Chemistry Commons^™

Telsam-Target Protein Fusions Can Form Diffraction-Quality Crystals Without Direct Inter-Polymer Contacts, Moriah Longhurst

Undergraduate Honors Theses

X-ray diffraction is a robust method for determining the detailed 3D structures of specific proteins. However, this requires the formation of well-ordered protein crystals, a process that is time-consuming, expensive, and only has about a 10-30% success rate. New methods are needed to enable the efficient crystallization of challenging proteins. One such technique is explored here, which utilizes a protein polymer (the sterile alpha motif domain of the human protein translocation Ets leukemia, or TELSAM) as a crystallization chaperone to form a more ordered crystal lattice of target proteins and drive crystallization. This method was successfully used to crystallize, collect …

Sources Of Formaldehyde In Bountiful Ut Data, Nitish Bhardwaj, Ariel Kelsch, Delbert Eatough, Ryan Thalman, Nancy Daher, Kerry Kelly, Isabel Cristina Jaramillo, Jaron Hansen

ScholarsArchive Data

Source of Formaldehyde in Bountiful, UT Data

This file contains the X and U matrix used in the positive matrix factorization analysis done on the data collected in Bountiful, UT. The X matrix contains the concentration of species measured and the U matrix is the calculated uncertainty in each measured value. This data is stored in the Excel format.

Included in this file is the two-hour averaged concentrations of formaldehyde and ozone, wind direction, time of day, and date that the data was collected at the Bountiful, UT air sampling site located at the Bountiful Utah High School. This data …

In Vitro Screening Of Tp5801 Against Kinases For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

Data from screen of TP-5801 against in vitro kinases

Improvement In 14-3-3 Binding Site Prediction, Katherine K. Mccormack

ScholarsArchive Data

The 14-3-3 family of phospho-binding proteins regulate a variety of major cellular processes through interaction with a network of dynamic proteins. Deregulation of the 14-3-3 interaction network contributes to a variety of degenerative disorders and cancers. Our lab focuses on identifying novel 14-3-3 interactions and understanding how 14-3-3 binding regulates protein function. A major gap in this process is that identifying the phospho-site where 14-3-3 docks on a given protein is time- and resource-consuming. Prediction algorithms have been developed to predict canonical 14-3-3 binding sites, however, there are many non-canonical sites that existing software is unable to predict. To fill …

Kinase Screen Data For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

A TNK1 peptide encompassing S502 was screened against 245 Ser/Thr kinases. This file contains kinase activity values (against S502) from an n=1 experiment. These data support a manuscript to be published in Nature Communications (Chan and Egbert et al.)

Building An Ins-1 Cdna Library For A Genome-Wide Crispr-Cas9 Screen, Idongesit Ekpo

Undergraduate Honors Theses

By the year 2040, an estimated 642 million people are expected to have diabetes globally. Diabetes results from an elevation of metabolic stressors, such as glucotoxicity, lipotoxicity, oxidative stress and apoptosis. In type 2 diabetes, these stressful conditions contribute to the malfunction and loss of functional insulin-producing β-cells. Current treatment methods for diabetes include insulin therapy, islet transplant and anti-diabetes medication. These treatments are not curative and ignore other factors that contribute to the pathogenesis of diabetes beyond insulin resistance and islet β-cell failure. Previous research on β-cells has focused on ways to replace functional β-cell mass, trigger β-cell proliferation, …

Preparation And Detailed X-Ray Photoelectron Spectroscopy And Spectroscopic Ellipsometryanalysis Of Ultrathin Protective Coatings, Brian Ivins Johnson

Theses and Dissertations

Ultra-thin films (UTFs) are important in many applications, seen in the semiconductor industry, in chromatography, in sensing, in microfluidics, in aerospace, and in robotics. They also protect materials from corrosion, change surface energies, limit water intrusion into materials, allow material self-cleaning and self-healing, provide scratch resistance, and impart other specific chemical properties. In many cases, UTFs drastically alter surface properties and therefore their applications. It is imperative that proper and consistent characterization be performed on coatings to confirm and understand their desired properties. In Chapter two, Al oxidation under MgF2 protective layers is studied using real time X-ray photoelectron spectroscopy …

