Digital Commons Network^™

Biomimetic Adhesive Thiol-Ene Films For Improved Adhesion, Laken L. Kendrick

Honors Theses

Current dental restoration materials fall short in adhesion and often pull away from the surface of the tooth upon curing. This project seeks to design polymers that can adhere to wet, heterogeneous surfaces as potential materials for dental restoration applications. The goal of this project is to mimic the structure and adhesive properties of natural adhesives containing 3,4-dihydroxyphenyl-L-alanine (DOPA). We will synthesize mono- and di-functional DOPA derivatives with catechol functionality and investigate their adhesion compared to their non-catechol-containing alternative through incorporation into a model thiol-ene photopolymerization. Functional group conversion, real time kinetics, and adhesion data will be used to analyze …

Distinguishing Macrophage Activation States By Mass Spectrometry, Matthias Manfred Knust

Graduate Theses and Dissertations

Macrophages are versatile and highly adaptive cells that are involved in a wide range of physiological processes including host defense, homeostasis or regeneration, as well as pathogenesis. They react to their microenvironment, assuming various roles based on chemical and/or physical cues, and can reversibly shift between these so-called activation states. Concurrently, the technique of immunohistochemistry is used to gain spatial information on activated macrophages on tissue sections. The aim of this work was to find mass spectral biomarkers that allow the differentiation of activation states, and establish conditions that can be used in imaging mass spectrometry (IMS) experiments to investigate …

Simulation In Algorithmic Self-Assembly, Jacob Hendricks

Graduate Theses and Dissertations

Winfree introduced a model of self-assembling systems called the abstract Tile Assembly Model (aTAM) where square tiles with glues on their edges attach spontaneously via matching glues to form complex structures. A generalization of the aTAM called the 2HAM (two-handed aTAM) not only allows for single tiles to bind, but also for "supertile" assemblies consisting of any number of tiles to attach. We consider a variety of models based on either the aTAM or the 2HAM. The underlying commonality of the work presented here is simulation. We introduce the polyTAM, where a tile system consists of a collection of polyomino …

Characterization Of Cellulase Enzyme Inhibitors Formed During The Chemical Pretreatments Of Rice Straw, Kalavathy Rajan

Graduate Theses and Dissertations

Production of fuels and chemicals from a renewable and inexpensive resource such as lignocellulosic biomass is a lucrative and sustainable option for the advanced biofuel and bio-based chemical platform. Agricultural residues constitute the bulk of potential feedstock available for cellulosic fuel production. On a global scale, rice straw is the largest source of agricultural residues and is therefore an ideal crop model for biomass deconstruction studies. Lignocellulosic biofuel production involves the processes of biomass conditioning, enzymatic saccharification, microbial fermentation and ethanol distillation, and one of the major factors affecting its techno-economic feasibility is the biomass recalcitrance to enzymatic saccharification. Preconditioning …

Inertial Force-Driven Synthesis Of Near-Infrared Plasmonic Nanosphere Composites: Physicochemical Characterizations, Joseph Noel Batta-Mpouma

Graduate Theses and Dissertations

Near-infrared (NIR) responsive nanoparticles (NPs) like gold nanorods (GNRs) are important in biomedical fields because of their transparency for biological tissues. Although GNRs are sought after as contrast agents for theranostics in cancer studies, capping ligands like cetyltrimethylammonium bromide (CTAB) for the GNR synthesis are toxic for biological tissues. The need for an alternative to toxic GNRs is of interest to alleviate the problem.

This work aimed to optimize the synthesis of NIR responsive nanosphere composites (NSCs) by inertial force (g-force) using colloidal gold NPs as model, elucidate the mechanism for the NSC formation, and study their detailed physicochemical characteristics. …

Analysis Of Free Solute Fractions And Solute-Protein Interactions Using Ultrafast Affinity Extraction And Affinity Microcolumns, Xiwei Zheng

Department of Chemistry: Dissertations, Theses, and Student Research

This dissertation describes the use of a high-performance affinity chromatography method based on ultrafast affinity extraction and microcolumns to study biological interactions.

