Chemistry Commons^™

Urine Proteomics Identifies Preeclampsia Subphenotypes, Michelle R. Axe

Undergraduate Honors Thesis Projects

Preeclampsia is a perinatal complication of unknown etiology, resulting in 76,000 maternal deaths and 500,000 infant deaths annually₁. The Nationwide Children’s Center for Perinatal Research was the first cohort to propose that preeclampsia is rooted in protein misfolding. We aimed to characterize the misfolded protein components of maternal urine samples and to determine if distinct molecular profiles exist for clinical preeclampsia phenotypes. A total of 86 maternal urine samples from Yale-New Haven Hospital were analyzed for this study, from six clinical preeclampsia subphenotypes- pregnant control (n=10), idiopathic proteinuria (n=15), mild preeclampsia (n=14), superimposed preeclampsia (n=12), typical severe preeclampsia …

Flavour Chemicals In Electronic Cigarette Fluids, Peyton A. Tierney, Clarissa D. Karpinski, Jessica E. Brown, Wentai Luo, James F. Pankow

Chemistry Faculty Publications and Presentations

Background: Most e-cigarette liquids contain flavour chemicals. Flavour chemicals certified as safe for ingestion by the Flavor Extracts Manufacturers Association may not be safe for use in e-cigarettes. This study identified and measured flavour chemicals in 30 e-cigarette fluids.

Methods: Two brands of single-use e-cigarettes were selected and their fluids in multiple flavour types analysed by gas chromatography/mass spectrometry. For the same flavour types, and for selected confectionary flavours (eg, bubble gum and cotton candy), also analysed were convenience samples of e-cigarette fluids in refill bottles from local ‘vape’ shops and online retailers.

Results: In many liquids, total flavour chemicals …

Development And Application Of Web-Based Open Source Drug Discovery Platforms, Yuri Pevzner

USF Tampa Graduate Theses and Dissertations

Computational modeling approaches have lately been earning their place as viable tools in drug discovery. Research efforts more often include computational component and the usage of the scientific software is commonplace at more stages of the drug discovery pipeline. However, as software takes on more responsibility and the computational methods grow more involved, the gap grows between research entities that have the means to maintain the necessary computational infrastructure and those that lack the technical expertise or financial means to obtain and include computational component in their scientific efforts. To fill this gap and to meet the need of many, …

Structural Insights Into The Cubic-Hexagonal Phase Transition Kinetics Of Monoolein Modulated By Sucrose Solutions, Caleb W. Reese, Zachariah I. Strango, Zachary R. Dell, Stephanie Tristram-Nagle

University Faculty Publications and Creative Works

Using DSC (differential scanning calorimetry), we measure the kinetics of the cubic-HII phase transition of monoolein in bulk sucrose solutions. We find that the transition temperature is dramatically lowered, with each 1 mol kg-1 of sucrose concentration dropping the transition by 20 °C. The kinetics of this transition also slow greatly with increasing sucrose concentration. For low sucrose concentrations, the kinetics are asymmetric, with the cooling (HII-cubic) transition taking twice as long as the heating (cubic-HII) transition. This asymmetry in transition times is reduced for higher sucrose concentrations. The cooling transition exhibits Avrami exponents in the range of 2 to …

Laboratory And Field Studies Of Chemical Processes Of Atmospheric Relevance, Bryant N. Fong

Student Theses and Dissertations

Atmospheric processes such as surface absorption and reflectance are dependent on aerosol composition and aging processes. Our studies examined four atmospheric processes. First, mole ratio effects on deliquescence of mixed binary particles were analyzed. Experimental mole ratio results match established atmospheric model calculations and show that binary component concentrations affect the deliquescence relative humidity (DRH). Second, hydrogen chloride (HCl) gas formation as a function of humidity was investigated. HCl production influences pH of aerosols and was found to be independent of humidity conditions. Third, particles collected in Northeast Arkansas were found to be indicative of urban or rural point sources. …

Aldehyde–Alkyne–Amine (A3) Coupling Catalyzed By A Highly Efficient Dicopper Complex, Hong-Bin Chen, Yan Zhao, Yi Liao

Chemistry and Chemical Engineering Faculty Publications

A dicopper(I) complex, CuI 2ðpipÞ 2 (pip ¼ (2-picolyliminomethyl)pyrrole anion), was utilized to catalyze A3 coupling reactions, which led to the formation of propargylamines. Aldehydes, alkynes and amines with a variety of structures have been tested. A low catalyst loading of 0.4 mol% was sufficient to give good to excellent yields. The low catalyst loading, broad scope of substrate and easy preparation make this dicopper complex a useful catalyst for A3 coupling.