The Investigation Of Secondary Particle Formation Initiated By Non-Prototypical Sources And The Role Of Amines In The Atmosphere, Emily Burrell

Theses and Dissertations

This dissertation is a collection of works that investigate non-prototypical sources leading to new particle formation in the atmosphere. Particles play a major role in atmospheric chemistry. For example, particles are a component of smog and are commonly found in high concentrations under conditions of atmospheric inversions. In order to reconcile the difference between measured and modeled particle concentrations new mechanisms from non-prototypical sources for particle formation need to be determined. Formation of particles has frequently been modeled using classical nucleation theory (CNT). The first step in CNT is the nucleation step where molecular clusters form. In a second step, …

Preparation, Functionalization, And/Or Characterization By X-Ray Photoelectron Spectroscopy Of Carbon Surfaces For Biosensors And Other Materials, Varun Jain

Theses and Dissertations

My dissertation is primarily divided into two parts. The first deals with the preparation, functionalization, and characterization of carbon surfaces prepared by direct current magnetron sputtering (DCMS) and high power impulse magnetron sputtering (HiPIMS) as substrates for bioarrays. Part two discusses applications of XPS peak fitting in surface chemical analysis. Chapter 1, the introduction, includes (i) a discussion of the construction of bioarrays and the preparation of sputtered surfaces, e.g., by DCMS and HiPIMS, and also functionalization (bioconjugate) chemistry with special emphasis on the importance of covalent functionalization of surfaces, and (ii) a discussion of the surface characterization techniques and …

Computational Studies Of High-Oxidation State Main-Group Metal Hydrocarbon C-H Functionalization, Clinton R. King

Theses and Dissertations

High-oxidation state main-group metal complexes are potential alternatives to transition metals for electrophilic C-H functionalization reactions. However, there is little known about how selection of the p-block, main-group metal and ligand impact C-H activation and functionalization thermodynamics and reactivity. Chapter 2 reports density functional theory (DFT) calculations used to determine qualitative and quantitative features of C-H activation and metal-methyl functionalization energy landscapes for reaction between high-oxidation state d10s0 InIII, TlIII, SnIV, and PbIV carboxylate complexes with methane. While the main-group metal influences the C-H activation barrier height in a periodic manner, the carboxylate ligand has a much larger quantitative impact …

The Development Of Individualized Anemia Treatments Using Point Of Care Diagnostics To Distinguish Anemia Caused By Infection Or Chronic Inflammation, Dr. Richard Watt

Journal of Undergraduate Research

Background: Anemia that accompanies inflammation is associated with negative outcomes for patients. Early intervention to treat anemia is an important step in improving the quality of life for anemic patients. Our lab proposed to develop simple diagnostic tests using a Lateral Flow Immunoassays (LFIs) to measure the presence of a hormone called hepcidin because hepcidin is the master regulator of iron homeostasis in the body and elevated hepcidin levels lead to anemia.

Rational Design Of Multifunctional Enzyme-Like Catalysts For Assembly-Line Chemical Synthesis, David Michaelis

Journal of Undergraduate Research

The main objectives of this proposal was to publish our preliminary findings in peptide catalysis and then submit applications for external funding. Both of these objectives were accomplished during the grant period. In the Fall of 2017, we published our first paper on the development of our new enzyme-like catalysts (ACS Catal. 2017, 7, 7704–7708). This publication should serve as a springboard for additional publications in the area (on which we are currently working) and help ensure external funding for this project. During 2017-2018, we submitted 3 grant applications to the NIH to help support this project. These submissions have …

Modeling Main Group Metal Alkane Functionalization Reactions In Highly Acidic Carboxylic And Sulfuric Acid Solvents, Lily H. Carlson, Daniel H. Ess

Journal of Undergraduate Research

Our group is interested in identifying the unknown mechanisms of main-group C-H functionalization reactions. In the long term, our goal is to use computational chemistry tools to develop general principles on mechanisms, intermediates, reactivity, and selectivity for hydrocarbon C-H functionalization reactions by p-block main-group compounds as well as provide prediction of new catalysts and reactions. However, in providing these predictions, it remains unclear if different mechanistic pathways and intermediates will be predicted if examined in a complete solvent sphere (see Figure 1 for technical details). This is especially important for non-aqueous solvents such as carboxylic acids and sulfuric acid. To …

