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The Interconnected Roles Of Residues N189, E168, And S220 In M. Tuberculosis Indole-3-Glycerol Phosphate Synthase Catalysis, Erik Domlija

Theses, Dissertations and Culminating Projects

Tuberculosis (TB) is an infectious disease caused by the bacteria Mycobacterium tuberculosis that primarily attacks the lungs. Drug resistance for M. tuberculosis is emerging and therefore new drug targets need to be identified. One way to target TB is through the inhibition of the tryptophan biosynthetic pathway of M. tuberculosis since production of tryptophan is essential for the replication of M. tuberculosis. The enzyme Indole-3-glycerol phosphate synthase (MtIGPS) was chosen as a potential drug target due to its role in tryptophan biosynthesis. Residue N189 interacts with active site residues E168 and S220. It is inferred from previous studies done with …

Nitroalkane Oxidase Inspired No-Transfer Agents, No Sensors, And The Computational Design Of Fluorescent Sensors, Thanh Thuy Thi Vuong

Chemistry & Biochemistry Dissertations - Archive

Flavin adenine dinucleotide and flavin mononucleotide are co-enzymes with biologically relevant redox potentials. They are involved in many chemical transformation processes in the biological system, such as one-electron and two-electron transfer reactions, dehydrogenase reactions, and intramolecular electron transfer reactions critical to cellular function. Their ability to be reoxidized under aerobic conditions has inspired us to investigate biomimetic transformations with their derivatives, especially in converting NO2 to NO. Besides that, a series of biosensors was designed and investigated to detect NO in the aqueous system. NO sensors were achieved with computational DFT calculations correctly predicting the fluorescence response.

The Effects Of Prior Calculus Classes On Success In Organic Chemistry, Tori Williamson

Theses/Capstones/Creative Projects

Within University of Nebraska – Omaha (UNO) chemistry-based degree programs, organic chemistry along with at least two semesters of calculus are required courses. There is, however, no requirement for the order in which these courses should be taken. This is mainly due to the notion that for chemistry courses, organic chemistry is detached from the typical quantitative concepts studied in other chemistry-based courses. This is untrue, however, as many organic chemistry concepts rely on three-dimensional spatial visualizations and manipulations. Spatial awareness skills are strengthened within higher-level calculus classes. A survey was administered to organic chemistry students enrolled in 2022-2023. The …

Battery Design, Construction, And Characterization For Small Motor Use Focusing On Anodic Zinc For Electron Flow, Amber Veach

Chemical Engineering Undergraduate Honors Theses

This thesis explores the construction, characterization, and application of anodic zinc batteries for powering a small electric motor for the ChemE Car competition. Two zinc galvanic cell batteries were studied: zinc-carbon and zinc-air batteries. Prototype batteries were constructed and tested for voltage, amperage, and power production. In the zinc-carbon trials, a 3:1 mixture of manganese dioxide and graphite was determined to be the best cathode for power production. The size which allowed for sufficient power while maintaining the smallest footprint on the car was a zinc can six cm tall and two cm in diameter. Analysis of paper zinc-air battery …

Spatial Metabolomics Reveals Glycogen As An Actionable Target For Pulmonary Fibrosis, Lindsey R. Conroy, Harrison A. Clarke, Derek B. Allison, Samuel Santos Valenca, Qi Sun, Tara R. Hawkinson, Lyndsay E. A. Young, Juanita E. Ferreira, Autumn V. Hammonds, Jaclyn B. Dunne, Robert J. Mcdonald, Kimberly J. Absher, Brittany Dong, Ronald C. Bruntz, Kia H. Markussen, Jelena A. Juras, Warren J. Alilain, Jinze Liu, Matthew S. Gentry, Peggi M. Angel, Christopher M. Waters, Ramon C. Sun

Saha Cardiovascular Research Center Faculty Publications

Matrix assisted laser desorption/ionization imaging has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application of high- dimensionality reduction/spatial clustering and histopathological annotation of matrix assisted laser desorption/ionization imaging datasets to assess tissue metabolic heterogeneity in human lung diseases. Using metabolic features identified from this pipeline, we hypothesize that metabolic channeling between glycogen and N-linked glycans is a critical metabolic process favoring pulmonary fibrosis progression. To test our hypothesis, we induced pulmonary fibrosis in two different mouse models with lysosomal glycogen utilization deficiency. Both mouse models displayed …

