Biochemistry, Biophysics, and Structural Biology Commons^™

Spectroscopic Studies Of Cu2+ And Zn2+ Binding To Prodigiosin Analogs, Karen Chichetu, Papireddy Kancharla, Shilah Bonnett, Kevin Reynolds

Student Research Symposium

Prodigiosins are a family of secondary metabolites that were first isolated from the bacterium Serratia marascens. These natural compounds are red pigmented and characterized by a tri-pyrrole skeleton with a C-4 methoxy group. They have been reported to have good biological properties that include anticancer, antimalarial, antimicrobial and immunosuppressive activities. We have synthesized analogs of the natural prodigiosins (prodiginines) to produce a library of biologically active compounds which have improved biological activity and reduced cytotoxicity in human cells. In this work we studied the interaction between prodiginines and Cu2+ and Zn2+ using UV and Mass Spectroscopy techniques. Early results show …

Finding Rna-Dna Hybrid Viruses, Jeremy Filip, Geoffery S. Diemer, Kenneth M. Stedman

Student Research Symposium

Until extremely recently it was thought that recombination between DNA and RNA viruses was practically nonexistent. The discovery of the "RNA-DNA Hybrid Virus" (RDHV) genome in a metavirome from a hightemperature acidic lake changed this view (Diemer and Stedman, 2012). We, and others, have discovered multiple examples of this recombination "hiding in plain sight" in multiple both published and unpublished metagenomes from many different environments and recent publications (Rosario et al., 2012 a Tae Woong Whon et al, 2012, Mitsuhiro Yoshida et al., 2013, and several others through personal communication). Comparing the proteins within these hybrid viruses against each other …

Polyethylenimine-Enhanced Alumina Nanoscale Adjuvant For Cancer Vaccine, Naoko Uno, Haiyan Li, Hong-Ming Hu, Jun Jiao

Student Research Symposium

Aluminum oxide nanoparticles (Al2O3 NPs) have been shown to increase the efficiency of cell-mediated immune response. Specifically, CD8 and CD4 immune response is required for T cell activation by dendritic cells. These nanoparticles, when functionalized with peptides and other molecules, can be used as vaccine in cancer treatment. In this study, Al2O3 NPs were attached to E6/E7 proteins. HPV-induced cervical cancer expresses E6/E7 antigens. E6/E7 proteins were attached using surface modification of the Al2O3 NPs; different types of molecules were tested to see which adhered the highest amount of protein and produced the strongest cell response. Protein measurements were done …

Molecular Characterization Of A Patient Presumed To Have Prader-Willi Syndrome, Marina Falaleeva, Carlos R. Sulsona, Horst R. Zielke, Kathleen M. Currey, Pierre De La Grange, Vahid Aslanzadeh, Daniel J. Driscoll, Stefan Stamm

Molecular and Cellular Biochemistry Faculty Publications

Prader-Willi syndrome (PWS) is caused by the loss of RNA expression from an imprinted region on chromosome 15 that includes SNRPN, SNORD115, and SNORD116. Currently, there are no mouse models that faithfully reflect the human phenotype and investigations rely on human post-mortem material. During molecular characterization of tissue deposited in a public brain bank from a patient diagnosed with Prader-Willi syndrome, we found RNA expression from SNRPN, SNORD115, and SNORD116 which does not support a genetic diagnosis of Prader-Willi syndrome. The patient was a female, Caucasian nursing home resident with history of morbid obesity (BMI 56.3) and mental retardation. She …

From Gibbons To Gymnasts: A Look At The Biomechanics And Neurophysiology Of Brachiation In Gibbons And Its Human Rediscovery, Emma Et Pennock

Student Works

This conference paper serves to examine the evolutionary linkages of a brachiating ancestor in humans, the biomechanical and neurophysiology of modern day brachiators, and the human rediscovery of this form of locomotion. Brachiation is arguably one of the most metabolically effective modes of travel by any organism and can be observed most meritoriously in Gibbons. The purpose of the research conducted for this paper was to encourage further exploration of the neurophysiological similarities and differences between humans and non-human primates. The hope is that in spurring more interest and research in this area, further possibilities for rehabilitating brain injury will …

Eastern Kentucky Farmer's Willingness To Grow Biomass For Emergy Production, Austin P. Jacobs

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Austin P. Jacobs in May of 2013.

