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Characterization Of Glycation Sites On Human Serum Albumin Using Mass Spectrometry, Omar S. Barnaby

Department of Chemistry: Dissertations, Theses, and Student Research

The modification of proteins by reducing sugars is a process that occurs naturally in the body. This process, which is known as glycation, has been linked to many of the chronic complications encountered during diabetes. Glycation has also been linked to changes in the binding of human serum albumin (HSA) to several drugs and small solutes in the body. While these effects are known, there is little information that  explains why these changes in binding occur. The goal of this project was to obtain qualitative and quantitative information about glycation that occurs on HSA. The first section of this dissertation …

Ultrafast Carrier Dynamics In Type Ii Znse/Cds/Znse Nanobarbells, Nishshanka N. Hewa-Kasakarage, Patrick Z. El-Khoury, Alexander N. Tarnovsky, Maria Kirsanova, Ian Nemitz, Alexander Nemchinov, Mikhail Zamkov

Chemistry Faculty Publications

We employ femtosecond transient absorption spectroscopy to get an insight into ultrafast processes occurring at the interface of type II ZnSe/CdS heterostructured nimocrystals fabricated via colloidal routes and comprising a barbell-like arrangement of ZnSe tips and CdS nanorods. Our study shows that resonant excitation of ZnSe tips results in an unprecedently fast transfer of excited Electrons into CdS domains of nanobarbells (<0.35 ps), whereas selective pumping of CdS components loads to a relatively slow injection of photoinduced holes into ZnSe tips (tau(h) = 95 ps). A qualitative thermodynamic description of observed electron processes within the classical limit of Marcus theory was used to identify a specific charge transfer regime associated with the ultrafast electron injection into CdS. Potential photocatalytic applications of the observed fast separation of carriers along the main axis of ZnSe/CdS barbells are discussed.

C - Reactive Protein Induced Rearrangement Of Phosphatidylcholine On Nanoparticle Mimics Of Lipoprotein Particles, Marilyn R. Mackiewicz, Heather L. Hodges, Scott M. Reed

Chemistry Faculty Publications and Presentations

Lipid-coated metal nanoparticles are developed here as a mimic of low-density lipoprotein (LDL) particles and used to study C-reactive protein (CRP) binding to highly curved lipid membranes. A 12 nm shift in the localized surface plasmon resonance (LSPR) was observed when CRP was added to the lipid-coated gold nanoparticles. Transmission electron microscopy (TEM) revealed that CRP induced a structural change to the lipids, resulting in clusters of nanoparticles. This clustering provides a visualization of how CRP could cause the aggregation of LDL particles, which is a key step in atherosclerosis. The cluster formation and resultant LSPR shift requires the presence …

Hrc Enews — 2010 Spring, Megan K. Svarz

Publications (HRC)

This issue contains staff accomplishments and announcements, event listings, a "new faces" listing for new staff, affiliates, and researchers, and an "of interest" section.

Volume 03, Cheryl Peck, Charles Hoever, Longwood Theater Department, Brittany Anderson, J. Ervin Sheldon, Richard Hayden, Yuri Calustro, Candice Fleming, Rebecca Franklin, Ashley Yocum, Danielle M. Jagoda, Cristina M. Valdivieso, Jameka Jones, Amy Ellis, Ashley Maser, Erikk Shupp, Jamie Yurasits, Joshua Davis, Alexander Leonhart, Kenny Wolfe, Sally Meadows, J. Haley, Amy Jackson, Morgan Howard, Adrienne Heinbaugh, Melissa Dorton, Ciarra Stalker

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

Little Shop of Horrors by Longwood Theater Department

Who Has the Hottest Hotsauce in Farmville: A Quantitative Comparison of Sauces from Local Restaurants by Cheryl Peck and Charles Hoever

Precipitation Effects on the Growth of White Oaks and Virginia Pines on the Mt. Vernon Plantation by Brittany Anderson

Design and Synthesis of Novel Ion Binding Molecules for Self-Assembly and Sensing Applications by J. Ervin Sheldon

