Biochemistry, Biophysics, and Structural Biology Commons^™

Partitioning The Fitness Components Of Rna Populations Evolving In Vitro, Carolina Diaz Arenas, Niles Lehman

Chemistry Faculty Publications and Presentations

All individuals in an evolving population compete for resources, and their performance is measured by a fitness metric. The performance of the individuals is relative to their abilities and to the biotic surroundings – the conditions under which they are competing – and involves many components. Molecules evolving in a test tube can also face complex environments and dynamics, and their fitnessmeasurements should reflect the complexity of various contributing factors as well. Here, the fitnesses of a set of ligase ribozymes evolved by the continuous in vitroevolution system were measured. During these evolution cycles there are three different catalytic …

Novel And Predominant Pathogen Responsible For The Enterovirus-Associated Encephalitis In Eastern China, Lei Zhang, Jie Yan, David M. Ojcius, Huakun Lv, Ziping Miao, Yin Chen, Yanjun Zhang, Jvying Yan

All Dugoni School of Dentistry Faculty Articles

Enteroviruses (EV) have been increasingly identified as the causative agent for unknown etiological encephalitis in many parts of the world, but the long period surveillance for enterovirus-associated encephalitis (EAE) was not reported in China. From 2002-2012 in Zhejiang, Coxsackieviruses A9, B1, B2, B3, B4, B5; and echoviruses 3, 4, 6, 9, 14, 25, 30 were detected from the unknown etiological encephalitis cases, with coxsackievirus B4 been identified here for the first time. From 2002-2004 and 2010-2012, echovirus 30 was found to be the periodically predominant serotype for in the EAE. The molecular typing results showed that all the EV isolates …

The Function Of Carmil1 In Migrating Cells, Marc Edwards

All Theses and Dissertations (ETDs)

This dissertation describes the physiological role of the Capping Protein- CARMIL interaction in migrating cells. I establish the CARMIL-CP complex as a key regulator of lamellipodial actin assembly and of lamellipodial dynamics. Membrane ruffling at the leading edge of motile cells and macropinocytosis were also found to be dependent on the CARMIL1-CP interaction. This is consistent with macropinocytosis and ruffling being dependent on a functional and dynamic lamellipodium.: Kerr and Teasdale, 2009).

In chapter two I demonstrate that the CBR of CARMIL1 is competent to inhibit CP in cells. I show that overexpression of the CBR in cells leads to …

Using Expression Profiling To Understand The Effects Of Chronic Cadmium Exposure On Mcf-7 Breast Cancer Cells, Zelmina Lubovac-Pilav, Daniel M. Borras, Esmeralda Ponce, Maggie Louie

Collected Faculty Scholarship

Cadmium is a metalloestrogen known to activate the estrogen receptor and promote breast cancer cell growth. Previous studies have implicated cadmium in the development of more malignant tumors; however the molecular mechanisms behind this cadmium-induced malignancy remain elusive. Using clonal cell lines derived from exposing breast cancer cells to cadmium for over 6 months (MCF-7-Cd4, -Cd6, -Cd7, -Cd8 and -Cd12), this study aims to identify gene expression signatures associated with chronic cadmium exposure. Our results demonstrate that prolonged cadmium exposure does not merely result in the deregulation of genes but actually leads to a distinctive expression profile. The genes deregulated …

Purifying The Human Rna-Lariat Debranching Enzyme, Ammar Saigal

Honors Program Theses and Research Projects

This project is my first official research endeavor and it involved becoming acquainted with a large variety of biochemistry and molecular biology techniques. The goal is to elucidate the structure of a protein common to most if not all cells of organisms within the Domain Eukarya, which is one of the three taxonomic domains into which all life is categorized. This is the domain most relevant to human beings as it includes plants, fungi, and animals (from a strictly biologically-taxonomic perspective, the species Homo sapiens to which you and I belong is considered belonging to the Kingdom Animalia [Animal]).

