Digital Commons Network^™

Stereospecific Cross-Coupling Reactions Of Enantioenriched Secondary Alkyltricyclohexyltin Nucleophiles, Meruyert Binayeva

Dissertations, Theses, and Capstone Projects

Transition metal-catalyzed cross-coupling reactions have evolved into a remarkable instrument for the formation of new bonds, and have significantly impacted how we approach to access complex organic molecules. Palladium is currently one of the most popular elements for catalytic applications due to its ability to facilitate powerful carbon-carbon and carbon-heteroatom couplings. Traditional Pd-catalyzed cross-coupling reactions have primarily concentrated on C(sp2)-C(sp2) cross-couplings, yielding planar products. Considering the use of C(sp3) nucleophiles would offer a viable control of the three dimensional arrangement in molecules. Herein, the first chapter details the history and development of Pd-catalyzed Stille cross-coupling reactions. The use of configurationally …

Studying The Stability Of Collagen/Heparin Coatings To Be Used In Cell Therapy Applications, Gavin Mussino

Biological Sciences Undergraduate Honors Theses

This honors thesis aims to investigate the reusability and performance of cell coatings for cell therapy applications. Cell therapy, which involves the use of human cells to repair or replace damaged tissues, holds immense potential for medical advancements. However, ensuring the survival and functionality of transplanted cells remains a significant challenge. We focused on studying the effectiveness of coatings applied to cells for improved cell growth and viability. The research project involved the preparation of the coatings using a layer-by-layer method and the subsequent seeding of cells. The coated cells were then subjected to a series of experiments to assess …

Protein Dynamics In Allostery And Computer-Aided Drug Design, Mayar Mohamed

Chemistry Theses and Dissertations

Molecular dynamics (MD) simulation is a powerful and versatile computational tool, that can be used in a wide range of applications from studying complex biological processes such as allostery to investigating the process of the protein-ligand binding in different computer-aided drug design implementations. In this work, various structural and drug discovery projects were performed by combining the state-of-art techniques molecular dynamics simulations, virtual screening, and binding free energy calculations with the innovative Markov State Model analysis and the machine learning techniques.

In the first project, the role of A’a helix as a key player in the transition between the light …

Synthesis Of Trifluoromethyl Ketones By (Diethylamino) Sulfur Trifluoride (Dast)-Mediated Nucleophilic Trifluoromethylation Of Benzoic Acids, Michael A. Vescio

Honors College Theses

Within the past few decades, the presence of fluorine containing

organic molecules has increased significantly. Many of the

current industrial production methods are not cost-effective,

practical, or inherently safe. This work describes a new methodology

for the synthesis of trifluoromethyl ketones. Our new method involves

the use of benzoic acid and trifluoromethyl trimethylsilane (TMSCF₃) as starting

materials along with diethylamino sulfur trifluoride (DAST) as a reagent

to obtain moderate to good yields of expected products in a short

reaction times.

Investigating Hops Production In Arkansas To Support Specialty Crop Growth, James Oliver Mcclellan

Graduate Theses and Dissertations

The hop plant (Humulus lupulus L.) is a perennial, climbing species within the Cannabaceae family that produces cones used for brewing. Hops are grown worldwide. In the United States most hops production occurs in the Pacific Northwest, but growth in the craft beer industry is driving efforts for hops production in other U.S. regions. Recommendations on hops cultivar suitability, fertility, and management are needed for the U.S. mid-south region. Objectives of this research on Arkansas-grown hops were to 1) assess the impact of cultivar and fertility rate on plant and cone attributes of six cultivars of Arkansas-grown hops and 2) …

Targeting Heat Shock 27 Kda Protein Induces Androgen Receptor Degradation, Yaxin Li

ETD Archive

Glioblastoma (GBM) is the most common and aggressive brain tumor, with very poor prognosis. Androgen receptor (AR) plays a significant role in the progression of GBM, and anti-androgen agents have the potential to be used for the treatment of GBM. However, AR mutation commonly happens in GBM, which makes the anti-androgen agents less effective. Heat shock 27 kDa protein (HSP27) is a well-documented chaperone protein to stabilize AR. Inhibition of HSP27 results in AR degradation regardless the mutation status of AR, which makes HSP27 a good target to abolish AR in GBM. Identified compound I ((N-(3-((2,5-dimethoxybenzyl)oxy)-4-(methylsulfonamido) phenyl)-4-methoxybenzamide) inhibits GBM cell …