In the first project, a new method was created and based on ultrafast affinity extraction to determine both the dissociation rate constants (k_d) and association equilibrium constants (K_a) for drug-protein interactions in solution. Various conditions to optimize the use of ultrafast affinity extraction for equilibrium and kinetic studies were considered.

The objective of the next portion of this dissertation was to develop a chromatographic approach to measure free drug fractions in more …

Chromatographic Analysis Of Drug-Protein Interactions During Diabetes And Characterization Of Human Serum Albumin Through Multidimensional Mass Spectrometry, Ryan E. Matsuda

Department of Chemistry: Dissertations, Theses, and Student Research

Diabetes is a metabolic disease that can lead to the non-enzymatic glycation of serum proteins such as human serum albumin (HSA). Previous studies have indicated that glycation can affect the structure and function of these proteins. This dissertation describes the development of tools and techniques based on high performance affinity chromatography (HPAC) and multidimensional mass spectrometry to analyze the effects of glycation on the function and structure of HSA.

A major portion of this research involved the utilization of HPAC to examine the effect of glycation on the binding of three second-generation sulfonylurea drugs and one third-generation sulfonylurea drug. These …

Investigations Into The Molecular Mechanisms Of Bacterial Pathogen–Host Interactions: Construction Of A Dual Plasmid System For Incorporation Of Unnatural Amino Acids Into Pseudomonas Syringae Pv. Tomato Dc3000, Scotty D. Raber

Department of Chemistry: Dissertations, Theses, and Student Research

A dual plasmid system for the incorporation of unnatural amino acids into plant pathogen, Pseudomonas syringae pv. tomato DC3000, has been designed. This invention is expected to allow (a) mutations of proteins synthesized by the bacterium, P. syringae pv. tomato DC3000, that can capture molecular targets, especially for such modified proteins secreted by the phytopathogen into the host plant cells of A. thaliana and S. lycopersicum, (b) expression of biological probes in the bacterial species to monitor changes in redox, nutritional, and other small molecule states over pre-, post- and in situ disease stages, and secretion of such biological …

Molecular Mechanism For The Biosynthesis Of Antifungal Hsaf And Antibacterial Wap-8294a2, Haotong Chen

Department of Chemistry: Dissertations, Theses, and Student Research

Bioactive natural products are a major source of anti-infectives. Many ubiquitous inhabitants of soil and water, such as the Gram-negative, prolific producers of natural products, Lysobacter, remain largely unexplored. This PhD thesis reports our studies of the biosynthetic mechanism for a novel antifungal natural product HSAF and a potent anti-MRSA natural product WAP-8294A2.

In the first chapter, we give a short review of the biosynthesis of polyketides, focusing on those which exhibit new biosynthetic features. In subsequent chapters, we present original research on the biosynthetic mechanisms of dihydromaltophilin, a heat stable antifungal factor (HSAF). HSAF is the main antifungal …

A Rapid Lc-Ms/Ms Method For Quantification Of Csuoh0901, A Novel Antitumor Agent, In Rat Plasma, Ramakrishna R. Voggu, Ravali Alagandula, Xiang Zhou, Bin Su, Bo Zhong, Baochuan Guo

Chemistry Faculty Publications

CSUOH0901, a novel anticancer derivative of nimesulide, exhibits very promising anticancer activities in various cancer cell lines. In order to support further pharmacological and toxicological studies of this promising anticancer drug candidate, an LC-MS/MS method was developed and validated in accordance with the US Food and Drug Administration guidelines. The drug molecules were extracted from plasma samples by protein precipitation and then analyzed with LC-ESI-MS/MS. An excellent analyte separation was achieved using a phenomenex C18 column with a mobile phase of 90% methanol and 5 m m of ammonium formate. The validated linear dynamic range was between 0.5 and 100 …

Beryllium Is A Potent And Unique Gsk-3Β Inhibitor With Potential To Differentially Regulate Glycogen Synthase And Β-Catenin, Ata Ur Rahman Mohammed Abdul

