Physical Sciences and Mathematics Commons^™

Metal-Protein Interactions For Proteomics Applications, Keerthi B Jayasundera

Open Access Dissertations

In the quest of deciphering biological mechanisms, the understanding of proteins and their functions is a vital component. However the complexity of the proteome poses an immense challenge for analytical chemists to explore it comprehensively. Currently mass spectrometry is at the forefront of proteome analysis, providing great capabilities to couple with modern separation techniques for wide applications. One major objective of current proteomic technologies is to identify proteins of interest among high background, in particular from complex biological samples. A variety of techniques have been developed over the years to simplify protein samples, which are broadly classified as enrichment, high …

Gas-Phase Ion/Ion Reactions Of Biomolecules: An Examination Of Carboxylate Reactivity And Arginine Based Non-Covalent Complexes, Nathan Zachary Barefoot

Open Access Theses

The advent of Electrospray Ionization with the ability to generate multiply charges ions has contributed significantly to the study of gas-phase ion/ion reactions. With the tools available in mass spectrometry it has been shown that these reactions are effective at transforming one type of gaseous ion into another through a series of reactions. This work examines some of these reactions and their application to field of proteomics specifically focusing on the amino acids of arginine and lysine. NHS reagents have been shown to react to both of these molecules with in the gas-phase under different conditions but have relies on …

Separation Of On-Column Labeled Model Proteins With Packed Capillary Electrophoresis, Yingxu Hao

Open Access Theses

Protein drugs are increasingly developed in the pharmaceutical company. Under the regulation of FDA, high purity of therapeutic proteins needs to be maintained. Before putting those drugs in the market, fast and efficient method is in need to achieve homogeneity. Traditionally, polyacrylamide gel electrophoresis (PAGE), capillary electrophoresis (CE), and size-exclusion chromatography (SEC) are used for the purification process. These methods have the disadvantages of low time and cost efficiency, and this quality assurance process has become the bottleneck of production. In our group, sub-micron silica colloidal particles with polyacrylamide layer on the surface are packed inside capillaries to increase the …

Physical And Chemical Attributes Of A Genetically Modified Fruit Pectin, Carl Patrick Littrell

Open Access Theses

Pectin is an important polymer used in the food industry as a thickening and gelling agent. Though pectin is ubiquitous in plants, chemical and structural differences among pectin molecules prevent most from being viable for industrial use. Enzymes found naturally in fruit cell walls during the ripening process impair many desirable attributes of fruit pectins, rendering them unsuitable for industrial applications. Pectin methylesterase (PME) is one such enzyme whose expression can be altered during ripening through the use of recombinant genetic engineering. Reduction in levels of PME results in increased degree of methylation and molecular size of pectin, greatly increasing …

Investigation Into The Control Of Melittin Secondary Structure And Antimicrobial Activity, Zachary B. Molinets

Open Access Theses

Antimicrobial resistance has been an exponentially growing problem since the discovery of antibiotics. Antibiotics have been misused for many years and this misuse has grown into a real problem for the medical community. While there are countless safeguards to prevent infection by a resistant strain of bacteria, there are still many plagued by it and must be treated with sometimes dangerous antibiotics. Melittin, along with many other peptides, contain potent antimicrobial properties, but are also toxic toward enthrocytes. The control of the secondary structure of peptides provides the key to adjusting their activity.

Synthesis And Characterization Of Crystalline Iron Nanoparticles From Zerovalent Iron Sandwich Complexes, Anh Tue Nguyen

Open Access Theses

In this project we present a systematic study on the synthesis of crystalline iron nanocubes by thermal decomposition of an iron sandwich complex, ( π-C₅H₅)Fe⁰(π-C ₆H₇), in the presence of oleylamine and oleylamine.HCl as surfactants and n-decane as a solvent. The presence of oleylamine.HCl is essential for the reproducible formation of crystalline iron cores.^ Reaction parameters such as temperature, surfactant concentration, effect of counterion, and organoiron reagent structure were investigated in order to obtain iron nanoparticles with uniform size and shape. The nanoparticles, which were characterized by …

Nitroxide Radicals For Low Frequency Electron Paramagnetic Resonance Imaging (Epri), Joshua R. Biller