A Statistical Analysis of Algorithms for Playing SameGame by Richard Hayden

Intersecting Cylinders at Arbitrary Angles by Yuri Calustro

Putting a Foot in the Revolving Door: Strategies for Reducing …

Conformational Dynamics Of Single Pre-Mrna Molecules During In Vitro Splicing, J. Abelson, M. Blanco, M. A. Ditzler, F. Fuller, P. Aravamudhan, M. Wood, T. Villa, D. E. Ryan, J. A. Pleiss, Corina Maeder, C. Guthrie

Chemistry Faculty Research

The spliceosome is a complex small nuclear RNA (snRNA)-protein machine that removes introns from pre-mRNAs via two successive phosphoryl transfer reactions. The chemical steps are isoenergetic, yet splicing requires at least eight RNA-dependent ATPases responsible for substantial conformational rearrangements. To comprehensively monitor pre-mRNA conformational dynamics, we developed a strategy for single-molecule FRET (smFRET) that uses a small, efficiently spliced yeast pre-mRNA, Ubc4, in which donor and acceptor fluorophores are placed in the exons adjacent to the 5′ and 3′ splice sites. During splicing in vitro, we observed a multitude of generally reversible time-and ATP-dependent conformational transitions of individual pre-mRNAs. The …

The Development Of An Effective Water-Soluble Receptor For Pyrene Derivative Dyes, Ashley Longstreet

Undergraduate Theses and Capstone Projects

A receptor with enhanced water solubility was synthesized from an existing receptor to be used as a pyranine fluorescence quencher in endovesiculation detection assays. The existing receptor consisted of a cyclen core with four protruding arms containing an aryl nitro group at each end. Its poor water solubility limited the accuracy and precision of the endovesiculation assay because the low concentration of receptor did not match the concentration of pyranine. To increase the water solubility, ethoxy groups were attached to the ends of each arm by first selectively reducing the nitro group to an amine with NaBHU4, H2, and a …

Relatin Dissolved Oxygen Concentration To Fish Distribution In Jarecki Lake, Adam Sutton

Department of Environmental Studies: Undergraduate Student Theses

Abstract Water temperature and dissolved oxygen (DO) profiles were measured once every month from mid July to mid February in a relatively deep sand-pit lake in southeast Nebraska. These profiles showed depleted DO concentrations below the thermocline during summer stratification indicating areas fish will likely avoid in summer months. Colder temperatures in fall caused complete mixing of the water column allowing fish to inhabit all depths of the lake. An inverse temperature stratification occurred directly below the ice during winter months as ice cover cooled the surface water to below 4 degrees Celsius. Ice cover also blocked air – water …

Herbicides And Amphibian Populations, Zach Shirk

Department of Environmental Studies: Undergraduate Student Theses

Amphibians are a unique class of species that are found worldwide except Antarctica and Greenland. They range in size from a few millimeters to over six feet long. Amphibian’s habitats are as various as their size, but one thing in common is that amphibians require an aquatic location to breed. Amphibians live in deserts, mountain prairies, rain forest, wetlands, and almost everywhere in between. Amphibians are an integrated part of most natural ecosystems across the world. Amphibians are a critical part of many food chains; they provide the important link between secondary and tertiary consumers. Amphibians are indicator species in …

Inhibitors Of NΑ-Acetyl-L-Ornithine Deacetylase: Synthesis, Characterization And Analysis Of Their Inhibitory Potency, J. Hlavacek, J. Picha, V. Vanek, J. Jiracek, J. Slaninova, V. Fucik, M. Budesinsky, Danuta M. Gillner, Richard C. Holz

Chemistry Faculty Research and Publications

A series of N ^α-acyl (alkyl)- and N ^α-alkoxycarbonyl-derivatives of l- and d-ornithine were prepared, characterized, and analyzed for their potency toward the bacterial enzyme N ^α-acetyl-l-ornithine deacetylase (ArgE). ArgE catalyzes the conversion of N ^α-acetyl-l-ornithine to l-ornithine in the fifth step of the biosynthetic pathway for arginine, a necessary step for bacterial growth. Most of the compounds tested provided IC₅₀ values in the μM range toward ArgE, indicating that they are moderately strong inhibitors. N ^α-chloroacetyl-l-ornithine (1g) was the best inhibitor tested toward ArgE providing an IC₅₀ value of 85 …