Essential Oils From Apple Mint (Mentha Suaveolens) And Passionflower Fruit (Passiflora Incarnata): Studies On Cognition, Coordination, And Chemical Components., Evelyn F. Patrick *, Jessie Bowers *, Shannon Read *, Brett R. Lackey, Christine Murphy, Sandra L. Gray

Journal of the South Carolina Academy of Science

Plant essential oils (EO) are used as perfumes, lotions and air fresheners because of their pleasant aromas, but EO also have the ability to elicit changes in mood and behavior. These activities are influenced by the mode of administration and by multiple signaling pathways. The EO aromas from organically grown apple mint (Mentha suaveolens) and passionflower fruit (Passiflora incarnata) were assessed for their effects on cognition and coordination. Participants completed two tasks designed to test working memory and bimanual task efficiency in rooms infused with apple mint, passionflower fruit or control EO. Bimanual coordination was assessed using the Intercept2 program …

The Rise Of Carbon Nanoscience In South Carolina, Apparao M. Rao

Journal of the South Carolina Academy of Science

No abstract provided.

On The Influence Of Ionic Strength On Radium And Strontium Sorption To Sandy Loam Soils, Brian A. Powell, Todd Miller, Daniel I. Kaplan

Journal of the South Carolina Academy of Science

Models which can estimate environmental transport of radioactive contaminants in natural and engineered systems are required to 1) deploy effective remediation strategies for contaminated sites, 2) design waste repositories for future waste streams, and 3) ensure protection of human and environmental health in all cases. These models require accurate transport parameters in order to correctly predict how these contaminants will move in the subsurface. This work aimed to determine more accurately the distribution coefficients for radium and strontium sorption to Savannah River Site (SRS) soils. Radium and strontium sorption to the soils was found to be highly dependent upon ionic …

Application And Development Of Computational Methods In Conformational Studies Of Bio-Molecules, Aleksandra Karolak

USF Tampa Graduate Theses and Dissertations

The work presented in my dissertation focuses on the conformational studies of bio-molecules including proteins and DNA using computational approaches. Conformational changes are important in numerous molecular bioprocesses such as recognition, transcription, replication and repair, etc. Proteins recognize specific DNA sequences and upon binding undergo partial or complete folding or partial unfolding in order to find the optimal conformational fit between molecules involved in the complex. In addition to sequence specific recognition, proteins are able to distinguish between subtle differences in local geometry and flexibility associated with DNA that may further affect their binding affinities. Experimental techniques provide high-resolution details …

Use Of Assessments In College Chemistry Courses: Examining Students' Prior Conceptual Knowledge, Chemistry Self-Efficacy, And Attitude, Sachel M. Villafañe-García

USF Tampa Graduate Theses and Dissertations

Students' retention in STEM-related careers is of great concern for educators and researchers, especially the retention of underrepresented groups such as females, Hispanics, and Blacks in these careers. Therefore it is important to study factors that could potentially influence students' decision to stay in STEM. The work described in this dissertation involved three research studies where assessments have been used in college chemistry courses to assess students' prior content knowledge, chemistry-self-efficacy, and attitude toward science. These three factors have been suggested to have an influence on students' performance in a course and could eventually be a retention factor.

The first …

Investigation Of Bioactive Metabolites From The Antarctic Sponge Dendrilla Membranosa And Marine Microorganisms, Chris G. Witowski

USF Tampa Graduate Theses and Dissertations

Natural products continue to be a valuable source of compounds in research involving chemical ecology and drug discovery. Secondary metabolites are biosynthesized to benefit the host organism in its environment (feeding deterrence from predators, antibiotic properties to avoid infection, etc.) but these compounds also serve as useful scaffolds in drug discovery applications. The research herein describes both aspects of these two branches of natural products chemistry. The Antarctic sponge Dendrilla membranosa produces diterpenes, of which membranolide A, deters feeding of the predatory amphipod Gondogenia antarctica. A metabolomic study of several sponges was undertaken to determine environmental factors that govern …

Reagent Pencils: A New Technique For Solvent-Free Deposition Of Reagents Onto Paper-Based Microfluidic Devices, Haydn T. Mitchell, Isabelle C. Noxon, Cory A. Chaplan, Samantha J. Carlton, Cheyenne H. Liu, Kirsten A. Ganaja, Nathaniel W. Martinez, Chad Immoos, Philip Costanzo, Andres W. Martinez

Chemistry and Biochemistry

Custom-made pencils containing reagents dispersed in a solid matrix were developed to enable rapid and solvent-free deposition of reagents onto membrane-based fluidic devices. The technique is as simple as drawing with the reagent pencils on a device. When aqueous samples are added to the device, the reagents dissolve from the pencil matrix and become available to react with analytes in the sample. Colorimetric glucose assays conducted on devices prepared using reagent pencils had comparable accuracy and precision to assays conducted on conventional devices prepared with reagents deposited from solution. Most importantly, sensitive reagents, such as enzymes, are stable in the …

The Phytotoxic Virulence Factor Bcsnod 1 From Botrytis Cinerea, Gnana Sreekar Nidadavolu, Hana Mcfeeters

Research Horizons Day Posters

No abstract provided.