UNLV Theses, Dissertations, Professional Papers, and Capstones

Glycogen Synthase Kinase-3β (GSK-3β) is an important serine/threonine kinase that phosphorylates/regulates diverse and metabolically important proteins. Some of the important substrates of GSK-3β are glycogen synthase, tau, β-catenin, cyclin D1, axin, c-jun, c-myc, Heat Shock Factor–1, BCL-3, CREB, Histone H1.5, mdm2, p21 (CIP1), pyruvate dehydrogenase and many more. De-regulation of GSK-3β has been implicated in diseases like cancer, Alzheimer’s disease, bipolar disorder and type 2 diabetes mellitus. Currently, GSK-3β is one of the most widely studied proteins and there is a great interest in developing potent and efficient GSK-3β-inhibitors for research as well as therapeutic purposes. We demonstrate that beryllium …

Novel Spectroscopic Tools To Differentiate Molecule-Dna Binding Interactions, Sense Dna And Track Dna Melting, Saad Hmoud Alotaibi

Dissertations

The discovery of DNA as a genetic material and its double helical structure led to numerous studies directed at understanding molecule-DNA interactions. These studies have played an integral role in medical diagnostics, forensics, imaging and therapeutics. Typically, molecule-DNA interactions have two prominent modes: intercalation and minor groove binding. Several optical techniques are available that can monitor molecule-DNA binding interactions, but they cannot differentiate between intercalation and minor-groove binding. The major goals of the research are to develop novel optical spectroscopic tools that can differentiate molecule-DNA binding interactions, selectively and sensitively detect one form of DNA over another, and track DNA …

Methanogen Metabolism In The Presence Of Iron Compounds: A Martian Environment Simulation, Monroe Phillip Cowan

Chemistry & Biochemistry Undergraduate Honors Theses

The climate on the face of Mars is hostile towards life. Thus, any organisms potentially living on Mars would likely inhabit a subsurface environment, in which conditions are wetter and warmer. However, organisms living beneath the surface would be significantly deprived of light and some organic compounds necessary for the sustenance of most life. The discovery of methane gas in Mars’ atmosphere has led to speculation that methanogens, obligate anaerobes which produce methane as waste, are the organisms most likely to survive in a subsurface environment. These members of domain Archaea subsist on water, hydrogen, and carbon dioxide. In addition, …

Synthesis Of Novel Dienes And Cyclic Compounds Via Olefin Metathesis Reactions Catalyzed By The Second Generation Grubbs Catalyst, Patrick Joseph Carey

Honors Theses

Transition metal-catalyzed olefin metathesis reactions play a significant role in chemical synthesis. These reactions are currently applied across several disciplines, and their full potential has not yet been reached. This project details the synthesis of spiro[3-cyclopentene-1,9’-[9H]fluorene], 1-(1-amino-2-methylpropyl)-3-cyclopentenol, and the eugenol dimer via olefin metathesis reactions catalyzed by the second generation Grubbs catalyst. The unique structural properties of each compound help demonstrate the widespread abilities of these reactions. Also reported are the novel three-dimensional crystal structures of both spiro[3-cyclopentene-1,9’-[9H]fluorene] and the eugenol dimer. These structures were determined via X-ray diffraction crystallography methods using a Bruker SMART X2S Single Crystal Diffractometer. Both …

Modifications Of Lysozyme By Substituted Benzoquinones, Hendrik J. Greve

Honors Theses

Amyloidosis, which involves the precipitation of mis-folded protein aggregates, is a prominent process that occurs in many neurodegenerative conditions such as Alzheimer's disease and Parkinson's disease; the protein aggregates being amyloid-β for Alzheimer’s disease and α-synuclein for Parkinson’s disease. This study has focused on lysozyme modifications induced by metabolites of the commonly found pollutants known as polycyclic aromatic hydrocarbons (PAHs). PAHs are found in substances ranging from grilled meats to cigarette smoke to cosmetics, and they can be metabolized into a family of biological toxins known as benzoquinones. The molecules of interest for this study were 1,4-benzoquinone (pBQ), 2-chloro-1,4-benzoquinone (CBQ), …

