Physical Sciences and Mathematics Commons^™

Characterization Of Cytidylyltransferase Enzyme Activity Through High Performance Liquid Chromatography, James Brault

Theses and Dissertations

The cytidylyltransferases are a family of enzymes that utilize cytidine 5â?? triphosphate (CTP) to synthesize molecules that are precursors to membrane phospholipids. There are four well known enzymes: CTP: phosphoethanolamine cytidylyltransferase (ECT), CTP: glycerol-3-phosphate cytidylyltransferase (GCT), 2-C-methyl-D-erythritol-4-phosphate cytidylyltransferase synthetase (CMS), and CTP: phosphocholine cytidylyltransferase (CCT). Previously, a radioisotope tagging method was employed to study cytidylyltransferase catalysis. Using CCT as a model, a method utilizing high performance liquid chromatography (HPLC) was developed to replace the radioisotope scintillation technique. The development of this new HPLC method is cheaper, more efficient, and more accurate than the previously established method.

The targets of separation …

Defining The Effects Of Gdf-2 On TgfB Signaling In Tumorigenic Epithelial Cells, Tirthankar Bandyopadhyay

Theses and Dissertations

Cancer cells can be viewed as such cells, which have disrupted/aberrant signaling pathways for maintaining cellular homoeostasis. Identifying such altered signaling mechanisms can help us target these pathways in a better way. GDF-2 (Growth and differentiation factor – 2) or BMP9 (Bone morphogenetic protein – 9), a multifunctional cytokine, is a member of the Bone Morphogenetic Protein subfamily, under TGFβ superfamily, with roles distinct from BMP2/4/7. While GDF-2 is known to be one of the most potent ectopic inducers of bone and cartilage formation, it rose to significance with the identification of its receptor ALK1 in endothelial cells. TGFβ’s role …

Supramolecular Coordination Networks Of S- And F-Block Metals Featuring The 1,8-Naphthalimide Tecton, Andrew Paul Leitner

Theses and Dissertations

The reactions of (S)-2-(1,8-naphthalimido)propanoic acid (HLala), and (S)-2-(1,8- naphthalimido)-3-hydroxypropanoic acid (HLser), protonated forms of ligands that contain a carboxylate donor group, an enantiopure chiral center and a 1,8-naphthalimide π...π stacking supramolecular tecton and in the case of HLser an alcohol functional group, with the appropriate alkali metal hydroxide followed by a variety of crystallization methods leads to the formation of crystalline K(Lala)(MeOH) (1), K(Lala)(H2O) (2), Na(Lala)(H2O) (3), KLser (4), CsLser (5) and CsLala (6). Each of these new complexes has a solid state structure based on six-coordinate metals linked into homochiral helical rod SBU central cores. In addition to the …

Two-Dimensional Transient Spectroscopy Measuring Heterogeneity In Electronic And Rotational Dynamics, Haorui Wu

Theses and Dissertations

Multiple population-period transient spectroscopy (MUPPETS) is a picosecond, time resolved experiment that uses a sequence of six laser pulses. It was previously known that MUPPETS could measure heterogeneity in electronic-state decay. This dissertation presents two projects that extend MUPPETS to new processes. One process is the extension from 2-level system into 3-level system, another new process extends the kinetics from electronic decay to rotational decay. In addition, a third, ongoing project on rotational dynamics in ionic liquids will also be discussed briefly. The first project consisted of two main parts. The first part focused on the biexciton decay in semiconductor …

Optimization Of Shell Growth And Influence Of Surface Ligands For Colloidal Cdse/Cds Core/Shell Quantum Dots, Rui Tan

Theses and Dissertations

Progress in the colloidal synthesis of semiconductor quantum dots (QDs) has triggered a burst of research toward applications in QD based light emitting diodes, biological imaging as fluorescent tags, and advanced solar cell designs. In order to adjust and optimize the photo physical properties of QDs, QD heterostructures have been introduced and widely explored. This dissertation is focused on studies of growth of semiconductor colloidal CdSe/CdS core/shell quantum dots and the influences of neutral surface ligands to their photo-physical properties. Chapter 1 provides an introduction of the concept of semiconductor colloidal nanoparticles, core/shell heterostructures and the synthesis methods as well …

