Digital Commons Network^™

Effects Of Ecologically Realistic Heating Profiles On Feeding In The Intertidal Hermit Crab, Pagurus Sameulis, Paige Davis

Student Scholar Symposium Abstracts and Posters

The intertidal zone is an ideal habitat to investigate effects of global warming because species living in it are very close to their physiological limits. Initial studies of invertebrate physiological responses to heat stress have employed relatively abrupt increases in temperature. My research investigates effects of ecologically more realistic temperature profiles on feeding in the intertidal hermit crab, Pagurus sameulis. Recent work in the Wright lab showed that feeding in this species is inhibited by an abrupt increase in temperature. Because temperature change in the natural environment of Pagurus is much more gradual, I hypothesize that such a gradual temperature …

Biological Degredation Of Acetaldehyde In Southern California Wetlands, Anthony Castagnola, Brandon Lamb, Mary Senstad, Sovandara Hok

Student Scholar Symposium Abstracts and Posters

Oxygenated hydrocarbons are ubiquitous in the atmosphere with levels ranging from low ppt (acetaldehyde) to low ppb(methanol). As an OH sink and an atmospheric HOx source, oxygenated hydrocarbons have a direct impact on the oxidative capacity of the atmosphere. A better understanding of the processes that produce and destroy these species in natural water would improve our understanding of the role that these systems play in cycling these species into or out of the atmosphere. These species can be lost to chemical, photochemical, and partical mediated (abiotic and biotic) processes in natural waters. Chemical loss and photochemical loss are believed …

Revealing Important Nocturnal And Day-To-Day Variations In Fire Smoke Emissions Through A Multiplatform Inversion, Pablo E. Saide, David A. Peterson, Arlindo Da Silva, Bruce Anderson, Luke D. Ziemba, Glenn Diskin, Glen Sachse, Johnathan Hair, Carolyn Butler, Marta Fenn, Jose L. Jimenez, Pedro Campuzano-Jost, Anne E. Perring, Joshua P. Schwarz, Milos Z. Markovic, Phil Russell, Jens Redemann, Yohei Shinozuka, David G. Streets, Fang Yan, Jack Dibb, Robert Yokelson, O. Brian Toon, Edward Hyer, Gregory R. Carmichael

Chemistry and Biochemistry Faculty Publications

We couple airborne, ground-based, and satellite observations; conduct regional simulations; and develop and apply an inversion technique to constrain hourly smoke emissions from the Rim Fire, the third largest observed in California, USA. Emissions constrainedwithmultiplatform data show notable nocturnal enhancements (sometimes over a factor of 20), correlate better with daily burned area data, and are a factor of 2–4 higher than a priori estimates, highlighting the need for improved characterization of diurnal profiles and day-to-day variability when modeling extreme fires. Constraining only with satellite data results in smaller enhancements mainly due to missing retrievals near the emissions source, suggesting that …

First Steps Of Putting Research Into Practice: Utilizing Concept Inventories To Identify Biochemistry Misconceptions And The Development Of A Guided Inquiry Activity To Correct The Identified Misconceptions, Ellen Humphreys

Master of Science in Chemical Sciences Theses

It is known that students leave science classes with an incomplete or incorrect understanding of some of the concepts covered in the courses. Identification of these misconceptions is difficult, as it usually involves conducting an hour long one-on-one interview with a student. Concept inventories were developed as a way for professors to identify misconceptions in their classroom in an efficient manner. However, there is no collection of biology, chemistry and biochemistry concept inventories and there has been no analysis of the quality of these inventories. One goal of the research was to collect these inventories and do the much needed …

Benchmark Structures And Harmonic Vibrational Frequencies Near The Ccsd(T) Complete Basis Set Limit For Small Water Clusters: (H2o)N = 2, 3, 4, 5, 6, J. Coleman Howard, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

A series of (H₂O)_n clusters ranging from the dimer to the hexamer have been characterized with the CCSD(T) and the 2-body: Many-body CCSD(T):MP2 methods near the complete basis set (CBS) limit to generate benchmark-quality optimized structures and harmonic vibrational frequencies for these important systems. Quadruple-ζ correlation-consistent basis sets that augment the O atoms with diffuse functions have been employed in the analytic computation of harmonic vibrational frequencies for the global minima of the dimer, trimer, tetramer, and pentamer as well as the ring, book, cage, and prism isomers of the hexamer. Prior calibration [J. Chem. Phys. 2013, …

