Chemistry Commons^™

Synthesis And Immunological Evaluation Of Type I, Type Ii, And Gamma Delta Nkt Cell Antigens, Brian L. Anderson

Theses and Dissertations

The purpose of the immune system is to protect our bodies from infection. One way it accomplishes this task is through the presentation of foreign pathogens to NKT cells. After an antigen is presented to the T cell receptor, activated NKT cells quickly release soluble chemical signals, termed chemokines and cytokines, that modulate the response of the immune system. Due to the immunological relevance of NKT cell activation, we developed and synthesised non-natural analogs of immunostimulatory type I, II, and gamma delta NKT cell antigens. The immunological evaluations of these analogs resulted in identification of sulfatide as a gamma delta …

An Alternative Ribozyme For The Rna Hypercycle, Ishak Elkhal

Student Research Symposium

In the quest to forward understanding of the prebiotic world (specifically, the RNA World Hypothesis), one of the most interesting paradigms to consider is the potential for cooperative networks that may have driven molecular evolution forward. Such a network may exist as an RNA hypercycle, as proposed by Eigen (1977). Much progress has been made towards an RNA hypercycle-like system, especially using the Azoarcus ribozyme system demonstrated by Vaidya et al. (2012). The current work is dedicated to constructing a second model as a cooperative RNA network, utilizing a group I intron from Coxiella burnetii (Cbu1917). The intron was constructed …

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 …

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 …

Investigations Toward Tunability Of Mechanical, Thermal, And Impact Properties Of Thiol-Ene Networks For Novel High Energy Absorbing Materials, Olivia Devon Mcnair

Dissertations

The UV polymerization of thiols with electron rich alkenes is a highly resourceful reaction that has been utilized by scientists within various disciplines to produce an even more versatile display of applications. This dissertation focuses on a newer application, thiol-ene network (TEN) materials for energy absorption devices. TEN networks display a host of positive polymer properties such as low stress, high optical clarity and uniformity, but they also suffer from unfavorable mechanical properties such as low toughness and elongation at break. The poor mechanical properties demonstrated by TENs prohibit them as choice materials for applications requiring thicker material forms, including …

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 …

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 …

Mesobiliverdin Ixα Enhances Rat Pancreatic Islet Yield And Function, Taihei Ito, Dong Chen, Cheng-Wei Tom Chang, Takashi Kenmochi, Tomonori Saito, Satoshi Suzuki, Jon Y. Takemoto

Chemistry and Biochemistry Faculty Publications

The aims of this study were to produce mesobiliverdin IXα, an analog of anti-inflammatory biliverdin IXα, and to test its ability to enhance rat pancreatic islet yield for allograft transplantation into diabetic recipients. Mesobiliverdin IXα was synthesized from phycocyanobilin derived from cyanobacteria, and its identity and purity were analyzed by chromatographic and spectroscopic methods. Mesobiliverdin IXα was a substrate for human NADPH biliverdin reductase. Excised Lewis rat pancreata infused with mesobiliverdin IXα and biliverdin IXα-HCl (1–100 μM) yielded islet equivalents as high as 86.7 and 36.5%, respectively, above those from non-treated controls, and the islets showed a high degree of …

Kinetics Of Atmospheric Reactions Of Biogenic Volatile Organic Compounds: Measurement Of The Rate Constant Ofthujone + Cl· At 296 K And Calculation Ofthe Equilibrium Constant For The Ho2ch2ch2o2· H2o Complex, Marie Coy Killian

Theses and Dissertations

Biogenic volatile organic compounds (VOCs) react with Cl and OH radicals and the resulting radicals combine with oxygen to form peroxy radicals RO2. Organic peroxy radicals can then react with NO to form NO2, a precursor of tropospheric ozone. The work presented here explored the initial reaction between Cl and thujone, a VOC emitted by Great Basin sagebrush. The rate constant for the reaction of thujone + Cl at 296 K was measured with the method of relative rates with FTIR for detection of reactants. LEDs were used to photolyze Cl2 to generate Cl in the reaction cell. Thujone was …

Side Chain Requirements For Affinity And Specificity In D5, An Hiv-1 Antibody Derived From The Vh1-69 Germline Segment, Alex Stewart, Joseph S. Harrison, Lauren K. Regula, Jonathan R. Lai

College of the Pacific Faculty Articles

BACKGROUND: Analysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464-5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the …

Multiscale Modeling Of Enzyme-Catalyzed Methanol Production By Particulate Methane Monooxygenase, Katherine K. Bearden

Doctoral Dissertations

In this work, the conversion of methane to methanol by the particulate Methane Monooxygenase (pMMO) enzyme is investigated using a multi-scale modeling approach. This enzyme participates in carbon cycling and aids in the removal of harmful atmospheric methane, converting it to methanol. The interaction between pMMO and a neighboring enzyme that is present in the same organism is studied, and the unknown pMMO active site is elucidated and tested for methane oxidation towards the production of methanol.