Electronic Theses and Dissertations

Optimization of nitroxides as probes for EPR imaging requires detailed understanding of spectral properties such as spin lattice relaxation times, spin packet linewidths, and nuclear hyperfine splitting. Initial measurements of relaxation times for six low molecular weight nitroxides at X-band stimulated further measurement at frequencies between 250 MHz and 34 GHz. The impact of tumbling was studied with perdeuterated 2,2,6,6-tetramethyl-4-piperidinyl-1-oxyl (PDT) in five solvents with viscosities resulting in tumbling correlation times, τ_R, between 4 and 50 ps. A set of three ¹⁴N/¹⁵N pairs of nitroxides in water was selected such that τ_R varied between …

An Investigation Of Poly(N-Isopropylacrylamide) For Applications With Microfluidic Paper-Based Analytical Devices, Haydn Thomas Mitchell

Master's Theses

N,N′-methylenebisacrylamide-crosslinked poly(N-isopropylacrylamide), also known as P(NIPAM), was developed as a fluid delivery system for use with microfluidic paper-based analytical devices (microPADs). MicroPADs are postage-stamp-sized devices made out of paper that can be used as platforms for low-cost, simple-to-use point-of-care diagnostic assays. P(NIPAM) is a thermally responsive polymer that absorbs aqueous solutions at room temperature and will expel the solutions to microPADs when heated. The fluid delivery characteristics of P(NIPAM) were assessed, and P(NIPAM) was able to deliver multiple solutions to microPADs in specific sequences or simultaneously in a laminar-flow configuration. P(NIPAM) was then shown to be suitable …

Ionic Liquids In Micro Extractions And Gas Chromatographic Stationary Phases, Ramkumar Dhandapani

Seton Hall University Dissertations and Theses (ETDs)

Ionic liquids are salts that exist entirely as ionic species. They are composed of cation, anion and side chain or linkage group. Due to the different combination of the these groups, the ionic liquid exhibits unique selectivity. Their applications are enormous in the field of analytical chemistry.

The interest of using ionic liquids as gas chromatographic stationary phase has increased in recent years. The low volatility, tailorable physico-chemical property and high thermal stability of ionic liquids make them an ideal choice for gas chromatographic stationary phase. For the present research, commercially available ionic liquid capillary columns were investigate for thermodynamics …

Glass Foundation Chemosensor Synthesis And Functionality Analysis, Justin D. Dancer

Master's Theses

Chemosensors are created through a series of reaction steps on controlled pore class (CPG) and terminate with a Cu²⁺ metal binding site. Each monolayer of reactant insures that the metal binding site exposed to solution would serve as an indicator displacement assay (IDA) sensor. The purpose of this research is to create a molecular sensor with a high density of terminal metal sites to quantify bidentate substrates. To accomplish this, each synthetic step of the sensor is examined in order to test the effects of new linkers, ligands, and variously sized dendrimers to see if small structural changes could …

Understanding The Plasmonic Properties Of Metallic Nanostructures With Correlated Photon- And Electron-Driven Excitations, Vighter Ozezinimize Iberi

Doctoral Dissertations

The collective oscillation of the conduction band electrons in metal nanostructures, known as plasmons, can be used to manipulate light on length scales that are smaller than the diffraction limit of visible light. In this dissertation, a correlated approach is used to probe localized surface plasmon resonances (LSPRs) in metallic nanostructures, and their application to surface-enhanced spectroscopy. This correlated approach involves the measurement of LSPRs with dark-field optical microscopy (resonance-Rayleigh scattering), and electron energy-loss spectroscopy (EELS) in a scanning transmission electron microscope (STEM). Structural parameters of the exact same nanostructures obtained from the STEM are subsequently used in performing fully …

Development Of Optical Sensors For Chemical Detection, Jonathan Kelly Fong

Doctoral Dissertations

Detection of biodiesel at low and high concentrations in diesel is highly desired in the aviation and fuel industries. Cross contamination of jet fuel with biodiesel may impact the thermal stability and freezing point which can cause deposits in the fuel system or cause the fuel to gel, leading to jet engine operability problems and possible engine flameout. A dye doped optical sensor utilizing the dye Nile Blue Chloride has been developed for quick and direct detection of biodiesel which mainly contains fatty acid methyl esters (FAME). The sensing mechanism relies on the solvatochromatic properties of the dye which undergoes …

The Development Of Apci Mass Spectrometry Based Systems For Quantitative Real-Time Monitoring Of Process-Scale Homogenous And Heterogeneous Reactions, Zhenqian Zhu

Doctoral Dissertations

The dissertation presents solutions to monitor industrial chemical processes quantitatively in real time by mass spectrometry. Chapter 1 presents the background of atmospheric pressure chemical ionization mass spectrometry (APCI-MS). Chapters 2-6 present methods developed based on flow injection analysis coupled to atmospheric pressure chemical ionization mass spectrometry (FIA/APCI-MS) for quantitative real-time monitoring of homogeneous and heterogeneous reactions conducted at molar concentrations.