Relative Reaction Rates Of The Amino Acids Cysteine, Methionine, And Histidine With Analogs Of The Anti-Cancer Drug Cisplatin, Cynthia A. Tope

Mahurin Honors College Capstone Experience/Thesis Projects

We are studying the reaction of analogs of the anticancer drug cisplatin with amino acids that differ in size and shape. The reaction of cisplatin with proteins likely precedes reaction with DNA in the body, forming a variety of products that may be toxic to the human body. The size and shape of the platinum(II) complexes often affects the rate of reaction with proteins, more so than with DNA. In this study, triamine cisplatin analogs are reacted with the amino acids cysteine, methionine, and histidine simultaneously. These reactions are monitored by NMR spectroscopy. The effect of the bulk of the …

Effects Of Anions And Amino Acids On Surface Tension Of Water, Diana Al Husseini

Senior Honors Projects, 2010-2019

Hofmeister series is a set of ions in order of their abilities to affect physical properties in aqueous solutions. Franz Hofmeister was the first to discover the specific ion effects on protein solubility in aqueous solutions. Although the Hofmeister phenomena are general, their mechanisms are still not fully understood. Herein, we use optical tensiometry by a pendant drop method to study the Hofmeister anion effects on the surface tension of water. It has been observed that the surface tension of water increases linearly as the salt concentrations increase. The effects of salts follow a specific trend with respect to the …

The Synthesis And Study Of The Biological And Colloidal Properties Of Bolaamphiphiles, Louis M. Damiano

Senior Honors Projects, 2010-2019

Over the past decade, antibiotic resistant bacteria have caused infections in patients throughout the world.^[1] The rise in antibiotic resistance is primarily due to the misuse and overuse of antibiotics. ^[1] To counter the increase in antibiotic resistance, infection control mechanisms have been aggressively researched in recent years. In particular, drug delivery has become a focal point to fight antibiotic resistant infections.^[2] Amphiphiles have a wide range of applications in the clinical setting, including the ability to inhibit bacterial transference because of their bactericidal activity. ^[3] Bolaamphiphiles are a subclass of amphiphiles that possess two or more hydrophilic …

Analysis Of Nitrogen And Phosphorus Nutrients In Lake Sediment, Kelsey L. Berrier

Senior Honors Projects, 2010-2019

Analytical methods for the determination of nitrogen and phosphorus nutrients (NO₃-N, NH₄-N and PO₄-P) in sediment were studied with the goal of developing extraction steps compatible with analysis by ion chromatography (IC). Research focused on extractant solution composition, Dionex OnGuard^® sample pretreatment cartridges for salt removal, and chromatographic resolution. Aqueous test samples, lake sediment samples and spiked lake sediment samples were analyzed. Dionex Ag, Ag/H, and H cartridges were studied for the pretreatment step. Silver (Ag) cartridges were found effective in removing >99% of interfering chloride ion to allow NO₃-N determination …

Facile Method For Large Scale Alignment Of One Dimensional Nanoparticles And Its Biomedical Application, Sheng Feng

Theses and Dissertations

Topographical cues can profoundly affect cellular behaviors. This thesis investigate how to utilize the topographical cues generated by two techniques, flow assembly and electrospinning, to regulate cellular behaviors.

First of all, a facile and robust method to align one-dimensional (1D) nanoparticles (NPs) in large scale has been developed. Using flow assembly, representative rod-like nanoparticles, including tobacco mosaic virus (TMV), gold nanorods and bacteriophage M13, have been aligned inside capillaries by controlling flow rate and substrate surface properties. The properties of 1D NPs, such as stiffness and aspect ratio, play a critical role in the alignment. Furthermore, these hierarchically organized structures …

Applications Of Organic Probes For Imaging And Analysis Of Different Cancer Cell Models, Hong Guan

Theses and Dissertations

Novel techniques for better studying cancer cell behavior and progression are extremely important. Our lab is interested in synthesizing specifically designed organic reagents and applying them in the studies of cancers. In this dissertation, we used organic probes to investigate cancer cells in the following topics: determination of amino acid concentration in different types of cancers, tumor toxicity of organic probes towards HER2 positive breast cancer cells, glycoproteins identification in breast cancer cells and development of enzyme activity assay for colon cancer cells.

