Biochemistry Commons^™

Site-Specific Modification Of Antibodies Utilizing Microbial Transglutaminase For Improved Immunoassay Performance, Emily Beitello

Theses and Dissertations

Immobilization strategies used for fixing antibodies to solid phase surfaces significantly contribute to the antigen capture capacity and influences the performance and sensitivity of immunoassays. Traditional methodologies result in the random orientation and/or the weak attachment of immobilized antibodies. Different formats of immunoassays scope in applicability to many fields of research and everyday use. Improving the efficiency of immobilizing antibodies in immunoassays is a beneficial endeavor to increase assay sensitivity. Here, we investigated the use of enzyme-mediated conjugation of antibodies to facilitate a highly oriented immobilization. Microbial transglutaminase (mTG) catalyzes the covalent bond formation between a plethora of primary amine …

Open Path Spectroscopic Detection Of The Hydroxyl Radical: A Comparison Between Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas) And Bbceas Coupled With A Fabry-Pérot Interferometer (Bbceas-Fp), Callum Flowerday, Ryan Thalman, Matthew C. Asplund, Samuel A. Badstubner, Adam K. Cook, Philip Lundrigan, Jaron C. Hansen

ScholarsArchive Data

Data collected by the BBCEAS and BBCEAS-FP instruments described in the paper "Open Path Spectroscopic Detection of the Hydroxyl Radical: A Comparison Between Broadband Cavity-Enhanced Absorption Spectroscopy (BBCEAS) and BBCEAS coupled with a Fabry-Pérot Interferometer (BBCEAS-FP)"

The Effect Of Polyethylene Glycol Surface Density Of Dense Brush Gold Nanoparticles On Insulin Fibrillation, Ethan Patrick Grier

Graduate Theses/Dissertations

The development of various neurodegenerative diseases such as Parkinson’s disease and Alzheimer’s disease has been linked to the fibrillation of various proteins within the brain. Parkinson’s disease is specifically linked to the fibrillation of α-Synuclein. During the fibrillation process, the proteins take the form of oligomers, and exposure to these oligomers has been linked to various cytotoxic and neurotoxic effects. Once the fibrillation process is complete, the fibrils made have been shown to be much less toxic than the oligomer stage. This fibrillation process is thermodynamically favorable and is largely irreversible, so one course of action for treatment of these …

Development Of Cyan And Blue Thermostable Fluorescent Proteins: Characterization And Structural Analysis, Acacia J. Jurkowski

Graduate Theses/Dissertations

Fluorescent proteins are commonly used as cell markers in living organisms. Modifications by mutation can be used to improve the qualities of these proteins including fluorescence, thermostability, pH stability, and chemical stability. The goal of this project is to use mutagenesis to improve the fluorescence of thermostable cyan and blue proteins derived from the thermal green protein (TGP). The first cyan protein developed by the DeVore lab (CTP 0.0) shifted the fluorescence to cyan but decreased the quantum yield (Φ_F) to 0.056. Further mutations were incorporated to increase the quantum yield through incorporating hydrogen bonding interactions to the …

Extended Inter-Laboratory Characterization Of The New Coastal Seawater Dissolved Organic Matter Reference Material Trm-0522, Alexander J. Craig, Lydia Babcock-Adams, Maxime C. Bridoux, Charlotte Brun, Juliana D'Andrilli, Aleksandar I. Goranov, Patrick G. Hatcher, Oliver Lechtenfeld, Hang Li, Rebecca Matos, Garrett Mckay, Amy M. Mckenna, Madelyn Miller, Sasha Wagner, Margot E. White, Alexander Zherebker, Jeffrey A. Hawkes