Mth1 Regulates The Interaction Between The Rgt1 Repressor And The Ssn6-Tup1 Corepressor Complex By Modulating Pka-Dependent Phosphorylation Of Rgt1, Adhiraj Roy, Yong Jae Shin, Kyu Hong Cho, Jeong-Ho Kim

Biochemistry and Molecular Medicine Faculty Publications

Glucose uptake, the first, rate-limiting step of its utilization, is facilitated by glucose transporters. Expression of several glucose transporter (HXT) genes in yeast is repressed by the Rgt1 repressor, which recruits the glucose-responsive transcription factor Mth1 and the general corepressor complex Ssn6-Tup1 in the absence of glucose; however, it is derepressed when Mth1 is inactivated by glucose. Here we show that Ssn6-Tup1 interferes with the DNA-binding ability of Rgt1 in the absence of Mth1 and that the Rgt1 function abrogated by Ssn6 overexpression is restored by co-overexpression of Mth1. Thus Mth1 likely regulates Rgt1 function not by modulating …

Patatin-Related Phospholipase Pplaiiiδ Increases Seed Oil Content With Long-Chain Fatty Acids In Arabidopsis, Maoyin Li, Sung Bahn, Chuchuan Fan, Jia Li, Tien Phan, Michael Ortiz, Mary Roth, Ruth Welti, Jan Jaworski, Xuemin Wang

Biology Department Faculty Works

The release of fatty acids from membrane lipids has been implicated in various metabolic and physiological processes, but in many cases, the enzymes involved and their functions in plants remain unclear. Patatin-related phospholipase As (pPLAs) constitute a major family of acyl-hydrolyzing enzymes in plants. Here, we show that pPLAIIId promotes the production of triacylglycerols with 20- and 22-carbon fatty acids in Arabidopsis (Arabidopsis thaliana). Of the four pPLAIIIs (a, b, g, d), only pPLAIIId gene knockout results in a decrease in seed oil content, and pPLAIIId is most highly expressed in developing embryos. The overexpression of pPLAIIId increases the content …

Section Abstracts: Structural Biology, Biochemistry And Biophysics

Virginia Journal of Science

Abstracts of the Structural Biology, Biochemistry and Biophysics Section for the 91st Annual Virginia Journal of Science Meeting, May 2013

Biophysical Studies Of Styrene-Maleic Acid Copolymer Stabilized Membrane Mimetics, Diane Yu

University Scholar Projects

Traditional methods of isolating membrane proteins involve the use of detergents that destabilize the membrane environment. Biophysical studies of membrane proteins are challenged by the requirement of a stable membrane platform. Lipodisq® nanoparticles are novel membrane mimetics that consist of 3:1 styrene-maleic acid copolymer encircling phospholipids to form discoidal species on the order of 10 nm in diameter. Bacteriorhodopsin was previously incorporated into Lipodisq® nano-particles from its native purple membrane without the addition of detergent. In this study, dynamic light scattering was used to investigate the stability of empty Lipodisq® nano-particles over time. These data show that Lipodisq® nano-particles are …

Spectroscopic Investigation Of The Interaction Of Fadh In Dna Photolyase With Uv-Damaged Dna, Kyle Luke Williams

Theses, Dissertations and Culminating Projects

Skin cancer is the most prevalent malignancy found in humans, with the diagnosis rate continuing to steadily increase. The primary cause of this disease is overexposure to harmful ultraviolet (UV) radiation from sunlight, which can induce damage to the nitrogenous bases in DNA via dimerization. The most prevalent UV-induced photoproducts in DNA are cyclobutane pyrimidine dimers (CPDs), most commonly between adjacent thymidines.

Organisms have implemented methods by which to repair these CPDs, the primary of which are nucleotide excision repair (NER) and photoreactivation by photolyases. Photolyases are blue-light activated flavoproteins that are more efficient at recognizing and repairing CPDs than …

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 91st Annual Virginia Journal of Science Meeting, May 2013

Aerobic Degradation Of Α-, Β-, Γ-Hexachlorocyclohexane By Narragansett Bay Bacterioplankton, Ian M. Rambo

Senior Honors Projects

Hexachlorocyclohexanes (HCHs) are a family of chlorinated organic compounds that were previously used as agricultural insecticides. HCHs are recognized as persistent organic pollutants due to their toxicity, recalcitrant properties, and tendency to bioaccumulate in food webs. Although HCH was first synthesized in 1825, its use was not widespread until the discovery of the insecticidal activity of the γ-HCH isomer in 1942. γ-HCH and its toxic waste isomers α-HCH and β-HCH were banned from production and use by the United Nations in 2009, yet these chemicals still present environmental problems due to their persistence in soils and surface waters. HCHs continue …