Separating The R Vs. S Enantiomers Of A Quinoline Aimed At Inhibiting The Allosteric Binding Pocket Of Hiv-1 Integrase, Madison Canfield

Honors Theses

HIV-1 is a retroviral disease that infects CD4+ T cells in the body. Once inside the body, HIV-1 uses human cell machinery to replicate and reproduce using several enzymes to reverse transcribe viral RNA to DNA and integrate the viral DNA into the human genome to reproduce. Several drugs, such as NRTIs, INSTIs, NNRTIs, and PIs, have been created to inhibit specific parts of the viral life cycle and are used in combination to fight HIV-1. However, these medications face challenges of viral mutation and resistance, which increases the importance of creating more potent and effective drugs. Recently, a new …

Separating The R Vs. S Enantiomers Of A Quinoline Aimed At Inhibiting The Allosteric Binding Pocket Of Hiv-1 Integrase, Madison Canfield

Honors Theses

HIV-1 is a retroviral disease that infects CD4+ T cells in the body. Once inside the body, HIV-1 uses human cell machinery to replicate and reproduce using several enzymes to reverse transcribe viral RNA to DNA and integrate the viral DNA into the human genome to reproduce. Several drugs, such as NRTIs, INSTIs, NNRTIs, and PIs, have been created to inhibit specific parts of the viral life cycle and are used in combination to fight HIV-1. However, these medications face challenges of viral mutation and resistance, which increases the importance of creating more potent and effective drugs. Recently, a new …

College Of Natural Sciences Newsletter, March - May 2023, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 4, Issue 2

Page 1 Dean's Message
Page 2-7 Awards and Recognition
Page 8 March 3rd Corothers Seminar
Page 9 54th Geography Convention
Page 10 Spring 2023 Day of Scholars
Page 11 2023 URSCAD Snaps
Page 12-14 Media Coverage of CNS
Page 15 Open PRAIRIE Data

Developing And Applying Computational Methods On Biomolecules, Shengjie Sun

Open Access Theses & Dissertations

Computational biophysics is an interdisciplinary subject that uses numerical algorithms to study the physical principles underlying biological phenomena and processes. Electrostatic interactions play an important role in computational molecular biophysics and their potential impact on disease mechanisms. At distances larger than several Angstroms, electrostatic interactions dominate all other forces, while the alteration of short-range electrostatic pairwise interactions can also have significant effects. The dual nature of electrostatic interactions, being dominant at long-range and specific at short-range, underscores their profound implications for wild-type structure and function. Any disruption of the complex electrostatic network of interactions may abolish wild-type functionality and could …

Structure Study Of Small Heat Shock Protein 27, Zhaobo Li

Open Access Theses & Dissertations

Molecular chaperones are a class of oligomeric proteins that play a critical role inpreventing the aggregation of non-native protein so that these proteins can later be refolded. Chaperones are ubiquitously expressed in all the kingdoms of life where their function is to counteract cellular stress and to maintain protein homeostasis. One subgroup of molecular chaperones is characterized by low molecular weight and are termed small heat shock proteins. The focus of the proposed research is the small heat shock protein 27 (Hsp27). Hsp27 is an ATP independent chaperone that is overexpressed in response to heat shock, radiation damage, oxidative damage, …

Repeated Low-Level Blast Exposure Alters Urinary And Serum Metabolites, Austin Sigler, Jiandong Wu, Annalise Pfaff, Olajide Adetunji, Paul Ki-Souk Nam, Donald James, Casey Burton, Honglan Shi

Chemistry Faculty Research & Creative Works

Repeated exposure to low-level blast overpressures can produce biological changes and clinical sequelae that resemble mild traumatic brain injury (TBI). While recent efforts have revealed several protein biomarkers for axonal injury during repetitive blast exposure, this study aims to explore potential small molecule biomarkers of brain injury during repeated blast exposure. This study evaluated a panel of ten small molecule metabolites involved in neurotransmission, oxidative stress, and energy metabolism in the urine and serum of military personnel (n = 27) conducting breacher training with repeated exposure to low-level blasts. The metabolites were analyzed using HPLC—tandem mass spectrometry, and the Wilcoxon …

Quantum Chemistry–Machine Learning Approach For Predicting Properties Of Lewis Acid–Lewis Base Adducts, Hieu Huynh, Thomas J. Kelly, Linh Vu, Tung Hoang, Phuc An Nguyen, Tu C. Le, Emily Jarvis, Hung Phan