Chemistry & Biochemistry Faculty Publications

Dissolved organic matter (DOM) reference materials are critical to ensuring reliable comparability of measurements across experiments and between labs. TRM-0522, isolated in 2022 from 45 m deep seawater off of Sweden’s west coast, fills the niche of a previously unavailable coastal marine DOM reference material. After its isolation, we detailed a limited number of metrics for TRM-0522, initially disclosing Orbitrap high-resolution mass spectrometry, nuclear magnetic resonance, carbon proportion, absorbance, and fluorescence data. With TRM-0522 becoming more widely used, a variety of labs have generated different metrics that help to characterize and define the chemical properties of this coastal reference material. …

Experimental Demonstration And Study Of Transmembrane-Electrostatically Localized Protons Prevail, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

In this review in relation to some interesting arguments from Silverstein, it is now reaffirmed that the experimental demonstration of transmembrane-electrostatically localized protons (TELPs) was successfully accomplished through 1) using an aluminum film as a TELPs sensor in a biomimetic anode water-membrane-water cathode system, 2) analyzing the water-electrolysis current curve, and 3) measuring bulk liquid phase pH. Formation of induced TELPs was subsequently discovered in an anode water-membrane-water-membrane-water cathode system. The discovery of induced TELPs enabled clean experimental tests on the cation-TELPs exchange process by using sodium bicarbonate or potassium bicarbonate solution in the central liquid chamber. The sodium/TELPs exchange …

Technological Development Of In-Cell Nmr: Microfluidic, Metabolomic, And Fluxomic Approaches, Nicholas Sciolino

Electronic Theses & Dissertations (2024 - present)

In the fields of structural biology, metabolomics, and fluxomics, there is a driving, technique-based concern when it comes to high-resolution spectrometry and its marriage to biological and physiological relevance. Sample preparation often involves cellular perturbation, lysate separation schemes, combinations with non-biological reagents, and timeline slack. Conceptually, the farther we get from the cell, the greater the potential disparity between what exists in vivo and our in vitro manipulations. This is particularly true when seeking to collect data on transfected targets of interest, and on sensitive metabolic equilibria that occur on the order of minutes. The question remains: if we are …

Redox Control In A Fused Electron Transfer Flavoprotein From A Thermophilic Archaeon And Expanded Significance Of A Hydrogen Bond From A Conserved Histidine Residue That Contributes To Flavin Redox Tuning And Activation For Covalent Modification, Debarati Das

Theses and Dissertations--Chemistry

In absence of O₂ as terminal electron acceptors in anaerobic bacteria and archaea, carbohydrate metabolism is 15 times less efficient compared to aerobic energy metabolism resulting in energy deficit conditions. Despite their meager resources these anaerobes were able to generate H₂ and a chemiosmotic potential able to drive energy demanding reactions such as CO₂ or N₂ fixation. These observations raised concerns as production of high energy reductants (H₂) from mediocre fuels (NADH) defied the laws of thermodynamics.

In 2008, a known mechanism “electron bifurcation” but with flavins as redox mediators instead of quinones was …

Assessment And Health Benefit Of Vitamin C Using A549 Cell, Yetunde Adepoju

College of Graduate Studies: Theses & Dissertations

Vitamin C (ascorbic acid) is a vital micronutrient recognized for its antioxidant capacity and essential bodily functions, such as collagen formation, neurotransmitter activity, and regulation of the immune system. This study explores how vitamin C can protect and potentially heal cells under oxidative stress and inflammation, using A549 cells, a human lung epithelial cell line, as the model system. The cells were exposed to varying concentrations of vitamin C dissolved in water, DMSO, and 5% DMSO. To assess the outcome, cell viability was measured with an MTT assay. In addition, the expression of key genes related to oxidative stress and …

Interactions Of The Sars-Cov-2 Viral Genome 3’-Untranslated Region With Viral And Host Rnas, Caleb Frye, Mihaela Rita Mihailescu

Electronic Theses and Dissertations

This dissertation focuses on the characterization of RNA-RNA interactions within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and with host microRNAs. As the causative agent of coronavirus disease 2019 (COVID-19), SARS-CoV-2 has evolved rapidly since its appearance. This has warranted prompt characterization of the virus particularly of its single stranded RNA (ssRNA) genome. By using a combination of bioinformatics, biophysics, and/or biological assays, we analyzed the SARS-CoV-2 viral genomic RNA and uncovered interactions of genomic RNA with host RNAs, highlighting an underutilized method of targeting RNA viruses. We showed here that the conserved elements in the viral genomic …

