Chemistry Commons^™

Use Of Solid-Phase Extraction To Enrich Protein Biomarkers Of Disease From Blood Serum, Peter F. Mclean, Dr Craig Thulin

Journal of Undergraduate Research

Biomarkers in blood serum are the keys needed for the early detection of several types of cancer, complications of pregnancy, and potentially many other diseases, to allow time for successful treatment. Blood serum is ideal because itp comes in contact with all parts of the body, its sampling is minimally invasive, and it is easily prepared with high reproducibility. There is a problem, however, that prevents the development and wide-scale utilization of this treasure chest of biological information. Pure blood serum is complex and cluttered with high-abundance non-target proteins which makes examination of the low-abundance and low-molecular weight potential biomarkers …

Antibiotic Thin Films, Timothy Jennings, Jason Nielsen, Brian Ratcliff, Nina Wallace, Xin Zhong Lai, Paul B. Savage

Journal of Undergraduate Research

Nosocomial infections lead to septicemia, a severe problem in the United States. The Savage group has developed a novel class of antibiotics (CSAs) that can be attached to polymers. Invasive medical equipment can be coated with CSA polymers, forming an antibiotic thin film. Testing has shown the ability of CSA polymers to kill bacteria, which will lead to further testing and future use in the medical field.

Biomimetic And Amino-Retinoid Compounds: Potential Applications In Cancer And Age-Related Macular Degeneration, Kam Lau, Dr. Heidi Vollmer-Snarr

Journal of Undergraduate Research

Cancer is the second leading cause of death in the United States. According to the American Cancer Society, about half of all men and one-third of all women in the US will develop cancer during their lifetimes. Today, millions of people are living with cancer or have had cancer.1 Even though there is still no ultimate treatment for cancer, chemotherapy, radiation therapy, and surgery are common existing treatments for different types of cancers. New kinds of anti-cancer agents, developed in our laboratory, called amino-retinoid compounds also show promise in treating cancer. Currently, retinoid compounds and germcitabine (a chemotherapy drug) are …

Removal Of Abundant Non-Informative Proteins From Blood Serum For Biomarker Discovery, Nathan Lewis, Dr. Craig D. Thulin

Journal of Undergraduate Research

Biomarkers play a key role in disease diagnosis and in guiding physicians in treatment selection. Blood serum is potentially the best tissue for biomarker discovery and detection for several reasons. First, blood is already routinely drawn for tests. Second, serum preparation is highly reproducible between differing labs because the serum preparation method is standardized. Third, the blood is in intimate contact with most other tissues and is often the route by which the body discards of cellular waste or by which endocrine signals are sent.

Three-Dimensional Modeling Of Two Forms Of The Hepatitis B Virus, Rebecca Baum, Dr. David M. Belnap

Journal of Undergraduate Research

The hepatitis B virus (HBV) is a pathogen that causes liver disease and death in over one million individuals per year. It is an enveloped retrovirus that is composed of a protein capsid surrounding a nucleic acid core. This nucleic acid core, depending upon the maturation state of the virus, consists of either RNA or DNA. The protein capsid of HBV is composed of four quasiequivalent subunits (subunits that have identical polypeptide (amino acid) sequences but slightly different tertiary structures). Each subunit forms an alpha-helical hairpin structure and dimerizes with another subunit. The result is the appearance of spikes on …

Genetic Analysis Of Protein Folding, Daniel Chan, Dr. Allen Buskirk

Journal of Undergraduate Research

Proteins are of the utmost physiological importance in their roles as enzymes, structural elements, and antibodies. Correctly formed proteins catalyze biochemical reactions, initiate proper immune system response, and even promote the development of hair, bones, skin, muscles, and blood. Likewise, incorrectly formed proteins cause Alzheimer’s disease, cystic fibrosis, various forms of cancer, and Creutzfeld-Jacob (mad cow) disease1. One of the fundamental problems that scientists face today is understanding how proteins fold to yield correct or incorrect structures. Proteins consist of building blocks called amino acids, each of which is encoded by certain DNA sequences. The conventional wisdom in the field …

Structural Identification Of The Bioactive Components Of The Samoan Fish Poison Plant Barringtonia Asiatica, Robert A. Burton, Dr. Noel L. Owen

Journal of Undergraduate Research

The seed of the Futu tree, Barringtonia asiatica, has been used by inhabitants of the Pacific islands for many years as a highly toxic fish poison.1 These ethnobotanical studies were responsible for the initiation of this investigation.

