Biochemistry, Biophysics, and Structural Biology Commons^™

Electrical Homeostasis Of The Inner Mitochondrial Membrane Potential, Peyman Fahimi, Lázaro A. M. Castanedo, P. Thomas Vernier, Cherif F. Matta

Bioelectrics Publications

The electric potential across the inner mitochondrial membrane must be maintained within certain bounds for the proper functioning of the cell. A feedback control mechanism for the homeostasis of this membrane potential is proposed whereby an increase in the electric field decreases the rate-limiting steps of the electron transport chain (ETC). An increase in trans-membrane electric field limits the rate of proton pumping to the inter-membrane gap by slowing the ETC reactions and by intrinsically induced electroporation that depolarizes the inner membrane. The proposed feedback mechanism is akin to a Le Chatelier's-type principle of trans-membrane potential feedback control.

Investigating The Role Of Fnci-1 In The Development And Function Of The C. Elegans Nervous System, Meagan Collins

Open Access Master's Theses

Fanconi Anemia (FA) is a rare human genetic disease caused by mutation of any of twenty-three genes on the FA pathway, which functions in the repair of DNA damage and the maintenance of genome stability. FA is clinically characterized by congenital abnormalities and a predisposition to aplastic anemia and malignancies. Recently, progressive neurological symptoms and abnormal neurological findings on imaging have been noted in FA patients, including cerebral and cerebellar lesions, calcification, necrosis, gliosis, and associated acute and chronic neurological symptoms; this constellation of symptoms has been termed Fanconi Anemia-Associated Neurological Syndrome (FANS).

To elucidate the molecular etiology of FANS, …

Investigating Regulation And The Regulome Of The Nucleic Acid Binding Protein Spovg Within Borrelia Burgdorferi, Timothy C. Saylor

Theses and Dissertations--Medical Sciences

Prior studies indicated Borrelia burgdorferi SpoVG protein was regulated, SpoVG binds specifically to a number of nucleic acids, and SpoVG binds to the non-variable section of the major virulence factor vlsE. Although a direct transcriptional activator or inhibitor was not elucidated, it is shown that SpoVG is regulated based on cell culture density independent of the growth rate of B. burgdorferi, indicating that SpoVG regulation is outside the scope of the alternative sigma factor RpoS. Using a dCas9 CRISPRi construct to target SpoVG resulted in protein expression trending towards upregulation of the BosR-RpoS regulon, and a marked decrease …

Characterization Of Dietary And Hormonal Influences On Renal Sodium Transporters And Channels In Rodent Models, Evelyn Chan

Scripps Senior Theses

Within kidneys, a diverse array of renal epithelial cells works to maintain electrolyte and water balance to regulate blood pressure and pH. These cells contain varying types of sodium transporters that adjust sodium reabsorption according to the body’s needs. Previous studies have observed sex-specific differences in renal sodium transporter regulation, which are thought to optimize reproduction in females. In this study, we performed high resolution microscopy and detailed characterization of cell type-specific expression and localization of major sodium transporters and channels in rodents in response to dietary and hormonal influences. Specifically, we examined the impact of dietary salt intake and …

Kinetic Model Of Glycolysis And Glutaminolysis Interplay Developed In Matlab Simbiology, Zohreh Mirveis, Hugh J. Byrne, Nitin Patil

Datasets

This dataset contains a kinetic model developed in MATLAB SimBiology to simulate the metabolic dynamics of glycolysis and glutaminolysis and their interconnection. The model was used in the study ‘Experimental and computational investigation of the kinetic evolution of the glutaminolysis pathway and its interplay with the glycolysis pathway’ (Mirveis et al., 2024). The dataset includes the original SimBiology project file together with the experimental data used for model training. These resources enable reproduction of the simulations reported in the publication and provide a reusable framework for further computational exploration of metabolic pathway kinetics.

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 …

Caspases Protect Against Hyperglycemia Induced Necroptosis-Like Cell Death In Brain Endothelial Cells, Aleena S. Mathew

Theses and Dissertations

Acute diabetes characterized by high spikes in blood glucose levels in association with severe hyperglycemia can lead to an increased risk of ischemic stroke in the brain. To better understand high blood glucose levels, hyperglycemia, in the brain we explored its effects on endothelial cells. Endothelial cells line the inner walls of blood vessels and are directly impacted in hyperglycemia. Brain endothelial cells are a major component of the blood brain barrier (BBB) which tightly regulates the brain’s microenvironment. The type of cell death such as apoptosis, caspase dependent, or necroptosis, caspase independent, can exacerbate diabetes associated complications. There is …

