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Intrinsic Buffer Hydroxyl Radical Dosimetry For Hydroxyl Radical Protein Footprinting, Addison Roush 2020 University of Mississippi

Intrinsic Buffer Hydroxyl Radical Dosimetry For Hydroxyl Radical Protein Footprinting, Addison Roush

Honors Theses

Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry is a powerful technique for the analysis of protein topography as it generates covalent mass labels that can survive downstream sample handling, and it is sensitive to the solvent accessibility of amino acid sidechains. Of the multiple platforms for HRPF, fast photochemical oxidation of proteins (FPOP) utilizes a pulsed 248 nm KrF excimer laser to label proteins by photolyzing hydrogen peroxide. FPOP is the most widely used HRPF platform because it labels proteins faster than unfolding can occur. Variations in FPOP sample conditions make it difficult to compare results between experiments ...


Nmr-Based Metabolic Profiles Of Intact Zebrafish Embryos Exposed To Aflatoxin B1 Recapitulates Hepatotoxicity And Supports Possible Neurotoxicity, Zain Zuberi, Muhamed N.H. Eeza, Joerg Matysik, John P. Berry, A. Alia 2020 Trinity College; Leiden University

Nmr-Based Metabolic Profiles Of Intact Zebrafish Embryos Exposed To Aflatoxin B1 Recapitulates Hepatotoxicity And Supports Possible Neurotoxicity, Zain Zuberi, Muhamed N.H. Eeza, Joerg Matysik, John P. Berry, A. Alia

Department of Chemistry and Biochemistry

Aflatoxin B1 (AFB1) is a widespread contaminant of grains and other agricultural crops and is globally associated with both acute toxicity and carcinogenicity. In the present study, we utilized nuclear magnetic resonance (NMR), and specifically high-resolution magic angle spin (HRMAS) NMR, coupled to the zebrafish (Danio rerio) embryo toxicological model, to characterize metabolic profiles associated with exposure to AFB1. Exposure to AFB1 was associated with dose-dependent acute toxicity (i.e., lethality) and developmental deformities at micromolar (≤ 2 µM) concentrations. Toxicity of AFB1 was stage-dependent and specifically consistent, in this regard, with a role of the liver and phase I enzyme ...


Phenolic Phytochemicals And Their Antioxidant Activities In Maine-Grown Asian, American-Hybrid, And European Plums, Hye Weon Hwang 2020 University of Maine

Phenolic Phytochemicals And Their Antioxidant Activities In Maine-Grown Asian, American-Hybrid, And European Plums, Hye Weon Hwang

Electronic Theses and Dissertations

Plum fruits of 16 plum cultivars derived from three species, Asian, American-hybrid, and European plums, and one cultivar of an interspecific hybrid between Asian plum and apricot were investigated to identify and quantify two major groups of phenolic phytochemicals, anthocyanins and hydroxycinnamic acids (HCAs) by HPLC–DAD/MS. The plums were harvested from 2014 to 2017. Some cultivars were analyzed through consecutive years to determine year-to-year differences and to evaluate the maturity impacts on the concentration of anthocyanins and HCAs from the partial-ripe stage and tree-ripe stage. Anthocyanins were present in red−purple colored plums, but their profiles varied among ...


Formation Of Nanoparticles For The Oral Delivery Of Small Molecules By Flash Nanoprecipitation, Jing Zhi Lo 2020 University of Pennsylvania

Formation Of Nanoparticles For The Oral Delivery Of Small Molecules By Flash Nanoprecipitation, Jing Zhi Lo

Master of Chemical Sciences Capstone Projects

Nanoparticles have shown considerable potential in many biological applications including drug delivery, bio-imaging, and medical diagnostics. Specifically, the development of nanoparticle-based drug formulations holds opportunities to improve the dissolution rate and oral availability of poorly water-soluble drugs. The goal of this project is to improve oral bioavailability of a small molecule drug (“G-1”) through the formation of nanoparticles using the flash nanoprecipitation (FNP) process. Interestingly, “G-1” formed ~80 nm particles that are electrostatically stabilized without the use of stabilizing polymers and concentration as high as 160 mg/mL of “G-1” formed nanoparticles. Additionally, trehalose was found to be an effective ...


