Physical Sciences and Mathematics Commons^™

Covalent Inhibition Of Enzyme Sortase A As A New Pathway Against Bacterial Resistance Of Staphylococcus Aureus, Umyeena Bashir

Master's Theses

The continued rise of antibiotic-resistant bacteria, such as MRSA (methicillin-resistant Staphylococcus aureus), has made the discovery of novel antibiotics critical. While bacteriostatic and bactericidal antibiotics inevitably exert evolutionary pressure on bacteria to develop resistance, small molecules that target mechanisms of bacterial virulence present a promising alternative for treatment. Sortase A (Srt A), a cysteine protease of S. aureus, promotes bacterial virulence by covalently attaching proteins such as pilin to the bacterial surface, enabling bacterial adhesion to mammalian cells. Inhibitory studies of this enzyme have gained prominent interest as a new pathway for drug development since blocking this enzyme's ability to …

Nanoparticles And The Environment: Biopolymer Grafted Cellulose And Screen-Printed Carbon Nanotube Composites, Dominique Henry Porcincula

Master's Theses

A host of environmental issues will define the state of the environment in the 21^st century, with plastic pollution and water shortages among them. While solutions to these problems require large-scale, multipronged solutions, one way we can address them is through material innovation and the use of nanoparticles.

In the first project, we address the issue of plastic pollution by creating nanocomposites of biodegradable polymers (PLA and PCL) with cellulose nanofibrils. Here, PLA and PCL are grafted from the surface of cellulose nanofibrils via ring-opening polymerization of cyclic ester monomers. Polymer-grafted cellulose (PGC) is characterized with structural analysis, solubility …

Design And Synthesis Of N-Succinyl-L,L-2.6-Diaminopimelic Acid Desuccinylase Inhibitors As Potential Novel Antibiotics, Thomas Dipuma

Master's Theses

N-Succinyl-L,L-2,6-Diaminopimelic Acid Desuccinylase (DapE) is a bacterial enzyme located in the lysine biosynthetic pathway of all Gram-negative and most Gram-positive species of bacteria including the notorious ESKAPE pathogens, or pathogenic strains of bacteria that have developed significant levels of resistance to currently available antibiotics. As a means to combat this challenge of growing antimicrobial resistance, we have identified the bacterial enzyme DapE as a conserved, novel enzymate target within these resistant bacterial strains,as DapE is responsible for the production of m-DAP and lysine which are ultimately employed in bacterial cell wall synthesis. The overall aim of this research is to …

Functional Nanocomposite Coatings For Use In Food Packaging, Camden N. Webb

Master's Theses

Plastics are a class of materials known for their cost and property advantages, increasing significantly in their usage worldwide. Unfortunately, these benefits come with an increasingly concerning environmental impact. A combination of inadequate disposal options and combinations of materials have led to environmental disasters that will impact generations. One of the worst areas for plastic waste is food packaging. Plastic as a material generally excels at durability and longevity, but as food packaging, it outlives its intended purpose by several orders of magnitude. This leads to plastic food packaging materials sitting in landfill or leading to the environment for hundreds …

Evaluating The Effect Of Resveratrol On Sirt1 With Different Peptide Substrates, Yujin Hur

Master's Theses

SIRT1 is an NAD+-dependent lysine deacetylase that is involved in many important cellular pathways. The protein has an extended N-terminal domain that seems to play a role in regulating its activity. Sirtuin Activating Compounds (STACs) are allosteric activators, such as resveratrol, that regulate the activity of SIRT1. STACs bind to the N-terminal STAC Binding Domain (SBD) in SIRT1. Past literature has found that SIRT1 activity can be increased, decreased, or remain unchanged by resveratrol depending on the identity of the peptide substrate. The goal of this study is to clarify the mechanism for substrate-specific allosteric regulation by resveratrol. The interactions …

Characterization And Evaluation Of Catalytic Activity Of Small Molecule Copper Complexes For Metallopolymer Design, Brenda Lu

Master's Theses

Catalysis is one of the driving forces in designing greener chemical processes for essential real-world applications. Enzymes, Nature’s catalysts, are known for their high selectivity, use of readily available metals and reagents, and ability to work under physiological conditions; three important qualities that synthetic chemists would like to mimic in their small molecule metal catalysts. Though most small molecule metal catalysts fall short of enzyme-like activity, we hypothesize that using a polymer scaffold as a secondary coordination sphere mimic around the metal complex will affect the microenvironment (steric and electronic) and enable enzyme-like activity. Previously, we synthesized ligand precursors and …