Sodium Mediates Developmentally Plastic Responses In Plants And Herbivores, Luis Santiago-Rosario

LSU Doctoral Dissertations

Sodium plays a crucial role in organismal performance, trophic-level interactions, and eco-evolutionary dynamics. For plants, sodium impacts osmoregulation, growth, and water uptake. For animals, sodium is essential influencing osmoregulatory processes, muscle and neural development, and blood regulation. My dissertation aims to disentangle why sodium mismatch affects resource-consumer interactions and its influence on morphological and behavioral plasticity. First, I identified how sodium impacts plant performance and sodium accumulation strategies. I initially focused my research on understanding how increasing substrate sodium affects plant growth and tissue sodium accumulation strategies in controlled settings using a systematic review approach. I found that saltier plants …

Chemistry And Functionality Of Plant Waxes: Applications Toward Postharvest Coatings, Francisco Miguel Angel Leyva Gutierrez

Doctoral Dissertations

The cuticle of all higher-plants is covered in lipidic layers of amorphous and crystalline waxes. The chemical composition and structure of cuticular waxes impart numerous functional properties to the surfaces of plants. Moreover, plant waxes are valuable industrial products with myriad applications; the postharvest coating of agricultural commodities for preservation serves as a salient example. There is an unfulfilled need in the agricultural sector for alternative wax materials to reduce reliance on imported waxes of botanical origin. Plant waxes are inherently complex mixtures composed of n-alkanes, as well as aliphatic alcohols, aldehydes, fatty acids, ketones, esters, and derivatives thereof. …

Fast Photochemical Oxidation And Footprinting Of Proteins Via Trifluoromethyl Radical Chemistry, Elaine Morrow

Honors Theses

Fast photochemical oxidation of proteins (FPOP) is a useful tool in proteomics because of the ability for modifications to occur on the scale of microseconds which reduces the modifications to tertiary and quaternary structure allowing for more accurate labeling of the protein. Labels for FPOP are generated from various radicals in our experiments which include hydroxyl radicals and trifluoromethyl radicals. Hydroxyl radicals are easily generated by using an excimer laser (KrF laser, 248 nm) or a UV flash lamp (as a part of the Fox™ System) by the photolysis of hydrogen peroxide. Trifluoromethyl radicals, however, need hydroxyl radicals to be …

Initial Characterization Of Prna From Burkholderia Ambifaria: Developing An Nadph-Dependent Activity Assay For Tryptophan Halogenation, Mahmuda Akter

Theses and Dissertations

Some bacteria produce a potent antifungal agent (pyrrolnitrin) from tryptophan using four dioxygen dependent steps to outcompete other microbes. Each step of this process is catalyzed by an oxygenase encoded by the prnABCD cassette. The first enzymatic step in pyrrolnitrin biosynthesis is the regioselective chlorination of tryptophan to form 7-chlorotryptophan. This halogenation is catalyzed by PrnA, a Flavin dependent oxygenase, which has been isolated and characterized from P. fluorescens. The pyrrolnitrin biosynthesis pathway (prnABCD) has been also observed in the Burkholderia genus. This thesis comprises my studies on the expression, purification, and characterization of PrnA from Burkholderia ambifaria. Beyond the …

Application Of Artificial Intelligence And Machine Learning In Chemistry, Niraj Verma

Chemistry Theses and Dissertations

In the last four years, I have been exposed to various topics in scientific research under the supervision of Dr. Kraka in the CATCO group. Numerous involved chemistry projects were undertaken to gain an understanding of the basic laws of nature involving vibrational spectroscopy, molecular acidity, and catalysts based on transition metals for halogen chemistry. The insights from computational chemistry were then applied to model and predict various complicated problems in chemistry via artificial intelligence. With the help of classical artificial intelligence, the non-covalent interactions governing the properties of proteins and water properties were analyzed. Significant improvements were made in …

Ahr Expression On Rorc-Expressing Immune Cells Is Essential For I3c-Mediated Protection Against Colitis, Michal C. Williams

Senior Theses

Colitis is an inflammatory bowel disorder (IBD) whose etiology is attributed to modification in the luminal microbiota and dysregulation in the immune response. Indole is a signaling molecule which is naturally produced by gut luminal microbiota. Indole-3- carbinol (I3C) is a compound commonly found in vegetables and a ligand for the aryl hydrocarbon receptor (AhR). Previous studies have detected decreased expression and activation on the AhR receptor in colitis patients, thought to possibly alter gut microbiota metabolism, subsequently promoting colitis. 1 AhR, expressed in a variety of immune and epithelial cells, contributes to gut homeostasis by affecting vital mediators such …