Raman Spectroscopy Study Of Delta-9-Tetrahydrocannabinol And Cannabidiol And Their Hydrogen-Bonding Activities, Kalee Sigworth 2020 University of Mississippi

Raman Spectroscopy Study Of Delta-9-Tetrahydrocannabinol And Cannabidiol And Their Hydrogen-Bonding Activities, Kalee Sigworth

Honors Theses

Cannabis and products containing its cannabinoids have grown rapidly in acceptance and use in recent years with legalization of cannabis in many countries and US states. Cannabidiol and Delta-9-Tetrahydrocannabinol are two primary cannabinoids in Cannabis that have been shown to produce analgesic effects along with many other positive side effects for the user. These two cannabinoids interact with receptors in the Central and Peripheral Nervous Systems. No spectroscopic study to our knowledge has been performed to analyze the hydrogen bonding effects of interactions between these two cannabinoids and solvents. Here, we employ theoretical Raman spectra through computational methods to study ...


Monolayer Self-Assembly Of Monodisperse Nanocrystals At The Liquid-Air Interface, Di An 2020 University of Pennsylvania

Monolayer Self-Assembly Of Monodisperse Nanocrystals At The Liquid-Air Interface, Di An

Master of Chemical Sciences Capstone Projects

The study of nanocrystals (NCs) self-assembly into monolayers have attracted significant interests, due to wide applications in sensors, catalysts, nanodevices and pattern transfer. Liquid-air interface self-assembly (LAISA) is a useful technique used for the monolayer fabrication. In this capstone project, a library of NCs is built for LAISA and binary superlattice study. Monodisperse iron oxide, gold and gadolinium fluoride NCs of various sizes were synthesized by modifying reported methods.9,10,20 The obtained NCs were characterized by TEM, SAXS, DLS and TGA, revealing their geometry, size and surface chemistry. The second part of this project is optimizing conditions of ...


Magnetic Ionic Liquids As Solvents For Rna Extraction And Preservation, Chenghui Zhu, Marcelino Varona, Jared L. Anderson 2020 Iowa State University

Magnetic Ionic Liquids As Solvents For Rna Extraction And Preservation, Chenghui Zhu, Marcelino Varona, Jared L. Anderson

Chemistry Publications

Ribonucleic acid (RNA) is particularly sensitive to enzymatic degradation by endonucleases prior to sample analysis. In-field preservation has been a challenge for RNA sample preparation. Very recently, hydrophobic magnetic ionic liquids (MIL) have shown significant promise in the area of RNA extraction. In this study, MILs were synthesized and employed as solvents for the extraction and preservation of RNA in aqueous solution. RNA samples obtained from yeast cells were extracted and preserved by the trihexyl(tetradecyl) phosphonium tris(hexafluoroacetylaceto)cobaltate(II) ([P66614+][Co(hfacac)3–]) and trihexyl(tetradecyl) phosphonium tris(phenyltrifluoroacetylaceto)cobaltate(II) ([P66614+][Co(Phtfacac)3–]) MIL with a ...