Modeling Amyloid-Ss Self-Assembly : Stability Of On-Pathway Aggregate Formation, Andrew Kevin Mauro

Theses, Dissertations and Culminating Projects

Protein misfolding and concomitant aggregation towards amyloid formation is the underlying biochemical commonality among a wide range of human pathologies. Amyloid formation involves the conversion of proteins from their native monomeric states (intrinsically disordered or globular) to well-organized, fibrillar aggregates in a nucleation-dependent manner. Understanding the mechanism of aggregation is important not only to gain better insight into amyloid pathology but also to simulate and predict molecular pathways. One of the main impediments in doing so is the highly stochastic nature of interactions that complicates the development of meaningful insights. In this study, we have utilized a well-characterized intermediate along …

Analysis Of The Chondroitinase Operon Of Flavobacterium Columnare, Erin L. Sorlien

Senior Honors Projects

Analysis of the chondroitinase operon of Flavobacterium columnare

Erin Sorlien

Major

Cell and Molecular Biology, Chemistry

Advisor

Dr. David R. Nelson

Date

May 2, 2013

Keywords

Flavobacterium columnare, columnaris disease, chondroitin AC lyase, complementation, csl operon

Abstract
Flavobacterium columnare, an opportunistic bacterial pathogen of fish, is the causative agent of columnaris disease (CD). The bacterium is a Gram-negative rod that exhibits gliding motility and avidly forms biofilms. CD affects both wild and cultured freshwater fish, and continues to cause large economic losses to the fish farming industry. According to an investigation conducted by the National Animal Health Monitoring System, CD …

The Use Of P53-Derived Stapled Peptides As Affinity Isolation Reagents, Kathryn Margaret Headley

Renée Crown University Honors Thesis Projects - All

The transcription factor p53 can induce apoptosis and cell cycle arrest in response to cellular distress. Cancer cells often display increased cell survival. In most cases, this is due to a p53-related defect, such as mutation, deletion, degradation, or sequestration. HDM2 and HDMX are homologous proteins that regulate the function of p53, and their over-expression can lead to an ineffective p53 response. Various inhibitors, including hydrocarbon stabilized alpha-helices of p53 (SAH-p53s), have been developed to target HDM2 and HDMX and restore functionality to the p53 pathway. It has been recently found that SAH-p53 factors also elicit cell death responses in …

Characterization Of Dap2 (Defense-­‐Associated Aspartic Protease-­‐2) In Arabidopsis Thaliana And Determining Its Role In Plant Defense Responses, Kemardo Kitaro Henry

Renée Crown University Honors Thesis Projects - All

Plants defend themselves from invading pathogens by coordinating activity of several plant defense-­‐associated genes. Defense-­‐Associated Aspartic Protease-­‐1 (DAP1) gene of Arabidopsis encodes for an atypical aspartic protease with a putative proteolytic activity. The DAP1 is a negative regulator of plant immunity and the transgenic plants ectopically expressing this genes support pathogen growth and pathogenicity. The Arabidopsis genome has another putative protese that has ~75% homology to DAP1 present in close proximity and therefore was named DAP2. Here, I describe the role of the DAP2 gene in plant defense responses. Two independent knockout dap2 mutants are found to be more susceptible …

Vitamin B12-Based Bioconjugate Probes For In Vitro And In Vivo Imaging, Anna Kahkoska

Renée Crown University Honors Thesis Projects - All

Cancer is the second leading cause of death in the United States. This year, an estimated 577,190 Americans will die as a result of this family of diseases. Finding cancer at its most treatable stage gives patients the greatest chance of recovery; novel imaging agents that target primary and metastasized tumors offer hope for improved prognoses in the future. Based on the hypothesis that vitamin B12 (B12) and its association with specific transport proteins could offer selective access to cancer cell lines, a series of B12-based imaging agents were synthesized, characterized, and assayed for both in vitro and in vivo …

Investigation Of Ghrelin Acylation By Ghrelin O-Acyltransferase, Edward P. Prybolsky