Synthesis And Characterization Study Of Biomimetic Tetradentate Ni Complexes, Nirupama Singh

Research Horizons Day Posters

No abstract provided.

Active Site Mimics Of Nickel Superoxide Dismutase, Victoria Grace Snider

Research Horizons Day Posters

No abstract provided.

High Mannose Binding Lectins - A New Class Of Attractive Antifungals, Tyler Hays Jones

Research Horizons Day Posters

No abstract provided.

Extent And Mechanism Of Translational Readthrough In Humans, Michael Porter, Dr. John Prince

Journal of Undergraduate Research

Introduction Proteins are an integral part of the cell. They are responsible for metabolism, DNA replication, transportation, and responding to changes in environment. Because of their importance to the cell, proteins are often drug targets due to the important roles they play in carrying out cellular function. Proteins are made by ribosomes which are responsible for translating proteins from mRNA. The end of translation is signaled by a stop codon in the RNA. However, in some organisms such as viruses and yeast, the stop codon may be bypassed in an event known as translational readthrough.

Microbial Pretreatment Of Waste For Anaerobic Digestion, Braden Myers, Jaron Hansen

Journal of Undergraduate Research

This project will demonstrate the technical feasibility of microbial pretreatment of lignocellulose for enhanced production of biogas when coupled with secondary anaerobic digestion as well as optimize the entire process.

Learning Chemistry Through Experimentation, Brent Kamba `, Dr. Jennifer Nielson

Journal of Undergraduate Research

There is a great need for students to learn scientific skills in Uganda. Very few students pass the national chemistry exams (about 40%) and even fewer go on to study science fields in higher education. The teaching methods in Uganda are a little bit old fashion where students often just learn facts and practise rote memorization. Rarely do they develop the critical and analytical skills to help them succeed in science jobs. Teachers also express that the curriculum is very theoretical, and not experimental.

Mitochondrial Membrane Lipids Regulator In B-Cll Leukemia Research, Brooke Keeton, Dr. John Prince

Journal of Undergraduate Research

B-cell chronic lymphocytic leukemia (B-CLL) is the most common type of leukemia in adults.1 Over 75% of patients diagnosed with B-CLL are over the age of 50 years old, and have a median survival between 18 months and 3 years.2 B-CLL originates from a mutation in the DNA of white blood cells, the potent infection fighters of the body. This genetic mutation produces abnormal white blood cells, rendering them nonfunctional and resulting in a weak immune system. While this mutation originally occurs in the bone marrow, it slowly invades other parts of the body, including the lymph nodes, liver, and …

Mega-Autophagosome Induction By Human Cox-3 And Human Nucleobindin, Gideon N. Logan, Daniel Simmons

Journal of Undergraduate Research

Cyclooxygenase (COX) isoenzymes catalyze the first step of prostanoid synthesis, which plays a role in various conditions including pain, inflammation, arthritis, and cancer. Recently our laboratory has shown that mammalian cell lines transfected with the COX-1 splice variant, COX-3, express translationally recoded proteins, including four unglycosylated lower molecular weight forms, 57kDa (57 rcCOX-3), 50kDa (50 rcCOX-3), 47kDa (47 rcCOX-3) and 44kDa (44 rcCOX-3.)

Bottom-Up Development Of Nanoelectronics Using Dna Origami Templates, John Jensen, Dr. Adam T. Woolley

Journal of Undergraduate Research

Introduction DNA origami is the method of folding a large single stranded DNA (ssDNA) with multiple smaller ssDNA “staple” strands into a predesigned shape, making it an attractive option in the bottom-up construction of nanoelectronic components, such as nanowires. These structures can be used as templates for placement of conductive species1, such as gold nanoparticles (Au NPs). In order to attach Au NPs to the structure, polyadenine (polyA) tails are added to ends of certain staple strands, allowing attachment of Au NP “seeds” that are functionalized with a thiolated polythymine (polyT) sequence. After attachment, the Au NP seeds are connected …

Molecular-Level Interactions Responsible For Retention In Liquid Chromatography, Jessica Jenkins, James Patterson

Journal of Undergraduate Research

Introduction In many fields of work, such as medicine or pharmaceutical research, it is necessary to separate chemically similar compounds. Liquid chromatography, which involves a mixture of compounds (analyte) dissolved in a mobile phase flowing through a packed column (stationary phase), is the most widely used chemical separation technique. Changes in operational parameters such as the mobile or stationary phase composition, temperature, pressure, pH, etc. affect retention time Operational parameters are currently chosen by trial-and-error because we understand very little about the molecular interactions between the analyte and the mobile phase/stationary phase interface. Specifically, it is unclear how enthalpy and …