Formation, Functionalization, Characterization, And Applications Of A Mixed-Mode, Carbon/Diamond-Based, Core-Shell Phase For High Performance Liquid Chromatography, Landon A. Wiest

Theses and Dissertations

My work has focused on a variety of different types of diamond-based, core-shell particles. These particles are formed with inert cores and poly(allylamine)/nanodiamond shells. Their intended purpose is to form an LC stationary phase that is stable from pH 1 – 14 and at elevated temperatures. At the beginning of my studies, the particles that had been made in the Linford laboratory were pH stable, but irregular and had poor mechanical stability. Since that time, I have worked to improve the particles by using more spherical zirconia and carbon cores, and I have improved their mechanical stability via chemical crosslinking …

Membrane Lipid-Modulated Mechanism Of Action And Non-Cytotoxicity Of Novel Fungicide Aminoglycoside Fg08, Sanjib Shrestha, Michelle Grilley, Marina Y. Fosso, Cheng-Wei Tom Chang, Jon Y. Takemoto

Chemistry and Biochemistry Faculty Publications

A novel aminoglycoside, FG08, that differs from kanamycin B only by a C8 alkyl chain at the 4″-O position, was previously reported. Unlike kanamycin B, FG08 shows broad-spectrum fungicidal but not anti-bacterial activities. To understand its specificity for fungi, the mechanism of action of FG08 was studied using intact cells of the yeast Saccharomyces cerevisiae and small unilamellar membrane vesicles. With exposure to FG08 (30 µg mL−1), 8-fold more cells were stained with fluorescein isothiocyanate, cells had 4 to 6-fold higher K+ efflux rates, and 18-fold more cells were stained with SYTOX Green in comparison to exposure to kanamycin B …

Investigate The Function Of The 5′ Leader In The Human At1 Angiotensin Receptor, Erik J. Petersen, Dr. Terry S. Elton

Journal of Undergraduate Research

A comparison of several published hAT1R cDNA sequences revealed that, although these clones shared an identical open reading frame, they differed in portions of their 5′-UTRs.1 Therefore these data suggest that alternative splicing events combine various 5′-UTR exons with the exon that harbors the hAT I R coding region.

Determination Of Angiotensin Ii Type 2 Receptor Protein Interactions Using The Yeast-Two Hybrid System, Emily Janeen Westover, Dr. Terry S. Elton

Journal of Undergraduate Research

The renin-angiotensin system plays a central role in water and salt homeostasis, electrolyte balance, and vascular tone maintenance. 1 Each component of this system is a potential effector in the etiology of hypertension. Angiotensin II (Ang II), a component of the reninangiotensin system, interacts with two distinct receptor types, the Angiotensin Type 1 Receptor (AT1R) and the Angiotensin Type 2 Receptor (AT2R). The receptor types 2 probably mediate opposite intracellular effects.3 However, all currently known effects of Ang II involve the AT1R. Because of its novelty and importance, we are investigating the 4 role of the AT2R by determining proteins …

Laboratory Characterization Of Pm Emissions From Combustion Of Wildland Biomass Fuels, S. Hosseini, S. P. Urbanski, P. Dixit, L. Qi, I. R. Burling, Robert J. Yokelson, T. J. Johnson, M. Shrivastava, H. S. Jung, D. R. Weise, J. W. Miller, D. R. Cocker Iii

Chemistry and Biochemistry Faculty Publications

[1] Particle emissions from open burning of southwestern (SW) and southeastern (SE) U.S. fuel types during 77 controlled laboratory burns are presented. The fuels include SW vegetation types: ceanothus, chamise/scrub oak, coastal sage scrub, California sagebrush, manzanita, maritime chaparral, masticated mesquite, oak savanna, and oak woodland, as well as SE vegetation types: 1 year, 2 year rough, pocosin, chipped understory, understory hardwood, and pine litter. The SW fuels burned at higher modified combustion efficiency (MCE) than the SE fuels resulting in lower particulate matter mass emission factor. Particle mass distributions for six fuels and particle number emission for all fuels …

Mechanism Of Translation Termination, Michael Pfeiffer, Dr. Allen Buskirk

Journal of Undergraduate Research

Each cell within our body contains thousands of different kinds of proteins, each with a different function. Proteins provide cellular structure and perform catalysis of chemical reactions in the cell. Every protein is synthesized as ribosomes link together amino acids in the order encoded by DNA. It is therefore crucial that ribosomes function with great accuracy and proficiency to synthesize proteins quickly and correctly.