Targeting Als: A Multi-Cellular Study On The Potential Therapeutic Role Of Azole-Based Compounds, Alisha R. Kennedy

Theses and Dissertations

Amyotrophic Lateral Sclerosis (ALS), also known as Lou Gehrig’s disease, is a progressive neurodegenerative disorder that leads to the degeneration of motor neurons, which control voluntary muscle movements such as eating, speaking, and breathing. As these neurons are damaged, voluntary movement ceases, leading to a fatal outcome. The survival time of ALS patients varies, ranging from a few months to up to 10 years. Chapter 1 of this thesis provides an overview of ALS, highlighting the role of transactive response DNA-binding protein 43 (TDP-43), a key feature in ALS and other neurodegenerative diseases. The aggregation of TDP-43, particularly due to …

Estrogen Receptor-Mediated Effects Of Resveratrol On Muscle Function, David Ayi-Bonte

Open Access Master's Theses

Artemis missions are set to send the next man and the first woman back to the moon and enable long-term missions on the lunar surface. However, exposure to lunar gravity has significant physiological effects characterized by loss of muscle mass, weakness and decreased bone density. Nutraceutical countermeasures such as Resveratrol (RSV), a naturally occurring polyphenol, have been identified as promising strategies to preserve musculoskeletal health; however, its pleiotropic effect hinders our ability to identify the primary cellular pathways through which it delivers its benefits. Furthermore, its efficacy in simulated lunar gravity is unknown. Based on the benefits observed with RSV …

Cloning, Expression, And Characterization Of Collagen Galactosyltransferases From Human, Sponge, And Sea Walnut, Jeong Seon Kim, Tingfei Chen, Botao Zhang, Tristin M. Miller, Marisa E. Gilliam, Houfu Guo

Molecular and Cellular Biochemistry Faculty Publications

Collagen is an extracellular matrix protein conserved across animals and viruses, with its function regulated by post-translational modifications of lysine residues. Specifically, certain lysine residues in collagen are hydroxylated to form hydroxylysine, which serves as an attachment site for hydroxylysine-linked glycosylation. This glycosylation process is initiated by collagen galactosyltransferases from the GT25 family, also known as GLT25D or COLGALT proteins. Despite their biological importance, efficient methods for expressing and isolating GLT25Ds have yet to be fully developed, and the biochemical mechanisms underlying their function still need to be better understood. To address this, we performed sequence alignment and phylogenetic analyses …

Positive Allosteric Modulation Of Glun1/Glun3 Nmda Receptors, Mia Ruth Johns

Graduate Student Theses, Dissertations, & Professional Papers

N-methyl-D-aspartate (NMDA) receptors are ionotropic glutamate receptors that mediate excitatory neurotransmission in the central nervous system (CNS) where they play critical roles in normal and pathological brain functions and neurodevelopment. While the glutamate/glycineactivated GluN2-containing NMDA receptors (GluN1/GluN2) have been extensively studied, the physiological roles and pharmacology of glycine-activated GluN3-containing receptors (GluN1/GluN3) remain less understood. Although GluN1/GluN3 receptors exhibit unique functional properties and play distinct roles in neuronal development and synapse maturation, studies of their precise roles in neurophysiology and circuit function are impeded by limited availability of GluN3-selective pharmacological tools. This study describes UCM-A86, a novel GluN3-selective positive allosteric …

Investigating Mono-Driver Versus Multi-Driver Oncogenesis Via Alterations To Cell Signaling Pathways, Abygail Chapdelaine

Open Access Dissertations

The latest edition of Global Cancer Statistics released by the American Cancer Society reported approximately 20 million newly diagnosed cancer cases worldwide in 2022 with 9.7 million deaths. This ranks cancer as the second leading cause of death worldwide. For the majority of cancer patients, the standard treatment approach is chemotherapy and/or radiation therapy, and while this has been successful in some patients, a lack of specificity to cancer cells causes severe side-effects when these agents damage healthy cells. Despite extensive efforts that have gone into developing targeted cancer therapeutics that block functions specific to cancer, they have not been …

Novel Methodology And Proof-Of-Concept For Proton Ct Using Spot Profile Rather Than Bragg Peak Location, Brett Albert Ruben