Chapter 2 introduces auto-sampling FIA/APCI-MS with the ability to overcome potential sample overloading when molar concentration samples were analyzed without sample pretreatment procedures. A homogenous Michael-addition reaction between phenethylamine and acrylonitrile was conducted at room temperature and monitored quantitatively …

Extraction Of Indicator Dyes Into Imidazolium-Based Ionic Liquids, Sarah Oplawski

Theses and Dissertations

Among the major classes of water pollutants, dyestuffs have proven to be particularly problematic, both in terms of the quantities released to the environment and the difficulties involved in their recovery from aqueous solution. Each year, textile mills worldwide discharge millions of gallons of dye-laden effluents, leading to significant adverse environmental impact as a consequence of the high chemical oxygen demand and toxicity of these effluent streams. For this reason, there has been considerable interest in the development of a means by which to remove dyes from aqueous waste streams. To accomplish this, textile mills generally employ a combination of …

The Analysis Of The Decomposition Of Hydrogen Peroxide Using A Schiff Base Copper Complex By Cyclic Voltammetry, Gavin James Rustin Mr.

Undergraduate Honors Theses

Copper(II) complexes of Schiff bases can be used in the catalysis of hydrogen peroxide to create water and oxygen. The mechanism and the kinetics of this disproportionation reaction by a dimeric copper(II) complex [CuSALAD]₂ are studied in this experiment, where SALAD refers to a Schiff Base ligand formed from salicyaldehyde and 1S,2S-D(+)-1-phenyl-2-amino-1,3-propanediol. By using cyclic voltammetry, the oxidation-reduction processes of a reaction may be monitored. The [CuSALAD]­₂ is initially reacted with a base such as imidazole to form the catalytic species, and the ratio of the copper(II) complex to the imidazole was found to be 1:4, consistent with …

Investigation Of Energy Alignment Models At Polymer Interfaces, Wenfeng Wang

USF Tampa Graduate Theses and Dissertations

The presented study investigated the Induced Density of Interface States (IDIS) model at different polymer interfaces by using photoemission spectroscopy in combination with electrospray deposition.

In recent years, organic electronics have attracted considerable attention due to their advantages of low-cost and easy-fabrication. The performance of such devices crucially depends on the energy barrier that controls the interface charge transfer. A significant effort has been made to explore the mechanisms that determine the direction and magnitude of charge transfer barriers in these devices. As a result of this effort, the IDIS model was developed to predict the energy alignment at metal/organic …

Using Ultra Performance Liquid Chromatography-Mass Spectrometric Based Metabolomics To Determine The Metabolic Differences Due To Low Temperature Or Genetic Mutation In Salmonella Enterica, Nicole Rhonda Mooney

Masters Theses

Metabolomics aims to identify and quantify all of the small molecules within a cell. The relative concentrations of metabolites within cells grown under different experimental conditions, or different species, can be compared using pool size data. Exposing cellular cultures to isotopically labeled compounds allows the progress of metabolites through metabolic pathways to be tracked, known as flux. In the first experiment, the metabolic effects of exposure to lower than optimal temperatures in wild type Salmonella enterica, i.e. cold shock, were determined. The metabolites involved in glycolysis, the citric acid cycle, and the pentose phosphate pathway had less efficient labeling …

Tip-Enhances Raman Spectroscopy, Enabling Spectroscopy At The Nanoscale, Nastaran Kazemi Zanjani

Electronic Thesis and Dissertation Repository

The knowledge on the chemical and the structural properties of substances benefits strongly from characterization methods that can provide access to the sample’s nanoscale building blocks. Not only should the sensitivity of these methods approach a high detection limit up to single molecule, but also the accessible spatial resolution must enable chemical imaging of individual nanoscale features of the substances. High resolution imaging is often provided by electron microscopes through methods such as transmission electron microscopy (TEM) and scanning electron microscopy (STM), nevertheless, these methods lack offering chemical information. Surface-enhanced spectroscopy was developed to improve the sensitivity of the chemical …