Thermodynamic Properties Of Nanoalumina Synthesis And Analysis Of Nanoalumina, Rebecca Olsen, Dr. Juliana Boerio-Goates

Journal of Undergraduate Research

Nanomaterials, possessing unique chemical, physical, and mechanical properties, can be used in a wide range of industrial, biomedical, and electronic applications. There are three general categories for producing nanomaterials: mechanical processing (milling), chemical processing (precipitation), or thermal processing (evaporation and condensation). Conventional methods often have drawbacks in controlling size, purity, surface morphologies, production amounts, cost, and time.1,2,3 Additionally, techniques developed for one metal oxide often do not transfer to other nano-oxides. A new method developed here at BYU overcomes many of these difficulties.

Enantioselective Synthesis Of Hasubanan Alkaloids, Daniel Nielsen, Laura Nielsen, Dr. Steven L. Castle

Journal of Undergraduate Research

In nature, many molecules exist in two different forms, referred to as enantiomers. These forms are structurally identical, yet they are mirror images of each other. One simple example of this is our hands. While both hands are structurally identical, there is no way that they can be superimposed. Our hands are enantiomers, and interact differently with certain objects. For example, a left hand cannot fit a right-handed glove. Such a phenomenon occurs on the molecular level as well. A left-handed enantiomer of a drug might react with the receptors in the body in a beneficial way, while the right-handed …

Does The Ribosome Cleave Mrna? Searching For The A-Site Endonuclease, Jeremy Goodson, Dr. Allen Burskirk

Journal of Undergraduate Research

Trans-translation can be broken down into 5 steps. , After a ribosome stalls, the mRNA in its aminoacyl-tRNA site (A-site) is cleaved and released, which leaves the A-site empty. The key molecule in ribosomal rescue, transfer-messenger RNA (tmRNA), then forms a complex with Small Protein B (SmpB). This complex is recruited into the empty A-site of the stalled ribosome. tmRNA contains a message in an open reading frame, which encodes a degradation tag that will be added to the protein later. In the next surprising step, the ribosome switches RNA templates from the stalled mRNA to tmRNA, resuming translation on …

Covalent Modification Of Hydrogen-Terminated Silicon Surfaces Through A One-Step Polymerization Process, Robert Blake, Dr. Matthew R. Linford

Journal of Undergraduate Research

Silicon is one of the most abundant elements on the earth and has been used throughout history in a variety of applications. Because silicon is so widely used in the semiconductor and electronics industries, recent research has focused on altering the properties of silicon wafers. Chemical modification of the silicon surface changes the properties of the silicon wafer and potentially presents new semiconductor applications. One method commonly used to modify silicon surfaces is to grow polymer brushes from them.

Short, Strong Halogen Bonding In Co-Crystals Of Pyridyl Bis-Urea Macrocycles And Iodoperfluorocarbons, Michael F. Geer, James Mazzuca, Mark D. Smith, Linda S. Shimizu

Faculty Publications

No abstract provided.

A Trojan Horse Approach To Cancer Treatment: A2da And A2noon As Potential Triggered And Targeting Chemotherapeutic Drugs, Jeremy Koontz, Dr. Heidi Vollmer-Snarr

Journal of Undergraduate Research

Despite the enormous amounts of time and money spent to research effective cures for cancer—the second leading cause of death in the United States —little is known today about how to kill cancer cells without harming normal cells. Current traditional forms of cancer treatment are chemotherapy, radiotherapy, and invasive surgery. However, the challenge with such treatments is they do not discriminate between normal cells and cancerous cells; these therapies struggle to balance toxicity and efficiency. In comparison, photodynamic therapy (PDT) offers a more favorable alternative to traditional methods of cancer treatment. In PDT drugs, called photosensitizers, are activated through specific …