Spectral Narrowing Accompanies Enhanced Spatial Resolution In Saturated Coherent Anti-Stokes Raman Scattering (Cars): Comparisons Of Experiment And Theory, Avinash Singh, Kalyan Santra, Xueyu Song, Jacob W. Petrich, Emily A. Smith 2020 Ames Laboratory

Spectral Narrowing Accompanies Enhanced Spatial Resolution In Saturated Coherent Anti-Stokes Raman Scattering (Cars): Comparisons Of Experiment And Theory, Avinash Singh, Kalyan Santra, Xueyu Song, Jacob W. Petrich, Emily A. Smith

Chemistry Publications

We demonstrate theoretically and confirm experimentally the mechanism by which spectral narrowing accompanies enhanced spatial resolution in a saturated coherent anti-Stokes Raman scattering (CARS) signal that is demodulated at the third harmonic (3f) of the pump modulation frequency (f). Under these modulation conditions, theory predicts a narrowing of the full width at half-maximum (FWHM) of the CARS spectrum by a factor of 2.0 with respect to that of the spectrum obtained by demodulation at the fundamental frequency. Theory also predicts an improvement of spatial resolution by a factor of 1.7. Experimentally, narrowing of the FWHM of the ...


Effect Of Charged Lipids On The Ionization Behavior Of Glutamic Acid Containing Transmembrane Helices, Brooke Nunn 2020 University of Arkansas, Fayetteville

Effect Of Charged Lipids On The Ionization Behavior Of Glutamic Acid Containing Transmembrane Helices, Brooke Nunn

Chemistry & Biochemistry Undergraduate Honors Theses

Transmembrane proteins make up critical components of living cells. Protein function can be greatly impacted by the charged state of its respective components, the side chains of amino acid residues. Thus far, in the lipid membrane, little is known about the properties of residues such as glutamic acid. To explore these properties, I have included glutamic acid in a suitable model peptide-lipid system for fundamental biophysical experiments. Within the system, I have placed a glutamic acid residue instead of leucine in the L14 position of the helical hydrophobic peptide GWALP23 (acetyl-GGALWLALALALAL14ALALWLAGA-amide). Substitutions of glutamine and aspartic acid serve ...


Molecular Dynamics Simulations Of Apolipoprotein A1 In Ionic Liquids, Benjamin Smith 2020 University of Tennessee at Chattanooga

Molecular Dynamics Simulations Of Apolipoprotein A1 In Ionic Liquids, Benjamin Smith

Honors Theses

High-density lipoprotein function is essential for the healthy processing of fats in the blood. The function of these proteins is determined by their conformational structure of chains of amino acids. Certain ionic liquids have been shown to interact with individual amino acids to affect the tertiary shape of the protein. These interactions can disrupt the native hydrogen bonds between amino acids which can either promote folding or denaturing of the protein. Our work focused on apoA-1, a high-density lipoprotein that binds to cholesterol for efflux from the body. We studied this protein in different ion-based liquids with sodium, chloride, and ...


Hplc Detection Of Organic Gunshot Residues With Silicone Wristbands, Yelyzaveta Zuy 2020 University of Tennessee at Chattanooga

Hplc Detection Of Organic Gunshot Residues With Silicone Wristbands, Yelyzaveta Zuy

Honors Theses

The analysis of gunshot residue (GSR) is frequently used to aid in investigating firearm-related crimes. Typically, Scanning Electron Microscopy (SEM) is applied for inorganic analysis of elements such as lead, barium, and antimony to study GSR. However, heavy metal-free ammunition creates the need for a different type of approach. This research focuses on studying the potential of detecting organic gunshot residue (OGSR) collected with silicone wristbands through passive sampling. This study has been directed towards the development of an optimal High Performance Liquid Chromatography (HPLC) procedure for the detection and separation of five selected compounds typically found in OGSR. The ...


Temperature-Dependence Of Electrostatic Dna Melting, Jeffrey Taylor 2020 University of San Francisco

Temperature-Dependence Of Electrostatic Dna Melting, Jeffrey Taylor

Creative Activity and Research Day - CARD

Electrostatic melting is a recently developed electrochemical tool that can be used to interrogate DNA stability, allowing for discrimination of double-stranded DNA (dsDNA) by base-pair sequence or the presence of mismatches, deletions, and other mutations (1). This type of analysis has potential applications in point-of-care diagnostics. Here we explore the dependence of temperature and potential on the kinetics of electrostatic melting in an effort to better understand the mechanism. Previous studies, by another group, have shown that the potential at which electrostatic melting occurs decreases with temperature in the range 10 – 18 °C, i.e. the melting becomes easier at ...