Applications Of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy For Forensic Analysis, Zhenyu Lu

Theses and Dissertations

Blood stains, which are among the traces encountered most frequently at crime scenes, are important for potential extraction and amplification of DNA for suspect identification, as well for spatter pattern analysis to reveal a sequence of events. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was used in detection of blood stains and age estimation because of signature absorbances in the mid-infrared region at 3300 cm-1 (Amide A), 2800-3000 cm-1 (Amide B), ~1650 cm-1 (Amide I), ~1540 cm-1 (Amide II) ,and 1200-1350 cm-1 (Amide III). Position and intensity shifts for amide peaks were observed due to aging changes occurring as …

Approaching Aromatic Interactions With Small Molecule Model Systems: Assessing N-Heteroarene In ∏ -Stacking And Ch-∏ Interactions, Crystal Engineering Of Atropisomeric Rotors, And Developing Responsive Organic Charge-Transfer Complex, Ping Li

Theses and Dissertations

Non-covalent interactions involving aromatic species are important in many areas in chemistry, biochemistry, and materials sciences. During the past two decades, small molecule model systems have emerged as a powerful tool to advance our knowledge of the stability trends for aromatic interactions in the condensed phase. Among these, the Cshape N-arylimide molecular balances developed by our laboratory have proven to be one most successful and versatile model systems that can be readily adapted to investigate various types of aromatic interactions. These molecular balances are particularly apt at isolating and accurately measuring the targeted weak aromatic interaction energies for different geometries. …

Optimized Spectral Processing Of Infrared Diffuse Reflection Spectra For The Detection Of Blood On Fabric, Stephanie Ann Dejong

Theses and Dissertations

The detection of bodily fluids such as blood on interfering backgrounds is important to the forensic community. Luminol, which participates in a chemiluminescent reaction with the heme groups of blood, is one of the most commonly used presumptive tests. Luminol has a few drawbacks, including the requirement of use in a dark environment and potential to degrade the amount of recoverable DNA in blood stains. A potential complementary method is infrared (IR) spectroscopy. These two methods are compared in this work. Infrared diffuse reflection (DR) spectroscopy works well to measure the IR spectrum of samples that are highly absorbing or …

Novel Block Copolymer Architectures For Lithography-Relevant Self-Assembly, Jeffery Hakim Hayat

Theses and Dissertations

This dissertation is focused on the synthesis, characterization, self-assembly, and materials processing of various functionalized block copolymer systems. A variety of monomers were prepared and polymerized through various polymerization techniques including atom transfer radical polymerization, reversible addition-fragmentation chain transfer polymerization, and ring-opening metathesis polymerization. Self-assembly of the functionalized block copolymers led to well-defined nanostructures in bulk and thin films. These materials have the capability to be utilized in various applications including ordered catalysts and templates for nanolithography. In Chapter 1, the overall background of diblock and triblock copolymers and their preparation methods is in this dissertation. Major research objectives of …

Spectroscopy And Chemometrics For Cultural Heritage And Forensics: Conservation Of Magnetic Tape By Identifying Degraded Polymer Signatures; And Characterizing The Chemiluminescent Reaction Of Luminol With Blood, Brianna Marie Cassidy

Theses and Dissertations

The first half of this manuscript focuses on the identification of degraded magnetic tape using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) and multivariate statistics. For several decades before the digital era, magnetic tape was the dominant audio and visual recording medium. A majority of magnetic tapes contain polyester urethane (PEU) binders, which are known to degrade via hydrolysis, making the retrieval of recorded data difficult and at times impossible. Degraded tapes are currently identified through visual inspection followed by playback on vintage equipment. However, if degraded tapes are played, they are likely to stick and shed onto player …

Optical Spectroscopy And Chemometrics For Discrimination Of Dyed Textile Fibers And Magnetic Audio Tapes, Nathan C. Fuenffinger

