Biochemistry Commons^™

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 …

Development And In Vitro Evaluation Of Novel Near-Ir Fluorescent Sensors For Egfr Kinase, Haniyeh Jadidi

Graduate Research Theses & Dissertations

This thesis presents the in vitro evaluation of a novel near-infrared (NIR) fluorescent small-molecule probe AB-139 that selectively binds to epidermal growth factor receptor (EGFR) kinase and operates through a turn-on fluorescence mechanism. The sensor addresses several limitations associated with conventional protein-based probes by offering small-molecule specificity, tunable modularity, deep-tissue imaging potential, and reduced background noise. AB-139 comprises four key components: A Zn-phthalocyanine fluorophore that serves as the NIR emission reporter; hydrophilic triethylene glycol chains that enhance aqueous solubility and reduce aggregation; cationic quaternary ammonium groups that facilitate cellular permeability; and a gefitinib-derived recognition anchor that targets the intracellular ATP-binding …

Characterization Of Lipids In Tenebrio Molitor Larvae And Pupae Under Various Extraction Methods, Nariman A. Ktil

Graduate Theses, Dissertations, and Problem Reports (ETD)

Tenebrio molitor, or the yellow mealworm is an edible insect widely recognized and consumed for its rich nutritional value. Mealworms are known for their flexible nature of adapting to various environmental conditions and being able to thrive under harsh conditions and low-value wastes. In this paper, our main goal was to investigate the mealworm’s ability to grow and develop while being reared on apple pomace, the biowaste from apple production, and the effect it would have on its nutritional value specifically its lipid profile. Then these reared insects were used for oil extraction and analyzing their fatty acid profiles. …

An Investigation Into How The Prostate And Androgens Mediate Greater Levels Of Uric Acid In Males Compared To Females, Rachel D. King

Graduate Theses, Dissertations, and Problem Reports (ETD)

Chronic elevated circulating uric acid (UA) levels (hyperuricemia) are associated with gout as well as cardiovascular, metabolic, and renal dysfunction. Men have greater mean circulating UA levels than women and are more likely to exhibit hyperuricemia. This may be partly driven by the hormonal regulation of renal UA transporters; however, a direct link between hormones and UA production has not been established. Production of UA is catalyzed by xanthine oxidoreductase (XOR / XDH), which is ubiquitously expressed but has the greatest specific activity in the liver. Interestingly, an extensive gout genome-wide association study (GWAS) recently revealed a robust genetic …

P23h Rhodopsin Accumulation Disrupts Synaptic Protein Levels In Rod Photoreceptors, Samantha Thompson

Graduate Theses, Dissertations, and Problem Reports (ETD)

Rod photoreceptors are specialized neurons located in the retina, the neural tissue that lines the back of the eye. Rod photoreceptors are necessary for dim light and peripheral vision through the photoactivation rhodopsin (Rho). Rho is synthesized in the inner segment of rods before being unidirectionally trafficked to the outer segment. In diseases such as retinitis pigmentosa (RP), Rho trafficking can be disrupted, leading to progressive rod cell death. In many cases of RP, Rho is mislocalized to the rod photoreceptor synapse (“spherule”). The impact of Rho mislocalization on spherule structure and protein organization is poorly understood. We hypothesize that …

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 …

Physiological Structure, Activity, And Interactions Of The Formin, Human Diaphanous Homologue 1, Aaron Premo

Electronic Theses & Dissertations (2024 - present)

Human Diaphanous Homologue 1 (DIAPH1) is a 143 kDa functional protein that plays a critical role in the regulation of actin dynamics within eukaryotic cells. As a formin, DIAPH1 facilitates the assembly of actin filaments from globular actin monomers, a process essential for cellular structure, motility, and other fundamental cellular processes. Beyond its structural role in actin polymerization, DIAPH1 is implicated in several diseases, including diabetes, cancer, and inflammation, as well as complications like hearing loss. Despite its significance in human health, the functional and structural properties of DIAPH1, particularly in human cells, remain less explored compared to related proteins, …

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 …

Unleashing Serine Palmitoyltransferase In Test Tubes And Mice, Matthew W. Peart

Theses and Dissertations

Canonically known both for structural contributions to lipid bilayers and roles in cell signaling, the sphingolipids comprise a dynamic, multifaceted class of molecules which are studied to understand homeostatic cell biology as well as pathophysiology. Sphingolipids contribute to tissue-specific structures such as myelin, a multilayer membrane that allows for rapid conduction of action potentials along neuronal axons. All sphingolipids are downstream products of the rate-limiting and initiating enzyme in the de novo sphingolipid synthesis pathway, Serine palmitoyltransferase (SPT). Demonstrative of its status as the enzyme that catalyzes a crucial step in a biochemical pathway, SPT activity is strictly regulated. This …

Impact Of Membrane Lipid Composition On The Structure And Function Of Uncoupling Proteins 1 And 2 From Arabidopsis Thaliana (Atucp1 And Atucp2), Elizabeth Silva

Theses and Dissertations (Comprehensive)

