Biochemistry, Biophysics, and Structural Biology Commons^™

Macromolecular Crowding Effects On Enzymes That Display Non-Hyperbolic Kinetics, Kelsey A. Aldrich

Electronic Theses and Dissertations

Macromolecules occupy up to 30% of a cell's volume, yet the in vitro study of biological processes is almost exclusively performed in dilute solutions that fail to approximate the crowded interior of a cell. A growing body of literature has identified that macromolecular crowding has significant effects on a number of biochemical processes, including enzymatic activity. However, changes in kinetic parameters with increased macromolecule concentrations have only been determined for enzymes that follow hyperbolic Michaelis-Menten kinetics, despite the fact that over 25% of enzymes deviate from this model. Here, we perform the first characterization of macromolecular crowding effects on …

Assimilating Satellite-Derived Snow Cover And Albedo Data To Improve 3-D Weather And Photochemical Models, Colleen Jones, Huy Tran, Trang Tran, Seth Lyman

Chemistry and Biochemistry Faculty Publications

During wintertime temperature inversion episodes, ozone in the Uinta Basin sometimes exceeds the standard of 70 ppb set by the US Environmental Protection Agency. Since ozone formation depends on sunlight, and less sunlight is available during winter, wintertime ozone can only form if snow cover and albedo are high. Researchers have encountered difficulties replicating high albedo values in 3-D weather and photochemical transport model simulations for winter episodes. In this study, a process to assimilate MODIS satellite data into WRF and CAMx models was developed, streamlined, and tested to demonstrate the impacts of data assimilation on the models’ performance. Improvements …

Role Of Pycr2 In Colorectal Cancer, Raju Lama Tamang

Theses & Dissertations

Despite significant progress in clinical management, colorectal cancer (CRC) remains the 3rd most common cause of cancer-related deaths. A positive association of PYCR2 (Pyrroline-5-carboxylate reductase-2), a terminal enzyme of proline metabolism, with CRC aggressiveness was recently reported including by us. However, how PYCR2 promotes colon carcinogenesis remains ill understood. In our studies, comprehensive in-silico and biochemical evaluations were performed along with genetic manipulations and in-vivo tumor growth assays to gain mechanistic understanding. Results showed that PYCR2 expression was significantly upregulated in CRC and associated with poor patient survival specifically among PYCR isoforms (PYCR-1, -2 and -3). Genetic inhibition of PYCR2 …

Determining If Cx45 Acts As An Arrythmogenic Substrate In The Diseased Myocardium, Stephen R. Sobota

Theses & Dissertations

Proper contraction of the heart relies on gap junction channels (GJCs) composed of Cx40 and Cx43 in the atrial and ventricular tissues which mediate electrical conductance in the working myocardium. Also expressed is Cx45, which is limited to the pacemaker system. Studies in diseased human hypertrophic cardiac tissue have shown expression of Cx45 and decrease of Cx43 in the myocardium. Cx43 and Cx45 in vitro form heterometric GJCs, where the channel characteristics (metabolite transfer, electrical conductance, etc.) resemble those of Cx45. There is little-to-no data showing whether GJCs composed of Cx43 and Cx45 in cardiac hypertrophy result in altered conductance. …

Rna Secondary Structures: Structure-Function Studies In Viral And Neurodegenerative Diseases, Caylee Cunningham

Electronic Theses and Dissertations

The studies within this dissertation highlight the importance of RNA structure and function, highlighting potential mechanisms in the pathogenesis of the SARS-CoV-2 virus and hallmarks of ALS. Specifically, the s2m, a 41-nt structure found within the hyper variable region of the 3’ UTR of the SARS-CoV-2 virus, was investigated as this element has no definitive role in viruses but its high conservation in several viral families warrants investigation. We used various biophysical techniques to determine if a palindromic sequence in the terminal loop could participate in dimerization activities, which may have implications in recombination and the longevity of the virus. …

Enpp1 Enzyme Replacement Therapy Improves Ectopic Calcification But Does Not Rescue Skeletal Phenotype In A Mouse Model For Craniometaphyseal Dysplasia, Ernst Reichenberger, Kevin O'Brien, Ayano Hatori, Thomas Carpenter, Koen Van De Wetering, Lisa Flaman, Jennifer Howe, Daniel Ortiz, Yves Sabbagh, I-Ping Chen