Theses and Dissertations

This dissertation focuses on the application of both novel and standard chemometric approaches toward societal problems of interest in the areas of forensic science and cultural heritage preservation. Microspectrophotometry (MSP), a technique enabling measurements of absorption of electromagnetic radiation by microscopic materials in the ultraviolet-visible (UV-Vis) region, is widely used by forensic examiners for comparisons of metameric textile fibers. These comparisons are often hindered, however, by the raw or normalized spectra showing little detail or having few points of comparison. Derivative preprocessing can enhance structure in some instances. We have demonstrated through the use of multivariate statistics that derivatives are …

Sustainable Polymeric Materials Derived From Novel Soybean Based Monomers And Polymers: From Synthesis To Applications, Nathan Trenor

Theses and Dissertations

In this thesis, monomers and polymers derived from high oleic soybean oil are investigated. The properties of these monomers and polymeric materials are characterized and discussed. Chapter 1 describes an overall background of bio-based resources, monomers, polymers, and their potential impact on society. Polymerization techniques are introduced, and the overall objective of my research is described. Chapter 2 outlines the large scale preparation of a soybean based monomer and the use of this monomer in thermoset elastomers. The synthetic procedures and characterizations of the monomers and polymers are discussed. A model study using oleic acid is described and proved to …

Hydroxy Polybenzimidazoles For High Temperature Fuel Cells And The Solution Polymerization Of Polybenzimidazole, Kayley Fishel

Theses and Dissertations

In this dissertation, two different hompolymers of polybenzimidazole (PBI) containing hydroxyl functional units were synthesized via the PPA Process to produce gel membranes. These polymers and their phosphoric acid doped membranes were characterized to further explore structure-property relationships in functionalized PBI's. Fuel cell performance of the doped membranes was evaluated and compared to previously reported PBI membrane chemistries. Copolymers of p-OH PBI and para-PBI were prepared at five different copolymer compositions to examine the effects of hydroxy content on membrane properties and compared to the respective homopolymers. The reactivity of the hydroxy groups and the formation of phosphate bridges were …

Arylboronates As H2o2 Or Photo-Inducible Dna Cross-Linking Agents: Design, Synthesis, Mechanism, And Anticancer Activity, Yibin Wang

Theses and Dissertations

Interest in the development of cancer therapies with improved selectivity and reduced host toxicity has been growing. In this thesis, we designed and synthesized a series of novel non-toxic arylboronic ester and biarylboronic ester derivatives that can be activated by hydrogen peroxide (H2O2) to induce DNA interstrand cross-link formation. The mechanism of DNA cross-linking induced by these arylboronates involves generation of phenol intermediates 1 followed by departure of leaving group (L) leading to quinone methides (QMs) 2, which directly cross-link DNA via alkylation. The QM formation is the rate-determining step for DNA cross-linking. The activity and selectivity of these compounds …

Part I. The Development Of Non-Secosteroidal Vitamin D Receptor Modulators Part Ii. The Development Of A Universal Gtp-Ase Assay, Kelly Ann Teske

Theses and Dissertations

The vitamin D receptor is a nuclear hormone receptor that regulates cell proliferation, cell differentiation, calcium homeostasis and immunomodulation. The receptor is activated by the vitamin D metabolite, 1,25-dihydroxyvitamin D3, which induces a cascade of events including the recruitment of coactivators that activate transcription of specific VDR target genes. Thousands of VDR agonists have been synthesized based on the secosteroid scaffold of 1,25-dihydroxyvitamin D3. However, most of these ligands are metabolically unstable, have sub-optimal drug-like properties, and induce hypercalcemia in vivo. The limited numbers of VDR antagonists reported bear the same secosteroid scaffold and thus exhibit similar problems encountered by …

Facile Sol-Gel Molten Salt Synthesis Of Double Perovskite La 2nimno6 As An Electrocatalyst For Oxygen Evolution Reactions, Padmini Kukkapalli