Optimizing Soluble Recombinant Expression Of The Aedes Aegypti Early Trypsin Protease, Neomi Millan

Master's Theses

The female Aedes aegypti mosquito is a primary vector for the transmission of blood–borne viral pathogens such as Chikungunya, Zika, Yellow Fever, and Dengue. The female mosquito will become infected with these pathogens through the uptake of a blood meal from an infected host. The midgut digestive enzymes are required to digest the blood meal to obtain necessary nutrients needed for the completion of the gonotrophic cycle. Blood meal digestion is biphasic and digestive enzymes are expressed at different time points after uptake of a blood meal. The focus of this study is on an early phase protease known as …

Single Chain Nanoparticles As Synthetic Enzyme Mimics, Tony Mo

Master's Theses

Enzymes, nature’s catalysts, are a crucial component in biological reactions because they help lower the activation energy and speed up these reactions. They display impressive selectivity, catalytic activity, and specificity. However, they can be difficult to produce synthetically, especially on a large scale, and they are not suitable for all reactions for which synthetic catalysts are needed. Metalloenzymes contain a transition metal active site inside the primary coordination sphere (PCS) (ligands directly bound to the metal) that is surrounded by a secondary coordination sphere (SCS) (made up of more distant amino acids) which provides steric bulk and intramolecular interactions between …

Acetylacetone Oxidation At Room Temperature: A Multiplexed Photoionization Mass Spectrometric Investigation, Study Of The Russell Intermediates In Gas Phase Reactions, And The Investigation Of Oxidation Reaction Products Of Ethanol At Room Temperature, Sara Gallarati

Master's Theses

This thesis presents the combustion study of acetyl acetone using synchrotron radiation coupled with multiplexed photoionization mass spectrometry at 298 K. The experiments were performed at the Chemical Dynamics Beamline 9.0.2 at the Advanced Light Source of the Lawrence Berkeley National Laboratory. The reaction of acetyl acetone with chlorine (Cl) radicals was analyzed based on their photoionization spectra and reaction kinetic profiles.

Additionally, a study of the Russell intermediate has been performed. Previous to experimentation at the Advanced Light Source, computational analysis has been investigated to evaluate compounds that could possibly lead to the formation of a stable species. The …

Understanding The Effects Of Temperature On Electrostatic Dna Denaturation, Jeffrey Taylor

Master's Theses

In this work, the electrostatic denaturation of 18-bp DNA duplexes was investigated via Square Wave Voltammetry (SWV) to determine the extent of melting (∆) and rate of melting (𝝉). Electrostatic denaturation was observed over the temperature range of 20-50 °C, and purely electrostatic melting was defined from 27.5°C. In contrast, electrostatic denaturation for 30 °C was defined as a mixture of thermal melting thiol desorption + electrostatic melting. Electrostatic denaturation is a temperature-dependent process, and the amount of melting of the dsDNA increased with temperature. It was also observed that the ∆ and 𝝉 values increase with temperature further …

Understanding Biogeochemical And Physical Controls On Methane Air-Sea Exchange Fluxes In The Pacific Ocean, Sarah Raney

Master's Theses

Methane and trace element samples were collected on GEOTRACES GP15 Pacific Meridional Transect (PMT) cruise conducted between the Aleutian Islands (57 °N) and Tahiti (20 °S) from September to November 2018. Uncertainty in methane air-sea exchange fluxes was determined using a propagation of errors approach. Fluxes ranged from -0.88 to 4.9 µmol CH₄ m^-2 d^-1. Average CH₄ flux along the Alaskan margin was 2.2 ± 2.9 µmol CH₄ m^-2 d^-1. Methane fluxes decreased moving southward and increased to their open ocean maximum around 20 °N before declining in equatorial waters. Near …

Synthesis And Characterization Of Ruthenium Complexes And Their Potential And Photosensitizers For Photodynamic Therapy, Keit Dine

Master's Theses

Cancer is one of the leading causes of death in the world with over 10 million people dying of the disease every year. Inorganic complexes supported by platinum metal centers are often used in cancer treatment. However, these complexes lack selectivity for tumor cells. As such, other alternatives to platinum have been explored. Ruthenium (Ru) complexes are one of the most promising candidates due to their ability to be used as photosensitizing drugs in photodynamic therapy. Herein, we report the design, synthesis, and characterization of two novel ruthenium-based complexes. One compound is a Ru(II) homoleptic complex, while the other is …