Chemistry and Biochemistry Faculty Works

Synthetic design allowing predictive control of charge transfer and other optoelectronic properties of Lewis acid adducts remains elusive. This challenge must be addressed through complementary methods combining experimental with computational insights from first principles. Ab initio calculations for optoelectronic properties can be computationally expensive and less straightforward than those sufficient for simple ground-state properties, especially for adducts of large conjugated molecules and Lewis acids. In this contribution, we show that machine learning (ML) can accurately predict density functional theory (DFT)-calculated charge transfer and even properties associated with excited states of adducts from readily obtained molecular descriptors. Seven ML models, built …

Quantitative Analysis Of The Proteomic Selectivity Of Acidic Reductive Alkylation Of Peptides, Connor Jewell

Honors Scholar Theses

Proteome quantification is a complicated process which takes on many methods, usually involving peptide derivatization and complex mass spectral analysis. Scores of techniques have been utilized to address issues of incomplete quantification. The implementation of IPTL labeling, or isobaric peptide terminal labeling, is a recent addition to the literature, which exploits the supposedly selective labeling of N-termini of tryptic peptides from the C-termini of lysine residues due to differences in basicity. This method has been shown to improve quantitation by reducing spectral complexity and provide more accurate and reproducible results on peptide abundance. Investigations into the selectivity of terminal derivatization …

Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel

Honors Scholar Theses

Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …

Spin Trapping Behavior Of Some Selected Melatonin Derivatives For Hydroxyl Radicals: A Computational Study, Aaron Caesar

Electronic Theses and Dissertations

Melatonin (N-acetyl-5-methoxytryptamin, MLT) is a naturally occurring antioxidant which has shown some potential for use as a spin trap. Spin traps react with short lived hydroxyl radicals (HO·) to produce more stable products called spin adducts which may be characterized by electron paramagnetic resonance spectroscopy. However, the relative stability of hydroxyl spin adducts of melatonin derivatives (MLTD) compared to 2-hydroxymelatonin (HO-MLT) has not been examined computationally. Computational studies have been done on four selected MLTD; methylmelatonin (Me-MLT), chloromelatonin (Cl-MLT), cyanomelatonin (CN-MLT), and nitromelatonin (NO₂-MLT). Geometry of the structures were optimized at the HF/6-31G(d), cc-pVXZ, (X=D and T) and …

Design And Synthesis Of Peripherally Selective Endocannabinoid Enzyme Inhibitors For Ocular Indications, Kezia Reji Thomas

Senior Honors Theses

Peripherally selective compounds have been found to stimulate endocannabinoid receptor activity, which has been observed to have positive physiological effects such as ocular wound healing and inflammation control. The activation of the cannabinoid 1 receptor via binding of the endogenous ligands, anandamide and 2-arachidonoylglycerol, has been indicated to elicit these effects. Both ligands are controlled by two hydrolase enzymes, fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL), which can be targeted for therapeutic inhibition. Sulfonamide derivatives of JZL195 containing carbamate functionalities in the southern region of the inhibitor compounds were produced using novel carbamate exchange reactions. Polar functionalities were …

Impacts Of Preferential Flow On Tc-99and Np-237 Vadose Transport In Soils At The Savannah River Site, Josh Parris

All Theses

Since the 1950s, the United States has produced approximately 90,000 metric tons of spent nuclear fuel (SNF) (Office of Nuclear Energy, 2022); however, no long-term storage solutions are available. Technecium-99 and neptunium-237, two fission products found in SNF, readily form highly mobile species in oxidizing conditions (Hu, 2008; Bondietti, 1979) and have respective half-lives of 2.13 x 10⁵ and 2.14 x10⁶ years (Hu, 2010). Considering these characteristics, ⁹⁹Tc and ²³⁷Np are two risk-driving isotopes found in SNF storage. The process of macropore-facilitated preferential flow, transport through cracks within a soil matrix, has been recognized to increase …

Determination Of Cadmium Uptake In Crassostrea Virginica Shell Under Controlled Conditions, Joseph John Pavelites Ii

Graduate Theses and Dissertations (2019 - present)

The objective of this thesis was to meet growing demand for the development of environmental biomonitors that protect ecosystems and public health. To do this, I determined the potential of oyster shell as a bioindicator of cadmium (Cd) in the environment by determining the mode of Cd uptake and relationships between Cd concentrations in the environment, shell, and soft tissues of juvenile eastern oysters (Crassostrea virginica Gmelin). I performed a review of the literature on the ability of oyster shell to retain metal contaminants and the factors that could affect this process (Chapter 2). I then reared C. virginica …