Ribonuclease A Modification Induced By 1,2-Naphthoquinone And 2-Hydroxy-1,4-Naphthoquinone, Michelle Dawn Smith

Honors Theses

Protein modifications may occur upon exposure to environmental toxins such as polycyclic aromatic hydrocarbon (PAH) molecules or their metabolites. In this context, our laboratory was interested in investigating protein modifications in the presence of select naphthoquinones, which were 2-hydroxy-1,4-naphthoquinone (HNQ) and 1,2-naphthoquinone (o-NQ). The effects of HNQ and o-NQ on the protein Ribonuclease A (RNase) were investigated through a variety of conditions. These modified incubation conditions included pH variation and the addition of metal ions to further mimic physiological conditions. Documentation of results was carried out through sodium dodecyl sulfate polyacrylamide gel electrophoretic analysis (SDS-PAGE). Of the two quinones, o-NQ …

Distributed Drug Discovery: Synthesis Of Unnatural Amino Acids As Potential Antimalarial Drugs, Amanda Dugan

Honors College

Through the collaboration of many institutions across the globe, the Distributed Drug Discovery project founded at Indiana University-Purdue University Indianapolis seeks to aid in the development of drugs for the developing world. In response to two antimalarial assay hits, our team at Abilene Christian University has synthesized many unnatural amino acid analogs using resin-based combinatorial chemistry. Proton nuclear magnetic resonance spectroscopy has been used to characterize the compounds and thin layer chromatography to determine purity. All compounds were purified on hypersep cyanosilica columns.

Aqueous Raft Polymerization Of Glycopolymers For Peptide Interaction Studies And Antimicrobial Peptide Mimics For Antimicrobial Activity And Selectivity Studies, Sarah Elizabeth Exley

Dissertations

The first section of this work describes the synthesis and characterization of novel glycopolymers synthesized to model GM1 gangliosides, a glycolipid found in neuronal cells. Glucose and galactose were attached to N-hydroxyethyl acrylamide, using chemistry that granted control over the stereochemistry at the C1’ carbon of each saccharide, and polymerized via aqueous RAFT (aRAFT). Homopolymers, targeting either 30 or 300 DP, and copolymers, with N-dimethyl acrylamide, were prepared as a glycopolymer platform for investigation of amyloid β (Aβ), a naturally occurring peptide associated with Alzheimer’s disease, aggregation. Aβ aggregation kinetics and aggregate size in the presence of glycopolymer were determined. …

Differentiation Of Human, Animal And Synthetic Hair By Atr Ftir Spectroscopy, Jeremy Manheim

Chemistry

Hair fibers are ubiquitous to every environment and are the most commonly found form of trace evidence at crime scenes. The primary difficulty forensic examiners face after retrieving a hair sample is determining who it came from. Currently, the methodology of microscopic examination of potential hair evidence is absent of statistical probability and is inherently subjective. Another method, involving DNA analysis, takes months to conduct and the majority of times is unsuccessful due to its degradation and absence from the hair. Here, Attenuated Total Reflectance (ATR) Fourier Transform Infrared (FTIR) Spectroscopy coupled with advanced statistics was used to identify a …

Removal Of Cobalt And Nickel From Water Using Mno2 And Mn3o4 Nanomaterials, Maria Dolores Pacheco

Theses and Dissertations - UTB/UTPA

Nanomaterials MnO2 and Mn3O4 were synthesized using a titration/precipitation technique and characterized with powder XRD. A pH assay determined the optimum binding for cobalt and nickel occurred at pH 5 for both nanomaterials. A time dependency study determined that cobalt and nickel required more time with MnO2 for maximum adsorption than Mn3O4. The binding capacity study showed cobalt and nickel have good binding capacity with both nanomaterials. Interfering ion assay in the presence of Na+ , Ca2+ and Mg2+ showed minimal difference in the adsorption of cobalt and nickel to MnO2 or Mn3O4. Cobalt and nickel showed a reduction in …

Effect Of Crimping, Multilayering, And Twisting On Polymer Fibers For Acl Replacement, Mariana Ocampo