Characterization Of The Ch Addition Product From Meta- And Ortho-Xylene + Ch Reaction And Direct Experimental Observation Of The Tetrabromine Cluster Br4 Using Synchrotron Photoionization Mass Spectrometry, Rory R. Mcclish

Master's Theses

This thesis is centered on the use of a unique gas-phase spectroscopy technique to characterize products and elucidate reaction mechanisms. Experiments were carried out at the Chemical Dynamics Beamline 9.0.2 of the Advanced Light Source located at the Lawrence Berkeley National Laboratory in Berkeley, CA. Computational work was performed on the scientific supercomputer at USF to supplement experimental findings. Chapter 1 contextualizes the work spurred in response to the deleterious interactions of anthropogenic emissions on Earth’s climate. Chapter 2 describes the theoretical manipulations foundational to the experimental design and interpretation. Chapter 3 delves into the physical details of the experimental …

Chitosan Graphene Composite Fabrication And Characterization For Treatment Of Harmful Algal Blooms And Toxins, Sarah Zetterholm

Master's Theses

Chitosan graphene composites were fabricated and characterized as a management strategy for harmful algal blooms (HABs) caused by various species of cyanobacteria. These chitosan graphene materials were compared to previously studied chitosan graphene-oxide composites in both material properties and HAB treatment. In previous studies, adsorption of the cyanobacteria onto the surface of the composite materials has been observed. Investigations of the pure materials for these composites are also included in this study to determine whether removal is a result of charge interactions with the composite, or as an inherent property of the graphene or graphene oxide. Initial results suggest that …

Comparison Of Supported Liquid Extraction And Solid Phase Extraction Of Methamphetamine From Urine And Method Validation By Gas Chromatography-Mass Spectrometry, Taylor Hood

Master's Theses

Applications of SLE (supported liquid extraction) is a relatively new extraction technique that is not widely used in forensic toxicology. SLE is also easier and less time consuming than traditional LLE (liquid-liquid extraction) and SPE (Solid phase extraction). This work will compare the extraction efficiencies between SLE and SPE for methamphetamine from urine with detection and quantitation using GC-MS (gas chromatography- mass spectrometry). The SLE cartridges provide better analyte recoveries, eliminate emulsion formation, and allow for shorter processing time than other extraction techniques. The SPE cartridges used have a mixed-mode non-polar/strong cation exchange retention mechanism to extract basic analytes like …

Exploring The Mechanism Of The Electrostatic Denaturation Of Double-Stranded Dna, Gayatri Raghu

Master's Theses

Electrostatic melting is an electrochemical tool that can be used to analyze the stability of DNA, allowing for the detection of various mutations in double-stranded DNA (dsDNA). Here, we explore the influence of electrostatic double layer formation on the unzipping of dsDNA to better comprehend the mechanism of this process. Previous studies by our lab show that the melting curve produced can distinguish between fully complementary 34-bp strands and a version of the same sequence in which one base pair has been replaced with a mismatch pair or detect and characterize the crosslinking of the dsDNA by anticancer drug cisplatin. …

Exposing The Effects Of Reaction Cavity In Solid-Phase Reaction Kinetics, Michael Carr

Master's Theses

Reactivity of molecular solids is governed by topochemical considerations, where minimizedmolecular movement dictates both product identity and kinetics. This Thesis explores the central role reaction cavity plays in the topochemical principle by using the highly varied cavities formed by the different facets of a tetracene crystal. The relative rates for ten different reaction cavities were measured via energy dispersive X-ray spectroscopy for the reaction of tetracene with vapors of maleic anhydride. Variance in cavities resulted in Diels-Alder reaction rates that differed by as much as a factor of 2.6. Effects were understood via molecular dynamic simulations which modeled the approach …

Eelgrass (Zostera Marina) Population Decline In Morro Bay, Ca: A Meta-Analysis Of Herbicide Application In San Luis Obispo County And Morro Bay Watershed, Tyler King Sinnott

Master's Theses

The endemic eelgrass (Zostera marina) community of Morro Bay Estuary, located on the central coast of California, has experienced an estimated decline of 95% in occupied area (reduction of 344 acres to 20 acres) from 2008 to 2017 for reasons that are not yet definitively clear. One possible driver of degradation that has yet to be investigated is the role of herbicides from agricultural fields in the watershed that feeds into the estuary. Thus, the primary research goal of this project was to better understand temporal and spatial trends of herbicide use within the context of San Luis …