A Study Of Gold Nanoparticles Of Different Sizes With Raman Labels For Surface Enhanced Raman Spectroscopic Detection, Melissa M. Hader

Undergraduate Honors Theses

According to the Center for Disease Control and Prevention, the second leading cause of death in the United States is cancer, with 602,350 cancer deaths in 2020. With the current cancer detection techniques, the detection of cancer is often at a stage when the cancer has progressed to dangerous levels. Therefore, being able to detect cancer at its early stages is pivotal and can be life altering for millions. Gold nanoparticles (AuNPs) have been widely explored in developing surface-enhanced Raman scattering (SERS) techniques for early detection of cancer biomarkers. Using gold nanoparticles conjugated with Raman reporter molecules, SERS is a …

Synthesis And Characterization Of Nanocomposite Sensing Films For Breath Sensors, Tara Mercer

Undergraduate Honors Theses

Lung cancer is one of the most common and fatal cancers today, infecting 1 in 16 people, and killing well over a million patients per year. Currently, lung cancer is detected usually in stages three and four by quite costly and invasive methods, which shows only a survival rate of 10%. Breath sensors provide a low-cost and non-invasive technique for early screening of lung cancer. The breath sensors use assemblies of gold nanoparticles to identify lung cancer, specifically by identifying and quantifying specific volatile organic compound (VOC) concentrations found in the breath of lung cancer patients. This thesis describes a …

Low-Cost Microstereolithography 3d Printing With Microfluidic Microsampling Applications, Lauren Twombly

Chemistry & Biochemistry Undergraduate Honors Theses

The growing field of stereolithography 3D printing has welcomed a new age ofmicrofluidic device fabrication techniques. When compared to previous planar fabrication techniques such as soft-lithography, stereolithography 3D printing offers highly automated procedures, reduced fabrication times, and greater complexity of device features. To date, the greatest tradeoff for 3D printing in microfluidic device fabrication is poorer resolution when compared to soft-lithography which can produce feature sizes on the nanometer scale. The poorer resolution of 3D printing limits the feasible size of features. While highly sophisticated 3D printers are capable of achieving sub 10 μm resolution, these instruments are incredibly expensive …

Design Of A Hyperstable Endocrine Acting Fibroblast Growth Factot, Sara Armstrong

Chemistry & Biochemistry Undergraduate Honors Theses

A novel chimera protein, consisting of the C-terminus of Fibroblast Growth Factor (FGF) 21 and super FGF1, a mutant of the wild-type FGF1, was studied. The protein retained the stability of sFGF1 and the endocrine acting behaviors and binding efficiency of FGF21, so that it could be more practical for therapeutic uses as a wound healing and angiogenic agent. sFGF1- FGF21 was expressed and purified before utilizing various biophysical techniques to measure its stability, secondary and tertiary characteristics, and metabolic activity.

Microwave Synthesis Of Carbon Dot Nanoparticles, Hayden Ferguson

Undergraduate Honors Theses

This study aimed to improve the known microwave method to produce carbon dot nanoparticles from ethylenediamine and citric acid. Carbon dots have recently gained much attention as they have diverse applications, such as bioimaging and drug delivery reagents as cancer theranostics. Research was focused on establishing the ideal time for the synthetic reaction to produce carbon dot nanoparticles with the microwave method. After several trials, the 16-minute trial provided the best results based on Fourier transform infrared spectroscopy, ultraviolet-visible spectroscopy, fluorescence spectroscopy, and ultraviolet exposure.

Separation Of Organic Acids Through Direct Catalysis From Sugars, Katelyn Robinson

Chemical Engineering Undergraduate Honors Theses

Society relies on plastic products, whether they are single use or durable. A downside of plastic is that the most common type is a product of oil and oil is not only a limited resource but also a climate-damaging resource. Polylactic acid (PLA) is a bio-based, biodegradable plastic. However, the process of converting biomass to polylactic acid polymer has the largest environmental impact of the PLA production process, so alternative methods of conversion are needed (Moretti et al., 2021). The polylactic acid polymer can be made with lactic acid, which can be converted from glucose.