Theses and Dissertations

Double perovskites have attracted a great attention recently for its high intrinsic activity in oxygen evolution reaction (OER) in electrochemical energy storage and conversion systems in alkaline media. In this study, we are the first to report the new approach of La2NiMnO6 double perovskite which was synthesized via Sol-gel molten-Salt synthesis method. However their stability and specific activity remain challenging that need to be addressed to meet the reqiurement for OER activities. Here in this study we synthesized three different samples with varying concentrations by taking molten salts NaNO 3 and KNO3 in (1:1) ratio such as 30:30, 60:60, 90:90. …

Porphyrin As A Spectroscopic Probe Of Net Electric Fields In Heme Proteins, Hannah Elizabeth Wagie

Theses and Dissertations

Heme proteins have diverse functions as well as varied structures but share the same organic, conjugated cofactor. Similarly varied approaches have been taken to deduce how heme can take on different roles based on its protein environment. A unique approach is to view the protein matrix as a constellation of point charges that generates a defined, reproducible, net internal electric field that has influence over the electronic properties of the heme cofactor. This work considers how porphyrins, the basic chromophore building block of heme, can be used as a native spectroscopic sensor of internal electric field at the active site …

Molecular Modeling And Mutational Mapping Of The Gpr119 Binding Site, Shane M. Askar

Theses and Dissertations

GPR119 receptor’s biological role in regulating glucose homeostasis has been studied extensively. Results in the scientific literature indicate that, when activated, GPR119 releases insulin in a glucose dependent manner. Currently the 3D structure of GPR119 has not been resolved.

The goal of this research is to use a combination of homology modeling and ligand docking studies to predict the binding mode of GPR119 ligands. Amino acids implicated to have direct interactions with docked ligands will further be assessed experimentally for their roll in binding and activation of GPR119. Our results indicate that residues W2656.48 and R813.28 are likely to be …

Advanced Data Analysis Tools And Multi-Instrument Material Characterization, Bhupinder Singh

Theses and Dissertations

My dissertation focuses on (i) the development of new analysis tools and methodologies for analyzing X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) data, and (ii) the comprehensive characterization of materials (nanodiamonds) using a multi-instrument approach. Chapter 1 contains (i) a discussion of the two techniques I focused on most in my work: XPS and ToF-SIMS, (ii) a discussion of the common chemometrics techniques used to analyze data from these methods, and (iii) the advantages/rationale behind the multi-instrument characterization of materials. Chapter 2 describes various good practices for obtaining reasonable peak fits in XPS, which can also …

Hand-Portable Capillary Liquid Chromatography Instrumentation, Sonika Sharma

Theses and Dissertations

This dissertation focuses on the development of hand-portable capillary liquid chromatography (LC) instrumentation. In this work, battery-operable nano-flow pumping systems (isocratic and gradient) were developed and integrated with portable UV-absorption detectors for capillary LC. The systems were reduced in size to acceptable weights and power usage for field operation. A major advantage of the pumps is that they do not employ a splitter, since they were specifically designed for capillary column use, thereby greatly reducing solvent consumption and waste generation. UV-absorption detectors were specifically designed and optimized for on-column detection to minimize extra-column band broadening. Initially, an isocratic nano-flow pumping …

High Flow Air Sampler For Rapid Analysis Of Volatile And Semi-Volatile Organic Compounds, Xiaofeng Xie

Theses and Dissertations

Volatile and semi-volatile organic compounds are ubiquitous, and some of them are hazardous. The ability to rapidly detect and identify trace levels of them in air has become increasingly important. The conventional device used today for sampling and concentrating them in air is thermal desorption tubes filled with specific sorbents, which can only collect air samples at flow rates of 100-200 mL/min. In order to detect low concentration (ppt level) VOC compounds, long sampling time (>2 h) and sensitive detection are required. At the same time, portable instrumentation for on-site analysis has been developing rapidly. The somewhat lower performance …

Synthesis And Characterization Of Neo-Confused Porphyrins And Related Systems, Arwa Salem Almejbel

Theses and Dissertations

Carbaporphyrins have been the focus of many studies, and a wide variety of related carbaporphyrinoid systems have been reported. N-confused porphyrins are a class of carbaporphyrins where one pyrrole unit has been inverted. In this work, a newly discovered family of porphyrin isomers where one of the pyrrolic subunits is connected to the meso-bridges in a 1,3-fashion, called neo-confused porphyrins, has been investigated.

