Biochemistry, Biophysics, and Structural Biology Commons^™

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Section Abstracts: Structural Biology, Biochemistry, And Biophysics

Virginia Journal of Science

Abstracts of the Structural Biology, Biochemistry, and Biophysics Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Neurotrophins And Their Effects On Breast Cancer Cell Proliferation And Migration, Kayla Elise Minser

Open Access Theses

Cancer is a large health issue in all parts of the world. In the United States alone, approximately 1 in 4 deaths are cancer related. Breast cancer is a particularly prevalent form, accounting for a little over 14 percent of all cancer incidence. The largest obstacle to overcome for breast cancer morbidity is metastasis. Over 90 percent of all breast cancer related deaths are due to metastasis. Because metastasis is a complex, multi-step process, it is difficult to treat. A recent observation in the Kirshner lab has revealed a type of phenotypic plasticity, where migratory cancer cells have a neuronal-like …

Pharmaceuticals And Personal Care Products: Emerging Contaminants In Aquatic Ecosystems, Jenny E. Zenobio

Open Access Theses

In recent years, the presence of pharmaceuticals and personal care products (PPCPs) in aquatic systems has led to research on their fate and effects. PPCPs have been found in mixture in wastewater effluents, surface, ground, and drinking water at low concentrations from areas of intense urbanization. Although adverse effects to human health from the current environmental concentrations are unlikely, the impacts to ecological receptors are not clear. We performed field and laboratory studies to quantify and evaluate effects of PPCPs on fish. First, a field study was conducted at the Baca National Wildlife Refuge, Colorado (2010-2012) because a portion of …

Developing An Unstructured Model To Investigate The Effect Of Ethanol On Product Yields For Glucose And Xylose Cofermentation In Saccharomyces Cerevisiae 424a (Lnh-St), Shane D. Clingenpeel

Open Access Theses

Production of bio-ethanol from lignocellulose requires the efficient fermentation of glucose and xylose, even in the presence of inhibitors. The desired product, ethanol itself, will inhibit the fermentation. A further understanding of how ethanol affects the organism is critical to overcoming its inhibition.

This thesis evaluated the effect of ethanol on the cofermentation of glucose and xylose in two different cases. The first case had an unstructured model created for Saccharomyces cerevisiae 424A (LNH-ST), a genetically modified strain of yeast capable of cofermenting glucose and xylose. The differential equations were based around sugar consumption, and the product yields were investigated …

Cd8Α Dendritic Cells Drive Establishment Of Hsv-1 Latency, Kevin R. Mott, Sariah J. Allen, Mandana Zandian, Bindu Konda, Behrooz G. Sharifi, Clinton Jones, Steven L. Wechsler, Terrence Town, Homayon Ghiasi

School of Veterinary and Biomedical Sciences: Faculty Publications

It is generally accepted that CD8 T cells play the key role to maintain HSV-1 latency in trigeminal ganglia of ocularly infected mice. Yet, comparably little is known about the role of innate immunity in establishment of viral latency. In the current study, we investigated whether CD8α DCs impact HSV-1 latency by examining latency in the trigeminal ganglia (TG) of wildtype (WT) C57BL/6 versus CD8α^‒/‒ (lack functional CD8 T cells and CD8α⁺ DCs), CD8β^‒/‒ (have functional CD8α⁺ T cells and CD8α⁺ DCs), and β2m^‒/‒ (lack functional CD8 T cells but have CD8α^{+ …}

The Role Of Sirtuin 1 And Ceramide In T10C12 Conjugated Linoleic Acid Induced Delipidation In 3t3-L1 Adipocytes, Wei Wang

Department of Animal Science: Dissertations, Theses, and Student Research

Project 1: Trans-10, cis-12 conjugated linoleic acid (t10c12 CLA) reduces triglyceride (TG) levels in adipocytes through multiple pathways, with AMP-activated protein kinase (AMPK) generally facilitating, and peroxisome proliferator-activated receptor γ (PPARγ) generally opposing these reductions. Sirtuin 1 (SIRT1), a histone/protein deacetylase that affects energy homeostasis, often functions coordinately with AMPK, and is capable of binding to PPARγ, thereby inhibiting its activity. This study investigated the role of SIRT1 in the response of 3T3-L1 adipocytes to t10c12 CLA by testing the following hypotheses: 1) SIRT1 is functionally required for robust TG reduction; …

Carbon Source-Dependent Alteration Of Puf3p Activity Mediates Rapid Changes In The Stabilities Of Mrnas Involved In Mitochondrial Function, Melanie Miller, Joseph Russo, Anthony Fischer, Florencia Leban, Wendy Olivas