Anion-Peptide Adduct Formation And Decomposition As Studied By Fourier Transform Ion Cyclotron Resonance (Ft-Icr) Mass Spectrometry, Xiaohua Liu

LSU New Orleans Theses and Dissertations

A new “best match” match model has been developed to account for adduct formation on multiply charged peptides observed in negative ion electrospray mass spectrometry. To obtain a stable adduct, the model necessitates an approximate matching of apparent gas-phase basicity (GBapp) of a given proton bearing site on the peptide with the gas-phase basicity (GB) of the anion attaching at that site. Evidence supporting the model is derived from the fact that singly charged adducts were only observed for lower GB anions: HSO₄^-, I^-, CF₃COO^-. Ions that have medium GBs (NO …

The Effects Of Chronic Simvastatin Treatment On The Expression Of Behavioral Symptoms In A Transgenic Mouse Model Of Huntington’S Disease, Ashley Whitmarsh

LSU New Orleans Theses and Dissertations

Huntington’s disease (HD) is a heritable, neurodegenerative disorder characterized by motor, cognitive, and psychiatric disturbances. An unstable CAG expansion within the gene normally encoding for the Huntingtin protein is responsible. The expanded mutant form of Huntingtin and the putative protein co-factor Rhes interact and cause cell death within the striatum. We hypothesized chronic treatment with simvastatin, a cholesterol lowering drug, would disrupt the biosynthetical pathway which gives both Rhes and its target cells binding sites and render Rhes inactive. Healthy and HD mice were treated with simvastatin or a vehicle. Animals’ motor behavior was assessed with three separate tests over …

The Effects Of Salinity, Ph, Temperature, And Dissolved Oxygen On Sensitivity Of Pcr Identification Of T4 Bacteriophage, Joesph F. Cannon, Nicholas A. Thurn, Paul E. Richardson

Journal of the South Carolina Academy of Science

Bacteriophages are used as indicators of pathogenic bacteria in drinking, and wastewaters. They also show potential in limiting aquatic bacterial populations through their lytic properties. The effect of different water characteristics (salinity, pH, dissolved oxygen, and temperature) on the sensitivity of the PCR identification of virus particles were analyzed to determine at what levels bacteriophage can be detected in environmental samples. Results from this preliminary study indicate that a PCR bacteriophage detection technique has potential as a relatively efficient and economical indicator of coliform contamination in multiple aquatic environments. While further evaluation is needed, the protocol appears to function in …

Valproic Acid Causes Proteasomal Degradation Of Dicer And Influences Mirna Expression, Zhaiyi Zhang, Paolo Convertini, Manli Shen, Xiu Xu, Frédéric Lemoine, Pierre De La Grange, Douglas A. Andres, Stefan Stamm

Molecular and Cellular Biochemistry Faculty Publications

Valproic acid (VPA) is a commonly used drug to treat epilepsy and bipolar disorders. Known properties of VPA are inhibitions of histone deacetylases and activation of extracellular signal regulated kinases (ERK), which cannot fully explain VPA's clinical features. We found that VPA induces the proteasomal degradation of DICER, a key protein in the generation of micro RNAs. Unexpectedly, the concentration of several micro RNAs increases after VPA treatment, which is caused by the upregulation of their hosting genes prior to DICER degradation. The data suggest that a loss of DICER protein and changes in micro RNA concentration contributes to the …

Molecular Evolution Of Protein-Rna Mimicry As A Mechanism For Translational Control, Assaf Katz, Lindsey Solden, S. Betty Zou, William Wiley Navarre, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Elongation factor P (EF-P) is a conserved ribosome-binding protein that structurally mimics tRNA to enable the synthesis of peptides containing motifs that otherwise would induce translational stalling, including polyproline. In many bacteria, EF-P function requires post-translational modification with (R)-β-lysine by the lysyl-tRNA synthetase paralog PoxA. To investigate how recognition of EF-P by PoxA evolved from tRNA recognition by aminoacyl-tRNA synthetases, we compared the roles of EF-P/PoxA polar contacts with analogous interactions in a closely related tRNA/synthetase complex. PoxA was found to recognize EF-P solely via identity elements in the acceptor loop, the domain of the protein that interacts with the …