The first chapter was focused on the determination of cysteine/homocysteine concentrations using turn-on sensors in cancer cells. …

A Review On The Bulk And Surface Chemistry Of Iron In Atmospherically-Relevant Systems Containing Humic Like Substances (Hulis), Hind A. Al-Abadleh

Chemistry Faculty Publications

As the fourth most abundant element by mass in the Earth’s crust, iron is ubiquitous and its chemistry is rich and interdisciplinary in nature. This review synthesizes the current state of knowledge of iron chemistry in multicomponent atmospheric aerosols, which is also applicable to other atmospherically-relevant systems that include iron-containing anthropogenic nanodust, ocean surfaces and buildings. Because of the abundance of humic-like substances (HULIS) in these systems, studies on their chemistry with iron and those used as models for HULIS are the focus of this review. Findings from field measurements and laboratory studies are summarized to highlight major themes in …

Section Abstracts: Chemistry

Virginia Journal of Science

Abstracts of the Chemistry Section for the 93rd Annual Meeting of the Virginia Academy of Science, May 21-23, 2015, James Madison University, Richmond, Virginia

A Rapid Lc-Ms/Ms Method For Quantification Of Csuoh0901, A Novel Antitumor Agent, In Rat Plasma, Ramakrishna R. Voggu, Ravali Alagandula, Xiang Zhou, Bin Su Ph.D., Bo Zhong, Baochuan Guo

Chemistry Faculty Publications

CSUOH0901, a novel anticancer derivative of nimesulide, exhibits very promising anticancer activities in various cancer cell lines. In order to support further pharmacological and toxicological studies of this promising anticancer drug candidate, an LC-MS/MS method was developed and validated in accordance with the US Food and Drug Administration guidelines. The drug molecules were extracted from plasma samples by protein precipitation and then analyzed with LC-ESI-MS/MS. An excellent analyte separation was achieved using a phenomenex C18 column with a mobile phase of 90% methanol and 5 m m of ammonium formate. The validated linear dynamic range was between 0.5 and 100 …

Ua66 Ogden College Of Science & Engineering Newsletter, Cheryl Stevens, Dean

Ogden College of Science & Engineering Publications

No abstract provided.

Comprehensive Quantification Of Triacylglycerols In Soybean Seeds By Electrospray Ionization Mass Spectrometry With Multiple Neutral Loss Scans, Maoyin Li, Emily Butka, Xuemin Wang

Biology Department Faculty Works

Soybean seeds are an important source of vegetable oil and biomaterials. The content of individual triacylglycerol species (TAG) in soybean seeds is difficult to quantify in an accurate and rapid way. The present study establishes an approach to quantify TAG species in soybean seeds utilizing an electrospray ionization tandem mass spectrometry with multiple neutral loss scans. Ten neutral loss scans were performed to detect the fatty acyl chains of TAG, including palmitic (P, 16:0), linolenic (Ln, 18:3), linoleic (L, 18:2), oleic (O, 18:1), stearic (S, 18:0), eicosadienoic (20:2), gadoleic (20:1), arachidic (20:0), erucic (22:1), and behenic (22:0). The abundance of …

Understanding The Molecular Level Interactions Of Cancer Inhibitor Imatinib With Human Fibroblast Growth Factor-1, Tulsi Modi

Masters Theses & Specialist Projects

Fibroblast growth factors (FGFs) lack signal sequences, and are exported through endoplasmic reticulum (ER)-Golgi-independent non-classical routes. FGFs work as modulators of various cellular activities like mitosis, differentiation, survival etc. Among the FGF family, which comprises of 23 different heparin proteins, human FGF-1 (hFGF-1), a potent angiogenic factors are one of the targets in cancer inhibition, as they are involved in blood vessel formation in tissues. There has been intensive research directed at the development of drugs that could effectively inhibit angiogenesis. In this context, the purpose of this study is to fully understand the molecular principles essential to determine probability …

Identification, Synthesis And Biological Activity Of Galloyl Inhibitors Of Human Low Molecular Weight Protein Tyrosine Phosphatase, Samuel T. Klinker

Honors Theses, 1963-2015

Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP) isoform 2 (IF2) has been found to be over expressed in many forms of aggressive cancer and has become a target for inhibition. Competitive inhibition of LMW-PTP IF2 by known inhibitor pyridoxal-5'-phosphate (PLP) shows a strong inhibition constant (Ki = 7.6 μM at pH 5.0); however, PLP is a cofactor for many other enzymes. In silico screening and in vitro testing identified NSC107022 (Ki = 10.8 ±1.0) from the National Cancer Institute's Diversity Set II as a lead compound for optimization as a LMW-PTP IF2 inhibitor. Utilizing NSC107022's galloyl group, compound libraries of …