Theses and Dissertations - UTB/UTPA

The Anterior Cruciate Ligament (ACL) is the most common knee injury in the United States; roughly 150,000 ACL surgeries are performed annually. The ACL lacks self-healing properties due to its location inside the knee’s intra – articular environment (IA). Treatments for ACL ruptures involve the use of autogenous grafts or allografts. More suitable treatments can be found in new bio engineered tissue scaffolds, composed of natural and synthetic polymers. The polymers provide stronger mechanical properties and the ability to promote cell adhesion. It is believed that mimicking the crimping pattern of human ligaments will enhance polymer properties. Four polymers were …

Synthesis And Characterization Of Five New Tetrakis(N-Phenylacetamidato) Dirhodium(Ii) Amine Complexes And One Molybdenum Cofactor Described Crystallographically, Cragin K. Harris

Electronic Theses and Dissertations

Six new crystal structures were determined using a Rigaku Mercurcy 375/MCCD(XtaLab mini) diffractometer. The structure of a molybdenum cofactor was solved resulting in an R1 (R1 = Σ ||Fo| - |Fc|| / Σ |Fo|) of 3.61% despite the presence of a disordered DMSO molecule. New Tetrakis(N-phenylacetamidato) Dirhodium(II) complexes were synthesized and characterized. Two 2,2-cis-[Rh2(NPhCOCH3)4]•(C3H4N2)x where x= 1 or 2 were successfully crystallized and solved with R1 values below 5%. Additional studies were conducted via NMR to observe formation of both products. Three potential catalysts were synthesized starting with 3,1-[Rh₂(NPhCOCH₃)₄]. The resulting compounds were a …

The Crystal Structure Of Nitrosomonas Europaea Sucrose Synthase Reveals Critical Conformational Changes And Insights Into The Sucrose Metabolism In Prokaryotes, Rui Wu, Matías D. Asención Diez, Carlos M. Figueroa, Matías Machtey, Alberto A. Iglesias, Miguel Ballicora, Dali Liu

Chemistry: Faculty Publications and Other Works

In this paper we report the first crystal structure of a prokaryotic sucrose synthase from the non-photosynthetic bacterium Nitrosomonas europaea. The obtained structure was in an open form, whereas the only other available structure from the plant Arabidopsis thaliana was in a closed conformation. Comparative structural analysis revealed a “hinge-latch” combination, which is critical to transition between the open and closed forms of the enzyme. The N. europaea sucrose synthase shares the same fold as the GT-B family of the retaining glycosyltransferases. In addition, a triad of conserved homologous catalytic residues in the family showed to be functionally critical …

Investigating Students' Use Of Multiple Representations Of The Arrow-Pushing Formalism, Yu Shen

All Theses

Over decades, research in STEM education has been conducted to investigate how students translate from one representation to another. Based on dual coding theory, multiple external representations (MERs) can be effective when the verbal/linguistic representations are provided along with the corresponded diagrammatic/pictorial representations. However, little is known about the difficulties that undergraduate students encounter when translating between the verbal and diagrammatic representations in the context of the arrow-pushing formalism used in organic reaction descriptions. Chemists use the arrow-pushing formalism to represent the electron flow in organic mechanistic processes. Yet, far less is known about the meaning that undergraduate students attribute …

Optimized Acid/Base Extraction And Structural Characterization Of Β-Glucan From Saccharomyces Cerevisiae, Shardrack O. Asare

Electronic Theses and Dissertations

β-glucan is a major component of the fungal cell wall consisting of (1→3)-β linked glucose polymers with (1→6)-β linked side chains. The published classical isolation procedure of β-glucan from Saccharomyces cerevisiae is expensive and time-consuming. Thus, the aim of this research was to develop an effective procedure for the extraction of glucans. We have developed a new method for glucan extraction that will be cost effective and will maintain the native structure of the glucan. The method that we developed is 80% faster and utilizes ¹/₃ of the reagents compared to the published classical method. Further, the method …

Increased Microdialysis Recovery Of Large Molecular Weight Analytes Via Ultrafiltration, Michael C. Elkins

