Chemistry Commons^™

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 …

Optimizing Metallization Of Dna-Templated Nanostructures, Andrew Dearden, Adam Woolley

Journal of Undergraduate Research

With countless technologies that rely on microprocessors, there is a great need for increasingly smaller microelectronic components. Traditionally, manufacturers have employed a “top-down” approach to build microelectronics – that is, they have attempted to scale functional microcircuitry components down in size, hoping for similar performance in a smaller circuit. This top-down approach is expensive, often costing manufacturers hundreds of dollars per part. A much more cost-effective approach to microelectronics has emerged over the past decade in the field of molecular science: that is, to develop circuitry from the “bottom-up” using macromolecules such as deoxyribonucleic acid (DNA). Scientists have now devised …

Immunoassays Of Potential Cancer Biomarkers In Microfluidic Devices, Jayson Virola Pagaduan

Theses and Dissertations

Laboratory test results are important in making decisions regarding a patient's diagnosis and response to treatment. These tests often measure the biomarkers found in biological fluids such blood, urine, and saliva. Immunoassay is one type of laboratory test used to measure the level of biomarkers using specific antibodies. Microfluidics offer several advantages such as speed, small sample volume requirement, portability, integration, and automation. These advantages are motivating to develop microfluidic platforms of conventional laboratory tests. I have fabricated polymer microfluidic devices and developed immunoassays on-chip for potential cancer markers. Silicon template devices were fabricated using standard photolithographic techniques. The template …

Supramolecular Chemistry For Undergraduate Students, David V. Dearden, Roger G. Harrison

Journal of Undergraduate Research

The goal of this proposal was to train graduate and undergraduate students through research experiences in supramolecular chemistry in a multi-group environment. Academically, our objective was to synthesize and characterize new supramolecular host molecules and to develop applications for these molecules. We believe we have been quite successful, as demonstrated by the presentations and publications listed below and as shown by the receipt of a National Science Foundation grant by one of the teams involved in this research, in a year when such grants were particularly difficult to obtain.

Byu Meg Report, Emily Bates

Journal of Undergraduate Research

The academic objectives were met by the proposal. Students learned to sequence DNA and to interpret the sequence to know if there was a rare genetic change occurring in the sequence that they interpreted. Students learned to write academic abstracts, introductions, results, and conclusions in the format of an academic journal. Furthermore, together the students determined that the genetic change in a family with an inherited syndrome of birth defects was not one that had previously been identified or described.

Mentoring Undergraduates Via Organic Synthesis, Steven L. Castle

Journal of Undergraduate Research

This report summarizes the results that were generated under the auspices of the mentoring environment in my laboratory from January 2013 to the present. A total of eight undergraduates participated in the mentoring environment during this period.

Autophagy-Mediated Mechanisms Of Chemoresistance In Cancer, David Broadbent, Dr. Joshua Andersen

Journal of Undergraduate Research

The resistance of tumor cells to chemotherapy is a critical problem in the clinic and is a common cause of mortality in cancer. Emerging data suggests that resistance to chemotherapy is caused by a tumor-expressed protein called 14-3-3ζ, yet the mechanism to explain 14-3-3ζ-mediated chemoresistance is not completely understood (1). Rapid growing tumors often outgrow their blood supply resulting in regions of hypoxia (low glucose and oxygen). These cells must adapt or die and those that do adapt often become metastatic and chemoresistant. A recently proposed mechanism by which cancer cells are able to adapt to hypoxia is via autophagy, …

Optimization Of Nonadsorptive Polymerized Polyethylene Glycol Diacrylate As A Material For Microfluidics And Sensor Integration, Chad Rogers

Theses and Dissertations

Microfluidics is a continually growing field covering a wide range of applications, such as cellular analysis, biomarker quantification, and drug discovery; but in spite of this, the field of microfluidics remains predominately academic. New materials are pivotal in providing tailored properties to improve device integration and decrease prototype turnaround times. In biosensing, nonspecific adsorption in microfluidic systems can deplete target molecules in solution and prevent analytes, especially those at low concentrations, from reaching the detector. Polyethylene glycol diacrylate (PEGDA) mixed with photoinitiator forms, on exposure to ultraviolet (UV) radiation, a polymer with inherent resistance to nonspecific adsorption. Optimization of the …