Electrostatic Assembly Of Gold Nanoparticles Mediated By Polyoxomolybdates, Shannon M. Walter

Renée Crown University Honors Thesis Projects - All

The electrostatic assembly of cationic gold nanoparticles (AuNPs) with core diameters of approximately 1.5 nm and 4.5 nm and the anionic sphere and wheel polyoxomolybdates (Mo-132a), (Mo‑132b), and (Mo‑154) was investigated. The AuNPs were capped with a trimethylammonium terminated ligand. Zeta potential and UV-Vis studies supported the successful assembly of the oppositely charged species. The ratio at which the precipitation of aggregates from solution occurred was consistent with the point of electroneutrality observed in the zeta potential results. The UV-Vis studies showed the loss of the surface plasmon resonance (SPR) band as this point of electroneutrality was approached.

In a …

Sulfur-Oxidation Enhances Nitrile Hydration In Bioinspired Ruthenium Complexes : Catalytic, Kinetic, And Dft Investigations., Davinder Kumar

Electronic Theses and Dissertations

The current dissertation focuses on the effects of sulfur‒oxidation on nitrile hydration activity of a series of ruthenium(II) complexes inspired by nitrile hydratase (NHase). NHase catalytically hydrates nitriles to amides at a low spin non‒heme Fe(III) or non‒corrin Co(III) metal center. The active‒site employs a N2S3X type donor set using two carboxamido nitrogens and three cofacial cysteinic sulfurs that are present in distinct oxidation states as sulfinate (RSO2¯), sulfenate (RSO¯), and thiolate (RS¯). The apical site is occupied by substrate or solvent. A lack of sulfur‒oxidation renders the enzyme inactive. Three precatalysts, LnRuPPh3 (n = 1‒3), are employed to assess …

Analysis Of Anacardic Acid On The Surface Of Pelargonium × Hortorum Using Matrix Assisted Laser Desorptoin Ionization Mass Spectrometry Imaging., Bryan Edward Wessel 1989-

Electronic Theses and Dissertations

The biosynthetic pathway leading to the production of anacardic acids (AnAcs) in glandular trichomes on the surface of geranium plants remains unclear. Anacardic acids are salicylic acid derivatives known to possess various medicinal benefits. Gene silencing techniques, such as RNA interference, could be useful in determining specific enzymes involved in the synthesis of AnAcs. However, it is first necessary to develop methodologies to image AnAcs. In this project, both fluorescence (FL) and mass spectral imaging (MSI) were tested. Our results indicate that cellular imaging of AnAcs, via FL, is not suitable because the spectral ranges of absorption and emission of …

Ph Sensing And Imaging With Nanoparticles And Implantable Films, Fenglin Wang

All Dissertations

pH is a very important parameter in biological systems. Monitoring pH in situ may provide useful information for studying pH regulated cellular events, diagnosing diseases and assessing treatment efficacy. Various strategies have been introduced for developing pH sensors. However, it is still challenging to monitor pH in biological systems with high specificity, especially through thick tissue. In this dissertation, we describe three types of pH sensors which are used to noninvasively monitor pH in living cells, monitor and map bacterial growth caused pH variation through thick tissue with minimal autofluorescence background. In Chapter 2, a pH nanosensor with high specificity …

One-Step Synthesis Of Kanamycin Functionalized Gold Nanoparticles With Potent Antibacterial Activity Against Resistant Bacterial Strains, Hitesh Kumar Waghwani

Masters Theses & Specialist Projects

On the verge of entering the post-antibiotic era, numerous efforts are in place to regain the losing potential of antibiotics which are proving ineffective against common bacterial infections. Engineered nanomaterials, especially gold nanoparticles (GNPs) capped with antibacterial agents are proving to be an effective and novel strategy against multi-drug resistant (MDR) bacteria. In this study, we report a one-step synthesis of kanamycin-capped GNPs (20 ± 5 nm) utilizing the combined reducing and capping ability of the aminoglycoside antibiotic, kanamycin. Antibacterial assays showed dosedependent broad spectrum activity of Kan-GNPs against Gram-positive (Staphylococcus epidermidis and Enterococcus durans), Gram-negative (Escherichia coli and Enterobacter …

Syntheses, Structures And Properties Of Metal-Organic Frameworks, Xin Liu

Masters Theses & Specialist Projects

Mercury is one of the most serious heavy metal pollution sources that threaten people’s health. For decades, people have developed many technologies and materials to capture mercury from flue gas of coal-fired plant. Currently, the most effective material for mercury absorption is powdered activated carbon, which shows increased efficiency when modified with halogen functional groups such as bromine. Metal-organic frameworks (MOFs) have potential applications in mercury capture due to their fantastic properties such as high porosity and high thermal stability. More important, their pore sizes and topology structures can be controlled through choosing different organic ligands in the syntheses. However, …