Open Access Dissertations

Proton radiation therapy offers a highly precise method for cancer treatment, theoretically providing superior dose deposition characteristics compared to conventional X-ray radiation therapy. Its steep and finite dose fall-off region allows for superior tumor coverage while reducing, though not eliminating, dose to surrounding healthy tissue. However, its full potential is limited by range uncertainties, particularly those arising from the reliance on X-ray-based imaging methods called computed tomography (CT) for proton-based treatment. CT image Hounsfield Units (HU) must be converted to stopping power ratios (SPR) as these ratios are the clinically relevant value for accurately planning particle interactions during proton therapy. …

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)"

Enhanced Cholesterol Efflux And Atherosclerosis Regression Via Ceh Gene Delivery Using Galactose-Functionalized Dendrimeric Nanoparticles, Huari Kou, Jing Wang, Paul J. Yannie, Da Huang, William J. Korzun, Genta Kakiyama, Siddhartha S. Ghosh, Hu Yang

Chemical and Biochemical Engineering Faculty Research & Creative Works

Cholesteryl ester hydrolase (CEH) is a critical enzyme in cholesterol ester hydrolysis, influencing cholesterol metabolism and efflux. This study demonstrates that CEH overexpression promotes free cholesterol efflux from macrophages, thereby reducing the lipid burden in existing atherosclerotic plaques. To enable targeted delivery, galactose-functionalized polyamidoamine (PAMAM) dendrimeric nanoparticles were utilized as nanocarriers for hepatic delivery of the CEH expression vector. The therapeutic potential of CEH plasmid-loaded dendrimeric nanoparticles was evaluated in Ldlr-/- mice. Results showed a significant reduction in total lesion area (21%) and aortic arch lesion area (23%) compared to baseline. Lesion component analysis revealed marked decreases in total cholesterol …

Investigations Of Proteins Including Yellow Thermal Protein, Blue Thermal Protein, Lactoperoxidase, And Thyroid Peroxidase, Cammi Dargatz

Graduate Theses/Dissertations

This research investigated four different proteins: yellow thermal protein (YTP), blue thermal protein (BTP), lactoperoxidase (LPO), and thyroid peroxidase (TPO). YTP and BTP were both engineered from the extremely stable and non-aggregative thermal green protein (TGP) by mutating one residue each to obtain proteins with shifted spectra while preserving the stability properties observed in TGP. Site-directed mutagenesis (SDM) was utilized to construct YTP by mutating a histidine at residue 197 to a tyrosine (H197Y) and BTP by mutating a tyrosine at residue 67 to a histidine (Y67H). These proteins were expressed in E. Coli and purified with nickel and diethylaminoethyl …

Human Serum Albumin Interaction With Organochlorine Pesticides, D. S. Sanford, R. Yadav, A. Mishra

Journal of the Arkansas Academy of Science

Human serum albumin (HSA) is the most abundant blood plasma protein and plays a crucial role in drug transport and physiological homeostasis. HSA has a highly flexible structure consisting of three domains, each with multiple binding sites lined with hydrophobic and hydrophilic residues. The structural properties of HSA make it a robust reservoir and receptor for various endogenous and exogenous compounds, including therapeutic drugs. Organochlorine pesticides (OCPs) are a subclass of pesticides characterized by their chlorine content. Once widely used, these compounds remain persistent in the environment and biological systems despite regulatory restrictions in many developed countries. The strong ligand-binding …

Long-Term Antibacterial Efficacy Of Silver (I) Cyanoximates Against Streptococcus Mutans Ua159 Biofilm Growth, Tiffany A. Rojas

Honors Program Theses

Streptococcus mutans is the primary causative agent of dental caries due to its ability to form resilient multispecies biofilms. These biofilms promote acid production and degradation of the protective layers of the tooth, making biofilm formation a target for novel treatments. Silver(I) cyanoximates are of interest as alternatives to traditional antimicrobials and antibiotics due to the high UV and heat resistivity as well as poor solubility of the cyanoxime ligand paired with the well-established antimicrobial silver ion. Previous research has shown that silver(I) cyanoximates can effectively inhibit S. mutans biofilm formation after 24 hours in vitro. This study aimed to …

Using Lateral Flow Assay To Assess The Prevalence Of Trachemys Hybridization, Lillian Groves

Honors Program Theses

The current study focuses on Trachemys species, which is a group of freshwater turtles found throughout the Greater Antilles. The role of studying an isolated island, such as the Dominican Republic, is significant because it serves as a way to better understand how the combined effects of species migration, mass tourism, and climate change can greatly impact isolated species. Of particular significance is how these forces interact in complex ways to reshape habitats and threaten biodiversity. Additionally, the introduction of a highly invasive species, Trachemys scripta elegans (T. scripta), in this environment pressures native species by acting as a source …