Pressure Driven Desalination Utilizing Nanomaterials, Fangyou Xie

Master's Theses

Nanomaterials such as graphene oxide and carbon nanotubes, have demonstrated excellent properties for membrane desalination, including decrease of maintenance, increase of flux rate, simple solution casting, and impressive chemical inertness. Here, two projects are studied to investigate nanocarbon based membrane desalination. The first project is to prepare hybrid membranes with amyloid fibrils intercalated with graphene oxide sheets. The addition of protein amyloid fibrils expands the interlayer spacing between graphene oxide nanosheets and introduces additional functional groups in the diffusion pathways, resulting in increase of flux rate and rejection rate for the organic dyes. Amyloid fibrils also provide structural assistance to …

Rheological Studies Of Fully-Formulated Coatings Thickened With Heur: Effects Of Surfactants, Brandon M. Bonilla

Master's Theses

Rheology modifiers such as hydrophobically-modified ethoxylated urethane (HEUR)thickeners are included in waterborne latex coatings to optimize shear-rate dependent viscosity and other rheological properties. While these HEUR polymers are commonly used in industry, the complex chemical interactions that contribute to rheological properties are still not completely understood. Prior work in this area has focused on understanding latex-HEUR and latex-surfactant-HEUR interactions that affect rheological properties. Additionally, studies have been previously conducted to understand the relaxation mechanisms of complex interactions present in HEUR-thickened waterborne latex coatings under various dynamic conditions. The objective of this work is to extend the experimental work to fully-formulated …

An Investigation Of Antenna, Ligand Side-Chain, And Metal Ion Effects On The Optical And Mri Properties Of Bimodal Lanthanide (Iii) Complexes, Marisa Poveda

Master's Theses

Magnetic Resonance Imaging (MRI) is a leading anatomical imaging modality for disease diagnosis. With the aid of Gd³⁺ based contrast agents, high resolution images of biological structures can be obtained. However, there is an increased need for contrast agents that are responsive to specific analytes and chemical environments. Paramagnetic Chemical Exchange Saturation Transfer (PARACEST) agents that utilize a paramagnetic lanthanide ion chelated with a ligand have shown great promise in this area. Lanthanide ions also possess luminescence properties that do not suffer from common limitations of conventional optical imaging agents such as autofluorescence and photobleaching. The projects described in …

Electrostatic Denaturation Of Dna-Cisplatin Adducts, Eddie Madrigal

Master's Theses

In this thesis, electrochemical approaches are used to determine the properties of deoxyribonucleic acid (DNA) by electrostatic denaturation. The electrochemical routine involves an application of a destabilization potential, an equilibration potential, and a square wave voltammogram (SWV) to monitor the extent of melting. Our method uses a monolayer consisting of thiol modified DNA and mercaptohexanol on a gold electrode. These electrodes are then incubated in a complementary sequence tagged with methylene blue. By using our electrostatic denaturation technique, different parameters are explored, such as surface densities, surface coverages, and ionic strengths. As proof of concept, these techniques were applied toward …

Freshwater Endmembers Impacting Carbonate Chemistry In The Mississippi Sound, Allison Savoie

Master's Theses

Coastal ecosystems are highly dynamic areas for carbon cycling and are likely to be negatively impacted by increasing ocean acidification. This research focused on dissolved inorganic carbon (DIC) and total alkalinity (TA) in the Mississippi Sound in order to understand the influence of local rivers that supply alkalinity to the area and buffer against ocean acidification. This area receives large fluxes of freshwater from local rivers, in addition to episodic inputs from the Mississippi River through a human-built diversion, the Bonnet Carré Spillway. Sites in the Mississippi Sound were sampled monthly during August 2018 to November 2019 and at weekly …

Antibacterial Coatings Derived From Novel Chemically Responsive Vesicles, Emily B. Mobley

Master's Theses

In order for a drug, or any material used for the purpose of eliciting a change in an organisms’ physical or chemical state, to be effective it must reach the intended target intact and for a sustained rate over time. Drug delivery systems encapsulate a drug to protect it from degradation, prevent side reactions, increase solubility, improve accumulation rates at target sites, and release drugs at a controlled rate. Controlled and sustained release of drugs is achieved by degradation of the carrier triggered by breaking dynamic chemical bonds caused by changes in the chemical environment such as pH or redox …