Synthesis Of Sultams From Vinyl Aziridines And 1,4-Diazabicyclo[2.2.2]Octane Bis(Sulfur Dioxide), John Gandara 2020 University of San Francisco

Synthesis Of Sultams From Vinyl Aziridines And 1,4-Diazabicyclo[2.2.2]Octane Bis(Sulfur Dioxide), John Gandara

Creative Activity and Research Day - CARD

Sultams are an important functional group found in medicinal compounds with anticancer and enzyme inhibition activity. Traditional methods for sultam synthesis often require harsh conditions and have limited substrate scope. This research focuses on developing a novel methodology for the production of sultams using DABSO (1,4-diazabicyclo[2.2.2]octane bis(sulfur dioxide)) and vinylic aziridines. Our synthetic strategy starts with a Corey-Chaykovsky epoxidation of cinnamaldehyde, followed by an epoxide-opening using sodium azide. The final vinylic aziridine is synthesized by mesylation and Staudinger reduction of the resulting azido alcohol. Reaction of this vinyl aziridine with DABSO may provide a ...


Investigating The Mechanism Of The E.Coli Atp-Binding Cassette Transporter Metni, Matthew Foronda 2020 University of San Francisco

Investigating The Mechanism Of The E.Coli Atp-Binding Cassette Transporter Metni, Matthew Foronda

Creative Activity and Research Day - CARD

Intracellular chemical homeostasis is vital for cell survival. A key component for the maintenance of this homeostasis is ABC (ATP-binding cassette) transporters. These highly-conserved transporters utilize the energy from ATP binding and hydrolysis to move a wide array of substrates against their chemical gradient. Mutations can lead to a variety of diseases including cystic fibrosis and drug-resistant tumors. In order to solve these issues, these transporters must be well-studied. This project focuses on the mechanism of the methionine importer MetNI in E. coli, a reliable model for many transporters. Using fluorescence anisotropy, the apo-form of the substrate-binding protein (SBP) was ...


Determining The Impact Of Double-Layer Formation On Electrostatic Dna Melting, Gayatri Raghu 2020 University of San Francisco

Determining The Impact Of Double-Layer Formation On Electrostatic Dna Melting, Gayatri Raghu

Creative Activity and Research Day - CARD

Electrostatic melting is an electrochemical tool that can be used to analyze the stability of the DNA double helix, allowing for the detection of various mutations in double stranded DNA (dsDNA).1 Here we explore the effect of electrochemical double layer formation on the electrostatic melting of dsDNA in an effort to better understand the mechanism of the aforementioned category of melting. Previous studies from our lab have shown that electrostatic melting curves can be used to distinguish between duplexes that are fully complementary and duplexes that contain a single mismatch.2 Electrostatic melting is assumed to result from the ...


Synchrotron Photoionization Study Of The O(3p) + Alpha-Angelica Lactone (Aal) At 550 And 700k, Golbon Rezaei 2020 University of San Francisco

Synchrotron Photoionization Study Of The O(3p) + Alpha-Angelica Lactone (Aal) At 550 And 700k, Golbon Rezaei

Creative Activity and Research Day - CARD

The purpose of this research is to study the oxidation of alpha-angelica lactone (AAL) initiated by O(3P) using the synchrotron radiation from the Advanced Light Source (ALS) at the Lawrence Berkeley National Laboratory. The reaction species are investigated by multiplexed photoionization mass spectrometry. Mass-to-charge ratios, time traces, and photoionization spectra are collected for each primary product to help in their identification. Their adiabatic ionization energies are also obtained. The observed primary products at 550 K are ketene (m/z 42), acetaldehyde (m/z 44), methyl ketene (m/z 56), methyl vinyl ketone (m/z 70), methylglyoxal (m/z 72 ...