Conformational Change And Topological Stability Of Proteins, Jeffrey Andrew Tibbitt

Chemistry & Biochemistry Theses & Dissertations

The conformation and topology of a protein changes when stabilizing forces are absent, but the mechanisms by which these changes occur remains elusive. This dissertation aims to broaden the understandings. On the conformational level, the M20 loop conformers of E. coli dihydrofolate reductase are interrogated to identify factors responsible for their stability as well as to determine how one conformer might change into another. Molecular dynamics is used to simulate the open, closed and occluded conformers (observed in X-ray crystal structures) under a series of different single ligand conditions. Analysis shows that all open conformers move to a similar new …

Molecular Characterization Of The Soluble Fraction Of Atmospheric Particulate Matter Obtained By Chemical Oxidation With Nitric Acid, Amanda Susan Priest

Chemistry & Biochemistry Theses & Dissertations

The availability of information regarding the composition of ambient atmospheric particulate matter and the transformations that these compounds may undergo upon atmospheric transit is surprisingly absent. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry is used in this study to rapidly evaluate the composition of the water-soluble organic fraction of standard and collected atmospheric particulate matter samples, and the changes that these mixtures undergo upon oxidation with nitric acid. The standard samples include representative particulate matter collected over the course of a year in Washington, D.C. and particulate matter from the exhaust of a diesel-powered engine. The collected sample …

Electrodeposited Silica Thin Films, Debbie Campbell-Rance

Theses and Dissertations

Sol-gel derived silica thin film synthesis has gained prominence because of the mild processing conditions and widespread understanding of the chemistry of the process. Traditionally, silicate films are prepared by spin- and dip-coating but these materials lack the desired porosity for sensing, separations and catalysis applications. Electrochemical deposition was proposed to improve the porosity of silicate films. The main aims of this work were threefold. First we wanted to elucidate what parameters influenced film formation during electrodeposition. Then we wanted to understand how these parameters affected the morphology of the materials prepared. These films were characterized by profilometry, AFM, and …

Metal-Organic Materials: From Design Principles To Practical Applications, Mohamed H. Alkordi

USF Tampa Graduate Theses and Dissertations

The works presented herein outline rational design approaches towards construction of solid state materials with great potentials to answer some of current demanding applications. Specifically, the materials targeted are metal−organic materials with desirable structural features and functional properties. Metal−organic materials are constructed from organic linker molecules and metal ions under relatively mild solvothermal reaction conditions that preserve the structural features of the relatively simple building blocks. Therefore, it is feasible to conceive a retrospective pathway of the reaction and thus deconstruct the desirable structures into simple, chemicallyrelevant, building blocks in an approach known as the molecular building block approach. Due …

Effects Of Uvb-Induced Oxidative Stress On Protein Expression And Specific Protein Oxidation In Normal Human Epithelial Keratinocytes: A Proteomic Approach, Marzia Perluigi, Fabio Di Domenico, Carla Blarzino, Cesira Foppoli, Chiara Cini, Alessandra Giorgi, Caterina Grillo, Federico De Marco, D. Allan Butterfield, Maria E. Schininà, Raffaella Coccia

Chemistry Faculty Publications

BACKGROUND: The UVB component of solar ultraviolet irradiation is one of the major risk factors for the development of skin cancer in humans. UVB exposure elicits an increased generation of reactive oxygen species (ROS), which are responsible for oxidative damage to proteins, DNA, RNA and lipids. In order to examine the biological impact of UVB irradiation on skin cells, we used a parallel proteomics approach to analyze the protein expression profile and to identify oxidatively modified proteins in normal human epithelial keratinocytes.