Fundamental knowledge of pMMO's mechanism is not fully understood. Understanding how this enzyme works in nature will provide information towards designing efficient synthetic …

Volume 05, Ian Karamarkovich, Jessica Cox, Kyle Fowlkes, Allison Pawlowski, Kaitlin Major, Carrie Dunham, Kelsey Scheitlin, Kathryn Grayson, Ashley Johnson, Jennifer Nehrt, Kelsey Stolzenbach, Kristin Mcquarrie, Sara Nelson, Melisa Michelle, Jessica Sudlow, Perry Bason, Danielle Dmuchawski, Mariah Asbell, Matthew Sakach, Timothy Smith Jr., Annaliese Troxell, T. Dane Summerell, Sarah Ganrude, Malina Rutherford, Hannah Hopper, John Berry Jr., James Early, Colleen Festa, Chelsea D. Taylor, Michelle Maddox, Kaitlyn Smith, Sarah Schu, Cabell Edmunds, Katherine Grayson, Kayla Tornai

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

The Tallis House as an Extension of Emily Tallis in McEwan's Atonement by Ian Karamarkovich

Graphic Design by Jessica Cox

Graphic Design by Kyle Fowlkes

Graphic Design by Allison Pawlowski

Incorporating Original Research in The Classroom: A Case Study Analyzing the Influence of the Chesapeake Bay on Local Temperatures by Kaitlin Major, Carrie Dunham and Dr. Kelsey Scheitlin

Graphic Design by Kathryn Grayson

Graphic Design by Ashley Johnson

Facing the Music: Environmental Impact Assessment of Building A Concert Hall on North Campus by Jennifer Nehrt, Kelsey Stolzenbach And Dr. Kelsey Scheitlin

Art by Kristin …

Facile Synthesis And Improved Pore Structure Characterization Of Mesoporous Γ-Alumina Catalyst Supports With Tunable Pore Size, Baiyu Huang

Theses and Dissertations

Mesoporous γ-alumina is the most extensively used catalysts support in a wide range of catalytic processes. The usefulness of γ-alumina relies on its favorable combination of physical, textural, thermal, and chemical properties. Pore structure properties are among the most important properties, since high surface area and large pore volume enable higher loading of active catalytic phases, while design of pore size and pore size distribution is critical to optimize pore diffusional transport and product selectivity. In addition, accurate determination of surface area (SA), pore volume (PV) and pore size distribution (PSD) of porous supports, catalysts, and nanomaterials is vital to …

Resorcinarene-Based Cavitands: From Structural Design And Synthesis To Separations Applications, Na Li

Theses and Dissertations

Resorcinarenes are cyclic tetramers that are synthesized by the condensation of resorcinol and various aldehydes. The upper and lower rims can be modified with substituents that provide specific selectivity and other chemical features. In this work, resorcinarene-based macrocyclic ligands with specific selectivities have been designed, synthesized and applied to chiral amine discrimination and transition metal ion separations.These resorcinarenes fall into two categories. In the first type, the upper rims of resorcinarenes were modified with amino acid groups, including chiral alanine groups. The lower rims were modified with --CH3, or --C11H23 groups. The structures were studied by nuclear magnetic resonance (NMR), …

Insights Into The Roles Of Desolvation And Π-Electron Interactions During Dna Polymerization, Edward A. Motea, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

This report describes the use of several isosteric non-natural nucleotides as probes to evaluate the roles of nucleobase shape, size, solvation energies, and π-electron interactions as forces influencing key kinetic steps of the DNA polymerization cycle. Results are provided using representative high- and low-fidelity DNA polymerases. Results generated with the E. coli Klenow fragment reveal that this high-fidelity polymerase utilizes hydrophobic nucleotide analogues with higher catalytic efficiencies compared to hydrophilic analogues. These data support a major role for nucleobase desolvation during nucleotide selection and insertion. In contrast, the low-fidelity HIV-1 reverse transcriptase discriminates against hydrophobic analogues and only tolerates non-natural …

Immunological And Reproductive Health Assessment In Herring Gulls And Black-Crowned Night Herons In The Hudson-Raritan Estuary, Keith A. Grasman, Kathy R. Echols, Thomas M. May, Paul H. Peterman