Chemistry & Biochemistry Undergraduate Honors Theses

Microdialysis is a sampling method based on the passive diffusion of solutes across a semi-permeable hollow-fiber membrane that is driven by a concentration gradient. The membrane has a defined molecular weight cutoff, which causes larger molecular solutes such as proteins with molecular weights of approximately 8-80 kDa to have low recoveries. The purpose of this research is to utilize ultrafiltration across the membrane through push-pull and vacuum ultrafiltration methods as a means to increase recovery of large molecular weight analyte. These experiments were carried out using Methyl Orange (MO), Fluorescein Isothiocyanate 4 kDa (FITC-4), and Fluorescein Isothiocyanate 40 kDa (FITC-40). …

Derivatives Of 3,4-Ethylenedioxythiophene (Edot) For Enzyme-Immobilized Conducting Polymer: Toward Development Of Biofuel Cells And Biosensors, Corinne Songer

Chemistry & Biochemistry Undergraduate Honors Theses

Biofuel cells are electrochemical cells that use biological processes to generate a current, and when paired with a biosensor, they can be used to power electronics within the human body.1 Monomers, such as hydroxymethyl-3,4-ethylenedioxythiophene (HM-EDOT), can be electropolymerized into a conducting polymer that is capable of a high rate of electron transfer, and can increase the flow of current on the electrode surface. HM-EDOT is a suitable monomer for this project because it has a hydroxyl functional group, which allows for increased solubility in aqueous environments. The monomer HM-EDOT can be functionalized and synthesized into carboxylic acid-3,4-ethylenedioxythiophene (COOH-EDOT)2, which gives …

Chemically Accurate Calculations Of Rate Constants Of Spin Trap-Hydroxyl Radical Addition Reactions, Hayden B. Short

Undergraduate Honors Theses

The DMPO type spin trap 5,5-Dimethyl-1-pyrroline N-oxide (DMPO) and the exceptionally similar spin trap 2-ethoxycarbonyl-2-methyl-3,4-dihydro-2H-pyrrole-l-oxide (EMPO) are widely studied in computational and theoretical works. This particular study examines the addition reactions that both these molecules undergo with the carcinogenic hydroxyl radical. This work used a relatively new approximation method, called the correlation consistent composite approach or ccCA, for carrying out quantum mechanical calculations to give the free energies of the products and reactants of the reactions. The free energies are to be used to extrapolate the rate constants of the reactions from the Arrhenius equation. Though both the spin traps …

A Study Of The Kinetics Of A Reaction Between Vo(Hedta)-1 And Hydrogen Peroxide, Elaina B. Campbell

Undergraduate Honors Theses

Vanadium is commonly used as an agent to make tools rust-resistant. As a transition metal, it can be used as a catalyst due to its ability to change oxidation states. VO(HEDTA)^-1, a complex of the vanadyl ion, VO²⁺ and HEDTA (N-(2-Hydroxyethyl)ethylenediamine-N,N’,N’-triacetic acid) was readily formed. This complex containing vanadium in the +4 oxidation state was reacted with hydrogen peroxide to form a vanadate complex. This vanadate complex was formed as a first step in simulating the vanadate(V)-dependent haloperoxidases in marine algae, a yet uncharacterized reaction. Electron absorption spectroscopy (UV-Vis) was used to observe the oxidation of V(IV) …

Synthesis And Characterization Of Carbonized Poly (Divinylbenzene) Microspheres For Carbon/Nanodiamond/Polymer-Based Core-Shell Materials And Applications Of This Mixed-Mode Phase To High-Performance Liquid Chromatography, Chuan-Hsi Hung

Theses and Dissertations

This work focuses on improving the quality of carbon-based core-shell materials for high performance liquid chromatography (HPLC) via the characterization of the core materials, and also the development of chromatographic methods (separations) for them. In the early part of this work, I applied organic synthesis to make uniform, spherical poly(divinylbenzene) (PDVB) microspheres, and then carbonized them to prepare carbon core materials for core-shell particle synthesis. Here, I studied in detail the surface and material properties of these particles with multiple instruments, which allowed me to describe the physical and chemical changes that took place during each treatment. The uniform, spherical …