Organocatalytic Aryl−Aryl Bond Formation: An Atroposelective [3,3]‑Rearrangement Approach To Binam Derivatives, Gong-Qiang Li, Hongyin Gao, Craig Keene, Michael Devonas, Daniel H. Ess, LaśZlóKüRti *

Journal of Undergraduate Research

Herein we disclose an organocatalytic aryl− aryl bond-forming process for the regio- and atropo- selective synthesis of 2,2′-diamino-1,1′-binaphthalenes (BINAMs). In the presence of catalytic amounts of axially chiral phosphoric acids, achiral N,N′-binaphthyl hydrazines undergo a facile [3,3]-sigmatropic rearrangement to afford enantiomerically enriched BINAM derivatives in good to excellent yield. This transformation represents the first

example of a metal-free, catalytic C(sp²)−C(sp²) bond

formation between two aromatic rings with concomitant de novo atroposelective installation of an axis of chirality. Density functional calculations reveal that, in the transition state for C−C bond formation, the phosphoric acid proton of …

Fluorescence Imaging Of Analyte Profiles In An Inductively Coupled Plasma With Laser Ablation As A Sample Introduction Source, Lance Moses

Theses and Dissertations

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has risen to among the top tier techniques for the direct analysis of solid samples. However, significant problems remain that must be solved to achieve the full analytical potential of LA-ICP-MS. Inefficient conversion of aerosol to ions within the ICP or transmission through the MS interface may decrease precision, sensitivity, and/or accuracy. Although fundamental mechanisms that govern ion production and transmission have been studied extensively in solution-nebulization (SN) ICP-MS instruments, significant gaps in our understanding remain. Furthermore, it is unclear to what extent differences between the aerosols generated during SN and LA …

Microchip Thermal Gradient Gas Chromatography, Anzi Wang

Theses and Dissertations

Although the airbath oven is a reliable heating method for gas chromatography (GC), resistive heating is needed for higher analytical throughput and on-site chemical analysis because of size, heating rate and power requirements. In the last thirty years, a variety of resistive heating methods were developed and implemented for both benchtop and portable GC systems. Although fast heating rates and low power consumption have been achieved, losses in column efficiency and resolution, complex construction processes and difficulties experienced in recovering damaged columns have also become problematic for routine use of resistively heated columns. To solve these problems, a new resistively …

Fabrication, Characterization, Optimization And Application Development Of Novel Thin-Layer Chromatography Plates, Supriya Singh Kanyal

Theses and Dissertations

This dissertation describes advances in the microfabrication of thin layer chromatography (TLC) plates. These plates are prepared by the patterning of carbon nanotube (CNT) forests on substrates, followed by their infiltration with an inorganic material. This document is divided into ten sections or chapters. Chapter 1 reviews the basics of conventional TLC technology. This technology has not changed substantially in decades. This chapter also mentions some of the downsides of the conventional approach, which include unwanted interactions of the binder in the plates with the analytes, relatively slow development times, and only moderately high efficiencies. Chapter 2 focuses primarily on …

Synthesis And Characterization Of Complex Molecular Assemblies On Surfaces, Nitesh Madaan

Theses and Dissertations

The research presented in this dissertation is focused on the construction of complex molecular structures on planar gold and silicon dioxide surfaces using a variety of surface modification techniques, along with thorough surface characterization at each modification step. The dissertation is structured into six separate chapters. In Chapter 1, an introduction to the importance and implications of molecular level surface modification, commonly employed surface modification methods, and available surface characterization techniques is presented. Chapter 2 shows applications of novel methodologies for the functionalization of gold surfaces using alkane dithiol self-assembled monolayers and thiol-ene click chemistry. The resulting functionalized gold substrates …