Jefferson Institute of Molecular Medicine Papers and Presentations

Craniometaphyseal dysplasia (CMD) is a rare genetic bone disorder, characterized by progressive thickening of craniofacial bones and flared metaphyses of long bones. Craniofacial hyperostosis leads to the obstruction of neural foramina and neurological symptoms such as facial palsy, blindness, deafness, or severe headache. Mutations in ANKH (mouse ortholog ANK), a transporter of small molecules such as citrate and ATP, are responsible for autosomal dominant CMD. Knock-in (KI) mice carrying an ANK_F377del mutation (Ank^KI/KI) replicate many features of human CMD. Pyrophosphate (PPi) levels in plasma are significantly reduced in Ank^KI/KI mice. PPi is a potent inhibitor of …

Exploring The Role Of Rb1 In Cellular Differentiation Using Patient-Derived Stem Cells, Ambily Vincent

Theses and Dissertations

The Retinoblastoma (RB1) gene, predominantly recognized as a tumour suppressor, plays a crucial role in early growth and development. Mice lacking the retinoblastoma gene do not survive and exhibit defects in the differentiation of various tissues, underscoring its involvement in cellular differentiation. This suggests that the functions of the RB1 gene extend beyond its role as a tumour suppressor, encompassing cell cycle regulation, maintenance of genomic stability, cellular senescence, and cellular differentiation.

While the tumour suppressor function of the RB1 has been extensively studied, its role in cellular differentiation remains incompletely understood. Existing literature, primarily based on animal models, has …

Stem-Loop And Circle-Loop Tads Generated By Directional Pairing Of Boundary Elements Have Distinct Physical And Regulatory Properties, Wenfan Ke, Miki Fujioka, Paul Schedl, James Jaynes

Department of Biochemistry and Molecular Biology Faculty Papers

The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation-dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary …

Integration Of Machine Learning And Quantum Mechanical Calculations For De Novo Drug Design, Ayesh Madushanka Mahamada Kalapuwage

Chemistry Theses and Dissertations

The drug designing process is an intricate and resource-intensive endeavor, spanning approximately 12 years to transform a lead compound into a functional drug. Computer-aided drug design (CADD) plays a fundamental role in this process, mitigating the risk of failures in the later stage and saving valuable time and money. In the last decade, Artificial intelligence (AI) has provided remarkable alternatives for practical challenges, including drug design. Simultaneously, advanced QM calculations have achieved near-experimental accuracy in simulating drug-target interactions. However, introducing QM and AI-based techniques into drug discovery presents considerable challenges. AI techniques require high- quality data and often struggle with …

Assessment Of Tripeptides Self-Assembly & Er Stress On Cell Viability And Exosome Secretion In Mda-Mb231, Azmat Parveen

Theses and Dissertations

This study delves into the effects of tripeptides KYpF and WYpK(NBD) on MDA-MB-231 cells, uncovering KYpF's ability to reduce cell proliferation and exosome secretion in peptide treated cells. Conversely, WYpK(NBD) demonstrated significant toxicity at 10 μM. These insights pave the way for optimizing peptide-based cellular treatments for exosome secretion purposes.

G12/13 Signaling In Asthma, Elizabeth L. Mcduffie, Reynold A Panettieri, Charles P. Scott

Department of Biochemistry and Molecular Biology Faculty Papers

Shortening of airway smooth muscle and bronchoconstriction are pathognomonic for asthma. Airway shortening occurs through calcium-dependent activation of myosin light chain kinase, and RhoA-dependent calcium sensitization, which inhibits myosin light chain phosphatase. The mechanism through which pro-contractile stimuli activate calcium sensitization is poorly understood. Our review of the literature suggests that pro-contractile G protein coupled receptors likely signal through G12/13 to activate RhoA and mediate calcium sensitization. This hypothesis is consistent with the effects of pro-contractile agonists on RhoA and Rho kinase activation, actin polymerization and myosin light chain phosphorylation. Recognizing the likely role of G12/13 signaling in the pathophysiology …

The Role Of Efflux Pump Inhibitor In Enhancing Antimicrobial Efficiency Of Silver Nanoparticles And Methylene Blue As An Effective Photodynamic Therapy Agent, Yaran Allamyradov

Masters Theses & Specialist Projects

Efflux pumps are critical active transport systems utilized by cells to expel toxic substances, including antibiotics and photosensitizer complexes, thereby contributing to antimicrobial resistance. Efflux pump inhibitors (EPIs), which are compounds that obstruct the transport of molecules through these pumps, play a pivotal role in enhancing the effectiveness of antimicrobial therapies against pathogens. This study investigates the effects of the EPI reserpine on the photodeactivation rate of pathogens when used in conjunction with silver nanoparticles (Ag NPs) and methylene blue (MB), a common photosensitizer.