Biochemical Assay Optimization And Computational Screening Efforts To Identify Potential Luxs Inhibitors, Keeshia Q. Wang

Master's Theses

Quorum sensing (QS) is a process of coordination of bacterial gene expression in response to cell population. System two QS is regulated by the small signaling molecule autoinducer-2 (AI-2) and is implicated in the infectious behaviors of various bacterial species. AI-2 is biosynthesized from S-ribosylhomocysteine (SRH) by the enzyme LuxS and induces interspecies cell-to-cell communication. Inhibition of LuxS would therefore inhibit interspecies QS. Herein, a search for novel molecular species that will competitively bind with SRH in the LuxS binding site is performed in silico. Computational screening results are then validated in vitro using an optimized LuxS inhibition …

Synthesis, Characterization, And Application Of High Surface Area, Mesoporous, Stabilized Anatase Tio2 Catalyst Supports, Rebecca Elizabeth Olsen

Theses and Dissertations

Nanomaterials have attracted substantial attention in the area of catalysis due to the unique properties they exhibit such as high surface areas, intricate pore networks and unique morphologies. TiO2 has attracted attention as a catalyst since the discovery of its high photocatalytic activity by Fuishima and Honda in 1972. Given its high thermal stability, low cost, low environmental impact, and versatility, TiO2 is a widely used commercial catalyst and catalyst support. TiO2 is used in many applications such as photocatalysis is also an excellent support material for noble metals in a number of oxidative synthesis and pollution-control reactions. Though TiO2 …

Nonlinear Spectroscopic Investigation Of Adsorption To C-18 Model Stationary Phase, Anthony D. Peterson

Theses and Dissertations

Reversed-phase liquid chromatography (RPLC) is a commonly used separation technique in chemistry. Nevertheless, the mechanistic interactions at the molecular level among the eluent, analyte, and the stationary phase are not fully understood. Because of this limited understanding, optimization of the separation must be done experimentally. Learning more about molecular interactions should aid in improving separations. We are currently using second-harmonic generation (SHG) spectroscopy to investigate how analytes adsorb to the surface. SHG is a spectroscopic technique that produces signal only at places of non-isotropic symmetry; this typically occurs at surfaces. SHG can be used to produce surface isotherms of test …

Making Chlamydomonas Reinhardtii A Better Model Organism: Tackling The Inefficiency Of Nuclear Transgene Expression And Improving Methods For The Generation And Characterization Of Insertional Mutant Libraries, Thomas M. Plucinak

Department of Biochemistry: Dissertations, Theses, and Student Research

The green algal species Chlamydomonas reinhardtii possesses many beneficial features that have made it a useful model organism for many decades. Many types of experimentation however are difficult to conduct with this organism due to the relative under-development of genetic tools available for use. Tasks such as transgene expression, overexpression of proteins of interest (POIs) or site specific genomic modification that are routine in other more facile microbial model organisms such as Escherichia coli and yeast are difficult to accomplish in C. reinhardtii. The second chapter of this thesis describes the development of a novel nuclear transgene expression system …

Metabolic Remodeling And Mitochondrial Dysfunction In Maladaptive Right Ventricular Hypertrophy Secondary To Pulmonary Arterial Hypertension, Jose Gomez-Arroyo

Theses and Dissertations

Right ventricular dysfunction is the most frequent cause of death in patients with pulmonary arterial hypertension. Although abnormal energy substrate use has been implicated in the development of chronic left heart failure, data describing such metabolic remodeling in failing right ventricular tissue remain incomplete. In the present dissertation we sought to characterize metabolic gene expression changes and mitochondrial dysfunction in functional and dysfunctional RV hypertrophy. Two different rat models of RV hypertrophy were studied. The model of right ventricular failure (SU5416/hypoxia) exhibited a significantly decreased gene expression of peroxisome proliferator-activated receptor- coactivator-1α, peroxisome proliferator- activated receptor-α and estrogen-related receptor-α. The …

Functional Analysis Of The Acetic Acid Resistance (Aar) Gene Cluster In Acetobacter Aceti Strain 1023, Elwood Mullins, T Joseph Kappock