Effect Of Polymer Design And Coating Formulation On The Water Uptake And Sensitivity Of Acrylic Water-Borne Films, William Z. Thompson

Master's Theses

Water-borne latex coatings represent a safer, more user-friendly, and environmentally responsible alternative to solvent-borne coatings, and are growing in popularity each year. However, these coatings often exhibit unfavorable performance when exposed to water for extended periods of time. This prolonged exposure often results in water uptake, which may give rise to other detrimental effects such as a decrease in modulus, blushing or water-whitening, reduced serviceable life, and softening of the film. In this study, various polymer composition latex design spaces are studied to develop an understanding of how water uptake can be modulated and minimized using common synthetic approaches. Factors …

Altering An Epoxy-Amine Thermoset's Performance Through Varying Mix Ratios, Kiersten M. Smith

Master's Theses

Epoxy resins are used in a number of different industries and therefore have application-specific material requirements, from satellites that require materials that operate in space, to paints and coatings that require high scratch resistance and mechanical durability, to medical devices, designed to be in continuous contact with biological fluids. Commercial epoxy products come with manufacturer’s information explaining the epoxy properties and recommended preparation processing conditions, which may include epoxy resin to curing agent mix ratio (Part A : Part B), cure time, and cure temperature, for example. Due to proprietary reasons, it can be difficult to understand why these values …

Investigation On The Morphology Of Charge-Transfer Complexes In Low Density Polyethylene, Wade Korf

Master's Theses

Fillers are used ubiquitously throughout the fields of polymer and material science to overcome many inherent limitations to polymeric materials (i.e. poor stiffness or strength) and to expand their potential applications. There is a need to develop controllable particle architectures to better understand fundamental structure-property relationships in particle reinforced polymer composites. Charge-transfer complexes (CTCs) can assemble in situ into various needle and dendritic shapes via simple fabrication processes and at low loading levels. In this study, the effect of tetrathiafulvalene (TTF) and 7,7,8,8-tetracyanoquinodimethane (TCNQ) CTC crystallites of various shapes and sizes on composite mechanical properties was investigated in an LDPE …

Thiol-Ene Click Chemistry For Solid State Triplet-Triplet Annihilation Upconversion And Parts-Per-Billion Pyrophosphate Sensing In Artificial Seawater, Abagail K. Williams

Master's Theses

Thiol-ene click chemistry is a robust approach to molecularly engineering polymers for many applications. Within this work, thiol-ene click chemistry is used to fabricate thiol-ene networks for TTA-UC and to synthesize a conjugated polyelectrolyte (CPE) used as a pyrophosphate (PPi) sensor in complex aqueous media. Chapter I focuses on the synthesis and upconversion performance of rubbery networks fabricated using thiol-ene click photopolymerization. The advancement of triplet-triplet annihilation based upconversion (TTA-UC) in emerging technologies necessitates the development of solid-state systems that are readily accessible and broadly applicable. We demonstrate that thiol-ene click chemistry can be used as a facile cure-on-demand synthetic …

Valorization Of Carrot Processing Waste, Alexandra M. Duval

Master's Theses

Commercial carrot processors produce up to 175,000 tons of carrot waste annually. Carrot Mash (CM) is the term referring to the waste by-product of peeled baby carrot processing. Transportation of carrot processing waste is expensive due to its high- water content (approx. 83-95%). High in bioactive compounds (carotenoids) and dietary fibers, it is expected that its conversion into a value-added by-product is of interest to the carrot processing industry. Hemicellulose-rich plant materials have proven to be a source of oligosaccharides, which are known for their beneficial prebiotic activity. The objectives of this research were to: 1) determine the effect of …

Implementation Of Multivariate Artificial Neural Networks Coupled With Genetic Algorithms For The Multi-Objective Property Prediction And Optimization Of Emulsion Polymers, David Chisholm

Master's Theses

Machine learning has been gaining popularity over the past few decades as computers have become more advanced. On a fundamental level, machine learning consists of the use of computerized statistical methods to analyze data and discover trends that may not have been obvious or otherwise observable previously. These trends can then be used to make predictions on new data and explore entirely new design spaces. Methods vary from simple linear regression to highly complex neural networks, but the end goal is similar. The application of these methods to material property prediction and new material discovery has been of high interest …