Biochemistry, Biophysics, and Structural Biology Commons^™

2016-01-A3dsrinp-Csc-Sta-Cmb-522-Bps-542, Raymond Pulver, Neal Buxton, Xiaodong Wang, John Lucci, Jean Yves Hervé, Lenore Martin

Bioinformatics Software Design Projects

Cholesterol is carried and transported through bloodstream by lipoproteins. There are two types of lipoproteins: low density lipoprotein, or LDL, and high density lipoprotein, or HDL. LDL cholesterol is considered “bad” cholesterol because it can form plaque and hard deposit leading to arteries clog and make them less flexible. Heart attack or stroke will happen if the hard deposit blocks a narrowed artery. HDL cholesterol helps to remove LDL from the artery back to the liver.

Traditionally, particle counts of LDL and HDL plays an important role to understanding and prediction of heart disease risk. But recently research suggested that …

A Novel Variant In Cmah Is Associated With Blood Type Ab In Ragdoll Cats, Barbara Gandolfi, Robert Grahn, Nicholas Gustafson, Daniela Proverbio, Eva Spada, Badri Adhikari, Janling Cheng, Gordon Andrews, Leslie Lyons, Chris Helps

Computer Science Faculty Works

The enzyme cytidine monophospho-N-acetylneuraminic acid hydroxylase is associated with the production of sialic acids on cat red blood cells. The cat has one major blood group with three serotypes; the most common blood type A being dominant to type B. A third rare blood type is known as AB and has an unclear mode of inheritance. Cat blood type antigens are defined, with N-glycolylneuraminic acid being associated with type A and N-acetylneuraminic acid with type B. Blood type AB is serologically characterized by agglutination using typing reagents directed against both A and B epitopes. While a genetic characterization of blood …

Non-Canonical Roles Of Trnas And Trna Mimics In Bacterial Cell Biology, Assaf Katz, Sara Elgamal, Andrei Rajkovic, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Transfer RNAs (tRNAs) are the macromolecules that transfer activated amino acids from aminoacyl‐tRNA synthetases to the ribosome, where they are used for the mRNA guided synthesis of proteins. Transfer RNAs are ancient molecules, perhaps even predating the existence of the translation machinery. Albeit old, these molecules are tremendously conserved, a characteristic that is well illustrated by the fact that some bacterial tRNAs are efficient and specific substrates of eukaryotic aminoacyl‐tRNA synthetases and ribosomes. Considering their ancient origin and high structural conservation, it is not surprising that tRNAs have been hijacked during evolution for functions outside of translation. These roles beyond …

High Salt Induces Anti-Inflammatory Mφ2-Like Phenotype In Peripheral Macrophages, Suneetha Amara, Margaret M. Whalen, Venkataswarup Tiriveedhi

Chemistry Faculty Research

Macrophages play a critical role in inflammation and antigen-presentation. Abnormal macrophage function has been attributed in autoimmune diseases and cancer progression. Recent evidence suggests that high salt tissue micro-environment causes changes in macrophage activation. In our current report, we studied the role of extracellular sodium chloride on phenotype changes in peripheral circulating monocyte/macrophages collected from healthy donors. High salt (0.2M NaCl vs basal 0.1M NaCl) treatment resulted in a decrease in MΦ1 macrophage phenotype (CD11b+CD14highCD16low) from 77.4±6.2% (0.1M) to 29.3±5.7% (0.2M, p<0.05), while there was an increase in MΦ2 macrophage phenotype (CD11b+ CD14lowCD16high) from 17.2±5.9% (0.1M) to 67.4±9.4% (0.2M, p<0.05). ELISA-based cytokine analysis demonstrated that high salt treatment induced decreased expression of in the MΦ1 phenotype specific pro-inflammatory cytokine, TNFα (3.3 fold), IL-12 (2.3 fold), CCL-10 (2 fold) and CCL-5 (3.8 fold), but conversely induced an enhanced expression MΦ2-like phenotype specific anti-inflammatory cytokine, IL-10, TGFβ, CCL-17 (3.7 fold) and CCR-2 (4.3 fold). Further high salt treatment significantly decreased phagocytic efficiency of macrophages and inducible nitric oxide synthetase expression. Taken together, these data suggest that high salt extracellular environment induces an anti-inflammatory MΦ2-like macrophage phenotype with poor phagocytic and potentially reduced antigen presentation capacity commonly found in tumor microenvironment.