Protein Conformational Studies By Hydrogen/Deuterium Exchange Mass Spectrometry, Antony D. Rodriguez

Electronic Thesis and Dissertation Repository

Proteins are biological macromolecules responsible for the majority of all physiological processes. In order to properly function proteins are required to adopt highly ordered structures. These structural aspects may be found within a single protein or arise from multi-protein complexes. Here hydrogen/deuterium exchange mass spectrometry (HDX-MS) is employed as a tool to determine the extent of protein higher order structure. Exposure to D₂O-based solvent causes the heavier isotope to exchange with amide hydrogens in the polypeptide backbone. This exchange is mainly dependent on protein conformation because the presence of stable hydrogen-bonded secondary structure will impede the incorporation of …

The Electrochemistry Of Hydrogen Peroxide On Uranium Dioxide And The Modelling Of Used Nuclear Fuel Corrosion Under Permanent Disposal Conditions, Linda Wu

Electronic Thesis and Dissertation Repository

This thesis reports a series of investigations examining the corrosion process of used nuclear fuel under permanent disposal conditions. The motivation of the project is that the safety assessment of deep geological disposal of spent nuclear fuel requires a fundamental understanding of the processes controlling fuel corrosion which could lead to the release of radionuclides to the geosphere from a failed container.

One primary objective of this project was to develop a computational model in order to simulate fuel corrosion under the disposal conditions. A series of simulations based on COMSOL were designed and developed to determine the influence of …

Reactivity Studies Of Tridhydropyridine Radical Cautions By Using Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry And Advancement Of Mass Spectrometric Analysis Of Asphaltenes And Degradation Products, Mohammad Sabir Aqueel

Open Access Dissertations

Aromatic organic molecules which have unpaired electrons play an important role in a variety of applications in the fields of organic synthesis, organic magnets, and biological activity of organic compounds. Several studies have been published on σ- type carbon-centered mono- and biradicals. Reactive intermediates with three formally unpaired electrons are known as triradicals. They can be defined as species with three electrons distributed in three degenerate or nearly degenerate orbitals, based on Salem's definition of biradicals from the electronic structure point of view. Very little is known about the reactivity of carbon-centered σ,σ,σ- triradicals due to the complexity of studying …

Protein Affinity Extraction Of Prostate Specific Antigen (Psa) Using Submicron Spheres, Yao Wang

Open Access Theses

PSA has been used as a biomarker for prostate cancer for a long time. To characterize different glycoforms of PSA using techniques like UHPLC and cIEF, concentration and purification of PSA from complex samples becomes necessary. Our group has developed submicron silica spheres based affinity beads to extract PSA through immunoprecipitation. This study focuses on measuring the bead performance when antibody type/amount was varied and PSA concentration was lowered for clinical use. To better satisfy the requirement of large-scale extraction, several attempts were made to increase the bead capacity. The results will be presented and future directions of the project …

Method Development And Analysis For Pharmaceuticals And Personal Care Products In Surface Water, Victoria Ruelas

All Capstone Projects

Pharmaceuticals and Personal Care Products (PPCP) in surface waters is a worldwide concern. Effluent from waste water treatment plants have tested positive for PPCP. Method development for a liquid chromatographic method was derived using columns with fused core technology. Analysis of spiked samples as direct injection and after solid phase extraction indicated detection of acetaminophen, caffeine, bisphenol-A and triclosan. Confirmation of acetaminophen, caffeine, bisphenol-A and triclosan was achieved using Agilent 1100 HPLC with Agilent MST Trap XCT. Solid phase extraction using Oasis HLB indicated reproducibility at 0.05ppm.

The Determination Of Mercury Levels In Aquatic Avian Populations Using Atomic Spectroscopy Techniques, Peter M. Klaeser

All Capstone Projects

Mercury contamination has been shown to have a negative impact in fish-eating birds, including impacts on behavior, reproductive success, and their overall survival. Higher than normal mercury levels have been detected in birds who depend on fish for their food. High levels of mercury have been detected in the bird’s blood and feathers using analytical techniques. The present accepted method of determining levels of mercury in feathers and blood is the use of atomic spectroscopy. The amount of mercury in feathers appears to depend on the growth of the feathers with more growth associated with lower levels of mercury contamination. …

Loading Peptides Into Dictyostelium Discoideum Using Pinocytosis, Electroporation, Cell Penetrating Peptides, And Myristoylation, Lorena Lazo De La Vega