RESULTS: The expression levels of fifteen proteins - involved in maintaining the cytoskeleton integrity, removal of damaged proteins …

Electrospray Ionization Mass Spectrometry For The Characterization Of Covalent And Noncovalent Polynuclear Platinum Compounds Interacting With Bio-Molecules, John Mangrum

Theses and Dissertations

Polynuclear platinum compounds represent a new class of potential platinum anticancer therapeutics. Derived from the most widely used platinum anticancer drug, cisplatin, these novel compounds are distinct in their interactions with bio-molecules. The effectiveness of platinum anticancer agents is influenced by three pharmacological factors: (i) their resistance to deactivating sulfur nucleophiles, (ii) the ability to gain cellular entry and efficient cellular uptake, and (iii) the ability to form stable and specific complexes with DNA. BBR 3464, the first multinuclear platinum compound to reach phase II clinical trials, has created a new approach to cancer drug design. Large, highly charged platinum …

Role Of Members Of The Phosducin Gene Family In Protein Translation And Folding, Nana Sono-Koree

Theses and Dissertations

G proteins regulate various physiological processes by way of transducing a wide variety of signals ranging from hormonal to sensory stimuli. Malfunctions in G protein signaling lead to numerous diseases. G protein signaling begins with binding of a ligand to a G protein-coupled receptor resulting in a conformational change that leads to the exchange of a GDP for a GTP on G α. The GTP bound α subunit dissociates for its stable Gβγ dimer partner. G α-GTP and Gβγ control the activity of effector enzymes and ion channels that ultimately orchestrate the cellular response to stimulus. Current reports have shown …

The Asymmetric Phase-Transfer Catalyzed Alkylation Of Imidazolyl Ketones And Aryl Acetates And Their Applications To Total Synthesis, Michael Andrew Christiansen

Theses and Dissertations

Phase-transfer catalysts derived from the cinchona alkaloids cinchonine and cinchonidine are widely used in the asymmetric alkylation of substrates bearing moieties that resonance stabilize their enolates. The investigation of α-oxygenated esters revealed decreased α-proton acidity, indicating the oxygen's overall destabilizing effect on enolates by electron-pair repulsion. Alkylation of α-oxygenated aryl ketones with various alkyl halides proved successful with a cinchonidine catalyst, giving products with high yield and enantioselectivity. The resulting compounds were converted to esters through modified Baeyer-Villiger oxidation. Alkylation with indolyl electrophiles gave products that underwent decomposition under Baeyer-Villiger conditions. Alternative N-methylimidazolyl ketones were explored. Alkylated imidazolyl ketones, obtained …

Atomic Details Of Near-Transition State Conformers For Enzyme Phosphoryl Transfer Revealed By Mgf3− Rather Than By Phosphoranes, Nicola J. Baxter, Matthew W. Bowler, Tooba Alizadeh, Matthew J. Cliff, Andrea M. Hounslow, Bin Wu, David B. Berkowitz, Nicholas H. Williams, G. Michael Blackburn, Jonathan P. Waltho

David Berkowitz Publications

Prior evidence supporting the direct observation of phosphorane intermediates in enzymatic phosphoryl transfer reactions was based on the interpretation of electron density corresponding to trigonal species bridging the donor and acceptor atoms. Close examination of the crystalline state of β-phosphoglucomutase, the archetypal phosphorane intermediate-containing enzyme, reveals that the trigonal species is not PO−3 , but is MgF−3 (trifluoromagnesate). Although MgF−3 complexes are transition state analogues rather than phosphoryl group transfer reaction intermediates, the presence of fluorine nuclei in near-transition state conformations offers new opportunities to explore the nature of the interactions, in particular the independent measures of local electrostatic and …

Reactive Layer-By-Layer Assembly Of Suspended Thin Films And Semipermeable Membranes At Interfaces Created Between Aqueous And Organic Phases, Maren E. Buck, David M. Lynn

Chemistry: Faculty Publications

Thin films of polymer suspended across the openings of pores, channels, and microcavities are of interest in a broad range of fundamental and applied contexts. A "reactive" layer-by-layer approach Is demonstrated for the fabrication of suspended thin films and semipermeable membranes that makes use of liquid/ liquid interfaces created between immiscible aqueous and organic phases as templates for film fabrication (see image). (Figure Presented).