Department of Biochemistry Faculty Publications

Vinegar production requires acetic acid bacteria that produce, tolerate, and conserve high levels of acetic acid. When ethanol is depleted, aerobic acetate overoxidation to carbon dioxide ensues. The resulting diauxic growth pattern has two logarithmic growth phases, the first associated with ethanol oxidation and the second associated with acetate overoxidation. The vinegar factory isolate Acetobacter aceti strain 1023 has a long intermediate stationary phase that persists at elevated acetic acid levels. Strain 1023 conserves acetic acid despite possessing a complete set of citric acid cycle (CAC) enzymes, including succinyl-CoA:acetate CoA-transferase (SCACT), the product of the acetic acid resistance (aar …

Comparative Lipid Profiles Of Milk Bank Breast Milk And Infant Formulas, Anya Oleynik, Tatiana Eliseeva, Jack Y. Vanderhoek

Biochemistry and Molecular Medicine Faculty Publications

Lipid profiles of seven human breast milk samples obtained from milk banks and four infant formulas were compared in view of the potential food hypersensitivities of certain infants to human milk.The cholesterol (0.15-0.26 mM) content of the human samples was about 50% lower than that found in the infant formulas whereas the triglyceride (TG, 173-386 mM) contents of these products were found to be comparable.The major saturated fatty acid (SFA) and mono-unsaturated fatty acid (MUFA) were 16:0 and 18:1 respectively. The major poly-unsaturated fatty acid (PUFA) was 18:2 with otherPUFA members of the C18, C20 and C22 families identified and …

Formation And Analysis Of Zinc Oxide Nanoparticles And Zinc Oxide Hexagonal Prisms And Optical Analysis Of Cadmium Selenide Nanoparticles, Jared M. Hancock

Theses and Dissertations

In this dissertation, methods to synthesize ZnO are reported. First, zinc oxide nanoparticles were synthesized with small amounts of transition metal ions to create materials called dilute magnetic semiconductors (DMS). We employed a low temperature sol-gel method that produces ZnO nanoparticles of reproducible size and incorporates cobalt, nickel, and manganese ions into the nanoparticles. Conditions were controlled such that a range of amounts of Co, Ni, and Mn were incorporated. The incorporation was tracked by color changes in the white ZnO powder to blue for Co, green for Ni and yellow for Mn. XRD measurements showed the nanoparticles were on …

Effects Of Water Availability And Pest Pressures On Tea (Camellia Sinensis) Growth And Functional Quality, Selena Ahmed, Colin M. Orians, Timothy S. Griffin, Sarabeth Buckley, Uchenna Unachukwu, Anne Elise Stratton, John Richard Stepp, Albert Robbat Jr, Sean Cash, Edward J. Kennelly

Publications and Research

Extreme shifts in water availability linked to global climate change are impacting crops worldwide. The present study examines the direct and interactive effects of water availability and pest pressures on tea (Camellia sinensis; Theaceae) growth and functional quality. Manipulative greenhouse experiments were used to measure the effects of variable water availability and pest pressures simulated by jasmonic acid (JA) on tea leaf growth and secondary metabolites that determine tea quality. Water treatments were simulated to replicate ideal tea growing conditions and extreme precipitation events in tropical southwestern China, a major centre of tea production. Results show that higher water availability …

Regulation Of Satiety Quiescence: Cyclic Gmp, Tgf Beta, And The Asi Neuron, Thomas Gallagher

Theses and Dissertations

The worm Caenorhabditis elegans is a well-studied model organism in numerous aspects of its biology. This small free living nematode has less than 1,000 cells, but shows clear conservation in both signaling and behavior to mammals in aspects of appetite control. This is of importance to humans, where failure of appetite control is a major factor in the unprecedented obesity epidemic that we see today. In general, worm behavior reflects its internal nutritional state and the availability and quality of food. Specifically, worms show a behavioral state that mimics aspects of the mammalian behavioral satiety sequence, which has been termed …