Heterodinuclear Co-Zr Compound Shows Increased Reactivity In Kumada Coupling, James Coombs, Daniel Ess

Journal of Undergraduate Research

Heterodinuclear compounds containing a metal–metal bond represent a potentially useful subclass of catalyst in organic synthesis. Heterodinuclear compounds offer the possibility of increased reactivity due to interactions between metal centers (Scheme 1A). These so-called cooperative effects can enhance reactivity by changing the electronic density, increasing nucleophilicity/electrophilicity of the reactive metal, and by lowering the energy barriers for changes in oxidation state. These changes in reactivity can allow a heterodinuclear compound to be an effective catalyst for many chemical reactions that would be unfeasible with a mononuclear analogue.

Cyclic Peptide Catalyst Design, Millicent Campbell, David Michaelis

Journal of Undergraduate Research

Enzymes found in nature are more efficient catalysts than those used in organic chemistry labs. However, natural enzymes are not ideal for organic synthesis because they only make one product and only work in specific conditions. The Michaelis lab designed a catalyst capable of mimicking enzyme-like reactivity in the lab. This catalyst consists of an alpha helix with an imidazolidinone catalyst and a thiourea catalyst (see figure 1). The imidazolidinone catalyst and thiourea catalysts are attached adjacent to each other on the alpha helix, which acts as a rigid scaffold that can mimic the proximity effects seen in natural enzymes. …

Computational Design And Analysis Of Molecular Ethylene Oligomerization Catalysts, Doo Hyun Kwon

Theses and Dissertations

Linear alpha olefins (LAOs) are key petrochemical precursors for the synthesis of larger polymers, detergents, plasticizers, and lubricants. Most catalytic ethylene oligomerization processes generate a wide distribution of LAO carbon chain lengths. A major ongoing industrial challenge is to develop homogeneous catalysts that result in selective and tunable ethylene oligomerization to 1-hexene and 1-octene alkenes. Quantum mechanical calculations coupled with rapidly advancing technology have enabled the ability to calculate small molecule systems with high accuracy. Employing computational models to advance from empirical to quantitative prediction of product selectivities has become an active area of exploration. In this work, we demonstrate …

The Investigation Of Nickel-Based Catalysts For The Oxidative Dehydrogenation Of Ethane, Justin Lane Park

Theses and Dissertations

The Investigation of Nickel-Based Catalysts for the Oxidative Dehydrogenation of Ethane Justin Lane ParkDepartment of Chemistry & Biochemistry, BYU Doctor of Philosophy Chemistry The advancement of creating ethylene from ethane via oxidative dehydrogenation (ODH) rather than the traditional direct dehydrogenation is right on the cusp of commercialization. The oxidative pathway provides a novel route that reduces the operating temperature of this reaction by 400-500°C. A variety of metals including Mo, V, and Ni that have redox properties suitable for the partial oxidation of small chain alkanes have been investigated. Currently, a MoVNbTe oxide is the most promising catalyst but it …

Multi-Instrument Surface Characterization Of Display Glass, Cody Vic Cushman

Theses and Dissertations

Flat panel displays (FPDs) are microfabricated devices that are often fabricated on specialized glass substrates known as display glass. The surface chemistry of the outer few nanometers of display glass can have an important influence on FPD performance and yield. Dsiplay glass surface characterization is difficult because (i) display glass surface composition varies significantly from its bulk composition; (ii) high-surface area forms of glass, such as fibers and powders, may not have the same surface composition as melt-formed planar surfaces, and (iii) the surface composition of display glass may be altered through exposure to chemical treatments commonly used during flat …

Selective Catalysis By Polymer-Supported Ruthenium Nanoparticlesand New Ligand Design For Cooperative And Bimetallic Catalysis, Seyed Hadi Nazari