Time-Resolved Infrared Spectroscopy And Density Functional Theory Study Of Weak Interactions Of Metal Carbonyls And Organic Solvents, Carolyn Evans Sheffield

Theses and Dissertations

Pulsed laser flash photolysis of M(CO)6 (M = Cr, W) in cyclohexane with a small amount of benzene results in three sequential reactions. The first is the photodissociation of the parent to yield a M(CO)5:C6H12 complex, which takes place faster than the time resolution of our experiments. The second reaction is the replacement of the cyclohexane ligand with benzene to form a M(CO)5:C6H6 complex, in which benzene is coordinated to the metal via one side of the ring. This complex then falls apart in solution as M(CO)5 coordinates with a trace impurity in the solution that is likely water. Kinetic …

An Electrochemical Cell For The Efficient Turn Around Of Wafer Working Electrodes, Nicholas Wozniak, Alyssa Frey, Lucas Osterbur, Timothy Boman, Jennifer R. Hampton

Faculty Publications

We present a new design for an electrochemical cell for use with wafer working electrodes. The key feature of the design is the use of half turn thumb screws to form a liquid-tight seal between an o-ring and the sample surface. The assembly or disassembly of the cell requires a half turn of each thumb screw, which facilitates the quick turn around of wafer samples. The electrochemical performance of the cell is demonstrated by cyclic voltammetry and double step chronoamperometry measurements of the ferricyanide/ferrocyanide couple.

Utilizing Service Learning In The Analytical Chemistry Classroom, Kimberly D. Chichester, Colleen Dugan, Amanda Lewis, Maryann Herman, Irene Kimaru

Chemistry Faculty/Staff Publications

Service learning has been incorporated into the Analytical Chemistry Laboratory to give students a real world sampling experience including both soil and water, alongside professionals in their fields. Analysis of the soil and water includes metals, suspended solids, phosphorus and nitrogen containing compounds requiring knowledge of several different instrumental and wet chemical techniques. Most educational experiences do not afford students the chance to see the real world applications of their classroom knowledge, but with the service learning aspects this deficiency has been resolved. In the soil experience, students provide homeowners from the Highland Park and South Wedge neighbors with lead …

Quasispecies-Like Behavior Observed In Catalytic Rna Populations Evolving In A Test Tube, Carolina Diaz Arenas, Niles Lehman

Chemistry Faculty Publications and Presentations

Background: During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous.

Results: Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen …

Selective Regulation Of Aromatase Expression For Drug Discovery, Robert W. Brueggemeier, Bin Su, Michael V. Darby, Yasuro Sugimoto

Chemistry Faculty Publications

Aromatase is a particularly attractive drug target in the treatment of hormone-responsive breast cancer, and aromatase activity in breast cancer patients is greater in or near the tumor tissue compared with the normal breast tissue. Complex regulation of aromatase expression in human tissues involves alternative promoter sites that provide tissue-specific control. Previous studies in our laboratories suggested a strong association between aromatase (CYP19) gene expression and the expression of cyclooxygenase (COX) genes. Additionally, COX selective inhibitors can suppress CYP19 gene expression and decrease aromatase activity. Our current hypothesis is that pharmacological regulation of aromatase can act locally to decrease the …

The Electrochemical Characteristics Of Cpo-Pll/Gc Electrode, Wen Zhao, Xia-Qin Wu, Zhong-Qing Lu, Wen-Jing Hou, He-Xing Li

Journal of Electrochemistry

Poly-L-lysine(PLL) was electropolymerized onto the surface of glassy carbon(GC) electrode.1[(3-dimethylamino)propyl]-3-ethylcarbodiimide hydrochloride(EDC) was used as a Cross-linking agent to immobilized Chloroperoxidase(CPO) onto the PLL/GC electrode.A pair of well-defined redox peaks was observed at CPO-PLL/GC electrode,which clearly suggested that PLL can promote the direct electron transfer between the CPO and the GC electrodes.The cyclic voltammetry results also showed that the electron transfer at CPO-PLL/GC is a surface adsorption-controlled quasi-reversible process,which is accompanied with proton transfer.The CPO-PLL/GC electrode exhibited a good electrochemical stability and excellently electrocatalytic activity for electrochemical reduction of O₂.