Investigations Involving Mononuclear And Dinuclear Transition Metal Catalysts For Photochemical Carbon Dioxide Reduction, Ansu Edwards

Honors Theses

There is currently a global energy crisis, which is in desperate need of solutions. New energy sources are required that will not pollute as much as our longstanding reliance on nonrenewable fossil fuels as an energy source. This pollution involves large amounts of greenhouse gas emissions, predominantly carbon dioxide (CO₂), that contribute to environmental problems such as climate change. In this context, a fairly recent research direction to address this problem is the development of transition metal catalysts that can convert CO₂ into reduced carbon products that can serve as chemical fuels. This work focuses on the …

Indolizine Donor-Based Dyes For Applications In Fluorescence Biological Imaging, William Meador

Honors Theses

NIR emissive fluorophores are intensely researched due to their potential to replace modern imaging procedures. Many molecular strategies have been employed in the literature to optimize fluorophores for deeper NIR absorption and emission, biocompatibility, and higher fluorescence quantum yields. Amongst the fluorophores studied to date, proaromatic indolizine donors are attractive alternatives to traditional alkyl amine and indoline based donors due to their 1) lower energy absorption and emission facilitated by proaromaticity, 2) large Stokes shifts due to increased dihedral angles about the π-system, 3) ease of functionalization and capacity for bioconjugation at the phenyl ring, and 4) potential for further …

Techniques To Enhance The Attributes Of Wines Produced From Grapes Grown In Arkansas, Sarah Mayfield

Graduate Theses and Dissertations

Grapevines (Vitis spp.) are one of the most widely-planted horticultural crops, and the United States plays a major role in grape and wine production. Arkansas has a long history of grape and wine production with grapes grown in Arkansas including mostly native species, such as muscadines, and hybrids (crosses of Vitis spp.), such as Chambourcin. In addition, the University of Arkansas System Division of Agriculture (UA System) grape breeding program has cultivars and selections that have shown potential for wine production. The objectives of this research were to: evaluate effects of specific inactivated yeast application to Chambourcin grapevines on attributes …

Development Of A Computer Algorithm For Generation Of Primers For Nucleic Acid Sequence Based Amplification (Nasba), Rohit Karnati

Honors Undergraduate Theses

Nucleic acid sequence based amplification (NASBA) is a primer based isothermal method of RNA/DNA amplification. Currently, primer design for NASBA has been restricted to hand creating sequences of oligonucleotides that must follow a set of rules to be compatible for the amplification process. This process of hand-creating primers is prone to error and time intensive. The detection of mutants, post amplification, also offers a benefit in point of care scenarios and the design of hybridization probes for sequences in the region of amplification is also an erroneous and time intensive process. By creating a program to design primers and hybridization …

Changes In Soil Microbial Communities After Long-Term Warming Exposure, William G. Rodríguez-Reillo

Doctoral Dissertations

Microbial metabolism is a key controller of ecosystem processes (e.g., carbon cycling). However, we are only starting to identify the molecular mechanisms and feedback in response to long-term warming. My dissertation integrates multi-omics techniques to capture changes in soil microbial communities after long-term warming exposure. The research projects leverage three warming sites (i.e., SWaN, Barre Woods, and Prospect Hill) located in Western Massachusetts at Harvard Forest. These sites provided a unique experimental setup to better understand microbes in response to long-term temperature change. For the three research projects, we delved into the (i) microbial biodiversity across all three warming sites, …

Study Of Blood Viscosity With Added Sodium Nitrate And Temperature Variance: A Potential Therapy To Regulate Blood Flow After Induced Hypothermia, Brianna Munnich

Pence-Boyce STEM Student Scholarship

The human body has natural systems for vasodilation which are fueled by nitric oxide production, but in cases of cardiac disfunction and stress nitric oxide can be inhibited. In this study, nitric oxide was studied as a mediator for the blood rush experienced from the warming after induced hypothermia. Nitric oxide (NO) was introduced through sodium nitrate, which was aimed to reduce the speed and turbulence of blood flow through interaction between NO and the active site of hemoglobin. A viscometer was used to examine the rate of blood flow, while the temperature was varied to simulate the conditions of …

Design And Synthesis Of Circadian Clock Modulators And The Study Of Lov Domain Protein Lkp2 In Arabidosis Thaliana And Brassica Rapa, Aditi Nagar

