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 …

Tempers Rising: The Effect Of Heat On Spite, Jake C. Cosgrove

Master's Theses

The relationship between heat and harmful outcomes is well documented, with research connecting various adverse economic outcomes to the climate. In the presence of increasing global warming and climate change, understanding why the climate leads to negative economic outcomes is essential for forming peaceful institutions of the future. We study how behavioral economic outcomes change in the presence of heat through a lab experiment involving 1,110 observations conducted in five different countries. This paper specifically focuses on the social preference outcome of spite. We find that increased time exposure to the treatment effect of heat is required to elicit an …

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 …

Formal And Informal Styles Of Clothing In The Assessment Of Female Political Candidates, Erma Kurtovic

Master's Theses

Abstract: This study will research the importance of dress code of female candidates on the confidence in leadership.The research question is: How Important is the Formality of Dress Code in the Assessment of Leadership of Female Political Candidates? It is addressed by using an experimental design carried out in India and the United States, using Qualtrics and Amazon Mechanical Turk. This research gathered 400 responses, 200 from each country. Primary data collection was used, with the implementation of two experiments. The experimental design of the two experiments consisted of two conditions, one in which the main political candidate is dressed …

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 …

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 …

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. …

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 …

The Workability Of Dominican University Of California (Duoc) Transitioning To A Community Choice Aggregation (Cca) Program Energy Supply, Alexandra Fuentes

Master's Theses

For almost 10 years Community Choice Aggregation (CCA), or community based energy programs, have been developing and or providing clean energy resources to both commercial and residential customers in various regions around the United States. Although there are several programs in communities in the surrounding regions of California, this study focuses on a specific California program known as MCE. This research examines the feasibility of Dominican University of California (DUoC) transitioning from Pacific Gas and Electric (PG&E) to becoming a client of MCE in the future. Out of the 19 community energy programs currently available in the state, MCE is …

The Investigation Of Methylidyne Radical (Ch) Reactions With Furan, 2-Methylfuran, And 2,5-Dimethlyfuran And The Photoionization And Photodissociation Of Valeric Acid, Erica Carrasco

Master's Theses

This thesis presents the combustion study of three furanic compounds 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 reactions of the three furanic compounds with methylidyne (CH) radicals were analyzed based on their photoionization spectra and kinetic profiles.

Additionally, the unimolecular dissociation of valeric acid was also studied and presented in this work using the double imaging photoelectron photoion spectrometry (i2PEPICO) coupled with synchrotron radiation from the VUV beamline. The experiments were carried out …

Synchrotron Photoionization Study Of 2,5-Dimethylfuran Oxidation Initiated By O(3p) Atoms, And Computational Studies Of Superalkali Species: Li3f2, Heejune Park

Master's Theses

This thesis presents the experimental study of a 2,5-dimethylfuran oxidation reaction initiated by atomic oxygen (O(³P)) and the theoretical investigation of superalkalis properties. The experiments were performed at the Chemical Dynamics Beamline 9.0.2 of the Advanced Light Source (ALS) located at the Lawrence Berkeley National Laboratory in Berkeley, CA. The first chapter discusses world energy consumption and progress towards new sustainable energy sources, mainly focusing on biofuels, along with a basic description of combustion. A description of the superalkalis and a brief history of synchrotron radiation are also presented in Chapter 1. Chapter 2 describes the components of …

Facilitating Greenhouse Gas Reduction And Climate Change Adaptation Within The Coastal Zone: A Policy Analysis For The California Coastal Commission, Nicole Young

Master's Theses

California is already experiencing impacts to its coastline due to climate change, and more severe impacts are anticipated if greenhouse gas emissions continue to rise. These climate change impacts are especially strong within the California coastal zone, which falls under the jurisdiction of the California Coastal Commission. The Commission has a history of rigorous environmental protection and is committed to protecting California’s coast through proactive planning and regulation, however they will need to initiate coastal policies with ambitious targets to facilitate effective climate change adaptation and mitigation. This study analyzed existing California climate policies and Coastal Commission policies to identify …

Wildfire Exposure To Critical Habitat Of Endangered And Threatened Species In California, Kristin Butcher