The Detection Of Multiple Human Papillomavirus (Hpv) Types Through The Development Of An Isothermal Dna Amplification Assay, Lauren Powell

Doctoral

Human Papillomaviruses (HPV) belong to the Papillomaviridae family, with over 200 known types classified into high-risk (HR-HPV) and low-risk (LR-HPV) groups based on their carcinogenic potential. While most HPV infections are asymptomatic and transient, persistent infection can lead to health issues, including cervical cancer. Given the high prevalence of HPV and its potential for malignant transformation, nucleic acid amplification assays have become a widely implemented tool for routine HPV testing. This study developed a real-time isothermal DNA amplification assay for the detection and differentiation of multiple HPV types. A universal primer set was designed to target a highly conserved region …

Target Cell-Associated Cd47 Suppresses Nadph Oxidase Activity In Macrophages During Antibody Dependent Cellular Phagocytosis, Seuly Akter

Electronic Theses and Dissertations

CD47-SIRPα signaling is a well-known immune checkpoint that suppresses macrophage-mediated antibody-dependent cellular phagocytosis (ADCP). In this study, we explored how CD47 influences reactive oxygen species (ROS) production driven by Fcγ receptor (FcγR) signaling. Our results show that macrophages produce significantly more ROS when encountering IgG coated target cells lacking CD47.Polarization with IFNγ further amplified this effect. ThusCD47-SIRPα interactions limit phagocytosis and suppress oxidative ROS production by macrophages. We found that CD47 blockade and IFNγ stimulation enhanced ADCP through distinct mechanisms. CD47 blockade removed the inhibitory "don't eat me" signal supporting ADCP and ADROS. Similarly, IFNγ enhances ADCP by upregulating FcγRI …

Expanding The Vibrating Sharp-Edge Spray Ionization Toolkit For Oligonucleotide Characterization, Sultan Mahmud

Graduate Theses, Dissertations, and Problem Reports (ETD)

A gentle or soft Ionization process is a critical component in native mass spectrometry (MS) to lift the biomolecules from the bulk solution into the gas phase environment of the mass spectrometer preserving their shape, topology and non-covalent interactions. Electrospray ionization (ESI) facilitates structural preservation of proteins, nucleic acids and their complexes and as a result it has been extensively used in native MS. However, in negative ion mode, ESI is somewhat limited in sensitivity due to corona discharge effect resulting from the requirement of a high amount of voltage. This often disrupts the ESI process and may not preserve …

Ciliary Arl14b In Vision, Alexis Breann Crockett

Graduate Theses, Dissertations, and Problem Reports (ETD)

Primary cilia are highly specialized organelles that regulate signaling, trafficking, and sensory perception across multiple tissues, including the retina. The small GTPase ADP Ribosylation Factor-Like Protein 13B (ARL13B) is an atypical ARF-family protein enriched in cilia. ARL13B acts as a guanine exchange factor (GEF) for another small GTPase ARF-like Protein 3 (ARL3). Mutations in ARL13B cause Joubert syndrome, a ciliopathy characterized by brain malformation, developmental delays, and retinal degeneration. Despite ARL13B’s known ciliary localization and clinical relevance, ARL13B’s precise functions in cilia remain poorly defined. This dissertation investigates the cilia-specific roles and GEF-specific roles of ARL13B in photoreceptors using two …

Bridging The Gap Between Structural And Cellular Biology: Insight Into The Organization Of Glycolytic Enzymes In Cells, Heather Hansen

Graduate Theses, Dissertations, and Problem Reports (ETD)

Glycolytic enzymes are spatially organized in the cytoplasm, and are shown to localize with cellular structures such as the plasma membrane, F-actin, mitochondria, or associate independently within the cytosol. The assembly of these enzymes is hypothesized to regulate pathway flux to meet the energetic needs of the cell. However, it is unclear whether all of these assemblies have the same mechanism of formation or function in the cell. We investigated the role of glycolytic enzyme assemblies in cells, using the glycolytic “gatekeeper” enzyme phosphofructokinase-1 (PFK1). PFK1 is extensively regulated by multiple mechanisms, including over 20 allosteric ligands, post translational modifications, …

Probing The 10-23 Dnazyme Catalytic Core: Insights From Structural And Mechanistic Studies, Evan Rhyse Cramer

Graduate Theses, Dissertations, and Problem Reports (ETD)