University Faculty Publications and Creative Works

Previous studies have shown inexplicable declines in breeding waterbirds within western New York/New Jersey Harbor between 1996 and 2002 and elevated polychlorinated dibenzo-p-dioxins and polychlorinated biphenyls (PCBs) in double-crested cormorant (Phalacrocorax auritus) eggs. The present study assessed associations between immune function, prefledgling survival, and selected organochlorine compounds and metals in herring gulls (Larus argentatus) and black-crowned night herons (Nycticorax nycticorax) in lower New York Harbor during 2003. In pipping gull embryos, lymphoid cells were counted in the thymus and bursa of Fabricius (sites of T and B lymphocyte maturation, respectively). The phytohemagglutinin (PHA) skin response assessed T cell function in …

Iapp Aggregation And Cellular Toxicity Are Inhibited By 1,2,3,4,6-Penta-O-Galloyl-Β-D-Glucose, Edward Bruno, Catalina Pereira, Karla P. Roman, Marisa Takiguchi, Pei-Yu Kao, Luiza A. Nogaj, David A. Moffet

Chemistry and Biochemistry Faculty Works

The polyphenol, 1,2,3,4,6-penta-O-galloyl-β-D-glucose (PGG) has been found to exhibit a host of positive pharmacologic activities, including anti-cancer and anti-diabetic. Little is known about the mode of action of PGG in yielding these positive activities. We show here that PGG is a potent inhibitor of IAPP (islet amyloid polypeptide, amylin) aggregation. Preventing the initial aggregation event of IAPP is one strategy for slowing, and possibly preventing, the toxic effects of IAPP oligomeric intermediates. Equal molar ratios of PGG to IAPP substantially reduced the ability of IAPP to bind thioflavin T. Atomic force microscopy revealed that PGG prevented amyloid-based fiber formation under …

Affinity Monolith Chromatography: A Review Of Principles And Recent Analytical Applications, Erika L. Pfaunmiller, Marie Laura Paulemond, Courtney M. Dupper, David S. Hage

David Hage Publications

Affinity monolith chromatography (AMC) is a type of liquid chromatography that uses a monolithic support and a biologically-related binding agent as a stationary phase. AMC is a powerful method for the selective separation, analysis or studies of specific target compounds in a sample. This review discusses the basic principles of AMC and recent developments or applications of this method, with particular emphasis being given to work that has appeared in the last five years. Various materials that have been used to prepare columns for AMC are examined, including organic monoliths, silica monoliths, agarose monoliths and cryogels. These supports have been …

Kinetic And Spectroscopic Studies Of Bicupin Oxalate Oxidase And Putative Active Site Mutants, Ellen W. Moomaw, Eric Hoffer, Patricia Moussatche, John C. Salerno

Faculty Articles

Ceriporiopsis subvermispora oxalate oxidase (CsOxOx) is the first bicupin enzyme identified that catalyzes manganese-dependent oxidation of oxalate. In previous work, we have shown that the dominant contribution to catalysis comes from the monoprotonated form of oxalate binding to a form of the enzyme in which an active site carboxylic acid residue must be unprotonated. CsOxOx shares greatest sequence homology with bicupin microbial oxalate decarboxylases (OxDC) and the 241-244DASN region of the N-terminal Mn binding domain of CsOxOx is analogous to the lid region of OxDC that has been shown to determine reaction specificity. We have prepared a series of CsOxOx …

Integrating Art And Science In Undergraduate Education, Daniel Gurnon

Chemistry & Biochemistry Faculty Publications

The prevailing vision for undergraduate science education includes increased collaboration among teachers of science, technology, engineering and math (STEM) and an overhaul of introductory courses [1]–[4]. But by staying within the borders of STEM, are we overlooking connections between the arts and innovative science? Likewise, are we missing an important opportunity to inspire and inform nonscientists? Here we explore how weaving the visual arts into a science curriculum can both help develop scientific imagination and engage nonscientists. As an example, we describe a recent collaboration between artists and scientists to create a series of science-inspired sculptures.