Reaction of pyrrole-3-carbaldehydes with acetoxymethylpyrroles and NaH in DMF gave neo-confused dipyrrylmethane dialdehydes. The resulting dialdehydes underwent an acid catalyzed condensation with a dipyrrylmethane to give neo-confused phlorins, and following oxidation with FeCl3 afforded new neo-confused porphyrins. …

Image-Charge Detection €“ Novel Instrumentation And Applications, Brandon Lee Barney

Theses and Dissertations

Image-charge detection is an analytical technique in which a highly-charged particle is detected by the magnitude of the image current that it generates in a detecting electrode. This current is represented as a voltage between the charged particle and the sensing electrode. It is a single particle detection method, ideal for the analysis of large, variable mass particles such as biological cells. Some of the physical properties of Bacillus subtilis spores were explored using different applications of image-charge detection. B. subtilis is a gram-negative spore-forming bacteria that has been shown to exhibit extremophile behavior. The particular extremophile behavior that was …

Mass Spectrometry Based Proteomics And Lipidomics Studies, Huan Kang

Theses and Dissertations

Mass spectrometry has emerged as having a vital role in various applications to biochemical fields. In this thesis, we have utilized a variety of mass spectrometry techniques for both bacteriophage proteomics and colostrum and milk lipidomics studies. Our first study was the proteome characterization of Great Salt Lake bacteriophage NS01 with SDS-PAGE GEL to separate the viral proteins and high performance liquid chromatography (HPLC) coupled with an LTQ Orbitrap to identify the proteins after in-gel digestion. In this project, we have successfully identified 11 proteins with high confidence, p-values < 0.01, including coat protein gp88 with a coverage of 91% and tail protein gp86 with a coverage of 40.96%, which facilitated the classification of NS01 as a T7-like phage. Our second study was the discovery of colostrum and milk biomarkers that can be used to predict the likelihood of development of production-related metabolic diseases (PRMDs) in dairy cows through a lipidomics approach. In this study, an electrospray ionization, time-of-flight mass spectrometer was applied to lipid profiling, quantification and significant biomolecule selection. A Q-Star quadrupole, orthogonal time-of-flight mass spectrometer and an Agilent 6530 accurate-mass quadrupole/time-of flight mass spectrometer were both used for lipid biomarker fragmentation and identification. According to linear discriminative statistical modeling, three panels of biomarkers were defined. A combination of 2 milk lipid predictors, including DG18:0/18:0 and TG 18:0/18:0/18:1, provided PRMD predictions with 75.0% sensitivity at 90.0% specificity. A combination of 3 colostrum lipid predictors, including TG16:0/18:1/18:3, DG16:0/16:0 and C₄₀H₆₀NO, provided PRMD prediction with 90.0% sensitivity at …

Synthesis And Characterization Of Naphthocarbaporphyrins And Related Systems, Eric Grabowski

Theses and Dissertations

Carbaporphyrins are porphyrin analogs in which one of more of the pyrrole units have been replaced with a carbocyclic ring. In this project the cyclopentadiene ring replacing a pyrrole ring has been fused with a naphthalene ring. This is done in order to observe the effects of the naphthalene ring on the spectroscopic properties and reactivity.

Utilization Of Antibody-Conjugated Gold Nanoparticles, Dynamic Light Scattering And Sers In Influenza Virus Detection, Yen Hoang Lai

Theses and Dissertations

Influenza A H3N2, H1N1, and influenza B viruses primarily cause winter illness in humans, leading to significant morbidity and mortality in the population of the very young, the elderly, and people with chronic disease. In addition to the regular seasonal epidemics of influenza, influenza pandemics associated with the emergence of new influenza A strains are threatening due to high levels of mortality, social disruption, and economic losses. These novel strains are not affected by the human immunity developed to older strains of influenza, therefore can spread readily and infect a vast number of people. The most recent flu pandemic outbreak …