Master's Theses

Researchers, fire ecologists and wildlife managers are concerned about impact to endangered and threatened species and their critical habitat due to the projected increase in future wildfires. Wildfires have been studied in California for the last six decades and have been increasing at an alarming rate since the 1980’s. In this study, I use the 2018 spatial dataset for critical habitat of federally endangered and threatened species located in the state boundaries of California and compare it to a spatial dataset for wildfires that have occurred over the span of 32 years (1984 to 2016). Trends are derived from spatial …

The Long-Run Effects Of Tropical Cyclones On Infant Mortality, Isabel Miranda

Master's Theses

In the United States alone, each tropical cyclone causes an average of $14.6 billion worth of damages. In addition to the destruction of physical infrastructure, natural disasters also negatively impact human capital formation. These losses are often more difficult to observe, and therefore, are over looked when quantifying the true costs of natural disasters. One particular effect is an increase in infant mortality rates, an important indicator of a country’s general socioeconomic level. This paper utilizes a model created by Anttila-Hughes and Hsiang, that takes advantage of annual variation in tropical cyclones using annual spatial average maximum wind speeds and …

Triple Bottom Line As A Method To Increase Business Value And Foster Positive Social And Environmental Change, Jayleene West

Master's Theses

The Triple Bottom Line (TBL) business model has transformed the business world by changing the way businesses operate. By focusing on the people and the environment, businesses have grown to see substantial profit and avoid risks along the way. Companies are using the TBL to build their brand and customer loyalty by enhancing the environment and society. This paper analyzes four companies that are leaders in their industry and are founded on the TBL; Seventh Generation, New Belgium Brewing, Patagonia, and Ben & Jerry’s. Recommendations have been made by performing a literature review on the advantages and disadvantages of the …

Detection And Melting Of Surface-Bound Dna Using A Purely Electrochemical Approach, Denny Ho

Master's Theses

In this thesis, we demonstrate an electrochemical approach for monitoring the electric-field induced melting of surface-bound double-stranded DNA. The electrochemical routine involves repeated chronoamperometry pulses to melt the duplex and square wave voltammetry to monitor the extent of melting. We utilize a scanning potential and constant potential technique to generate melting curves and access the stability and kinetics of the DNA duplexes. Our method uses a mixed monolayer of thiol-modified DNA oligomers and mercaptohexanol on gold electrodes, are subsequently incubated with target DNA covalently modified with electroactive methylene blue. Under room temperature, 10 mM Tris, and optimized electrochemical parameters, DNA …

The Investigation Of The Chlorine Initiated Oxidation Of 2-Phenylethanol And Stability Of Superalkali Lithium Substituted Silyls., Adam Otten

Master's Theses

This thesis investigates the combustion potential of 2-phenylethanol and the superalkali properties of small lithium substituted silicon compounds. All combustion experiments were performed at the Advanced Light Source of Lawrence Berkeley National Laboratory at the Chemical Dynamics Beamline 9.0.2. The chlorine initiated oxidation of 2PE was investigated at 298 and 550 K using a multiplex photoionization mass spectrometer, coupled with the tunable vacuum ultraviolet radiation. Reaction products were identified using kinetic time traces and photoionization spectra.

Additionally, the stability of small superalkali silicon-lithium compounds has also been investigated. All structures and energetics were calculated using the CBS-QB3 composite method.

The …

Electropolymerization Of Polyaniline In The Presence Of Ferricyanide: Electrochemical, Spectroscopic And Gravimetric Studies, Lucas Marinelli

Master's Theses

In this work, ferricyanide-doped polyaniline (PANI) is electropolymerized by constant current and cyclic voltammetry (CV) measurements with simultaneous monitoring of mass changes using electrochemical quartz crystal microbalance (eQCM). Raman spectroscopy, Fourier transform infrared spectroscopy and CV measurements confirm the incorporation of the ferricyanide into the film and indicate modified electrical conductivity. UV-Vis absorbance spectroscopy and Raman spectroscopy confirm the conducting ‘emeraldine-salt’ state and confirm the presence of polarons, i.e. charge carriers.