Quantitative Mass Spectrometry Reveals Changes In Histone H2b Variants As Cells Undergo Inorganic Arsenic-Mediated Cellular Transformation, Matthew Rea, Tingting Jiang, Rebekah Eleazer, Meredith Eckstein, Alan G. Marshall, Yvonne N. Fondufe-Mittendorf

Molecular and Cellular Biochemistry Faculty Publications

Exposure to inorganic arsenic, a ubiquitous environmental toxic metalloid, leads to carcinogenesis. However, the mechanism is unknown. Several studies have shown that inorganic arsenic exposure alters specific gene expression patterns, possibly through alterations in chromatin structure. While most studies on understanding the mechanism of chromatin-mediated gene regulation have focused on histone post-translational modifications, the role of histone variants remains largely unknown. Incorporation of histone variants alters the functional properties of chromatin. To understand the global dynamics of chromatin structure and function in arsenic-mediated carcinogenesis, analysis of the histone variants incorporated into the nucleosome and their covalent modifications is required. Here …

Determining The Role Of Erbeta In The Activation Of Erk1/2 By The Environmental Estrogens, Cadmium Chloride And Sodium Arsenite, In Human Lung Adenocarcinoma Cells, Jeffrey Hyzer

Undergraduate Theses

Estrogen is involved in the proliferation of adenocarcinoma lung cells. However, the proliferative role of two endocrine disrupters, cadmium chloride and sodium arsenite, in lung adenocarcinoma is less clear. Previous studies have shown that these two heavy metals can induce cellular proliferation and activate phosphorylation of ERK1/2 in a human lug adenocarcinoma cell line, NCI-H1793. Induced phosphorylation of ERK1/2 by these compounds is decreased in the presence of an estrogen receptor antagonist, ICI-182,780, suggesting that cadmium and arsenite stimulate these responses, in part, via a non-genomic estrogen signaling pathway. There are three known estrogen receptors, but it is unclear which …

A Pilot Study Analyzing Solvents In Electronic Cigarette “E-Liquid” Using High Performance Liquid Chromatography, Austin Matranga, Olivia Sellers, Matthew Gartner

Student Scholar Symposium Abstracts and Posters

Introduction: Electronic cigarettes, also known as an e-cigarette, are battery-powered devices that use a heating element to convert a liquid (“e-liquid”) into an inhalable aerosol. Their advertised use is as a nicotine delivery system minus the harmful chemicals. Since “e-liquids” and the electronic cigarettes are not regulated by the Food and Drug Administration, it is not well known under what conditions, if any, carcinogenic compounds are produced. There has been little research on the toxicity of electronic cigarettes. The aim of this study was to determine if formaldehyde or acetaldehyde are formed from the e-liquid by the high heat of …

Connecting The Physiological And Behavioral Response To Heat Stress On A Warming Planet, Anastasia Kalyta

Student Scholar Symposium Abstracts and Posters

Intertidal communities are considered good models of the biological effects of climate change on ecosystems, as their resident organisms are subjected to heat spells during daytime low tides. The increasing heat exposure can elicit behavioral as well as physiological responses in intertidal organisms. We studied the relationship between these responses to heat stress in the blue-banded hermit crab, Pagurus samuelis, by inducing a “heat shock” with elevated water temperature of 29 °C for 2.5 h. The behavioral effect of heat-shock was quantified using a 30-minute feeding assay, measuring the mass of a standard squid pellet consumed by individual hermit crabs. …

Novel Cell Penetrating Peptides Effect Endosomal Escape And Deliver Protein Cargos Into Living Cells, Verra M. Ngwa

Master of Science in Chemical Sciences Theses

Over the last decade a number of peptides that are rapidly internalized by mammalian cells have been discovered or designed. Cell-penetrating peptides (CPPs) are capable of mediating penetration of the plasma membrane, allowing delivery of macromolecular cargoes to the cell interior. We have developed a novel CPP-adaptor protein technology that allows any user-defined cargo delivery and release into the cytoplasm. Our hypothesis is that a CPP-adaptor with a moiety allowing high-affinity but reversible non-covalent cargo binding would lead to more efficient penetration and release than current CPP delivery strategies. Delivery of proteins to the interiors of cells has many applications. …