Biology Department Faculty Works

The Puf family of RNA-binding proteins regulates gene expression primarily by interacting with the 3′ untranslated region (3′ UTR) of targeted mRNAs and inhibiting translation and/or stimulating decay. Physical association and computational analyses of yeast Puf3p identified >150 potential mRNA targets involved in mitochondrial function. However, only COX17 has been established as a target of Puf3p-mediated deadenylation and decapping. We have identified 10 new targets that are rapidly degraded in a Puf3p-dependent manner. We also observed changes in Puf3p activity in response to environmental conditions. Puf3p promotes rapid degradation of mRNA targets in the fermentable carbon source dextrose. However, Puf3p-mediated …

Sudemycin E Influences Alternative Splicing And Changes Chromatin Modifications, Paolo Convertini, Manli Shen, Philip M. Potter, Gustavo Palacios, Chandraiah Lagisetti, Pierre De La Grange, Craig Horbinski, Yvonne N. Fondufe-Mittendorf, Thomas R. Webb, Stefan Stamm

Molecular and Cellular Biochemistry Faculty Publications

Sudemycin E is an analog of the pre-messenger RNA splicing modulator FR901464 and its derivative spliceostatin A. Sudemycin E causes the death of cancer cells through an unknown mechanism. We found that similar to spliceostatin A, sudemycin E binds to the U2 small nuclear ribonucleoprotein (snRNP) component SF3B1. Native chromatin immunoprecipitations showed that U2 snRNPs physically interact with nucleosomes. Sudemycin E induces a dissociation of the U2 snRNPs and decreases their interaction with nucleosomes. To determine the effect on gene expression, we performed genome-wide array analysis. Sudemycin E first causes a rapid change in alternative pre-messenger RNA splicing, which is …

Redox Regulation Of Protein Translation In Eukaryotes, Maxim Gerashchenko

Department of Biochemistry: Dissertations, Theses, and Student Research

Gene expression may be controlled at multiple levels, e.g., through genomic architecture, transcription and translation. In the current work, we focused on regulation of protein synthesis. Historically, the investigation of the regulation of gene expression at the level of translation lagged behind the transcriptional control because of the lack of accessible high-throughput methods. Our research has begun with the finding of the use of alternative non-AUG start codon in thioredoxin-glutathione reductase (TGR), a selenoprotein involved in redox control during male reproduction. The use of this codon, CUG, relies on the Kozak consensus sequence and ribosomal scanning mechanism. However, the CUG …

Overexpression Of Thioredoxin Binding Protein (Tbp-2) Increases Oxidation Sensitivity And Apoptosis In Human Lens Epithelial Cells, Yibo Yu, Kuiyi Xing, Rilwan Badamas, Charles A. Kuszynski, Hongli Wuand, Marjorie F. Lou

School of Veterinary and Biomedical Sciences: Faculty Publications

Thioredoxin (Trx) is an important redox regulator with cytosolic Trx1 and mitochondrial Trx2 isozymes. Trx has multi-physiological functions in cells and its bioavailability is negatively controlled through active site binding to a specific thioredoxin binding protein (TBP-2). This paper describes the delicate balance between TBP-2 and Trx, and the effect of overexpression of TBP-2 in the human lens epithelial cells. Cells overexpressing TBP-2 (TBP-2 OE) showed a 7- fold increase of TBP-2, and a nearly 40% suppression of Trx activity but no change in Trx expression. The TBP-2 OE cells grew slower and their population decreased to 30% by day …

A Course-Based Research Experience: How Benefits Change With Increased Investment In Instructional Time, Christopher D. Shaffer, Cheryl Bailey, Students And Tas In Genomics Education Partnership Courses

Department of Biochemistry: Faculty Publications

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge.We have developed a bioinformatics project that provides a coursebased research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment …

Do Omnivorous Shrimp Influence Mayfly Nymphs In A Tropical Island Stream?, Nicholas A. Macías, Jose Checo Colón-Gaud, Jonathan W. Duggins, Alonso Ramírez

Biology: Faculty Publications

Interspecific interactions can play an important role in determining habitat selection and resource use between competing species. We examined interactions between an omnivorous shrimp and a grazing mayfly, two co-dominant taxa found in Puerto Rican headwater streams, to assess how predator presence may influence mayfly resource use and instantaneous growth in a tropical rainforest ecosystem. We conducted a series of behavioral and growth experiments to determine the effects of the freshwater shrimp, Xiphocaris elongata, on the growth rate and resource selection of mayfly nymphs in the family Leptophlebiidae. For resource choice assessments, we conducted a series of five day laboratory …

Stress Responses And Energy Storage In Drosophila Melanogaster Selected For Resistance To A Gram-Positive Bacillus Cereus Spores, Zhen Hu

School of Biological Sciences: Dissertations, Theses, and Student Research

A survival response study was carried out by using D. melanogaster and the opportunistic pathogen B. cereus as the agent of selection. The spores of B. cereus, a gram-positive bacteria that can cause the human pathogen disease, were applied in our artificial laboratory selection. Selected lines were treated with B. cereus spores. Wound control lines were punctured with a needle dipped into sterile H₂O. Control lines did not apply any treatment. Three different environmental treatments were used within each line type (autoclaved spores of B.cereus, sterile H₂O and no treatment). The autoclaved spores were …