The addition of ferricyanide during electropolymerization of the PANI film results in an increase of polymerization rate as confirmed using eQCM. A decrease in counter ion ingress/egress and an …

Investigation On The Dissociative Photoionization Mechanism Of Furfural, Investigation Of The Absolute Photoionization Cross Sections Of Three Potential Propargylic Fuels, And Ab Initio Analysis On Potential Superbases Of Several Hyperlithiated Species: Li3f2o And Li3f2(Oh)N (N = 1, 2, 3), Matthew Winfough

Master's Theses

This thesis presents the study photoionization cross sections of three different propargylic biofuels; dipropargyl ether, propargyl alcohol, and propargylamine, in chlorine radical-initiated combustion experiments at the Chemical Dynamics Beamline (9.0.2) at the Advanced Light Source of the Ernest Orlando Berkeley National Laboratory in Berkeley, California. Additionally, the unimolecular dissociative photoionization mechanism of furfural was studied using photoelectron photoionization coincidence (PEPICO) spectroscopy at the vacuum ultraviolet beamline at the Swiss Light Source of the Paul Scherrer Institut in Villigen, Switzerland. Dissociation products and mechanisms for furfural were identified over a photon energy range of 10.9 to 14.5 eV. Lastly, a study …

Mineral Warfare: The Dark Side Of Technology And International Mediation, Priyanka Basnyat

Master's Theses

Conflict surrounding the extraction and trade of natural resources is not an uncommon phenomenon. Especially in the case of the Democratic Republic of Congo (DRC), which has historically suffered from the negative impacts of the resource curse since their mineral wealth was first discovered by their Colonial administrators. The importance of Congo’s minerals has fluctuated over the years but has peaked during recent times, as their use in technological advancements are becoming more vital. The global demand for these mineral ores have sky rocketed and consequentially, the largely informal trade has benefitted certain rebel groups, playing a pivotal role in …

What’S At Steak? The Political Discourse Of Emissions Intensity And Implications Of Animal Agriculture, Kalyn Simon

Master's Theses

This thesis analyzes the international discourse of greenhouse gas emissions in relation to livestock production. Specific government ministries, research institutes, and multilateral organizations are framing a new strategy to mitigate emissions by using emissions intensity metrics. Emissions intensity is a ratio comparing emissions produced per unit of animal product as oppose to measuring absolute emissions. This research is acknowledged as a win-win scenario which allows for a reduction of greenhouse gas emissions while continuing production more efficiently. This thesis outlines the emergence of this metric in international discourse and the implications this shift has on the livestock sector globally. Ultimately, …

Planning Cities, Economically Or Communally: A Comparative Study Of Amsterdam And San Francisco, Raina Dawn Whittekiend

Master's Theses

Globalization has spun “community” off its axis. What once defined community is no longer the current state of the community. Increased economic transactions have led to the instability of communities that once depended on one another at the local level. These communities are now dependent on systems that do not know nor understand their actors. This lack of relationship between development and subject is witnessed and highly scrutinized in developing countries all over the world and has been intensely researched in academic literature. This thesis intends to better understand why in modernized global cities these same processes of development and …

Development Of An Improved Synthesis Of S-D-Ribosyl-L-Homocysteine (Srh) And Progress Toward Srh Analogs Modified At The C3 Position, Emily Rouse

Master's Theses

Quorum sensing is a system that facilitates bacteria turning on and off gene expression depending on population density. System 2 quorum sensing is utilized by both Gram positive and Gram negative bacteria, and the quorum sensing molecule used in this system is AI-2. AI-2 is biosynthesized by the enzyme LuxS from the precursor SRH. This thesis describes an improved synthesis of SRH through the exploration of different protecting group strategies. The knowledge gained from the improved synthesis of SRH is then applied toward the synthesis of SRH analogues with increased steric bulk installed through use of a stereoselective anti-Mannich reaction. …

The Investigation And Characterization Of The Reaction Of 2-Methylfuran And 2-Methyl-3-Buten-2-Ol With O(3p) And The Photodissociation Of Xylyl Bromide Isomers, Yasmin Fathi

Master's Theses

This thesis has studied the oxidation behavior of different biofuels or additives, 2-methyl-3-buten-2-ol and 2-methylfuran, in combustion experiments at the Chemical Dynamics Beamline held at the Advanced Light Source of the Lawrence Berkley National Laboratory. The oxidation of these fuels were initiated through O(³P) and the combustion experiments were analyzed using a multiplexed chemical kinetics photoionization mass spectrometer with tunable synchrotron radiation. Products of the different reactions were identified using kinetic profiles and further characterized using the photoionization spectra. The amount of each species was calculated using branching fractions.