The Foundations Of Network Dynamics In An Rna Recombinase System, Jessica Anne Mellor Yeates

Dissertations and Theses

How life originated from physical and chemical processes is one of the great questions still unanswered today. Studies towards this effort have transitioned from the notion of a single self-replicating entity to the idea that a network of interacting molecules made this initial biological leap. In order to understand the chemical kinetic and thermodynamic mechanisms that could engender pre-life type networks we present an empirical characterization of a network of RNA recombinase molecules. We begin with 1-, 2-, and 3-molecular ensembles and provide a game theoretic analysis to describe the frequency dependent dynamics of competing and cooperating RNA genotypes. This …

The Spliceosomal Protein Sf3b5 Is A Novel Component Of Drosophila Saga That Functions In Gene Expression Independent Of Splicing, Rachel Stegeman, Peyton J. Spreacker, Selene K. Swanson, Robert Stephenson, Laurence Florens, Michael P. Washburn, Vikki M. Weake

Department of Biochemistry Faculty Publications

The interaction between splicing factors and the transcriptional machinery provides an intriguing link between the coupled processes of transcription and splicing. Here, we show that the two components of the SF3B complex, SF3B3 and SF3B5, that form part of the U2 small nuclear ribonucleoprotein particle (snRNP) are also subunits of the Spt-Ada-Gcn5 acetyltransferase (SAGA) transcriptional coactivator complex in Drosophila melanogaster. Whereas SF3B3 had previously been identified as a human SAGA subunit, SF3B5 had not been identified as a component of SAGA in any species. We show that SF3B3 and SF3B5 bind to SAGA independent of RNA and interact with …

Searching For Potential Binding Partners Of Arabidopsis Β-Amylase2 Using Yeast 2-Hybridization, Megan E. Hines

Senior Honors Projects, 2010-2019

BAM2 is a chloroplast-targeted member of the β-amylase gene family that currently has an unknown function in starch hydrolysis. Previous research indicated that BAM2 did not have significant catalytic activity, but, because the gene is highly conserved and there is a starch-excess phenotype in older plants lacking BAM2, it was hypothesized that BAM2 may instead have a regulatory function. Many regulatory proteins function by interacting with other proteins, so we wanted to test for potential protein binding partners for BAM2 using the yeast two-hybrid system. A plasmid containing the BAM2 gene from Arabidopsis thaliana was co-transformed into Y190-strain yeast ( …

The Purification And Characterization Of Beta-Amylase6 In Arabidopsis Thaliana, Catherine E. Torres

Senior Honors Projects, 2010-2019

Experimental evidence indicates that the family of beta-amylase (BAM) proteins is largely responsible for the hydrolysis of starch in land plants. In Arabidopsis thaliana there are nine BAM genes, six of which are targeted to the chloroplast, but only four of those are presumed to be catalytically active: BAM1, -2, -3, and -6. Currently, little is known about the expression, characterization, or function of BAM6. Our study of starch accumulation in Arabidopsis indicates that BAM6 may be playing a role in older plants, although it has a minimal role in young plants. To further investigate the function of BAM6 we …

Epigenetic Characterization Of Human Retina Cells, Nicholas R. Dunham

Senior Honors Projects, 2010-2019

DNA methylation is an epigenetic modifier that modulates gene expression in plant and vertebrate genomes. The aim of this study was to characterize the role of DNA methylation in the human retina, particularly within rod and cone photoreceptor retinal neurons. Previous studies investigating DNA methylation in murine retinal cells and retina-derived human retinoblastoma immortalized cell culture lines demonstrate an inverse relationship between DNA methylation and transcriptional activity. Here, we used gene-specific bisulfite pyrosequencing analysis to measure DNA methylation in the genomes of human ocular cells in an effort to characterize the role of this important epigenetic modifier. These results can …

Exploitation Of The Ligand-Binding Properties Of The Mannose 6-Phosphate/Insulin-Like Growth Factor Ii (Igf-Ii) Receptor To Inhibit Igf-Ii-Dependent Growth Of Cancer Cells, Megan Zavorka Thomas