Chimeric Rhinoviruses Displaying Mper Epitopes Elicit Anti-Hiv Neutralizing Responses, Guohua Yi, Mauro Lapelosa, Rachel Bradley, Thomas M. Mariano, Denise Elsasser Dietz, Scott Hughes, Terri Wrin, Chris Petropoulos, Emilio Gallicchio, Ronald M. Levy, Eddy Arnold, Gail Ferstandig Arnold

Publications and Research

Background: The development of an effective AIDS vaccine has been a formidable task, but remains a critical necessity. The well conserved membrane-proximal external region (MPER) of the HIV-1 gp41 glycoprotein is one of the crucial targets for AIDS vaccine development, as it has the necessary attribute of being able to elicit antibodies capable of neutralizing diverse isolates of HIV.

Methodology/Principle Findings: Guided by X-ray crystallography, molecular modeling, combinatorial chemistry, and powerful selection techniques, we designed and produced six combinatorial libraries of chimeric human rhinoviruses (HRV) displaying the MPER epitopes corresponding to mAbs 2F5, 4E10, and/or Z13e1, connected to an immunogenic …

One-Pot Anti-Markovnikov Hydroamination Of Unactivated Alkenes By Hydrozirconation And Amination, Alexandra E. Strom, John F. Hartwig

Chemistry: Faculty Publications

A one-pot anti-Markovnikov hydroamination of alkenes is reported. The synthesis of primary and secondary amines from unactivated olefins was accomplished in the presence of a variety of functional groups. Hydrozirconation, followed by amination with nitrogen electrophiles, provides exclusive anti-Markovnikov selectivity. Most products are isolated in high yields without the use of column chromatography.

Ectodermal Dysplasia In Family Arises From Unidentified Dominantly Inherited De Novo Mutation, Phil Young, Dr. Emily Bates

Journal of Undergraduate Research

Ectodermal dysplasia (ED) is a genetic disorder dealing with improper formation of tissues derived from the ectoderm, such as skin and sweat glands. Many clinical manifestations of the disorder exist, which has led to the classification of over 170 types of ectodermal dysplasia (1). The observed phenotypes of the disorder include: conical teeth, missing or sparse eyebrows, inability to sweat, craniofacial defects, and digit malformation. Many genetic causes have been identified. A novel mutation in an individual’s DNA sequence has caused ectodermal dysplasia in several members of a Caucasian, American family we identify as Kindred 214. The family pedigree shows …

Protein Similarity Networks Reveal Relationships Among Sequence, Structure, And Function Within The Cupin Superfamily, Richard Uberto, Ellen W. Moomaw

Faculty Articles

The cupin superfamily is extremely diverse and includes catalytically inactive seed storage proteins, sugar-binding metal-independent epimerases, and metal-dependent enzymes possessing dioxygenase, decarboxylase, and other activities. Although numerous proteins of this superfamily have been structurally characterized, the functions of many of them have not been experimentally determined. We report the first use of protein similarity networks (PSNs) to visualize trends of sequence and structure in order to make functional inferences in this remarkably diverse superfamily. PSNs provide a way to visualize relatedness of structure and sequence among a given set of proteins. Structure- and sequence-based clustering of cupin members reflects functional …

Dominantly Inherited Mutation Of Ectodermal Dysplasia, Ella Wyllie, Dr. Emily Bates

Journal of Undergraduate Research

Ectodermal Dysplasia is a genetic disorder associated with the abnormal development of hair, teeth, nails, tear ducts, sweat glands, and occasionally gross craniofacial or digit structure. ED is caused by a defective in the growth and development of the ectoderm where their tissues are derived. There are several different types of ED; to determine exactly what is causing each form of ED several genes have been investigated1. TP63, Ectodysplasin A, EDAR, tumer necrosis factor receptor associated factor 6, dentin sialophophoprotein, Dlx3, TBX22, Wnt10, Plakophilin-1 (PKP1), gap junction beta-6 protein (GJB6), porcupine homolog (PORCN), and EVC have all been identified with …

Comparison Of Arsenic Uptake And Oxidative Stress By Christmas Fern And Spider Brake Fern, Paul Lkanich, Pratheek Koneru, Robert Wei