The Synthesise Of Electron-Conducting Redox Hydrogel And Its Application In Microbial Fuel Cell, Kai-Peng Wang, Sheng-Li Chen

Journal of Electrochemistry

Efficient electron transfer between the microbe and the anode is key for the electricity generation in Microbial fuel cell(MFC).Through the modification of anode,the rate of electron transfer can be accelerated,therefore the performance of MFC can be enhanced.In this paper,we report the synthesis of a type of electronconducting and bio-compatible redox hydrogel and its application.The hydrogel consists of poly(4-vinylpyridine) as backbone and neutral red as the redox center.By immobiliazing neutral red on the backbone through covalent bond,the secondary contamination due to the soluble redox mediator to external environment can be prevented.MFCs using the hydrogel-modified carbon anode significantly exhibit shorter acclimation period,and …

Nmr Dynamics Investigation Of Ligand-Induced Changes Of Main And Side-Chain Arginine N-H’S In Human Phosphomevalonate Kinase, Andrew L. Olson, Sheng Cai, Timothy J. Herdendorf, Henry M. Miziorko, Daniel S. Sem

Chemistry Faculty Research and Publications

Phosphomevalonate kinase (PMK) catalyzes phosphoryl transfer from adenosine triphosphate (ATP) to mevalonate 5-phosphate (M5P) on the pathway for synthesizing cholesterol and other isoprenoids. To permit this reaction, its substrates must be brought proximal, which would result in a significant and repulsive buildup of negative charge. To facilitate this difficult task, PMK contains 17 arginines and eight lysines. However, the way in which this charge neutralization and binding is achieved, from a structural and dynamics perspective, is not known. More broadly, the role of arginine side-chain dynamics in binding of charged substrates has not been experimentally defined for any protein to …

Remarkable Iodine-Catalyzed Synthesis Of Novel Pyrrole- Bearing N-Polyaromatic B-Lactams, Debasish Bandyopadhyay, Gildardo Rivera, Isabel Salinas, Hector Aguilar, Bimal K. Banik

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Because of their interesting biological properties various methods for the synthesis of substituted pyrroles are described in the literature. However, synthesis of pyrroles fused with a β-lactam ring has not been reported. Our group has demonstrated synthesis and biological evaluation of various β-lactams as anticancer agents. The anticancer activities of these compounds have prompted us to study the synthesis of pyrroles bound to the β-lactams. We have identified an expeditious synthetic method for the preparation of pyrroles fused with β-lactams by reacting 3-amino β-lactams with acetonylacetone in the presence of catalytic amounts (5 mol%) of molecular iodine at room temperature. …

Water-Soluble Soa From Alkene Ozonolysis: Composition And Droplet Activation Kinetics Inferences From Analysis Of Ccn Activity, A. Asa-Awuku, A. Nenes, Song Gao, R. C. Flagan, John H. Seinfeld

Chemistry and Physics Faculty Articles

Cloud formation characteristics of the water-soluble organic fraction (WSOC) of secondary organic aerosol (SOA) formed from the ozonolysis of alkene hydrocarbons (terpinolene, 1-methlycycloheptene and cycloheptene) are studied. Based on size-resolved measurements of CCN activity (of the pure and salted WSOC samples) we estimate the average molar volume and surface tension depression associated with the WSOC using Köhler Theory Analysis (KTA). Consistent with known speciation, the results suggest that the WSOC are composed of low molecular weight species, with an effective molar mass below 200 g mol−1. The water-soluble carbon is also surface-active, depressing surface tension 10–15% from that of pure …