A Novel Algorithm For Validating Peptide Identification From A Shotgun Proteomics Search Engine, Ling Jian, Xinnan Niu, Zhonghang Xia, Parimal Samir, Chiranthani Sumanasekera, Zheng Mu, Jennifer L. Jennings, Kristen L. Hoek, Tara Allos, Leigh M. Howard, Kathryn M. Edwards, P. Anthony Weil, Andrew J. Link

Chemistry Faculty Research

Liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) has revolutionized the proteomics analysis of complexes, cells, and tissues. In a typical proteomic analysis, the tandem mass spectra from a LC–MS/MS experiment are assigned to a peptide by a search engine that compares the experimental MS/MS peptide data to theoretical peptide sequences in a protein database. The peptide spectra matches are then used to infer a list of identified proteins in the original sample. However, the search engines often fail to distinguish between correct and incorrect peptides assignments. In this study, we designed and implemented a novel algorithm called De-Noise to …

Dna Damage Repair Genes Controlling Human Papillomavirus (Hpv) Episome Levels Under Conditions Of Stability And Extreme Instability, Terri Edwards, Thomas Vidmar, Kevin Koeller, James Bashkin, Chris Fisher

Chemistry & Biochemistry Faculty Works

DNA damage response (DDR) genes and pathways controlling the stability of HPV episomal DNA are reported here. We set out to understand the mechanism by which a DNA-binding, N-methylpyrrole-imidazole hairpin polyamide (PA25) acts to cause the dramatic loss of HPV DNA from cells. Southern blots revealed that PA25 alters HPV episomes within 5 hours of treatment. Gene expression arrays identified numerous DDR genes that were specifically altered in HPV16 episome-containing cells (W12E) by PA25, but not in HPV-negative (C33A) cells or in cells with integrated HPV16 (SiHa). A siRNA screen of 240 DDR genes was then conducted to identify enhancers …

Lysine Biosynthesis In Bacteria: A Metallodesuccinylase As A Potential Antimicrobial Target, Danuta M. Gillner, Daniel P. Becker Ph.D., Richard C. Holz

Chemistry: Faculty Publications and Other Works

In this review, we summarize the recent literature on dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) enzymes, with an emphasis on structure–function studies that provide insight into the catalytic mechanism. Crystallographic data have also provided insight into residues that might be involved in substrate and hence inhibitor recognition and binding. These data have led to the design and synthesis of several new DapE inhibitors, which are described along with what is known about how inhibitors interact with the active site of DapE enzymes, including the efficacy of a moderately strong DapE inhibitor.

Utilizing Nmr Spectroscopy And Molecular Docking As Tools For The Structural Determination And Functional Annotation Of Proteins, Jaime Stark

Department of Chemistry: Dissertations, Theses, and Student Research

With the completion of the Human Genome Project in 2001 and the subsequent explosion of organisms with sequenced genomes, we are now aware of nearly 28 million proteins. Determining the role of each of these proteins is essential to our understanding of biology and the development of medical advances. Unfortunately, the experimental approaches to determine protein function are too slow to investigate every protein. Bioinformatics approaches, such as sequence and structure homology, have helped to annotate the functions of many similar proteins. However, despite these computational approaches, approximately 40% of proteins still have no known function. Alleviating this deficit will …

Metallization Of Dna And Dna Origami Using A Pd Seeding Method, Yanli Geng

Theses and Dissertations

In this dissertation, I developed a Pd seeding method in association with electroless plating, to successfully metallize both lambda DNA and DNA origami templates on different surfaces. On mica surfaces, this method offered a fast, simple process, and the ability to obtain a relatively high yield of metallized DNA nanostructures. When using lambda DNA as the templates, I studied the effect of Pd(II) activation time on the seed height and density, and an optimal activation time between 10 and 30 min was obtained. Based on the Pd seeds formed on DNA, as well as a Pd electroless plating solution, continuous …

Psychosine, The Cytotoxic Sphingolipid That Accumulates In Globoid Cell Leukodystrophy, Alters Membrane Architecture, Jacqueline Hawkins-Salsbury, Archana Parameswar, Xuntian Jiang, Paul Schlesinger, Ernesto Bongarzone, Daniel Ory, Alexei Demchenko, Mark Sands

Chemistry & Biochemistry Faculty Works

Globoid cell leukodystrophy (GLD) is a neurological disease caused by deficiency of the lysosomal enzyme galactosylceramidase (GALC). In the absence of GALC, the cytotoxic glycosphingolipid, psychosine (psy), accumulates in the nervous system. Psychosine accumulation preferentially affects oligodendrocytes, leading to progressive demyelination and infiltration of activated monocytes/macrophages into the CNS. GLD is characterized by motor defects, cognitive deficits, seizures, and death by 2–5 years of age. It has been hypothesized that psychosine accumulation, primarily within lipid rafts, results in the pathogenic cascade in GLD. However, the mechanism of psychosine toxicity has yet to be elucidated. Therefore, we synthesized the enantiomer of …

04. Botany, University Of Central Oklahoma

Oklahoma Research Day Abstracts

No abstract provided.