Theses and Dissertations

The abstract is the summary of three different projects all centered around the generalidea of catalysis which is the general theme of research in the Michaelis laboratory. The firstproject focuses on development of a new heterogeneous catalyst for selective catalysis. In theMichaelis lab, we were interested in the potential of nanoparticle catalysts for regioselectivetransformations. We showed that polymer supported ruthenium nanoparticles performed as areliable catalyst for regioselective reduction of azide to amine. In our study of regioselectivereduction of multiple azide containing substrates, we observed that in presence of ourruthenium nanoparticle catalysts, the least sterically hindered azide group reduced to aminefunctional …

Applications Of Pattern Recognition Entropy (Pre) And Informatics To Data Analysis, Shiladitya Chatterjee

Theses and Dissertations

The primary focus of my work is the application of informatics methods to the fields of materials science and analytical chemistry. The statistical analysis of data has become increasingly important in understanding the properties of materials and analytes. Statistical methods like principal component analysis (PCA) and multivariate curve resolution (MCR) are widely used for analysis in chemistry and other fields given their ability to categorize spectra in an unsupervised way. PCA is relatively easy to apply and has appealing mathematical properties. However, the results can be challenging to interpret, even for experienced users. In contrast, MCR results can be more …

Nonlinear Optical Characterization Of Solids, Alex Farnsworth

Undergraduate Honors Theses

Vibrational Sum Frequency Generation (VSFG) and the similar Second Harmonic Generation (SHG) are both classified as nonlinear optical phenomena, with the hallmark trait being that the input and output frequencies are different. Both of these systems are remarkable tools due to their surface specific nature. Still, there is much that is not known about the response from these systems, especially the nonresonant SFG response. We have worked to better understand SFG signal, specifically the nonresonant temporal profile. We have also collected results that call into question some underlying assumptions about time-based suppression methods when working with single crystal substrates.

As …

Application Of The Entropy Concept To Thermodynamics And Life Sciences: Evolution Parallels Thermodynamics, Cellulose Hydrolysis Thermodynamics, And Ordered And Disordered Vacancies Thermodynamics, Marko Popovic

Theses and Dissertations

Entropy, first introduced in thermodynamics, is used in a wide range of fields. Chapter 1 discusses some important theoretical and practical aspects of entropy: what is entropy, is it subjective or objective, and how to properly apply it to living organisms. Chapter 2 presents applications of entropy to evolution. Chapter 3 shows how cellulosic biofuel production can be improved. Chapter 4 shows how lattice vacancies influence the thermodynamic properties of materials. To determine the nature of thermodynamic entropy, Chapters 1 and 2 describe the roots, the conceptual history of entropy, as well as its path of development and application. From …

Creation And Use Of Software For Analysis Of Kinetic Proteomic Experiments, Bradley C. Naylor

Theses and Dissertations

In this dissertation, I will review the history and general strategies for performing kinetic proteomics. I will then demonstrate that I have published an open source, user-friendly program for other scientists to use to perform kinetic proteomics data analysis, as well as publishing a novel discovery of key ribosomal subunits being replaced within the lifetime of the ribosome, which was discovered through use of kinetic proteomics. Finally, I will discuss work that is ongoing to improve my software tool for use in human subjects, and work being done to combine kinetic proteomics with other global analysis methods to make novel …

Progress Toward Synthetically Simplified Natural Anticancer Peptide, David W. Kastner, Steven L. Castle

Library/Life Sciences Undergraduate Poster Competition 2018

Yaku’amide A was isolated in late 2010 from the deep-sea sponge Ceratopsion sp. and exhibits potent inhibitory activity against 39 human cancer cell lines via a potentially novel mode of action. However, the total synthesis requires many steps and produces low yields. In this study, we determined two simpler YA analogues that may retain its anticancer properties and can be synthesized in larger quantities. The analogues replace dehydroisoleucine with either dehydroethylnorvaline or dehydrovaline.