Chaperone-Mediated Folding And Assembly Of Β-Propeller Proteins Into Cellular Signaling Complexes, Rebecca L. Plimpton

Theses and Dissertations

G protein signaling depends on the ability of the individual subunits of the G protein heterotrimer to assemble into a functional complex. Formation of the G protein βγ (Gβγ) dimer is particularly challenging because it is an obligate dimer in which the individual subunits are unstable on their own. Recent studies have revealed an intricate chaperone system that brings the Gβ and Gγ subunits together. This system includes the cytosolic chaperonin containing TCP-1 (CCT) and a co-chaperone phosducin-like protein 1 (PhLP1). Two key intermediates in the Gβγ assembly process, the Gβ-CCT and the PhLP1-Gβ-CCT complexes, were isolated and their structures …

Ion Structure And Energetics In The Gas Phase Characterized Using Fourier Transfom Ion Cyclotron Resonance Mass Spectrometry, Chad A. Jones

Theses and Dissertations

In this dissertation, I use Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to study the structure and energetics of gas phase ions. Infrared multiphoton dissociation spectroscopy (IRMPD) is a technique for measuring the IR spectrum of gas phase ions in a Penning trap. I use this technique to investigate the conformation of cucurbituril complexes, terminal diamines, and protonated amino acids. Cross sectional areas by Fourier transform ion cyclotron resonance mass spectrometry (CRAFTI) is a technique developed by the Dearden lab to measure the cross section of gas phase ions. In this work, I further develop a fundamental understanding of …

Simple, Label-Free And Non-Instrumented Analyte Quantitation By Flow Distance Measurement In Microfluidic Devices, Debolina Chatterjee

Theses and Dissertations

Rapid determination of the concentrations of molecules related to diseases can provide timely information for treatment options. However, most biomarker quantitation methods require costly and complex equipment. On the other hand, point-of-care systems have less complex instrumentation needs than laboratory-based equipment, but often provide less information; for example, biomarker presence or absence instead of concentration. A complete analysis setup addressing key limitations of both laboratory-based and portable systems is highly desirable. I developed microfluidic devices with visual inspection readout of a target’s concentration from microliter volumes of solution flowed into a microchannel. Microchannels are formed within polydimethylsiloxane (PDMS), and the …

Synthesis Of 4'-Ester Resveratrol Analogues, Chromium Trioxide Oxidation Of Terpenes, And Synthesis Of Mimics Of (-)-Englerin A, Mark Jeffrey Acerson

Theses and Dissertations

4’ -ester analogues of resveratrol were synthesized using reaction conditions developed to produce mono-ester products in the presence of two other unprotected phenols. Basic conditions were employed to deprotonate the most acidic 4’ phenol followed by addition of anhydrides or acid chlorides to give the ester product. The reaction favored 4’-ester formation in polar aprotic solvents with DMSO being the optimal solvent.

(—)-Englerin A is a guaiane-type sesquiterpene containing two ester side chains. Mimics of (—)-englerin A were proposed that retained the ester side chains while replacing the non-polar core with less complicated structures. These proposed mimic cores would maintain …

High-Performance Polymer Monoliths For Capillary Liquid Chromatography, Pankaj Aggarwal

Theses and Dissertations

This dissertation focuses on improving the chromatographic efficiency of polymeric organic monoliths by characterizing and optimizing the bed morphology. In-situ characterization techniques such as capillary flow porometry (CFP), 3-dimensional scanning electron microscopy (3D SEM) and conductivity measurements were developed and implemented to quantitatively characterize the morphology of poly(ethylene glycol) diacrylate (PEGDA) monoliths. The CFP measurements for monoliths prepared by the same procedure in capillaries with different diameters (i.e., 75, 150, and 250 μm) clearly showed a change in average through-pore size with capillary diameter, thus, certifying the need for in-situ measurement techniques. Serial sectioning and imaging of PEGDA monoliths using …