Senior Theses and Projects

The phospholipid bilayer of the cell is fluid and allows transport of small, hydrophobic compounds across the membrane. However, larger molecules such as peptides cannot cross the bilayer as easily. Therefore, my goal is to identify and optimize a method for loading exogenous peptides, such as reporters, hormones, or drugs, through the cell membrane. For these studies, we are using Dictyostelium discoideum as a model organism to test four peptide loading methods: pinocytosis, electroporation, cell-penetrating peptides and myristoylation. Pinocytosis uses changes in osmotic pressure to load the peptides through vesicles. The cells were exposed to a hypertonic solution for 10 …

Surface Functionalization And Bioconjugation Of Nanoparticles For Biomedical Applications, Longyan Chen

Electronic Thesis and Dissertation Repository

Colloidal inorganic nanoparticles (NPs) have been attracting considerable interest in biomedicine, from drug and gene delivery to imaging, sensing and diagnostics. It is essential to modify the surface of nanoparticles to have enhanced biocompatibility and functionality for the in vitro and in vivo applications, especially in delivering locally and recognizing biomolecules. Herein, the goal of this research work is to develop advanced NPs with well-tailored surface functionalities and/or bio-functionality for the applications in cell tracking and analytes detection.

In the first project, quantum dots incorporating with gelatin nanoparticles (QDs-GNPs) have been developed for bioimaging applications. Two different approaches have been …

Investigation And Characterization Of Pt-Modified Au Catalysts And Polymer Composites By Electrochemistry, Raman And Surface Enhanced Raman Spectroscopy (Sers), Ranjani Muralidharan

USF Tampa Graduate Theses and Dissertations

This dissertation thesis consists of six chapters. The main focus of this study is the need for understanding the reaction mechanism and intermediates formed on Pt-modified Au surface as anode catalysts in the formic acid fuel cells. Chapter 1 gives an introduction to formic acid and methanol fuel cells, an overview of the current catalysts employed at the anode of the fuel cells, specifically the Pt-modified Au electrodes as potential catalysts and the different deposition methods for preparing this catalytic surface. Information about different electrochemical methods used like cyclic voltammetry and potential step method along with other characterization methods and …

Ionic Liquid Extraction Unveils Previously Occluded Humicbound Iron In Peat Porewater, Timothy J. Veverica

Dissertations, Master's Theses and Master's Reports - Open

Extracellular iron reduction has been suggested as a candidate metabolic pathway that may explain a large proportion of carbon respiration in temperate peatlands. However, the o-phenanthroline colorimetric method commonly employed to quantitate iron and partition between redox species is known to be unreliable in the presence of humic and fulvic acids, both of which represent a considerable proportion of peatland dissolved organic matter. We propose ionic liquid extraction as a more accurate iron quantitation and redox speciation method in humic-rich peat porewater. We evaluated both o-phenanthroline and ionic liquid extraction in four distinct peatland systems spanning a gradient of physico-chemical …

Hiv-1 Rna Dimerization At Single Molecule Level, Hansini R. Mundigala

Wayne State University Dissertations

The Dimerization Initiation Sequence (DIS) is a conserved hairpin-loop motif on the 5' UTR of the HIV-1 genome. It plays an important role in genome dimerization through formation of a "kissing complex" intermediate between two homologous DIS sequences. This bimolecular kissing complex ultimately leads to the formation of an extended RNA duplex. Understanding the kinetics of this interaction is key to exploiting DIS as a possible drug target against HIV. We wish to report a novel study that makes an important contribution to understanding the dimerization mechanism of HIV-1 RNA in vitro. Our work has employed single-molecule fluorescence resonance energy …

Environmental Assessment Of Used Motor Oil In The Ciudad Juarez-El Paso Area, Alma Leticia Figueroa

Open Access Theses & Dissertations

As a hazardous waste generated in large amounts worldwide, used motor oil (UMO) is an important issue for environmental science. UMO contains the carcinogenic and mutagenic compounds Polycyclic Aromatic Hydrocarbons (PAHs). Unless properly managed and disposed of PAHs remain in the environment, principally in sediments and soil. From such environmental sinks, PAHs can migrate to watersheds contaminate drinking water, and damage ecosystems and human health.

Generators of used oil include "businesses that handle used oil through commercial or industrial operations or from the maintenance of vehicles and equipment," (United States Environmental Protection Agency (USEPA), 2013). An example of such a …