Renée Crown University Honors Thesis Projects - All

Ghrelin is a peptide hormone involved in hunger signaling and other physiological processes. To become active, ghrelin first must be acylated by ghrelin O-acyltransferase (GOAT). This enzyme carries out a post-translational modification that attaches an octanoyl group to the side chain of the serine 3 (S3) residue of ghrelin. With ghrelin linked to hunger signaling, memory, and other physiological processes, GOAT has been identified as a potential drug target. However, inhibitor design is difficult because not much is known regarding the active site structure and catalytic mechanism of GOAT. This study reports the design of a novel fluorescence-based assay that …

Development Of Protein Farnesyltransferase Variants With Altered Substrate Selectivity, Susan Zhang

Renée Crown University Honors Thesis Projects - All

Post-translational modifications play an essential role in regulating protein structure and function. Enzymes catalyzing these modifications must often recognize and modify multiple substrate proteins from among a plethora of non-substrates with similar structures and amino acid sequences. For example, protein farnesyltransferase (FTase) catalyzes the addition of an isoprenoid group to a cysteine near the C-terminus of a substrate protein and is proposed to modify a pool of substrates numbering more than one hundred. We seek to understand the interactions in the FTase active site that engender substrate selectivity. By mutating two residues within FTase, we have developed FTase variants with …

Design Of Metalloproteins For Catalysis And Bioimaging, Krystyna Zhezherya

Renée Crown University Honors Thesis Projects - All

Abstract

Metalloenzymes constitute a large subclass of proteins with diverse functions including metal-sensing, signal transduction pathways, and metal transport. In this report, I aim to study the intricate relationship between structure and function as it relates to metalloproteins in the fields of catalysis and bioimaging. For catalysis, I used existing platforms in addition to de novo design to study small scaffolds with varying secondary structure, and their function in catalyzing the hydrolysis of a p-nitrophenol ester. For bioimaging, I used an existing enzyme known as human carbonic anhydrase I, hCA, to develop a bioimaging agent that can be fused to …

Structural And Functional Studies On The Role Of The Retinoblastoma Binding Protein Five (Rbbp5) In The Histone Methyltransferase Activity Of The Mixed Lineage Leukemia (Mll1) Core Complex, Melody Sanders

Biology - Theses

Cells employ elaborate mechanisms to introduce structural and chemical variation into chromatin in the form of covalent post-translational modifications. Covalent modifications of histones contribute to the dynamic states of chromatin structure that govern nearly all of DNA-coupled processes such as transcription, replication, and repair. The mechanism by which covalent modifications of histones contribute to these activities remains a central question to understanding genome regulation and its dysfunction in human disease. Although there is extensive literature documenting the identification of many of the enzymes that place histone modifications, far less is known about how the enzymes are targeted and how their …

Manipulating Aktivated Metabolism Via Mtorc1, Ivan Von Hack Prestinary

HIM 1990-2015

Although poorly understood, normal cells and cancerous cells of the same type exhibit different patterns of nutrient consumption, processing and utility of metabolic substrates. Differences in substrate uptake, preference, and alternately emphasized metabolic pathways offer opportunities for selective targeting of cancer versus stroma. This may be accomplished by using a sequential approach of nutrient deprivation and pharmaceutical perturbation of metabolic pathways to inhibit cellular proliferation. The purpose of this study was to investigate the effects of restricting glucose and glutamine concentrations, in vitro, to levels that resemble a potential human fasting state. The mammalian target of rapamycin (mTOR), a mediator …

Effects Of Mtn Enzyme Deficiency On E. Coli O157:H7 Growth And Virulence, Reece Knippel

Boise State University Theses and Dissertations

The bacterial enzyme Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTN) is involved in methionine and adenine salvage from the by-products of S-adenosylmethionine (SAM, AdoMet) dependent reactions. MTN plays a critical role in alleviating product inhibition of SAM dependent reactions, including methylation reactions and the synthesis of polyamines, vitamins, and autinducer signals. Due to its absence from humans and its importance to bacterial metabolism, MTN is a potential target for the development of novel antibiotics to treat microbial infections. In this study, a MTN gene knock-out (MTN KO) strain of the pathogen E. coli O157:H7 was created to study the impact of MTN activity …

The Effects Of Glutathione And Its Derivatives On The Survival Of Mycobacterium Bovis-Bcg Vegetative And Persistent Organisms, Neil Patel