Synthesis Of Self-Immolative Rhodamine Based Theranostic Agent, Jonathan Alexander, Alessandra Rivera, Nathaniel Garrison 2020 University of San Francisco

Synthesis Of Self-Immolative Rhodamine Based Theranostic Agent, Jonathan Alexander, Alessandra Rivera, Nathaniel Garrison

Creative Activity and Research Day - CARD

Theranostic agents, a class of molecules that simultaneously serve both a diagnostic and therapeutic function, enable in vivo imaging for early diagnosis and targeted drug delivery within a single entity. Due to recent advances in the synthesis and photophysical properties of the rhodamine scaffold, rhodamine dyes present a promising new direction for theranostic research. Toward the goal of exploring rhodamine dyes as self-immolative prodrugs for theranostic applications, we have synthesized a rhodamine precursor via a telescoped radical bromination/hydrolysis. Upon completion of the full rhodamine synthesis, we will explore and optimize the kinetics of its “turn-on” fluorescence and drug release ...


Oxidation Of Alpha-Pinene Initiated By O(3p) And Analyze Via Synchrotron Radiation, Ryan Rodriguez 2020 University of San Francisco

Oxidation Of Alpha-Pinene Initiated By O(3p) And Analyze Via Synchrotron Radiation, Ryan Rodriguez

Creative Activity and Research Day - CARD

Alpha-pinene oxidation is initiated via photolytically generated atomic oxygen O(3P). Reactions were analyzed at 550 K under 4 torr and 750 K at 5 torr. Reaction products are analyzed using multiplexed photoionization mass spectrometry. Vacuum ultraviolet synchrotron radiation is generated at the Advanced Light Source at the Lawrence Berkeley National Laboratory. Kinetic time traces are used to identify primary products, which are then characterized by comparing the experimental photoionization spectra to literature and/or simulated spectra. Calculations using the CBS-QB3 composite method suggest oxygen addition is the favorable pathway vs hydrogen abstraction, agreeing with experimental data. Branching fractions have ...


Determining The Mechanical Properties Of The E. Coli Methionine Transporter, Kha Andy Tran 2020 University of San Francisco

Determining The Mechanical Properties Of The E. Coli Methionine Transporter, Kha Andy Tran

Creative Activity and Research Day - CARD

Adenosine Triphosphate Binding Cassette (ABC) transporters constitute a superfamily of active transporters embedded in the cellular membrane. They consist of two highly conserved nucleotide-binding subunits which bind and hydrolyze ATP, and two diverse transmembrane subunits which provide a pathway for the substrate to pass through the membrane. ABC transporters serve a broad range of vital functions. Various conditions like cystic fibrosis and Stargardt disease are caused by defunct ABC transporters, and certain medical complications like antibiotic drug resistance are linked to promiscuous ABC transporters. Despite the importance of these transporters in crucial biological processes, the mechanisms of many transporters are ...


Extraction Of Thyme Leaves And Analysis Of Antibacterial Properties: An Adaptation For Usf Analytical Chemistry Lab Course, Kevin Do, Matthew Barnett 2020 University of San Francisco

Extraction Of Thyme Leaves And Analysis Of Antibacterial Properties: An Adaptation For Usf Analytical Chemistry Lab Course, Kevin Do, Matthew Barnett

Creative Activity and Research Day - CARD

We streamlined and adapted the thyme leaf extraction and analysis experiment developed by Purcell et al. at the University of California, Berkeley for the analytical chemistry lab course at the University of San Francisco. This experiment used the extraction and analysis of thyme leaves to familiarize students with an integrated laboratory approach, which is becoming increasingly popular in undergraduate chemistry education. The first goal of our research was to adapt the parameters of the experiment to the science writing heuristic (SWH), which moves away from verification-based activities and towards problem-based learning. A lab manual formatted for the SWH gives students ...


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