Non-Destructive Imaging Of Phytosulfokine Trafficking In Plants Using Fiber-Optic Fluorescence Microscopy, Bernard Abakah

Electronic Theses and Dissertations

Plants secrete peptide ligands and use receptor signaling to respond to stress and control development. Understanding these phenomena is key to improving plant health and productivity for food, fiber, and energy applications. Phytosulfokine (PSK), a sulfated peptide hormone, regulates plant cell division, growth, and stress tolerance via specific phytosulfokine receptors (PSKRs). This study uses fiber-optic fluorescence microscopy to elucidate trafficking of PSK in live plants. The microscope features two-color optics and an objective lens connected to a 1-m coherent imaging fiber mounted on either a conventional upright microscope body or 5-axis positioning system (X–Y–Z plus pitch and yaw). PSK and …

Supramolecular Pi-Donor/Acceptor Arrays Based On Redox-Active Metal-Organic Coordination Assemblies, Paola Benavides

All Dissertations

Coordination-driven self-assembly is an attractive strategy for constructing thermodynamically stable supramolecular coordination complexes, ranging from discrete metallacycles and cages to infinite coordination polymers and metal-organic frameworks for a variety of applications.

Chapter 1 discusses strategies for preparing supramolecular charge-transfer π-donor/acceptor assemblies and their potential applications.

Chapter 2 demonstrates that tricomponent self-assembly method, which was believed to yield 3D-cages, based on tetrapyridyl porphyrin (M’TPP, M’ = Zn or H₂), dicarboxylate ligands (XDC), and caped cis-Pt(II) corners, actually yields 2D-bowties featuring an M’TPP core and two parallel XDC linkers held together by four heteroligated PtII(N,O) corners. The 2D-bowties showed …

Synthesis, Radiolabeling And Evaluation Of A Suite Of Tracers With 44Sc For Detecting Extracellular Dna, Zhiyao Li

McKelvey School of Engineering Graduate Student Theses & Dissertations

Neutrophil extracellular traps involve the rapid translocation of DNA to the outside of the cell under certain stimuli. This structure forms a fibrous network that is able to limit the spread of pathogens and to kill microorganisms. It has also been shown to be present in various pathological processes such as inflammation, autoimmune diseases, and cancer metastasis. Currently, the formation process of NETs in vivo is being extensively studied. However noninvasive detection and quantitation has yet to be achieved. A class of PET tracers are described here that consists of a DNA dye as the backbone that is labeled with …

Different Approaches To Overcome Antibiotic Resistance, Samantha Biaesch

Chemistry

In the recent years, there has been a growing demand for the development of antibiotic treatments as bacterial infections have acquired defense mechanisms to commonly used antibiotics, such as penicillin. During the growth of bacterial cells, resistant mutants are able to survive antibiotic treatment and continue proliferation. Thus, creating a resistant bacterial cell population that can no longer be targeted through antibiotic treatment. Due to the recent need of new approaches, there has been an explosion of research in developing techniques that combat bacterial resistance. Both bacteriophage-RNA aptamer binding and modifications in bacterial tRNA show potential to be exploited for …

An Experimental Study Into Tholin's Solubility With Liquid Hydrocarbons On Titan, Katherine Dzurilla

Graduate Theses and Dissertations

Titan’s production of organics in its atmosphere and the liquid hydrocarbon lakes present on its surface make it a prime target for astrobiologists. Many previous studies on laboratory analogs of these organics, called "tholins", have found amino acids, nitriles, and other building blocks necessary for life. The potential solubility of tholins in the lakes of Titan presents an opportunity to create physical and chemical changes within the organics. While the lakes of Titan are primarily comprised of nonpolar compounds (methane and ethane), many predict that very small amounts of polar hydrocarbons are also present. To better understand these processes, researchers …

Dpd Guided Insight On The Formation Process Of Polyethersulfone Membranes By Nonsolvent Induced Phase Separation And The Effects Of Additives, Eric Ledieu

Graduate Theses and Dissertations

Dissipative particle dynamics (DPD), a coarse grain simulation method, was applied to the membrane formation process of non-solvent induced phase separation (NIPS) to gain further insight on the mechanism of certain variables and how they affect the final morphology. NIPS involves two solutions, an organic polymer dissolved in an organic solvent colloquially called the dope and an aqueous coagulation bath, brought into contact with one another. The solvents then mix, causing the polymer to fall out of solution as an asymmetric membrane with a dense surface layer and a more open subsurface layer in response to the decreasing solubility. Polyethersulfone …