Identification Of Disulfide Bond Formation Between Mitoneet And Glutamate Dehydrogenase 1, Morgan E. Roberts, Jacquelyn P. Crail, Megan M. Laffoon, William G. Fernandez, Michael A. Menze, Mary E. Konkle

Faculty Research & Creative Activity

MitoNEET is a protein that was identified as a drug target for diabetes, but its cellular function as well as its role in diabetes remains elusive. Protein pull-down experiments identified glutamate dehydrogenase 1 (GDH1) as a potential binding partner. GDH1 is a key metabolic enzyme with emerging roles in insulin regulation. MitoNEET forms a covalent complex with GDH1 through disulfide bond formation and acts as an activator. Proteomic analysis identified the specific cysteine residues that participate in the disulfide bond. This is the first report that effectively links mitoNEET to activation of the insulin regulator GDH1.

Identification Of Disufide Bond Formation Between Mitoneet And Glutamate Dehydrogenase 1, Morgan E. Roberts, Jacquelyn P. Crail, Megan M. Laffoon, William G. Fernandez, Michael A. Menze, Mary E. Konkle

Faculty Research & Creative Activity

MitoNEET is a protein that was identified as a drug target for diabetes, but its cellular function as well as its role in diabetes remains elusive. Protein pull-down experiments identified glutamate dehydrogenase 1 (GDH1) as a potential binding partner. GDH1 is a key metabolic enzyme with emerging roles in insulin regulation. MitoNEET forms a covalent complex with GDH1 through disulfide bond formation and acts as an activator. Proteomic analysis identified the specific cysteine residues that participate in the disulfide bond. This is the first report that effectively links mitoNEET to activation of the insulin regulator GDH1.

The Glycine And Proline Reductase Systems: An Evolutionary Perspective And Presence In Enterobacteriaceae, Joshua Witt

HIM 1990-2015

The Glycine and Proline Reduction systems are two of the best characterized selenoenzymes in bacteria and have been found to occur in a wide variety of clostridia [1-5]. These enzymes are utilized to reduce glycine or D-proline to obtain energy via substrate level phosporylation or membrane gradients, respectively [6, 7]. This includes the pathogens C. difficile and C. botulinum [5, 8]. Strains of C. difficile are activate toxigenic pathways whenever either of these pathways is active within the cell [5, 8]. Though evolutionary studies have been conducted on ammonia producing bacteria [9] none has been done to directly characterize these …

Severe, Fatal Multisystem Manifestations In A Patient With Dolichol Kinase-Congenital Disorder Of Glycosylation., Michelle T Lieu, Bobby G Ng, Jeffrey S. Rush, Tim Wood, Monica J Basehore, Madhuri Hegde, Richard C Chang, Jose E Abdenur, Hudson H Freeze, Raymond Y Wang

Molecular and Cellular Biochemistry Faculty Publications

Congenital disorders of glycosylation are a group of metabolic disorders with an expansive and highly variable clinical presentation caused by abnormal glycosylation of proteins and lipids. Dolichol kinase (DOLK) catalyzes the final step in biosynthesis of dolichol phosphate (Dol-P), which is the oligosaccharide carrier required for protein N-glycosylation. Human DOLK deficiency, also known as DOLK-CDG or CDG-Im, results in a syndrome that has been reported to manifest with dilated cardiomyopathy of variable severity. A male neonate born to non-consanguineous parents of Palestinian origin presented with dysmorphic features, genital abnormalities, talipes equinovarus, and severe, refractory generalized seizures. Additional multi-systemic manifestations developed …

Ferritin-Based Photo-Oxidation Of Biomass For Nanoparticle Synthesis, Bioremediation, And Hydrogen Evolution, Oscar Petrucci

Theses and Dissertations

The cell is the basic unit of all living organisms. It is an amazing machine capable of self-replicating, growing, and synthesizing and shuttling thousands of compounds. To perform all of these activities the cell needs energy. The original source of energy for all living beings is the Sun. The energy of the sun is collected by the autotrophs (mostly plants) through photosynthesis and stored in the chemical bonds of carbohydrates and lipids through carboxylic acid intermediates; animals use these compounds to obtain the energy for their cells. Most of the energy extracted by the cell comes from the citric acid …