Theses & Dissertations

The mannose 6-phosphate/insulin-like growth factor II receptor (M6P/IGF2R) is a multifunctional, type I transmembrane receptor that is a member of the P-type lectin family. A large, extracytoplasmic (EC) region of the M6P/IGF2R binds various ligands, allowing the receptor to regulate multiple biological functions, including the role as a tumor suppressor. Two major classes of ligands, M6P-glycosylated (i.e. any proteins that bear M6P due to post-translational modification in the trans-Golgi network (TGN)) and non-glycosylated (i.e., the mitogen insulin-like growth factor II (IGF-II)), bind within distinct regions of the EC of the receptor and are trafficked to the lysosome. The M6P/IGF2R as …

Molecular Mechanisms Regulating Myc And Pgc1Β Expression In Colon Cancer, Jamie L. Mccall

Theses & Dissertations

Identification and characterization of pathways specific to tumor cell survival, but absent in normal tissues, provide opportunities to develop effective cancer therapies with reduced toxicity to the patient. Kinase suppressor of Ras 1 (KSR1) is required for the survival of colorectal cancer (CRC) cells, but dispensable in normal cells. Using KSR1 as a reference standard, we identified EPH (erythropoietin-producing hepatocellular carcinoma) receptor (EPHB4) as a KSR1 functional analog.

We show here that, like KSR1, EPHB4 is aberrantly overexpressed in human CRC cells and selectively required for their survival. Both KSR1 and EPHB4 support tumor cell survival by promoting the expression …

The Role Of Oncogenic Kras In Initiation, Progression And Maintenance Of Pancreatic Cancer, Nirakar Rajbhandari

Theses & Dissertations

Pancreatic cancer is a lethal disease that is almost invariably associated with a KRAS gene mutation. Due to a very high frequency of gain-of-function mutations within the KRAS gene, and its proven role in initiation of pancreatic cancer in animal models, mutant KRAS is considered a rational therapeutic target. To determine the potential role of oncogenic KRAS in pancreatic tumor maintenance in vivo, we generated a mouse model with a Doxycycline regulated expression of oncogenic KRAS (KRAS^G12D) in pancreas. Using this reversible model, we demonstrated that the expression of oncogenic KRAS in a Cdkn2a deficient background was …

Role Of Stemloop D In Terminally Deleted Coxsackievirus B3 Replication, Lee K. Jaramillo

Theses & Dissertations

Coxsackievirus B3 (CVB3) is an enterovirus with no known form of latency. However, assays designed to detect enteroviral RNA have shown that CVB3 RNA can persist for weeks beyond the acute infection both naturally and experimentally. Our previous work with coxsackievirus revealed an inhibited version of enteroviral replication where the progeny virus, termed terminally deleted (TD) virus, was missing a maximum of 49 nucleotides from the beginning of the 5’ non-translated region (NTR). The largest terminally deleted virus, TD50, effaced stem a, stemloop b, and stemloop c from the secondary structure, the cloverleaf. We hypothesized that further deletion beyond those …

Role Of Akt2 In Cell Survival, Establishment And/Or Maintenance Of Colorectal Cancer Metastasis, Ekta Agarwal

Theses & Dissertations

There is extensive evidence for the role of aberrant cell survival signaling mechanisms in cancer progression and metastasis. Akt acts as a key signaling node that bridges oncogenic receptors to many essential pro-survival cellular functions, and is perhaps the most commonly activated signaling pathway in human cancer. Akt has three isoforms, Akt1, 2 and 3. Variable phenotypic differences are observed following the genetic inactivation and/or removal of the Akt isoforms, which suggests that the isoforms have distinct non-redundant functional characteristics despite sharing a high level of structural homology and similar mechanisms of activation.