Undergraduate Research Posters 2013

Plants are widely considered the most cost effective and environmentally friendly way to clean soils and waters contaminated with toxic metals, e.g. arsenic and mercury. We have focused our research on the uptake of arsenic and its biochemical effect on two species of fern, Spider brake fern and Christmas fern. Spider brake fern is known to be capable of accumulating significant amounts of arsenic. We wish to determine whether the levels of arsenic uptake in Christmas fern are comparable to Spider Brake fern (>1g kg-1 plant biomass) when both are grown under the same conditions. Another aim of the …

Climate Change From Oxygen Isotopic Variation Of Pore Water From Sediments In Punderson Lake, Northeast Ohio, Rachel Daley, Fasong Yuan

Undergraduate Research Posters 2013

The environment in Ohio has changed over time. The hydroclimate, which is the climate of the water, shows changes from the Industrial Revolution to the present. Evidence for these changes can be found in levels of δ18O and δ2H isotopes in the layers of sediment and water in the lakes of Northeast Ohio. Mass spectrometry can be used to test the levels of δ18O and δ2H isotopes from pore water samples within sediment cores. In this study, surface soil and water samples were collected from cores in Punderson Lake at Punderson State Park in Newbury, Ohio. Pore water was extracted …

Development Of Novel Reaction-Based Fluorescent Probes, Weimin Xuan

Chemistry and Chemical Biology ETDs

Fluorescent probes have been proved to be very valuable tools in chemical and biological applications, and extensive exploration has been made. Recently, reaction-based fluorescent probes became a new design trend and displayed great potential with remarkable implementation to the conventional design method. However, this field is still underdeveloped, and a lot of problems remain to be solved. As part of our groups research interest, my Ph.D. study centered on the development of new reaction-based fluorescent probes. Firstly, our previous research on Hg²⁺ was continued. In this work, we developed a novel ratiometric fluorescent probe for Hg²⁺ with impressive …

Self-Assembled Dna Origami Templates For The Fabrication Of Electronic Nanostructures, Elisabeth Pound Gates

Theses and Dissertations

An important goal of nanoscience is the self-assembly of nanoscale building blocks into complex nanostructures. DNA is an important and versatile building block for nanostructures because of its small size, predictable base pairing, and numerous sequence possibilities. I use DNA origami to design and fold DNA into predesigned shapes, to assemble thin, branched DNA nanostructures as templates for nanoscale metal features. Using a PCR-based scaffold strand generation procedure, several wire-like nanostructures with varying scaffold lengths were assembled. In addition, more complex prototype circuit element structures were designed and assembled, demonstrating the utility of this technique in creating complex templates. My …

Lipidomic Analysis Of Metastatic Kidney Cancer, Brendan Coutu, Dr. John Prince

Journal of Undergraduate Research

Cancer not only affects individuals and families but has the greatest economic effect worldwide than any other premature cause of death.1 Diverse aspects of cancer biology are under investigation to better understand the mechanism of action of different cancer types, that biomarkers can be identified for early diagnosis, and, most importantly, that a lasting cure can be discovered.32 In the development of cancer, cells undergo a number of phenotypic changes, known as the hallmarks of cancer.2 The hallmarks of cancer are described as sustained proliferative signaling, evading growth suppressors, activating invasion and metastasis, enabling replicative immortality, inducing angiogenesis, and resisting …

Phosphoester Bond Stabilization For Enhanced Cid Phosphoproteomics, Stewart Morley, Dr. John Prince

Journal of Undergraduate Research

Proteomics uses highly sensitive mass spectrometers to measure peptide fragment masses from enzymatically digested proteins. Measuring the mass of the peptide and fragments produced in the mass spectrometer allows for identification of its parent protein. Phosphoproteomics analyzes peptides that have been phosphorylated. Phosphoproteomics identifies phosphorylation sites, network relationships between proteins, and how cells respond to changes in their environment. Mass spectrometers typically ionize peptides to carry positive charges. This charge aids to draw molecules into the instrument. Phosphate modifications reduce charge on their molecules, reducing the positive charge on phosphopeptides, creating neutral, or negatively charged species. The lack of charge …