Chemistry Theses and Dissertations

Circadian rhythms are self-autonomous endogenous clocks synchronized with the rotation of the Earth. With the Earth’s rotation and revolution on its axis, the internal clock undergoes oscillation in the period of ~24 hour and governs day to day activities in most organisms. In humans, it regulates the day to day physiological activities. Today’s modern lifestyle has an impact on health: shift work, jet lag, and irregular eating habits contribute to the misalignment of the endogenous circadian oscillator, thereby, increasing the risk of many metabolic disorders including diabetes, irregular blood pressure, sleep disorders, obesity, depression, and cancer. The primary goal of …

Structural And Functional Characterization Of Plant And Fungal Lov Proteins, Jameela Lokhandwala

Chemistry Theses and Dissertations

The plant blue light photoreceptor proteins Flavin binding Kelch F-box protein-1 (FKF1) and LOV Kelch protein-2 (LKP2) play an important role in maintaining circadian rhythmicity and photo-periodic flowering responses. These proteins along with light sensitive Light Oxygen Voltage (LOV) domain contain F-box and Kelch repeat domains. Therefore, these proteins control blue light mediated degradation of various protein targets to regulate circadian rhythmicity, growth, and photo-periodic flowering. Blue-light excitation of these proteins leads to formation of a cysteinyl-flavin adduct, which then decays depending upon various factors. Therefore, spectral studies were conducted to measure the kinetics of light–dark recovery. Size Exclusion Chromatography …

Biomimetic Macromolecules For Macrophage Targeting And Modulation, Joshua Whited

ETD Archive

Carbohydrate recognition has come to the forefront of biological aiming to uncover the mechanisms of physiological and pathological processes. Cell surface glycans are involved in processes including cellular adhesion, cell signaling, and immune response. A new approach for profiling cell surface glycans has great potential for a wide range of biomedical applications. Lectins have been conventionally used to determine the structure and function of glycoproteins, however, their numbers are still restricted compared to the number of glycan structures. Boronic acid has proven a remarkable small molecule capable of binding diols in aqueous solution. This interaction indicates boronic acid derived molecules …

Quantitative Analysis Of Bleomycin In Rat Plasma By Lc-Ms/Ms, Huawen Li

ETD Archive

Bleomycin is the most commonly used compound in its group of antineoplastic drugs. It works on tumor cells by single and double stranded DNA cleavage after its activation, in which it blocks tumor cells’ DNA replication or transcription activities to inhibit tumor cells’ growth. Bleomycin sulfate (Blenoxane) is the most popular preparation used in clinical research, and contains Bleomycin fractions of A2 and B2, which causes difficulties in quantitative analysis. This work uses the metal chelating property of Bleomycin as an advantage to simplify and improve sensitivity of existing quantitative methods. Copper was spiked in excess to plasma samples, followed …

Computational Investigation Of Protein Assemblies, Sm Bargeen Alam Turzo

ETD Archive

Selective nitrosylation of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) at Cys-247 affects gene regulation through the interferon-gamma (IFN- γ) activated inhibitor of translation (GAIT) complex. Oxidized low-density lipoprotein (LDL_ox) and INF-γ induce assembly of the nitrosylase complex composed of inducible nitric oxide synthase (iNOS), S100A8, and S100A9 proteins. Crystal structure of the complex of GAPDH and S100A8A9 is not known, structural prediction method were employed by protein-protein docking and binding energy calculation with PatchDock and FIREDock respectively. Candidate models were selected, based on a weight factor calculated, from the computational method developed from the "artificial protease" cleavage mapping Fe(III) (s)-1-(p- …

Il-17 Drives Copper Uptake And Activation Of Growth Pathways In Colorectal Cancer Cells In A Steap4-Dependent Manner, Evan Martin

ETD Archive

Colorectal cancer is a disease characterized by abnormal, invasive cell growth beginning in the colon or rectum. The third most common type of cancer worldwide, approximately one million new cases of the disease are diagnosed across the globe annually, resulting in an estimated 700,000+ deaths. One major risk factor associated with development of colorectal cancer is the presence of chronic inflammation in the large intestine, also known as colitis. Inflammation is a complex immune response against harmful stimuli, characterized by symptoms including heat, redness, swelling and pain. One important molecular mediator of this process is interleukin 17 (IL-17), a pro-inflammatory …