Molten Flux Synthesis Of Plutonium (Iv) Silicates K2Pusi2O7 And Rb2Pusi6O15, Travis K. Deason, Gregory Morrison, Amir Mofrad, Jake Amoroso, David Diprete, Theodore M. Besmann, Shanna L. Estes, Hans Conrad Zur Loye

Faculty Publications

Few plutonium containing silicates have been reported in the literature and only one other tetravalent plutonium silicate structure has been reported using the flux growth method. With the goal of understanding actinide incorporation into silicates, we describe herein two new plutonium (IV) silicates, Rb2PuSi6O15 and K2PuSi2O7, synthesized using a mixed alkali chloride/alkali fluoride flux growth. Both structures crystallize in the C2/c space group with lattice parameters a=24.2980(10) Å, b=7.1466(3) Å, c=17.2025(8) Å and 96.6560(10)° for Rb2PuSi6O15, and a=9.9478(2) Å, b=5.59820 (10) Å, c=13.1848(2) Å, and 105.7400(10)° for K2PuSi2O7. Comparisons to the synthesis of other reported alkali actinide silicates (Ce, U, …

Capacity-Weighted Figures-Of-Merit For Battery Transport Metrics, Cj Sturgill, Christopher Sutton, Julian Schwenzel, Morgan Stefik

Faculty Publications

New battery materials with improved transport are needed. Typical measurements yield widely varying voltage-dependent diffusivities and reporting practices are diverse. Some materials (e.g. first-order phase change) have most redox occur at a specific voltage and may be sufficiently represented by singular transport metrics. Many rapid intercalation materials, however, exhibit second-order phase transitions with redox over a broad voltage range. How should such cases be compared? The use of capacity-weighted average values is suggested where voltage-dependent metrics are consolidated into representative descriptors as figures-of-merit. Examples are elaborated where differential capacity (dQ/dV) is used to derive a …

Design, Synthesis, And Nmr-Guided Characterization Of A Targeted Covalent Inhibitor-Like Molecule Against Ivyp1 From P. Aeruginosa, Samuel Taylor Moore

Master's Theses

Multi-drug resistance poses a serious threat to future generations and historical antibiotic pipelines; consequently, the medical and economic burdens associated with treating multidrug-resistant bacteria are substantiated. In this context, P. aeruginosa (PA) emerges as one of the most significant healthcare challenges, being a leading cause of resistance-associated mortality worldwide. Despite modern efforts to combat these poor outcomes, drug-resistant cases continue to rise, and the need for novel antibiotic treatment is apparent. To this end, we investigated relevant resistance mechanisms and past antibiotic targets within PA, and in doing so, we identified relationships between peptidoglycan biology and a periplasmic protein, Inhibitor …

Na2B12Si6Se18: A Novel B12-Cluster-Containing Quaternary Selenoborate Framework Material, Gopabandhu Panigrahi, Hunter B. Tisdale, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

We report the successful synthesis of the new quaternary, three-dimensional Na₂B₁₂Si₆Se₁₈ material using a solid-state synthesis route. This compound is characterized by a unique framework structure that features the rare icosahedral [B₁₂]¹⁰⁺ cation which is connected via Si2Se6 polyhedral units into a 3D framework structure with Na+ ions located inside the channels. The Na₂B₁₂Si₆Se₁₈ compound crystallizes in the cubic crystal system in the space group Im, with lattice parameter a = 11.91110(10) Å and unit cell volume of 1689.88(4) ų. …

D101n: A Unique And Ill-Understood Familial Als-Related Sod1 Mutant, Analisa Lott

Honors Program Theses and Research Projects

Background: Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease, with 90% of documented cases considered sporadic and about 10% showing a hereditary link; such cases are deemed as familial ALS (fALS). Superoxide dismutase (SOD), a copper-zinc binding enzyme that protects cells from damaging free radicals, has been linked to fALS with certain toxic gain of function mutations, such as the D101N mutant. The human SOD1 D101N mutant has been shown to be associated with rapidly progressing neurodegeneration yet is less prone to aggregation than similar mutants, but its deviation from wild-type (WT) SOD1 remains misunderstood.