Discovery Of An Allosteric Site On Furin, Contributing To Potent Inhibition: A Promising Therapeutic For The Anemia Of Chronic Inflammation, Andrew Jacob Gross

Theses and Dissertations

Release Date: October 2017

Anemia of chronic inflammation (ACI) is a condition that develops in a setting of chronic immune activation. ACI is characterized and triggered by inflammatory cytokines and the disruption of iron homeostasis. Hepcidin, a small peptide hormone, is the master regulator of iron homeostasis, and rapidly responds to iron supply and demand. Under conditions of chronic inflammation, hepcidin is elevated, and alters the way that iron is absorbed and disrupted throughout the body, resulting in disrupted iron homeostasis through inhibition of the iron exporter protein ferroportin. Anemia arises when insufficient erythropoietic activity combined with inadequate iron supply …

Bioinformatic Solutions To Complex Problems In Mass Spectrometry Based Analysis Of Biomolecules, Ryan M. Taylor

Theses and Dissertations

Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation. The complexity and volume of data produced by modern MS-omic instrumentation challenges biological interpretation, while the complexity of the instrumentation, sample noise, and complexity of data analysis present difficulties in maintaining and ensuring data quality, validity, and relevance. We present a corpus of tools which improves …

Laser-Induced Fluorescence Imaging Of Calcium And Barium Ion Beams In The Second Vacuum Stage Of A Commercial Inductively Coupled Plasma Mass Spectrometer, Alisa Jane Edmund

Theses and Dissertations

Inductively coupled plasma-mass spectrometers (ICP-MS) have become the workhorses of many analytical labs over the past few decades. Despite the instruments' high sensitivities and low detection limits there is still a demand for improvements in several aspects of their performance. One area of improvement is in the understanding of "space charge effects" Space charge effects are classified as problems associated with the ion beam. Problems are created when the mutual repulsions of the ions make consistent focusing of the ion beam difficult. This is particularly problematic with samples containing a low concentration analyte contained within a high salt solution matrix, …

Discovery Of Novel Serum Biomarkers For Diagnosing And Staging Alzheimer's Disease, Dipti Jigar Shah

Theses and Dissertations

Discovery of Novel Serum Biomarkers for Diagnosing and Staging Alzheimer’s DiseaseDipti Jigar ShahDepartment of Chemistry and Biochemistry, BYUDoctor of PhilosophyAlzheimer’s disease (AD) is an untreatable neurologic disease affecting more than 5 million Americans, most over 60 years of age. Protein plaques and neurofibrillary tangles typify AD brain pathology and are thought to cause the progressive dementia and brain shrinkage observed in AD. Currently there are no methods to diagnose the disease at a time before damage becomes irreversible.Biochemical tests for AD using cerebrospinal fluid analysis or neuroimaging are not yet sufficiently sensitive and specific, and they are invasive. This points …

Kir2.1 Effects On Craniofacial And Limb Development In Knockout Mice, Joy Williams, Dr. Emily Bates

Journal of Undergraduate Research

Birth defects arise because of both genetic and environmental factors. Children with genetic alteration of the inwardly-rectifying potassium ion channel Kir2.1 channel have heart arrhythmias, impaired cognitive function, and facial and limb abnormalities. Children that suffer from Fetal Alcohol Syndrome have cognitive and social development problems, heart defects, and facial abnormalities—including small eyes, small head, small upper jaw, and a small upper lip1. Kir2.1 is bound and blocked by alcohol2 and thus we predicted that it is the molecular target of Fetal Alcohol Syndrome. We designed experiments to determine how Kir2.1 is required during development and found that within 14 …

The Use Of Alpha-1-Antitrypsin (Aat) In The Downregulation Of Nuclear Factor Kappa-Light-Chain-Enhancer Of Activated B Cells (Nf-Κb) As A Treatment For Acquired Immunodeficiency Syndrome (Aids), Aaron Mcbride, Dr. Gregory F. Burton