A Multilaboratory Comparison Of Calibration Accuracy And The Performance Of External References In Analytical Ultracentrifugation, Huaying Zhao, Rodolfo Ghirlando, Carlos Alfonso, Fumio Arisaka, Ilan Attali, David L. Bain, Et Al. ..., Donald F. Becker, Peter Schuck

Department of Biochemistry: Faculty Publications

Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy …

Kinetic Isotope Effect Of The ¹⁶O+³⁶O₂ And ¹⁸O+³²O₂ Isotope Exchange Reactions: Dominant Role Of Reactive Resonances Revealed By An Accurate Time-Dependent Quantum Wavepacket Study, Zhigang Sun, Dequan Yu, Wenbo Xie, Jiayi Hou, Richard Dawes, Hua Guo

Chemistry Faculty Research & Creative Works

The O + O₂ isotope exchange reactions play an important role in determining the oxygen isotopic composition of a number of trace gases in the atmosphere, and their temperature dependence and kinetic isotope effects (KIEs) provide important constraints on our understanding of the origin and mechanism of these and other unusual oxygen KIEs important in the atmosphere. This work reports a quantum dynamics study of the title reactions on the newly constructed Dawes-Lolur-Li-Jiang-Guo (DLLJG) potential energy surface (PES). The thermal reaction rate coefficients of both the 18O + 32O₂ and 16O + 36O₂ reactions obtained using the …

Toward The Synthesis Of [4.2.1]Di-Azabicyclic Systems, Carlos Abel Gomez

Theses, Dissertations and Culminating Projects

Conformationally restricted bicyclic amines have been found to be very useful scaffolds in medicinal chemistry. Examples can be found in the chemical literature for the application of conformationally restricted diamines. These molecules can be used as enzyme inhibitors or GPCR ligands. Conformational restriction can improve affinity and selectivity toward receptors. The stereochemical diversity-oriented approach is a method that explores stereochemical effects in small molecule ligands for proteins. It is an effective strategy when the bioactive conformation of a ligand and the pharmacophore of the binding site are unknown. These concepts are applied in the design the target [4.2.1]di-azabicyclic compounds. The …

Novel Fluorescent Sensors For Cations With Additional Pet Pathways To Suppress Signals From Protons, Lesly C. Gomez

Theses, Dissertations and Culminating Projects

A large number of fluorescent sensors for cations that use a photoinduced electron transfer (PET) process to signal cation binding have been developed over the past three decades.1 The PET process of some of these sensors depends on having a tertiary nitrogen atom as a part of the receptor for cations. While these sensors work well as cation sensors, they also generate a fluorescent signal due to protonation of these receptors. The goal of this project is to design a fluorescent sensor that uses the same cation receptors but would not generate a signal for protons. Our new sensor has …

Green Chemistry As A Tool For Understanding The Toxic Substances Control Act: A Lecture Module For Undergraduate Students, Molly R. Blessing

Honors Scholar Theses

The Toxic Substances Control Act (TSCA) is the central form of chemical regulation existent in the United States today, yet scientists are often unaware or uncertain of its provisions. Violations of TSCA by unknowing chemists set industry and government unnecessarily at odds. A lecture on TSCA was developed for undergraduate students that uses the concept of green chemistry to promote interest and incentivize learning. Green chemistry methods are cleaner and less wasteful than traditional chemical ones, and many companies using them are at the forefront of technological innovation. The lecture explains both green chemistry and TSCA, includes company case studies, …

The Use Of Shape Memory Polymers As A Tool To Study Human Fibrosarcoma And Murine Mesenchymal Stem Cell Migration, Justin N. Elkhechen

Renée Crown University Honors Thesis Projects - All

Shape memory polymers (SMPs) are a class of “smart” materials that can transform between two distinct conformations through external stimuli, such as heat or electricity. Their usage in bioengineering has led to a promising field of research that lies at the interface of cell and mechanobiology, potentially providing insight into cancer therapies and tissue development—two processes that exist in dynamic environments in vivo. The present work involves creating new, shape changing, scaffolds for studies to analyze cell migration upon changes to the environmental topography. Specifically, this Capstone has been primarily focused on the development of a “half and half” fibrous …