Objective: Although the D101N …

Synthesis Of Novel Chromenone Esters For Biochemical Assays, Andrew Dean Helmerich

Undergraduate Honors Thesis Collection

This project details the synthesis of a variety of novel chromenone esters to be used as enzymatic probes. A robust, initial library of 22 chromenone esters was successfully synthesized with differences in chain length, branching, and the incorporation of cyclic and heteroatomic moieties. These new chromenones were fully characterized by 1HNMR, 13CNMR, DEPT HRMS, 19FNMR, and HSQC. The utility of these compounds comes from the fact that they will fluoresce upon cleavage of the ester; thus, this property makes them ideal candidates to be used in the monitoring of enzymatic activity of esterases. Elucidating the enzyme-substrate structure activity relationship (SAR) …

Decoding Fgf/Fgfr Signaling: Insights Into Biological Functions And Disease Relevance, Oshadi Edirisinghe, Gaetane Ternier, Zeina Alraawi, Thallapuranam Krishnaswamy Suresh Kumar

Chemistry & Biochemistry Faculty Publications and Presentations

Fibroblast Growth Factors (FGFs) and their cognate receptors, FGFRs, play pivotal roles in a plethora of biological processes, including cell proliferation, differentiation, tissue repair, and metabolic homeostasis. This review provides a comprehensive overview of FGF-FGFR signaling pathways while highlighting their complex regulatory mechanisms and interconnections with other signaling networks. Further, we briefly discuss the FGFs involvement in developmental, metabolic, and housekeeping functions. By complementing current knowledge and emerging research, this review aims to enhance the understanding of FGF-FGFR-mediated signaling and its implications for health and disease, which will be crucial for therapeutic development against FGF-related pathological conditions.

Investigation Of Magnesium-Potassium Phosphates As Potential Nuclear Waste Form For The Immobilization Of Minor Actinides, Hans Conrad Zur Loye, Petr Vecernik, Monika Kiselova, Vlastislav Kašpar, Hana Korenkova, Vlastimil Miller, Petr Bezdicka, Jan Šubrt, Natalija Murafa, Volodymyr Shkuropatenko, Sergey Sayenko

Faculty Publications

Several recent studies have evaluated technologies of spent nuclear fuel processing specifically for solidifying transuranic (TRU) waste as a by-product of fission. Of the TRU group, plutonium and the minor actinides will be responsible for the bulk of the radiotoxicity and heat generation of spent nuclear fuel in the long term (300 to 20,000 years). In this study, we investigated magnesium potassium phosphate (MKP)-based compounds as host waste forms for the encapsulation of inactive trivalent Nd and Sm as analogues of the minor trivalent actinides, Am and Cm. Waste forms were fabricated under ambient atmospheric conditions by adding 5 wt.% …

Functionalized Carbon Quantum Dots: A Promising Nanomaterial For Investigating Their Potential In Neurodegenerative Disease Treatment, Sherin M. El Morsy

Open Access Theses & Dissertations

Neurodegenerative diseases such as Parkinson's Disease (PD), Alzheimer's Disease (AD), and Huntington's Disease (HD) remain incurable, despite extensive research into therapeutic development. In the United States of America, the annual cost of PD and AD in terms of patient care and lost productivity is approximately $200 billion. Consequently, there is a critical and unaddressed need for the development of innovative drugs and drug delivery systems that can decelerate, stop, or ideally reverse neurodegenerative diseases. The dissertation presented here focuses on devising strategies to target PD through multiple mechanisms, including the inhibition of protein aggregation and the reduction of oxidative stress. …