14-3-3zeta Role In Promoting Survival Of Cells To Facilitate Progression Of Cancer, Katie Pennington, Eranga Roshan, Joshua Andersen, Katherine K. Mccormack

Student Works

The regulatory protein 14-3-3z promotes cellular growth and survival, and high expression levels of 14-3-3z are associated with mortality in multiple cancer types. 14-3-3z binds cellular proteins in a phosphorylation-dependent manner to modulate their functions. We have been characterizing the interactome of 14-3-3z which will likely lead to candidates for novel therapies for chemoresistant cancers. Tumor cells must be able to survive in a variety of stresses within the tumor microenvironment, including hypoxia, which occurs when tumors lack adequate blood supply. Previous data from our lab suggested that 14-3-3z promotes the adaptation of tumor cells to hypoxic stress. Our hypothesis …

Contribution Of Bulky <&Alpha>,<&Beta>-Dehydroamino Acids To The Proteolytic Stability Andenhanced Folding Of <&Beta>-Hairpins And Progress Towards The Total Synthesis Of Yaku<'>Amide A, Ankur Jalan

Theses and Dissertations

This dissertation primarily covers the impact of bulky ,-dehydroamino acids on the proteolytic stability and enhanced folding of -hairpins. It partly describes the progress towards the total synthesis of yakuamide A, a potent anticancer peptide with an IC50 value of 14 ng/mL against leukemia cells. Proteins and peptides are a very attractive source of potential medicinal agents as they can target various protein“protein interactions that are implicated in several diseases and disorders. The global sales of peptide drugs in 2013 were estimated to be about $28 billion and are constantly rising at an appreciable rate. However, peptide drugs have a …

Ion Trajectory Simulations And Design Optimization Of Toroidal Ion Trap Mass Spectrometers, Jessica Marie Higgs

Theses and Dissertations

Ion traps can easily be miniaturized to become portable mass spectrometers. Trapped ions can be ejected by adjusting voltage settings of the radiofrequency (RF) signal applied to the electrodes. Several ion trap designs include the quadrupole ion trap (QIT), cylindrical ion trap (CIT), linear ion trap (LIT), rectilinear ion trap (RIT), toroidal ion trap, and cylindrical toroidal ion trap. Although toroidal ion traps are being used more widely in miniaturized mass spectrometers, there is a lack of fundamental understanding of how the toroidal electric field affects ion motion, and therefore, the ion trap's performance as a mass analyzer. Simulation programs …

Capacity Of Human Immunodeficiency Virus Targeting Chimeric Antigen Receptor T Cells To Eliminate Follicular Dendritic Cells Bearing Human Immunodeficiency Virus Immune Complexes, Matthew T. Ollerton

Theses and Dissertations

An important obstacle to a functional cure for HIV/AIDS is the persistence of viral reservoirs found throughout the body in various cells and tissues. Reservoirs can be latently infected cells, or in the case of follicular dendritic cells (FDC), non-infected cells that trap infectious virus on their surface through immune complexes (HIV-IC). Although several strategies have been employed to target and eliminate viral reservoirs, they are short-lived and ineffective. In an attempt to provide a long-term approach, chimeric antigen receptor T (CAR-T) cells were designed to eliminate native HIV on FDCs. Although effective at eliminating HIV-infected cells, and halting spreading …

Semiconductor Terahertz Electronics And Novel High-Speed Single-Shot Measurements, Parker Dean Salmans

Theses and Dissertations

Ultrafast spectroscopy is used to study essential characteristics of solid-state materials. We use ultrafast techniques to study semiconductors at THz frequencies, as well as demonstrate new single-shot measurement techniques. The future of electronics is in the THz regime. We study a crucial characteristic of semiconductors used in devices: the critical field at which the material becomes conductive. GaAs is a promising semiconductor for high-speed devices, and we use enhanced THz electric fields to measure the critical fields at 0.7, 0.9, 1.1, and 1.5 THz frequencies. Single-shot spectroscopy is a technique used to measure ultrafast time scale laser pulses. We show …

Electrokinetically Operated Integrated Microfluidic Devices For Preterm Birth Biomarker Analysis, Mukul Sonker

Theses and Dissertations

Microfluidics is a vibrant and expanding field that has the potential for solving many analytical challenges. Microfluidics shows promise to provide rapid, inexpensive, efficient, and portable diagnostic solutions that can be used in resource-limited settings. Microfluidic devices have gained immense interest as diagnostic tools for various diseases through biomarker analysis. My dissertation work focuses on developing electrokinetically operated integrated microfluidic devices for the analysis of biomarkers indicative of preterm birth risk. Preterm birth (PTB), a birth prior to 37 weeks of gestation, is the most common complication of pregnancy and the leading cause of neonatal deaths and newborn illnesses. In …