The 10-23 DNAzyme is a catalytically active DNA oligonucleotide capable of cleaving RNA at purine-pyrimidine junctions in the presence of divalent metal ions, most notably magnesium. Despite its promise as a programmable RNA knockdown tool, its clinical and biotechnical utility has been hampered by limited structural characterization, low catalytic efficiency under physiological conditions, and poor understanding of its in-cell activity. This dissertation presents a comprehensive framework for the structural and functional analysis of DNAzymes using the 10-23 DNAzyme as a model system. In the absence of high-resolution structures, we first employed detailed in vitro biochemical assays to map essential residues …

The Role Of Fruiting Bodies In Protecting A Community Of Myxococcus Xanthus Spores From The Environment, Dave Lall

Wayne State University Dissertations

Environmental microorganisms have evolved a variety of strategies to survive fluctuations in environmental conditions, including the production of biofilms and differentiation into spores. Myxococcus xanthus are ubiquitous soil bacteria that produce starvation-induced multicellular fruiting bodies filled with environmentally resistant spores (a specialized biofilm). Isolated spores have been shown to be more resistant than vegetative cells to heat, ultraviolet radiation, and desiccation. The evolutionary advantage of producing spores inside of fruiting bodies is not clear. Here, we examine a hypothesis that the fruiting body provides additional protection from environmental insults. We developed a high-throughput method to compare the recovery (outgrowth) of …

Synthesis And Characterization Of Free Radical Scavenging Dendrimer Nanogels Via Cross-Linking Reaction-Enabled Flash Nanoprecipitation, Lin Qi, Da Huang, Huari Kou, Anna Chernatynskaya, Nuran Ercal, Hu Yang

Chemistry Faculty Research & Creative Works

This work reports the development and evaluation of dendrimer-based nanogels based on Poly amidoamine (PAMAM) dendrimer generation 5, engineered to act as a carrier with reactive oxygen species (ROS)-scavenging capabilities. We developed a cross-linking reaction-enabled flash nanoprecipitation method in which the cross-linking reaction occurs during the flash nanoprecipitation process to form a cross-linked nanostructure. Using this approach, an N-hydroxy succinimide (NHS)-functionalized ROS-responsive thioketal cross-linker (TK-NHS) was synthesized and utilized to cross-link DAB-core PAMAM dendrimer G5, resulting in the formation of G5-TK nanogels. The resulting nanogels were characterized using dynamic light scattering and transmission electron microscopy, and their cytocompatibility, irritancy, cellular …

Cholesterol Modulation Of Bk Currents And Cerebral Artery Diameter Via Channel-Forming Alpha-Subunit, Elizabeth Schneider

Theses and Dissertations (ETD)

Voltage- and calcium-gated, large conductance potassium channels (BK; MaxiK) are ubiquitously expressed and subsequently mediate numerous physiological processes. Cholesterol is consumed in high amounts with the diet and accumulates in cellular membranes when plasma levels become elevated. Cholesterol is a known inhibitor of BK channels and is suspected of contribution to many pathophysiological issues via its interaction with these channels. However, the molecular mechanisms that drive cholesterol inhibition of BK channels remain largely unexplored. This dissertation hypothesized that cholesterol inhibits BK currents via binding to specific amino acid(s) of the channel-forming alpha subunit, and involving distinct modifications of channel gating. …

Examining The Biotic And Abiotic Degradation Of Simple Phenols, Madeline Gruenberg

Browse all Theses and Dissertations

Plant secondary metabolites are a diverse class of compounds that encompass small phenols to large polymeric structures such as tannins. Smaller compounds such as phenolic acids can serve as substrates for soil microbes and enzymes. We monitored the degradation of three small phenols pyrogallol, gallic acid, and benzoic acid in biotic and abiotic conditions. They were chosen to observe the impacts of specific functional groups on both degradation processes and act as model compounds to mimic larger tannin reactivity. Both abiotic and biotic degradation of pyrogallol resulted in the formation of a stable quinone, while abiotic degradation of gallic acid …

The Role Of Fbxl16 In Regulating Erk3 Stability And Cell Migration, Seth Charles Murdock

Browse all Theses and Dissertations

Extracellular signal-regulated kinase 3 (ERK3) is a member of the atypical mitogen-activated protein kinase (MAPK) family. While ERK3’s role in promoting cell migration and invasion in multiple types of cancer has been well-documented, its activation and regulation remain poorly understood. Unlike other typical MAPK proteins, whose activation is regulated via the phosphorylation of an upstream kinase, ERK3 is regulated through its abundance, as it is constitutively phosphorylated when present in the cell. While USP20 has been established as a deubiquitinating protein that stabilizes ERK3 by preventing its degradation, both TRIM21 and FBXW7 have been identified as E3 ligases that target …