The major goal of the work presented …

Secretory Mucin Muc5ac In Gastrointestinal Malignancies, Shiv Ram Krishn

Theses & Dissertations

Secretory mucin MUC5AC is an extensively glycosylated high molecular weight protein that forms a polymeric gel layer over the epithelial layers under physiological conditions, to protect these surfaces from myriad of insults. MUC5AC is known to be implicated in various malignancies including pancreatic cancer and colorectal cancer. MUC5AC is overexpressed in pancreatic cancer compared to no expression in normal pancreas. However, its functional implications and associated mechanistic basis in pancreatic cancer remains obscure. Therefore, we investigated the role of MUC5AC in onset and progression of pancreatic cancer. Our study showed that MUC5AC expression is elevated during pancreatic cancer progression while …

Investigation Of A Mycobacteriophage Transcription Repressor, Kathryn Orban

Honors Thesis

Mycobacteriophage HelDan is a lysogenic, or temperate, phage (virus) of the bacterium Mycobacterium smegmatis, which is a fast-growing, close relative of Mycobacterium tuberculosis, the causative agent of tuberculosis. The phage replication cycle is dependent on time-coordinated gene expression events. In order to study the regulation of gene expression during phage replication, HelDan protein gp73, a putative transcriptional repressor, was studied. Characterization of gp73 structure and function, such as DNA binding activity and affinity, was done using both bioinformatics and biochemical analyses. To this end, the gene encoding gp73 was cloned and the ability of the recombinant gp73 protein …

Development Of A Novel Self-Propagating Prssv-Vsv G Hybrid Replicon As A Vector For Inducing Broad Prrsv Protection, Asit K. Pattnaik

School of Veterinary and Biomedical Sciences: Faculty Publications

Throughout successive cycles of Pork Check-off funding, our laboratories (Pattnaik’s and Osorio’s labs) have consistently produced new and fundamental information on: (i) the immunologic mechanisms that are important for protection against PRRSV infection, (ii) the structural basis for induction of PRRSV-neutralizing antibodies which are significant for conferring protective immunity, (iii) the possibility of producing a rationally-designed new generation DIVA vaccine that would offer more efficacious protection, and (iv) the presence of conserved B- and T-cell epitopes in the structural and nonstructural proteins (NSPs) of PRRSV.

A Mutation In Ltbp2 Causes Congenital Glaucoma In Domestic Cats (Felis Catus), Markus H. Kuehn, Koren A. Lipsett, Marilyn Menotti-Raymond, S. Scott Whitmore, Todd E. Scheetz, Victor A. David, Stephen J. O'Brien, Zhongyuan Zhao, Jackie K. Jens, Elizabeth M. Snella, N. Matthew Ellinwood, Gillian J. Mclellan

Chemistry Faculty Publications

The glaucomas are a group of diseases characterized by optic nerve damage that together represent a leading cause of blindness in the human population and in domestic animals. Here we report a mutation in LTBP2 that causes primary congenital glaucoma (PCG) in domestic cats. We identified a spontaneous form of PCG in cats and established a breeding colony segregating for PCG consistent with fully penetrant, autosomal recessive inheritance of the trait. Elevated intraocular pressure, globe enlargement and elongated ciliary processes were consistently observed in all affected cats by 8 weeks of age. Varying degrees of optic nerve damage resulted by …

The Effects Of Chronic Partial Sleep Deprivation And Chronic Voluntary Alcohol Consumption On Δfos B Accumulation, Kristian Ponder

Masters Theses, 2010-2019

The present study explores the relation between sleep restriction and alcohol use and the neural substrates that result from chronic behaviors. Accumulation of the transcription factors ΔFosB is suggested as a possible outcome of chronic behaviors, such as addiction. Sleep is discussed as possible mediating factor in the relationship between ΔFosB and chronic alcohol consumption. There were four experimental groups in this study: Control (C), Sleep Deprivation only (SD), Alcohol Exposure only (AO), and both sleep deprivation and alcohol exposure (B). Levels of ΔFosB accumulation in the Nucleus Accumbens (NAc) revealed a significant main effect of sleep deprivation, but no …

Zn(Ii), Cu(Ii), Sn(Ii), And Ni(Ii) And Other Metal Cations Do Not Prevent The Aggregation Of Hiapp, Charles Hoying

Honors Thesis

The Zn(II) metal ion has been shown to interact with Islet Amyloid Polypeptide (IAPP), a protein implicated in the progression of Type II Diabetes Mellitus, in such a way as to prevent the protein from aggregating into toxic fibers. We set out to find whether other metal ions might similarly prevent IAPP aggregation. Using Thioflavin T (ThT) spectroscopic assays, which measure fluorescence of ThT upon binding to aggregated IAPP, we observed a decrease in aggregation when incubated with Zn(II), Cu(II), Ni(II), and Sn(II). Atomic Force Microscopy (AFM), which can visualize fibril formation, revealed that the metals were not inhibiting IAPP …