Enantiospecific Stereospecific Strategy For The Total Synthesis Of Sarpagine And Macroline Related Oxindole Alkaloids: First Total Synthesis Of Affinisine Oxindole, Isoalstonisine, Alstofoline, Macrogentine, N(1)-Demethylalstonisine, Alstonoxine A And Second Generation Synthesis Of Alstonisine, German Oscar Fonseca Cabrera

Theses and Dissertations

The (7R)-sarpagine/macroline related oxindole alkaloids (-)-isoalstonisine (27) and (-)-macrogentine (31) together with the (7S)-sarpagine/macroline related oxindole alkaloids (-)-affinisine oxindole (24), (-)-alstonoxine A (19), (+)-alstonisine (8, second generation total synthesis), (+)-Na-demethylalstonisine (17) and (+)-alstofoline (18) were concisely synthesized during these studies.

These oxindole alkaloids were isolated from plants of the genus Alstonia which is characterized by the preponderance of sarpagine/macroline-type indole and oxindole alkaloids. Plants that belong to this genus are mainly distributed over tropical regions of Central America, Africa, and Asia where they are used locally in traditional medicine, for example, in the treatment of malaria and dysentery. The main …

Asymmetric Synthesis Of All-Carbon Α-Aryl Quaternary Carbonyl Compounds By Palladium-Catalyzed Asymmetric Allylic Alkylation (Pd-Aaa) And Their Application To The Synthesis Of Biologically Important 3,3′-Disubstituted Oxindole And Α-Disubstituted Quaternary Β-Lactone Frameworks, Md. Sharif Al Asad

Theses and Dissertations

The development of catalytic, enantioselective methods for the construction of all-carbon quaternary stereocenters is an outstanding achievement in the recent history of organic chemistry. The palladium-catalyzed asymmetric allylic alkylation (Pd-AAA) reaction has played a key role in creating such stereocenters and has allowed researchers to synthesize a vast number of biologically potent natural products. However, synthetic methodologies to access compounds containing α-aryl groups to the quaternary carbon stereocenters are still rare. The increasing appearance of these all-carbon α-aryl quaternary stereocenters in a growing number of biologically active natural products and pharmaceutical agents creates a pressing need for the ability to …

Mechanistic Study Of Heme Protein-Mediated Nitric Oxide Dioxygenation Using Photolytically Produced Nitric Oxide, Karl Joseph Koebke

Theses and Dissertations

The previously reported NO precursor [Mn(PaPy2Q)(NO)]ClO4 (1), where (PaPy2QH) is N,N-bis(2-pyridylmethyl)-amine-N-ethyl-2-quinoline-2-carboxamide, was synthesized and proven capable of producing as much as 180 µM NO when irradiated by a single 3 mJ 500nm laser pulse, in a 0.15 cm path cell, without the need for additional sacrificial reductants or oxidants. Species 1 was first used to study the reaction of nitric oxide with oxy-myoglobin (oxyMb) to form ferric myoglobin (metMb) and nitrate. This reaction had long been assumed to proceed via the same iron-bound peroxynitrite intermediate (metMb(OONO)) as the metMb-catalyzed isomerization of peroxynitrite to nitrate. Recent research showed that the metMb-catalyzed …

Design, Fabrication, And Optimization Of Miniaturized Devices For Bioanalytical Applications, Suresh Kumar

Theses and Dissertations

My dissertation work integrates the techniques of microfabrication, micro/nanofluidics, and bioanalytical chemistry to develop miniaturized devices for healthcare applications. Semiconductor processing techniques including photolithography, physical and chemical vapor deposition, and wet etching are used to build these devices in silicon and polymeric materials. On-chip micro-/nanochannels, pumps, and valves are used to manipulate the flow of fluid in these devices. Analytical techniques such as size-based filtration, solid-phase extraction (SPE), sample enrichment, on-chip labeling, microchip electrophoresis (µCE), and laser induced fluorescence (LIF) are utilized to analyze biomolecules. Such miniaturized devices offer the advantages of rapid analysis, low cost, and lab-on-a-chip scale integration …