induced bone growths cause bone pain and fractures. Therefore, understanding the molecular mechanisms contributing to PCa bone metastasis is required in order to find better prognostic tools and suitable targets for metastasis treatment and/ or prevention. Previous work in our laboratory showed increased expression of cadherin-11 (Cad11), a mesenchymal cadherin, during PCa progression. Furthermore, Cad11 expression endows PCa cells with increased migratory potential and metastasis to bone. Deletion of the Cad11 …

Mapping The Human Vasculature By In Vivo Phage Display, Julianna Bronk

Dissertations & Theses (Open Access)

In vivo phage display screenings by intravenous injection of a random phage-displayed peptide library allow for the selection of peptides that localize to specific vascular beds. At the University of Texas MD Anderson Cancer Center, we have had the opportunity to perform phage display screenings in cancer patients in order to select for cancer specific targets directly in humans. These targets serve to define biochemical diversity of endothelial cell surfaces and can be validated and explored towards the design of vascular-targeted pharmacology. In the most recent patient screen, samples were recovered from hepatocellular carcinoma (HCC) as well as 26 additional …

Egfr Modulates Microrna Maturation In Response To Hypoxia Through Phosphorylation Of Argonaute2, Jia Shen

Dissertations & Theses (Open Access)

MicroRNAs (miRNAs) are generated by two-step processing to yield small RNAs that negatively regulate target gene expression at posttranscriptional level. Deregulation of miRNAs has been linked to diverse pathological processes, including cancer. Recent studies have also implicated miRNAs in regulatory roles to cope with a spectrum of stresses, such as hypoxia, which is frequently encountered in the poorly angiogenic core of a solid tumor. However, the upstream regulators of miRNA biogenesis machineries remain obscure, raising the question of how tumor cells efficiently coordinate and impose specificity on miRNA expression and function in response to stresses. Here, we show that EGFR, …

Pi3k- And Mtor-Dependent Mechanisms Of Lapatinib Resistance And Resulting Therapeutic Opportunities, Samuel Brady

Dissertations & Theses (Open Access)

Breast cancers with HER2 amplification represent 20-25% of breast cancer cases and are frequently responsive to the HER2 kinase inhibitor lapatinib, but generally for only short duration. We aimed to understand how breast cancers with HER2 amplification become resistant to lapatinib, in order to identify potential therapies that can overcome lapatinib resistance. To establish lapatinib resistance models we treated three HER2+ breast cancer cell lines with lapatinib for several months until they became lapatinib-resistant. We then compared lapatinib-sensitive (parental) cells with their lapatinib-resistant (LapR) counterparts to identify changes conferring lapatinib resistance. We found that activation of PI3K, specifically the p110α …

Energy Stress Causes Chaperones To Assemble Into Cytoplasmic Complexes, Kimberly J. Cope

Dissertations & Theses (Open Access)

The majority of proteins require molecular chaperones to assist their folding into tertiary and quaternary structures. Certain stresses can compromise the weak hydrophobic forces responsible for these structures and lead to protein unfolding, misfolding, and aggregation. Aggregates of proteins are hallmarks of devastating diseases such as Alzheimer’s, Parkinson’s, and Huntington’s diseases. Fortunately, bacteria, plants, and fungi have a potent disaggregase, named Hsp104 in Saccharomyces cerevisiae. Recently, heat-induced aggregates, termed Q-bodies, were found to contain three molecular chaperones: Hsp70, Hsp104, and Hsp42. Their coalescence from small puncta into larger inclusions required Hsp104. During glucose deprivation, a stress that isn’t known to …

Cloning And Expression For The Future Characterization Of The Air2 Protein, Emily Sue Frampton

Undergraduate Honors Capstone Projects

Air2 is a eukaryotic protein involved in multiple biological processes including protein-protein interactions as well as RNA binding. Air2 plays a critical role in RNA quality control and also helps regulate post-translational modification of various proteins. Although previous studies have revealed information regarding Air2's roles within a cell, the molecular and structural basis for Air2 function is unclear. Using a codon-optimized version of the Air2 gene, various constructs were created that improved the expression and solubility of Air2. Additionally a co-expression complex of Air2 with a PRMTI mutant, K13S, was made to obtain the Air2 protein with a native binding …

Synthesis And Characterization Of Novel Platinum(Ii) And Platinum(Iv) Complexes Containing 4,4′--Disubstituted--2,2′--Bipyridine Ligands For The Treatment Of Cancer, Van Vo

UNLV Theses, Dissertations, Professional Papers, and Capstones

Three series of platinum(II) and platinum(IV) complexes containing 4,4′-disubstituted-2,2′-bipyridine ligands have been synthesized and characterized by 1H NMR, 13C NMR spectroscopy, elemental analysis, mass spectroscopy, and differential scanning calorimetry measurements. The MTS cell proliferation assay was used to examine the in vitro anti-proliferative activities of these complexes in various human breast, lung, and prostate cancer cells. The cell's response to the complexes varies between different cell lines; however, the low EC₅₀ values determined from the MTS data indicate that several of the complexes are much more potent than cisplatin.