Investigating The Role Of Tetherin Protein In Multivesicular Bodies Fusions In Lung Cancer Cells, Md. Rakib Miah

Electronic Theses and Dissertations

Cells rely on the secretion of exosomes to communicate with one another and this process is potentially mediated by a protein called tetherin, which anchors exosomes to the cell surface to limit their spread. Tetherin protein has attracted a lot of attention because of its capacity to hinder the propagation of viruses by attaching virions to the surface of host cells. Treatment with interferon-alpha (IFNα) increases the production of tetherin, although it is not known how this affects tetherin localization and exosome-mediated communication. This thesis looks at how the expression of tetherin, which IFNα boosts, affects the dynamics of intercellular …

Examination Of Photoinduced Radicals In Two Crystal Forms Of Triphenylamine Bis-Urea Macrocycles, Md Faizul Islam, Gamage Isuri P. Wijesekera, Anmon J. Sindt, Mark D. Smith, Linda S. Shimizu

Faculty Publications

This study probes two solvates of triphenylamine (TPA) bis-urea macrocycle 1 and their activated structures to evaluate their maximum photoinduced radicals (PIRs), the subsequent decay of the radicals, and their regeneration. The hierarchical assembly of TPAs shows promise in stabilizing less substituted derivatives, potentially expanding the utility of TPAs that lack stabilizing para-substituents. Single crystal structure analysis reveals that host 1 adopts a planar conformation with the two ureas pointing in opposite directions when dimethoxyethane (DME) is encapsulated within the channel. Whereas previously, 1 adopted a bowl-shaped conformation with the two ureas pointing in the same direction (syn …

Examination Of Photoinduced Radicals In Two Crystal Forms Of Triphenylamine Bis-Urea Macrocycles, Md Faizul Islam, Gamage Isuri P. Wijesekera, Ammon J. Sindt, Mark D. Smith, Linda S. Shimizu

Faculty Publications

This study probes two solvates of triphenylamine (TPA) bis-urea macrocycle 1 and their activated structures to evaluate their maximum photoinduced radicals (PIRs), the subsequent decay of the radicals, and their regeneration. The hierarchical assembly of TPAs shows promise in stabilizing less substituted derivatives, potentially expanding the utility of TPAs that lack stabilizing para-substituents. Single crystal structure analysis reveals that host 1 adopts a planar conformation with the two ureas pointing in opposite directions when dimethoxyethane (DME) is encapsulated within the channel. Whereas previously, 1 adopted a bowl-shaped conformation with the two ureas pointing in the same direction (syn …

Enzyme Encapsulation Within The Hk97 Virus-Like Particle: An Investigation Of Substrate Inhibition Kinetics Within A Confined And Crowded Environment, Joseph B. Lively

Chemistry Theses

Substrate inhibition is a paradoxical phenomenon observed in enzyme kinetics where increasing substrate concentrations lead to a marked decrease in the rates of enzyme-catalyzed reactions. Affecting an estimated 20% of studied enzymes, substrate inhibition poses significant challenges to the understanding of their function in essential biological processes and to their exploitation in industrial and therapeutic contexts. Studies show substrate inhibition to be a real limitation in vitro and rational conclusions have been drawn to explain the relevance of substrate inhibition in the self-regulation of biological pathways. However, there is currently no consensus on what role substrate inhibition plays in vivo …

Crystal Archer: Profile Of The Newest Chbc Faculty Member, Danna Jaimes-Fajardo, Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

Presents the research profile of Crystal Archer, Assistant Professor, Chemistry and Biochemistry department. It highlights her research interests, education, and impact of her research.