Journal of Undergraduate Research

Current Human Immunodeficiency Virus (HIV) treatment is greatly hindered due to viral reservoirs throughout the body prolonging and perpetuating infection.i Large stores of HIV exist in the follicular dendritic cell (FDC) microenvironment, located primarily in the lymph nodes and spleen. Free-floating virus has a half-life of less than two hours; however, FDC-trapped virus has a half-life of over eight weeks and can be rescued in its infectious state longer than nine months after the initial infection,ii showing the role of FDCs as an HIV reservoir.iii Studies in the Gregory Burton laboratory focus on the interactions between HIV, FDCs, and CD4+ …

Structure Of The Phlp1-Gβ-Cct Complex Reveals A Molecular Mechanism For Gprotein Β Subunit Folding And Βγ Dimer Assembly, Devon Blake, Dr. Barry Willardson

Journal of Undergraduate Research

Cells detect and respond to a myriad of extracellular signals via seven-transmembrane G protein-coupled receptors and their associated G protein signaling pathways. The pathway is initiated by the binding of a signaling molecule, such as a hormone or neurotransmitter, to its binding site on the extracellular side of the receptor. This interaction activates the G protein heterotrimer, composed of Gβ, Gβ, and Gβ subunits, which functions by propagating the signal throughout the cell. First, however, the G protein heterotrimer must be assembled from its nascent polypeptides. The initial step in this process is the formation of the Gβγ dimer. Gβγ …

Splicing Of Chicken Cyclooxygenase-2, Matthew Lelegren

Journal of Undergraduate Research

As described in the proposal, my goal was to further understand the mechanisms of mRNA processing of the chicken gene called Cyclooxygenase (COX)-2. There are many mechanisms by which mRNA molecules are modified in order to produce proteins that fulfill the needs of a given cell. The mechanism I chose to study was called alternative splicing, a process through which sequences are removed from the mRNA thereby altering the structure and function of the protein to be translated from its sequence. In brief summary splicing mechanisms, the cells possess machinery that recognize certain sequences, called splice sites, as a guide …

Estrogen Signaling In Migraine Pathogenesis, Sarah Bahr, Dr. Emily Bates

Journal of Undergraduate Research

Migraine is a disorder that can include aura, headache, nausea, and hypersensitivity to all sensory modalities. It affects over thirty million people in the US. Migraines affect men and women equally until puberty, but overall migraines affect 3x more women than men. They also increase in frequency and severity during periods of estrogen fluctuation and often subside after menopause. Moreover, hormone supplements and birth control can affect migraine patterns. These correlations of migraine episodes to the menstrual cycle and increased pain sensitivity in response to estrogen suggest that differences in estrogen signaling contribute to migraine. We hypothesized that estrogen receptor …

Acetylation Of Sod1 As A Regulator Of The Tumor Stress Response, Matthew Whited, Dr. Joshua L. Andersen

Journal of Undergraduate Research

In cancer patients, a lack of cell apoptosis (programmed cell death) coupled with increased levels of cell proliferation leads to the formation of a tumor. Among the available treatment options, cytotoxic chemotherapy is the most common. The primary purpose of this treatment is to induce tumor cell apoptosis. In many cases, tumor cells develop chemoresistance, rendering chemotherapy ineffective as a method to activate apoptosis. Understanding the mechanisms that lead to chemoresistance is a critical step toward developing methods to increase the effectiveness of chemotherapy treatments.

Synthesis And Purification Of The Glycosphingolipid Csa-13, Tyler Olsen, Dr. Paul Savage

Journal of Undergraduate Research

The need for novel antibiotic mechanisms is prevalent. Common antimicrobial medicines such as penicillin, ampicillin and vancomycin have started becoming obsolete as resistant strains of bacteria become more widespread. The main problem with antibiotics is the rapid mutations that bacteria undergo. Eventually one cell will develop resistance, and then have that mutation selected for as patients undergo antibiotic therapy. Bacteria are rapidly changing to combat the many new antibiotic variants that have come out.