Additionally, the unimolecular dissociation of the xylyl bromide isomers …

The Acquisition And Analysis Of Electroencephalogram Data For The Classification Of Benign Partial Epilepsy Of Childhood With Centrotemporal Spikes, Jessica A. Scarborough

Master's Theses

In this thesis, I will expand upon each step in the process of acquiring and analyzing electroencephalogram (EEG) for the classification of benign childhood epilepsy with centrotemporal spikes. Despite huge advancements in the field of health informatics—natural language processing, machine learning, predictive modeling—there are significant barriers to the access of clinical data. These barriers include information blocking, privacy policy concerns, and a lack of stakeholder support. We will see that these roadblocks are all responsible for stunting biomedical research in some way, including my own experiences in acquiring the data for the second chapter of this thesis.

This second chapter …

C(Sp2)–H Functionalizations Employing 2-Aminophenyl-1h-Pyrazole As A New Removable Directing Group, Wan-Chen Lee

Master's Theses

2-Aminophenyl-1H-pyrazole (2-APP) was discovered as a novel removable bidentate directing group for copper-mediated aerobic oxidative C(sp2)–H bond amidation and sulfonamidation bearing a wide range of sulfonamides, When Cu(OAc)2 was employed as the copper source, 1,1,3,3-tetramethylguanidine (TMG) as an organic base, the reaction, optimally carried out overnight in DMSO at 80 °C in open air, produced a variety of products in moderate to excellent yields. In addition, C(sp2)–H bond chlorination has been developed by using this auxiliary, employing trichloroacetamide as a new chlorine source. Furthermore, this unprecedented directing group also can assist copper-mediated regio-selective hydroxylation, and ortho-alkynylation/annulation by using Cu(OAc)2 as …

Characterization Of Etbe + Cl And Isooctane + Cl Combustion Products Using Synchrotron Photoionization, Rong Yao

Master's Theses

The low temperature (298 – 700 K) oxidation characterizations of a series of fuel additives (ETBE and isooctane) were studied at advanced light source in Lawrence Berkley National lab, using a multiplexed chemical kinetics photoionization mass spectrometer with tunable synchrotron radiation. Using Cl atoms as initiators in presence of oxygen, photoionization data were collected. Data analysis was performed via characterization of the reaction species photoionization spectra and kinetic traces, from which the products and also the intermediates were identified. Relevant reaction dynamics on potential energy surfaces were calculated, reaction enthalpies of each individual step were presented using the CBS-QB3 composite …

Dendrimer Modified Silica Nanoparticles As Fluorescent Chemosensors For The Detection Of Copper And Cyanide Ions, Alicia Luhrs

Master's Theses

A series of silica nanoparticle-based fluorescent chemosensors were synthesized for the sensitive and selective detection of Cu²⁺ ions in aqueous solution and subsequent CN^- ion detection. Silica nanoparticles (SNP) were modified with branching polyamidoamine (PAMAM) dendrimers, which function as selective turn-off Cu²⁺ ion chelators and platforms for the attachment of rhodamine isothiocyanate (RITC) or fluorescein isothiocyanate (FITC) fluorescent dyes. In the presence of Cu²⁺ ions, the emission of the fluorescent dye is quenched by Forster resonance energy transfer (FRET) and is dependent upon dendrimer generation, pH, fluorescent dye, and surface charge. The quenching effectiveness was analyzed …

Photooxidation Reactions Of Small-Chain Methyl Esters, Aerosol Photoelectron Spectroscopy, And The Photodissociation Of Ethylenediamine, Giel Muller

Master's Theses

Research conducted at the University of San Francisco is presented within this masters thesis, including the Cl-initiated photooxidation reactions of methyl propanoate, methyl butanoate, and methyl valerate (pentanoate), the aerosol photoelectron spectroscopy of isoprene and gamma-valerolactone, and the TPEPICO investigation of ethylenediamine. Experiments were conducted at the Lawrence Berkeley National Lab Advanced Light Source (ALS), the National Synchrotron Radiation Research Center in Hsinchu City (NSRRC), and the University of Stockton in California, respectively.