Accurate Crystal Structure Prediction Of New 2d Hybrid Organic–Inorganic Perovskites, Nima Karimitari, William J. Baldwin, Evan W. Muller, Zachary J.L. Bare, W. Joshua Kennedy, Gábor Csányi, Christopher Sutton

Faculty Publications

Low-dimensional hybrid organic–inorganic perovskites (HOIPs) are promising electronically active materials for light absorption and emission. The design space of HOIPs is extremely large, as a variety of organic cations can be combined with different inorganic frameworks. This not only allows for tunable electronic and mechanical properties but also necessitates the development of new tools for in silico high throughput analysis of candidate materials. In this work, we present an accurate, efficient, and widely applicable machine learning interatomic potential (MLIP) trained on 86 diverse experimentally reported HOIP materials. This MLIP was tested on 73 experimentally reported perovskite compositions and achieves a …

A Preliminary Fuzzy Inference System For Predicting Atmospheric Ozone In An Intermountain Basin, John R. Lawson, Seth N. Lyman

Mathematics and Statistics Faculty Publications

High concentrations of ozone in the Uinta Basin, Utah, can occur after sufficient snowfall and a strong atmospheric anticyclone creates a persistent cold pool that traps emissions from oil and gas operations, where sustained photolysis of the precursors builds ozone to unhealthy concentrations. The basin's winter-ozone system is well understood by domain experts and supported by archives of atmospheric observations. Rules of the system can be formulated in natural language ("sufficient snowfall and high pressure leads to high ozone"), lending itself to analysis with a fuzzy-logic inference system. This method encodes human expertise as machine intelligence in a more prescribed …

Michael Mcgraw: Profile Of The Newest Chbc Faculty Member, Danna Jaimes-Fajardo, Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

Presents the research profile of Michael McGraw, Assistant Professor, Chemistry and Biochemistry department. It highlights his research interests, education, and impact of his research.

Incorporating Solvation Thermodynamic Mapping In Computer-Aided Drug Design, Yeonji Ji

Dissertations, Theses, and Capstone Projects

Advancements in computational techniques have revolutionized structure-based drug design, substantially improving the efficiency and effectiveness of the drug discovery process by reducing time, costs, and labor requirements. These advancements include various methods, such as investigating small molecule ligands binding to proteins, exploring alternative protein conformations, and solvation mapping on the protein surfaces. Among these methods, understanding the correlation between protein-ligand binding and the role of solvation is important.

A fundamental concept in protein-ligand binding is shape and electrostatic complementarity, which is complicated by the inherent flexibility of proteins. In the absence of small molecule ligands, proteins are complementary to surface …

Improvement Of Single-Crystal Structures Of Very Heavy Element Compounds By Refining Anomalous Dispersion Parameters, Florian Meurer, Gregory Morrison, Birgit Hischa, Hans Conrad Zur Loye, Christoph Hennig, Michael Bodensteiner

Faculty Publications

Refining the anomalous dispersion parameters of the four uranium compounds NaUF5, NaU2F9, Cs2(UO2)TiO4, and Cs2(UO2)Ti2O6 gave insights into the crystallographic model improvement of very heavy atoms. We found that the values for the dispersive and absorptive parts, f′ and f″, closely followed the X-ray absorption spectra on their L3, L2, and L1 edges. The obtained values are sensitive to the chemical environment at each crystallographically independent position. An incorrect treatment of the anomalous dispersion correction can lead to a wrong crystallographic model. The above-mentioned, already published structures were improved by this process. General guidelines were given for the crystal structure …

Sequence Specificity Of Non-Structural Protein 15 From Sars-Cov-2, John Vincent Mcguire

Electronic Theses and Dissertations

The SARS-CoV-2 virus was recently able to cause a global pandemic, largely due to the asymptomatic period that occurs during initial infection. During this period, patients are infectious but do not exhibit symptoms, resulting in the unintentional spread of the virus. This occurs because the virus effectively avoids detection by the immune system during the early stages of infection, and as symptoms are the result of immune system activation, they never manifest. Non-structural Protein 15 (Nsp15) is one of the tools the virus uses to remain undetected, via its degradation of Pathogen-Associated Molecular Patterns (PAMPs) that would otherwise be recognized …