Quest Toward The Design And Synthesis Of Functional Metal-Organic Materials (Moms): A Supermolecular Building Layer Approach (Sbl), Hasnaa Mouttaki

USF Tampa Graduate Theses and Dissertations

Metal-Organic Materials (MOMs) represent an important division of coordination chemistry. They are self-assembled through the linking of metals with organic ligands. They gained their spotlight among scientists for their aptitude for design and facile synthesis via their multi-component coordination, and their readiness to functionalization. MOMs have been targeted for specific industrial and environmental applications such as gas storage, catalysis and CO₂ sequestration.

Throughout the past decade, studies have been conducted to develop systematic approaches toward the design and synthesis of functional MOMs. Their synthesis from targeted building units has facilitated their rational design and functionalization. The Molecular Building Block …

Synthetic Methods Of Cts And Czts Nanocrystals, Rachel R. Bohling, Michael M. Davis, Blake J. Gerold, Ted M. Pappenfus

Undergraduate Research Symposium 2015

The synthesis of various morphologies of copper zinc tin sulfide (Cu2ZnSnS4) and copper tin sulfide (Cu2SnS3) nanocrystals were explored to find a more energy efficient synthesis. Reactions were all carried out at 220°C under either inert atmospheres or normal conditions. Variations in synthetic methods included reaction time and solvents used. Products were analyzed with powder X-Ray diffraction and compared to simulated powder patterns of zincblende and wurtzite nanocrystals. The synthesis of CTS nanocrystals required the reaction to be heated to 220°C overnight under an inert atmosphere. The reaction used for the synthesis of CZTS nanocrystals required less energy and only …

Modification Of Mof-5 Hydrostability For Peptide Absorption Studies, Margareta E. Nivision, Zachary L. Mensinger

Undergraduate Research Symposium 2015

Metal-organic frameworks (MOFs) are an intriguing class of hybrid materials that consist of infinite crystalline lattices formed by metal ions bridged by organic linkers. Their porous interiors have highly variable properties, depending on the metal ions and linkers used. To date, MOFs have primarily been examined for uses such as gas separation and storage and catalysis, but recently researchers have described the adsorption of proteins and peptides, such as cytochrome C and a trypsin digest of bovine serum albumin, in MOF pores. The MOF pore provides a stable, ordered environment in which to isolate and characterize peptides. Our research thus …

Study Of The Protonation States Of The Curcumin Molecule And Their Visible Absorption Spectra In Aqueous Solution Using M06, Smd, And Tddft And Compared To Experiment, Joseph D. Alia, Peter Braegelmann, Timothy Roettgen, Hannah Goemann

Chemistry Publications

Curcumin, the primary natural dye from the spice turmeric, has been of recent interest due to its possible health benefits as an antioxidant and possible anti cancer and anti Alzheimer's properties. Limited solubility and instability in water are of primary importance when considering curcumin's possible uses as a pharmaceutical. DFT computations were carried out using B3LYP and MO6 density functionals and the SMD solvent model for water. TDDFT computations were carried out on geometries optimized in water as described by the SMD solvent model. It is found that M06 with the 3-21G* basis set and SMD solvent model gives accurate …

Non-Covalent Affinity Materials For Protein Structure Determination Via Single Particle Reconstruction Analysis Cryo-Electron Microscopy, Minji Ha

Open Access Theses

Single particle analysis (SPA) by cryogenic electron microscopy (Cryo-EM) is one of the powerful tools for determining biological macromolecule structure, particularly when combined with computational methods or X-ray crystallography. However, the SPA is challenged by sample processing efficiency. In this work, polyrotaxane (PRTx) was designed and synthesized such that laterally and rotationally mobile lysine nitrolicacetic acid (Lys-NTA) modified α-cyclodextrins (α-CD) were threaded onto a polyethylene glycol (PEG) core. Polyrotaxanes threaded with amine modified α-CD were also designed and synthesized for stoichiometric control of His-tagged protein capture by PRTx. For higher efficiency of single particle analysis along a single strand of …

Assessment Of Silk Degradation Using Pyrolysis, Conor Makepeace

Honors Projects in Science and Technology

The purpose of this research is to investigate the molecular constitution of silk and the specific causes of post-production degradation in silk material. This capstone project focused specifically on the conditions and degradation of ancient Chinese silk products provided by the Chinese National Silk Museum. Modern silk products were artificially degraded and compared to the ancient silk using Py-GC-MS and comparative analytic techniques. This investigation revealed that the ancient silk products most likely underwent degradation in elevated temperatures while in the presence of moisture and the absence of sunlight or UV radiation during long term burial.