Flow cytometric analysis of selected compounds revealed induction of apoptosis …

Single Tube, Multiple Enzyme Reaction For Detection Of Uv And Oxidative Damage In Forensic Physiological Stains, Nicholas J. Eurek

Department of Biochemistry: Dissertations, Theses, and Student Research

For decades, the use of DNA as a biological tool has revolutionized forensic investigations. The primary use of this genetic evidence is for identification of a victim or suspect through short tandem repeat (STR) profiling. However, the usefulness of this evidence can be compromised through inhibition of PCR, damage to the DNA, or low copy number. Here, we investigate damage induced to DNA by environmental factors. UV light is known to damage DNA by the formation of cyclobutane pyrimidine dimers, 6-4 photoproducts, and strand breaks. These lesions can stall polymerase action or misincorporate bases during extension. Oxidative damage is also …

Synthesis Of 4'-Ester Resveratrol Analogues, Chromium Trioxide Oxidation Of Terpenes, And Synthesis Of Mimics Of (-)-Englerin A, Mark Jeffrey Acerson

Theses and Dissertations

4’ -ester analogues of resveratrol were synthesized using reaction conditions developed to produce mono-ester products in the presence of two other unprotected phenols. Basic conditions were employed to deprotonate the most acidic 4’ phenol followed by addition of anhydrides or acid chlorides to give the ester product. The reaction favored 4’-ester formation in polar aprotic solvents with DMSO being the optimal solvent.

(—)-Englerin A is a guaiane-type sesquiterpene containing two ester side chains. Mimics of (—)-englerin A were proposed that retained the ester side chains while replacing the non-polar core with less complicated structures. These proposed mimic cores would maintain …

Biophysical And Computational Investigations Into G-Quadruplex Structural Polymorphism And Interaction With Small Molecules., Huy Tuan Le

Electronic Theses and Dissertations

In the cell, guanine-rich nucleic acids can self-assemble into unique four stranded tertiary structures known as G-quadruplexes. G-quadruplex formation in the telomere leads inhibits telomerase, an enzyme activated in cancer cells to maintain the telomere and allowing for cancer cells to achieve immortality. G-quadruplex formation in the promoters and 5’-untranslated regions regulates the expression of many oncogenes. Furthermore, G-quadruplex formation during cellular replication promotes genomic instability, a characteristic which enables tumor development. Because of their implication in cancer, G-quadruplex structures have emerged as attractive drug targets for anti-tumor therapeutics. In the current dissertation work, we present three experimental approaches to …

Genetic And Mechanistic Analysis Of Rat Mammary Cancer Susceptibility., Jennifer Sanders

Electronic Theses and Dissertations

Breast cancer is a complex disease, which is influenced by genetic, epigenetic and environmental components. Genetic susceptibility to breast cancer is made up of high, moderate and low penetrance alleles. High and moderate penetrance alleles are rare and constitute only a small percentage of the genetic susceptibility. Most variation in genetic susceptibility is controlled by low- penetrance, common polymorphisms. Comparative genetics uses model organisms to study human disease. Rat strains exhibit different susceptibility phenotypes to chemical induced carcinogenesis. The Wistar-Furth (WF) rat strain is susceptible to chemically induced mammary carcinogenesis, while the Wistar-Kyoto (WKy) and Copenhagen (COP) rat strains are …

Antiviral Responses In Mouse Embryonic Stem Cells: Differential Development Of Cellular Mechanisms In Type I Interferon Production And Response, Ruoxing Wang

Dissertations

Embryonic stem cells (ESCs) have been recognized as a promising cell source for regenerative medicine. Intensive research over the past decade has led to the possibility that ESC-derived cells will be used for the treatment of human diseases. However, increasing evidence indicates that ESC-derived cells generated by the current differentiation methods are not fully functional. It is recently recognized that ESC-derived cells lack innate immunity to a wide range of infectious agents and inflammatory cytokines. When used in patients, ESC-derived cells would be placed in wounded sites that are exposed to various pathogens and inflammatory cytokines; therefore, their viability and …

Characterization Of A Recently Purified Thermophilic Dnase From A Novel Thermophilic Fungus, Kyle Landry, Robert Levin

Kyle S Landry

The Demethylating Agent 5-Aza Reduces The Growth, Invasiveness, And Clonogenicity Of Uveal And Cutaneous Melanoma, F. Rajaii, L. Asnaghi, Raymond Enke, S. Merbs, J. Handa, C. Eberhart

Ray Enke Ph.D.

No abstract provided.

Purification And Characterization Of Sweet Potato (Ipomoea Batatas) Peroxidase, Mamouna Diao, Brice N’Cho Ayékoué, Crépin I. Dibala, Soumaïla Dabonné, Mamoudou H. Dicko Prof.

Pr. Mamoudou H. DICKO, PhD

Peroxidase (POX), a biotechnologically important enzyme was purified from bulb of Ipomoea batatas and characterized for use in the bioconversion of phenolic compounds from industrial wastewater. Purified peroxidase (POXp) was obtained using the gel-filtration chromatography and anion exchange chromatography. A final yield of 18 % was obtained with 20.5 as purification fold. Electrophoresis on SDS-PAGE and native-PAGE showed that POXp is monomeric with a molecular weight of 44 kDa. The optimum pH and optimum temperature were respectively 6.0 and 45 ° C. All enzyme activity was retained for 2 hours at pH values between 4.0 to 9.0. While the enzyme …

High-Performance Polymer Monoliths For Capillary Liquid Chromatography, Pankaj Aggarwal

Theses and Dissertations

This dissertation focuses on improving the chromatographic efficiency of polymeric organic monoliths by characterizing and optimizing the bed morphology. In-situ characterization techniques such as capillary flow porometry (CFP), 3-dimensional scanning electron microscopy (3D SEM) and conductivity measurements were developed and implemented to quantitatively characterize the morphology of poly(ethylene glycol) diacrylate (PEGDA) monoliths. The CFP measurements for monoliths prepared by the same procedure in capillaries with different diameters (i.e., 75, 150, and 250 μm) clearly showed a change in average through-pore size with capillary diameter, thus, certifying the need for in-situ measurement techniques. Serial sectioning and imaging of PEGDA monoliths using …