Comparison Of Two Separation Methods For Biological Particles: Field-Flow Fractionation (Fff) And Sucrose Density Gradients, Cody E. Garrison

OES Theses and Dissertations

Sucrose gradient centrifugation and Field-flow fractionation (FFF) are two different particle separation methods that overcome the problems of similar size microorganisms clumping together during standard filtration methods. FFF separates particles based on size and density via the parabolic velocity profile of laminar flow in a ribbon-like channel. The sucrose method separates particles via centrifugation in a density gradient. Both techniques worked well in separating eukaryotic from prokaryotic microbes, with the preferred method depending on the type and relative abundance of organisms to be separated. Minicells were separated from mother cells in transformed Escherichia coli cultures, heterotrophic flagellates (e.g., Diplonema papillatum …

Pathogenic Mechanisms And Signaling Pathways In Plasmodium Falciparum, Jennifer L. Sedillo

USF Tampa Graduate Theses and Dissertations

Plasmodium falciparum is a human intracellular parasite that is the causative agent of a deadly form of malaria. This species alone is responsible for 200 million cases of malaria annually resulting in over 1 million deaths worldwide. The excessive mortality due to P. falciparum infection is due to its ability to cause severe pathogenesis through hyperparasitemia and cytoadherence defined as the ability of infected red blood cells to adhere to host vasculature. Cytoadherence is mediated through the export of parasite proteins to the surface of the infected red blood cell (RBC). Exported proteins have been identified but the pathway for …

Molecular Evidence For Vector Implication Of Onchocerca Lupi In Los Angeles County, Ca, Shanna June Bolcen

USF Tampa Graduate Theses and Dissertations

Onchocerca is a genus of roundworm most commonly associated with the human infection onchocerciasis, or river blindness. While typically a zoonotic infection of ungulate populations, canine cases (Onchocerca lupi) have been identified in the United States and Greece. In 2012, Los Angeles County, Veterinary Public Health Program identified 3 cases of Onchocerca spp. infections in domestic canines. Samples from the ensuing blackfly collections were sent to the Global Health Infectious Disease Research Unnasch Laboratory for parasite isolation and vector species identification. Species-specific primers were designed and optimized for O. lupi using a non- specific cytochrome oxidase (COI) gene target (689bp) …

Sigma Factor N: A Novel Regulator Of Acid Resistance And Locus Of Enterocyte Effacement In Escherichia Coli O157:H7, Avishek Mitra

USF Tampa Graduate Theses and Dissertations

In enterohemorrhagic E. coli (EHEC) sigma factor N (σ^N) regulates glutamate-dependent acid resistance (GDAR) and the locus of enterocyte effacement (LEE), discrete genetic systems required for transmission and virulence of this intestinal pathogen. Regulation of these systems requires nitrogen regulatory protein C, NtrC, and is a consequence of NtrC/σ^N-dependent reduction in the activity of sigma factor S (σ^S). This study elucidates pathway components and stimuli for σ^N-directed regulation of GDAR and the LEE in EHEC. Deletion of fliZ, the product of which reduces σ^S activity, phenocopies rpoN (σ^N) …

Transcriptional Control Of Toxoplasma Development, Joshua Byran Radke

USF Tampa Graduate Theses and Dissertations

Toxoplasma gondii is an obligate intracellular protozoan parasite of animals and man. The asexual life cycle of Toxoplasma involves three very distinct, but tightly coordinated developmental stages. In nature, the sporozoite (contained within an oocyst) and bradyzoite (contained within a tissue cyst) initiate infection of the intermediate host, followed by rapid differentiation into the actively replicating tachyzoite. When countered by an effective host response, the tachyzoite differentiates back into the latent bradyzoite and this unique ability of Toxoplasma to interconvert between the replicating tachyzoite and the latent bradyzoite within a single host is the cause of life long infection. The …

Exploration Of Mutations In Erythroid 5-Aminolevulinate Synthase That Lead To Increased Porphyrin Synthesis, Erica Jean Fratz

USF Tampa Graduate Theses and Dissertations

5-Aminolevulinate synthase (ALAS; EC 2.3.1.37) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the first committed step of heme biosynthesis in animals, the condensation of glycine and succinyl-CoA yielding 5-aminolevuliante (ALA), CoA, and CO2. Murine erythroid-specific ALAS (mALAS2) variants that cause high levels of PPIX accumulation provide a new means of targeted, and potentially enhanced, photosensitization. Transfection of HeLa cells with expression plasmids for mALAS2 variants, specifically for those with mutated mitochondrial presequences and a mutation in the active site loop, caused significant cellular accumulation of PPIX, particularly in the membrane. Light treatment of HeLa cells expressing mALAS2 variants revealed …