A proton gradient across the inner mitochondrial membrane (IMM) is required for the synthesis of adenosine triphosphate (ATP) via ATP synthase. In other words, generation of the proton gradient is coupled to the synthesis of ATP. Interestingly, uncoupling proteins (UCPs), also located in the IMM, dissipate the proton gradient, meaning that the gradient is not efficiently used for the production of ATP.¹ The mechanism of proton transport activity of UCPs has been hypothesized and widely debated for the past 20 years to also reduce oxidative stress by reducing the production of reactive oxygen species (ROS).² The majority of …

Characterizing The Targeting Of Toc159 Receptors To The Chloroplast Outer Envelope Membrane And Their Role In The Assembly Of Distinct Toc Complexes, Michael Fish

Theses and Dissertations (Comprehensive)

Global agriculture and food security face challenges from climate change, population growth, and other human-driven pressures. Enhancing our understanding of plant biology, particularly chloroplast function, is critical for improving crop yield and stress resilience. As the sites of photosynthesis and key regulators of plant responses to environmental cues, chloroplasts depend on the precise import of thousands of nuclear-encoded proteins to maintain their biogenesis and function. While much is known about the core translocon components in the chloroplast outer envelope membrane that form the TOC complex, the mechanisms underlying their targeting, assembly, and regulation remain incompletely understood.

Plastids, including chloroplasts, evolved …

Reversible Degradation Of Peptidoglycan By Lytic Transglycosylases, Aaron Devereaux

Theses and Dissertations (Comprehensive)

Antimicrobial resistance continues to be a burden on the global healthcare system with an estimated cost of billions of dollars and millions of deaths each year. Recently, there has been little to no development on new antibiotics to treat bacterial infection, and any that are developed become resisted to within a few years. Both Gram-positive and Gram-negative bacteria contain a mesh-like layer called peptidoglycan (PG) that surrounds their cells providing strength, cell shape, and protection from their environments. This layer is a polymer of N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) connected via a b-1,4-glycosidic bond, with each strand being cross-linked …

Evaluation Of The Dnazyme Gr5 For The Determination Of Lead Speciation In Natural Waters, Gaganprit Gill

Theses and Dissertations (Comprehensive)

This thesis explores the development and application of a DNAzyme-based biosensor designed to detect labile metal species in environmental samples. Real time and on-site monitoring of labile metal fractions would make a valuable contribution to environmental management, as these fractions are the most bioavailable and pose significant toxicity risks to aquatic organisms. Conventional methods for detecting labile metals, while effective, are often burdened by high costs, complexity, and lengthy processing times, making them less ideal for rapid and widespread environmental assessments.

The first manuscript of this thesis (chapter 2) establishes the fundamental capabilities of the Pb²⁺-specific DNAzyme GR5 …

Structural Insights Into Peptidoglycan O-Acetylation In Gram-Negative Bacteria, Tyler Malloch

Theses and Dissertations (Comprehensive)

The Centres for Disease Control has acknowledged that we are entering a post-antibiotic era, where increasing numbers of bacterial pathogens are becoming resistant to known antibiotics. One of the most successfully targeted features of bacteria is also the main component of the cell wall, peptidoglycan (PG). PG is a heteropolymer of alternating sugar residues, namely N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) which are joined together by b-(1,4)-glycosidic bonds and crosslinked via stem peptide chains. PG is a target, readily lysed by exogenous and endogenous autolysins, such as lysozyme and lytic transglycosylase, respectively. This event leads to cell death …

Exploring The Interconnections Between Mitochondrial Carrier Proteins Involved In Energy Transfer: The Case Of Uncouplig Proteins 2 And 4, Adenine Nucleotide Translocase, And Phosphate Translocase, Marzieh Tabefam

Theses and Dissertations (Comprehensive)

Mitochondrial carrier (MC) proteins play an essential role in cellular energy metabolism by mediating the transport of solutes and protons across the mitochondrial inner membrane (MIM). This thesis explores the structural and functional characteristics of three groups of MC proteins—Uncoupling Proteins (UCPs), Adenine Nucleotide Translocase (ANT), and Phosphate Translocase (P_iT)—to elucidate their individual and interrelated cooperative roles in mitochondrial proton transport and energy regulation.

The study develops and applies novel methodologies for the overexpression, purification, and reconstitution of MC proteins into model lipid bilayers mimicking the native mitochondrial inner membrane environment. These methods ensure proteins maintain their native-like …

Near-Infrared Hemicyanine And Bodipy Sensors For Monitoring Mitochondrial Viscosity In Live Cancer Cells, Drosophila Melanogaster Larvae, And Adpkd Kidney Tissue, Joseph Peters

Dissertations, Master's Theses and Master's Reports

Two near-infrared fluorescent sensors, sensor A and sensor B, were synthesized and characterized. Sensor A was a hemicyanine derived structure, and sensor B was a BODIPY derived sensor. The sensors were tested to measure their ability to monitor viscosity, and sensor A was used to monitor viscosity in live cells. Both sensors were found to be effective in monitoring the viscosity level through optical measurements with glycerol. Sensor A was found to be successful in monitoring mitochondrial viscosity in HeLa MBA-MD-453 and MDA-MB-231 cell lines. It was also successful in monitoring viscosity in Drosophila melanogaster larvae as well as …