Measuring The Impact: An Evaluation Of Communities In Harmony, Michael Carl Owens

Senior Theses

In the study reported below, a program evaluation was performed for the student organization Communities in Harmony, a music-based community service organization at the University of South Carolina that works with homeless and socioeconomically disadvantaged children and young adults. This organization is about to enter its fifth year and is in the process of transitioning between leadership teams at the time of publication. The purpose of this study is to evaluate the strengths and weaknesses of the organization so that it can continue to grow and effectively serve its target populations. This study has found that the organization excels at …

The Evolution Of The Surface Of The Mineral Schreibersite In Prebiotic Chemistry, Nikita L. La Cruz, Danna Qasim, Heather Abbott-Lyon, Claire Pirim

Faculty Articles

We present a study of the reactions of the meteoritic mineral schreibersite (Fe,Ni)3P, focusing primarily on surface chemistry and prebiotic phosphorylation. In this work, a synthetic analogue of the mineral was synthesized by mixing stoichiometric proportions of elemental iron, nickel and phosphorus and heating in a tube furnace at 820 °C for approximately 235 hours under argon or under vacuum, a modification of the method of Skála and Drábek (2002). Once synthesized, the schreibersite was characterized to confirm the identity of the product as well as to elucidate the oxidation processes affecting the surface. In addition to characterization of the …

Single-Cell Transcriptional Analysis Of Normal, Aberrant, And Malignant Hematopoiesis In Zebrafish, Finola E. Moore, Elaine G. Garcia, Riadh Lobbardi, Esha Jain, Qin Tang, John C. Moore, Mauricio Cortes, Aleksey Molodtsov, Melissa Kasheta, Christina C. Luo, Amaris J. Garcia, Ravi Mylvaganam, Jeffrey A. Yoder, Jessica S. Blackburn, Ruslan I. Sadreyev, Craig J. Ceol, Trista E. North, David M. Langenau

Molecular and Cellular Biochemistry Faculty Publications

Hematopoiesis culminates in the production of functionally heterogeneous blood cell types. In zebrafish, the lack of cell surface antibodies has compelled researchers to use fluorescent transgenic reporter lines to label specific blood cell fractions. However, these approaches are limited by the availability of transgenic lines and fluorescent protein combinations that can be distinguished. Here, we have transcriptionally profiled single hematopoietic cells from zebrafish to define erythroid, myeloid, B, and T cell lineages. We also used our approach to identify hematopoietic stem and progenitor cells and a novel NK-lysin 4⁺ cell type, representing a putative cytotoxic T/NK cell. Our platform …

Purification Of A Bacteriophage Protein Involved In Host Range Specificity, Alec Brown

Honors Projects

The Escherichia coli ferric hydroxamate uptake receptor FhuA serves as the receptor for ferrichrome-Fe(III) complexes, with TonB protein energizing the active transport of the complex. The FhuA receptor is exploited by a variety of bacteriophages as a conduit into the cell. Interestingly, certain of these phages carry a gene called “Cor”, the product of which, when cloned and expressed from a plasmid, blocks transport by FhuA. In the present study, components of the cor gene from the bacteriophage ϕ80 were used to construct an IPTG-inducible MalE-Cor-His6 fusion protein, which allowed for affinity purification of the Cor protein. At 61 residues …

Stabilizing The Cold Plasma-Stimulated Medium By Regulating Medium’S Composition, Dayun Yan, Niki Nourmohammadi, Ka Bian, Ferid Murad, Jonathan H. Sherman, Michael Keidar

Biochemistry and Molecular Medicine Faculty Publications

Over past several years, the cold plasma-stimulated medium (PSM) has shown its remarkable anti-cancer capacity in par with the direct cold plasma irradiation on cancer cells or tumor tissues. Independent of the cold plasma device, PSM has noticeable advantage of being a flexible platform in cancer treatment. Currently, the largest disadvantage of PSM is its degradation during the storage over a wide temperature range. So far, to stabilize PSM, it must be remained frozen at −80 °C. In this study, we first reveal that the degradation of PSM is mainly due to the reaction between the reactive species and specific …