Il-17 Drives Copper Uptake And Activation Of Growth Pathways In Colorectal Cancer Cells In A Steap4-Dependent Manner, Evan Martin

ETD Archive

Colorectal cancer is a disease characterized by abnormal, invasive cell growth beginning in the colon or rectum. The third most common type of cancer worldwide, approximately one million new cases of the disease are diagnosed across the globe annually, resulting in an estimated 700,000+ deaths. One major risk factor associated with development of colorectal cancer is the presence of chronic inflammation in the large intestine, also known as colitis. Inflammation is a complex immune response against harmful stimuli, characterized by symptoms including heat, redness, swelling and pain. One important molecular mediator of this process is interleukin 17 (IL-17), a pro-inflammatory …

A Comprehensive Analysis Of Aromatic-Proton Mediated Hydrogen Bonds, Mona S. Alshamrani

Electronic Theses and Dissertations

Hydrogen bonds play critical role in folding, structure and recognition of biological macromolecules (e.g., proteins, RNA, DNA). In addition to classical hydrogen bonds (e.g., ─OH---O=, ─OH---O─, ─NH---O─ etc.), structural analysis of protein and nucleic acids, almost a decade ago, showed that hydrogen bonds (e.g., CH---O) with hydrogen atoms on aliphatic carbon atoms (hereafter, aliphatic-protons) also play very important role in the structure and function of biomolecules. Even though, protons of aromatic ring systems (hereafter, aromatic-protons) are more polar than the aliphatic-protons, systematic analysis of hydrogen bonds of aromatic-protons have not been carried out. Therefore, I carried out a systematic analysis …

Differentiation Of Potential False Positives From Human Saliva Using Raman Spectroscopy For Forensic Purposes, Selina Casadei

Legacy Theses & Dissertations (2009 - 2024)

Traces of body fluids can be found at a crime scene. Being able to identify and differentiate the body fluids while preserving DNA is fundamentally important for forensic applications. Saliva is an important body fluid that can be found on bite marks, cigarette butts, and more, being an excellent source for DNA extraction. Current tests for saliva and other body fluids are destructive and body fluid specific, and are prone to false positives. Our laboratory has developed a universal method for identification of all main body fluids; saliva, semen, sweat, peripheral blood, and vaginal fluid, using Raman spectroscopy combined with …

Vineyard Age Effect On Juice Chemistry, Anthocyanins, And Total Phenolics, Eric L. Camera

Wine and Viticulture

Grapevines (cv Zinfandel) planted in the same vineyard 100 years apart were analyzed for juice chemistry and phenolic content of the fruit. The vineyard was dry farmed, and vines from the original 1890 vineyard were compared to vines inter-planted in 1990. As “old vine” wines can command higher prices in the market due to a perceived difference in fruit characteristics. This study attempted to observe if there was a measurable difference in fruit characteristics, or if it is simply an effective marketing strategy. There has been little research conducted in the wine industry attempting to observe a difference of old …

Impacts Of Anthropogenic Noise On Litter Chemistry And Decomposition Processes In A Semi-Arid Ecosystem, Peggy Martinez

Boise State University Theses and Dissertations

Chronic anthropogenic noise in ecosystems can change avian/arthropod/plant interactions, but it is unclear how changes in herbivory pressure affects functional traits of plants. We asked how anthropogenic noise, mediated through changes in arthropod abundance, altered timing of leaf senesce, chemical composition (i.e. C/N ratios, total phenolics) and decomposition rates of leaf litter in Wyoming big sagebrush (Artemisia tridentata spp. wyo.). Additionally, we asked if changes in arthropod abundance altered secondary metabolites (i.e. monoterpenes) in foliage. We broadcasted recorded gas compressor station noise (24hrs/day) from April through October 2015 in a sagebrush steppe ecosystem of Idaho, USA. We quantified …

Characterization And Mechanisms Of Anthocyanin Degradation And Stabilization, Nathan Blaine Stebbins

Graduate Theses and Dissertations

Anthocyanins (ACYs) are polyphenol compounds found in nature, which contribute vivid colors to many fruits and vegetables, while also possessing significant health benefits. These pigments range in color from orange-red to blue-violet and could serve as natural colorants to replace artificial additives. There is a great demand from consumers to have fewer artificial compounds in their foods. However, the relatively instability of ACYs must be further understood in order to limit color degradation before they can completely replace synthetic colorants.

ACYs slowly degrade over time, but there is a knowledge gap on their fate and mechanisms causing degradation. In order …