Raman Spectroscopic Investigation Of Chondroitinase Abc Treatment After Spinal Cord Injury In An Organotypic Model, Shane Ruberto

Theses - ALL

This study investigated (1) the ability of an organotypic model of spinal cord injury (SCI) to recapitulate significant pathobiological events of in vivo SCI from a Raman spectroscopic perspective, and (2) the Raman spectroscopic effects of chondroitinase ABC (cABC) treatment on said model of SCI. Tissue from mouse spinal cords was excised, sectioned, and placed into culture, before being systematically injured to induce trauma. Cultures with and without cABC treatment were assessed using Raman spectroscopy at varying times post-injury. We demonstrate that Raman spectral phenomena characteristic of SCI can be observed using an organotypic model. By comparing these phenomena with …

Severe, Fatal Multisystem Manifestations In A Patient With Dolichol Kinase-Congenital Disorder Of Glycosylation., Michelle T Lieu, Bobby G Ng, Jeffrey S Rush, Tim Wood, Monica J Basehore, Madhuri Hegde, Richard C Chang, Jose E Abdenur, Hudson H Freeze, Raymond Y Wang

Molecular and Cellular Biochemistry Faculty Publications

Congenital disorders of glycosylation are a group of metabolic disorders with an expansive and highly variable clinical presentation caused by abnormal glycosylation of proteins and lipids. Dolichol kinase (DOLK) catalyzes the final step in biosynthesis of dolichol phosphate (Dol-P), which is the oligosaccharide carrier required for protein N-glycosylation. Human DOLK deficiency, also known as DOLK-CDG or CDG-Im, results in a syndrome that has been reported to manifest with dilated cardiomyopathy of variable severity. A male neonate born to non-consanguineous parents of Palestinian origin presented with dysmorphic features, genital abnormalities, talipes equinovarus, and severe, refractory generalized seizures. Additional multi-systemic manifestations developed …

Recombinant Expression, Purification, And Characterization Of An Hiv-1 Tat-Human Cyclin T1 Chimera, Collin Lesley Fischer

Dissertations - ALL

Efficient transcription of the human immunodeficiency virus type 1 (HIV-1) requires the interaction of the viral protein Tat with the trans-activation response (TAR) stem-loop of the long-terminal repeat (LTR) portion of nascent viral RNA. The production of viable transcripts is enhanced dramatically by the interaction of HIV-1 Tat with the host protein human Cyclin T1. Interaction with hCycT1 remodels Tat protein contributing a single cysteine residue that is critical to the formation of the second of two zinc fingers (Zn2). Here we suggest that it is the presence of this critical cysteine residue and not the presence of arginine residues …

Monodentate, Bidentate And Photocrosslinkable Thiol Ligands For Improving Aqueous Biocompatible Quantum Dots, Hiroko Takeuchi

Graduate Theses and Dissertations

Water-soluble Quantum Dots (QDs) are highly sensitive fluorescent probes that are often used to study biological species. One of the most common ways to render QDs water-soluble for such applications is to apply hydrophilic thiolated ligands to the QD surface. However, these ligands are labile and can be easily exchanged on the QD surface, which can severely limit their application. As one way to overcome this limitation while maintaining a small colloidal size of QDs, we developed a method to stabilize hydrophilic thiolated ligands on the surface of QDs through the formation of a crosslinked shell using a photocrosslinking approach. …

Development Of Novel Subunit Vaccine Against H5n1 Influenza, Lu Zhang

Graduate Theses and Dissertations

Influenza is a common infectious disease resulting from a frequently mutated RNA virus. Vaccination is currently the most effective method to prevent people from seasonal or pandemic influenza. The production of traditional egg-based influenza vaccine is time-consuming and provides limited effect against new strains. Therefore, it is necessary to develop a rapid method to produce influenza vaccines. We proposed a novel influenza vaccine based on the E.coli expression system. Hemagglutinin (HA) is the major target surface protein of influenza virus for vaccine development. In this study, we sub-cloned the HAs encoding gene into an E. coli expression vector; the signal …