Honors College Theses

Mycobacterium tuberculosis is responsible for nearly 2 million deaths yearly. Upon inhalation,mycobacteria are engulfed by alveolar macrophages. These cells produce reactive oxygen and nitrogen intermediates (ROI’s and RNI’s), which normally kill pathogens, but are ineffective against invading mycobacteria. What ensues, is the formation of a tubercle to sequester the infected macrophages, and the initiation of a latent tuberculosis infection, in which the mycobacteria enter a state of non-replicative persistence (NRP). Glutathione (GSH), a host tripeptide thiol-based detoxification molecule, protects host cells from ROI/RNI toxicity.Recently, it has been demonstrated that GSH is toxic to in vitro and early infection mycobacteria, but …

Amphetamine Elicits Opposing Actions On Readily Releasable And Reserve Pools For Dopamine, Dan P. Covey, Steven A. Juliano, Paul A. Garris

Faculty Publications – Biological Sciences

Amphetamine, a highly addictive drug with therapeutic efficacy, exerts paradoxical effects on the fundamental communication modes employed by dopamine neurons in modulating behavior. While amphetamine elevates tonic dopamine signaling by depleting vesicular stores and driving non-exocytotic release through reverse transport, this psychostimulant also activates phasic dopamine signaling by up-regulating vesicular dopamine release. We hypothesized that these seemingly incongruent effects arise from amphetamine depleting the reserve pool and enhancing the readily releasable pool. This novel hypothesis was tested using in vivo voltammetry and stimulus trains of varying duration to access different vesicular stores. We show that amphetamine actions are stimulus dependent …

Increased Production And Extraction Efficiency Of Triacylglycerides From Microorganisms And An Enhanced Understanding Of The Pathways Involved In The Production Of Triacylglycerides And Fatty Alcohols, Robert M. Willis

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The continued increase in the demand for fossil fuels combined with their ever dwindling supply has prompted the search for a suitable alternative fuel. The research contained within this dissertation seeks to increase the lipid (fat) content of cellular feedstocks, improve extraction efficiencies of lipids, and to understand the pathways involved in the production of fatty alcohols and triacylglycerides, compounds commonly used in many industrial processes, from microbial feedstocks. This work has been done in an attempt to increase the overall economic viability of microbial biofuels production.

The production of biofuels from microalgae used as a feedstock allows for the …

The Phosphoramidase Competency Of Prototypical Phosphatase Catalytic Motifs, Mark P. Haney

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Phosphorylation of proteins is ubiquitous. Phosphorylation can activate proteins, deactivate proteins, assist in signaling, or serve other roles depending upon the biochemical pathway. Attaching phosphate to proteins is accomplished by enzymes called kinases; removing phosphate from proteins is accomplished by enzymes called phosphatases. Cells must regulate their biochemical pathways, and the antipodal roles of kinases and phosphatases represent the yin-yang of phosphorylation.

Phosphorylation of proteins is known to occur on serine, threonine, and tyrosine. This creates a phosphoester bond. Phosphoester bonds have a phosphorus-oxygen (P-O) bond. The ability of phosphatases to cleave such phosphoester bonds is well studied. Phosphorylation of …

What Can Biochemistry Students Learn About Protein Translation? Using Variation Theory To Explore The Space Of Learning Created By Some Common External Representations, Thomas J. Bussey

UNLV Theses, Dissertations, Professional Papers, and Capstones

Biochemistry education relies heavily on students' ability to visualize abstract cellular and molecular processes, mechanisms, and components. As such, biochemistry educators often turn to external representations to provide tangible, working models from which students' internal representations (mental models) can be constructed, evaluated, and revised. However, prior research has shown that, while potentially beneficial, external representations can also lead to alternative student conceptions.

Considering the breadth of biochemical phenomena, protein translation has been identified as an essential biochemical process and can subsequently be considered a fundamental concept for biochemistry students to learn. External representations of translation range from static diagrams to …

The Role Of Oswrky71 And Its Interacting Proteins In Seed Germination And Early Growth Of Cereal Grains, Margaret Ja Shin

UNLV Theses, Dissertations, Professional Papers, and Capstones

During seed germination and early seedling growth, complex molecular and physiological events occur in rice (Oryza sativa) and other cereal grains. As the seed transitions to vegetative tissue, it responds to both favorable and unfavorable environmental conditions and is vulnerable to attack by predation and disease. Although seeds are relatively small and tender in size, extensive and sophisticated molecular networks enables the immobile seed to grow, survive and adapt in its environment. One of the networks I am interested in is in the crosstalk between the gibberellin (GA) and abscisic acid (ABA) signaling pathways. These pathways are interesting because they …