Our research reveals that the application of reserpine, in combination with Ag NPs and MB, leads …

Unique Oncostatin M Functions Within The Context Of Estrogen Receptor Positive Breast Cancer And Therapeutic Development For Patients, Cody L. Wolf

Boise State University Theses and Dissertations

In the United States, it is estimated that over 295,000 women will be diagnosed with breast cancer, and over 43,000 breast cancer patients will die in 2024. Mortality in breast cancer is due in large part due to distant metastasis to organs such as the bone, lung, liver, and brain. The IL-6-family cytokine oncostatin M (OSM) plays a crucial role in initiating metastasis by secreting pro-metastatic molecules such as VEGF, LOXL2 and IL-6, and increasing circulating tumor cell numbers and metastases to lung in vivo. More recent work within our lab has identified unique roles for OSM within the varying …

Detection Of Cryptosporidium Spp. In Surface Water And Tissues Of Bivalves In Waterways Of Coney Island, New York (Usa), Manasvi Patel

Biochemistry and Molecular Biology

Combined sewer overflows (CSOs) are major sources of pollutants such as microbial pathogens, total suspended solids (TSS), oxygen depleting substances, toxicants, and nutrients. Untreated wastewater contains parasites like Giardia, Cryptosporidium and Entamoeba which impact human health. Cryptosporidium is the leading cause of diarrheal diseases which spreads through contaminated water supplies. Our research on Coney Island in Brooklyn investigated the amount of Cryptosporidium oocysts found in the water and bivalves/shellfish tissue and to supports a parallel study examining both people's use of waterways around Coney Island (for religious ceremonies, fishing, foraging, swimming, etc.) and their perceptions of how polluted the …

Furthering Ascidian Taxonomy Using Molecular Biology, Nicholas Gulnick

Electronic Theses and Dissertations

Ascidians are our closest invertebrate relatives and comprise nearly 3,000 species separated into three orders: Aplousobranchia (most speciose), Stolidobranchia, and Phlebobranchia (least speciose). Ascidians can be classified as either solitary or colonial organisms. Species delimitation using morphological characters alone has had varied results. Well known, widely distributed, morphological species have turned out to be catch all species comprised of several cryptic species. Molecular markers can help mitigate some of the issues presented by strictly using morphological observations, including resolving the status of cryptic species, and accessing the expert knowledge required to identify a species. By incorporating molecular markers and pairing …

Deciphering The Wheat Seed Core Mycobiome Of Two Egyptian Cultivars (Giza 171 And Sids 14) By Using High Throughput Amplicon Sequencing Of The Its2 Region, Sobhy S.H. Abdelsalam, Muziri Mugwanya, Ahmed G. Gad, Ayman B.A. Basyony

Faculty Journal Articles

Wheat (Triticum aestivum L.) is an important food crop throughout the world. The seed mycobiome is the primary inoculum affecting the overall health and productivity of wheat plants. Seed-borne fungi can have an impact on the production of wheat and cause health complications upon consumption. Therefore, for durable and sustainable wheat production, it is imperative to characterise the wheat mycobiome. The rationale of this study was to investigate the wheat seed mycobiome of two Egyptian wheat cultivars (Sids 14 and Giza 171) using a culture-independent technique. The fungal community in 6 wheat seed samples was identified by high-throughput amplicon sequencing …

Lanthanide-Dependent Methanol Metabolism In Sinorhizobium Meliloti, Enish Pathak

Masters Theses

Lanthanides, also known as rare earth elements, were thought to be biologically inert. However, the recent discovery of XoxF, a lanthanide-dependent methanol dehydrogenase, shed new light on the roles of lanthanides in biology. Lanthanide-dependent methanol metabolism was even found in bacterial genera that previously have not been described as methylotrophs, including Sinorhizobium. A homolog of the xoxF gene was found to be present in Sinorhizobium meliloti. S. meliloti is a soil bacterium that undergoes a symbiotic relationship with alfalfa plants by fixing atmospheric nitrogen within root nodules. While many studies on lanthanide-dependent methylotrophy have been performed mainly in the model …

Structure-Function Relationships In Neurodegenerative And Infectious Diseases: Biophysical Characterization Of Rna Secondary Structures By Computational Techniques, Kendy Guarinoni

Electronic Theses and Dissertations

The research described in this dissertation focuses on the investigation of the structure and dynamics of regions of RNA implicated in two diseases: COVID-19 and amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). Both studies sought to create experimentally corroborated models that were used to characterize the structure and dynamics of the C9orf72 repeat expansion and the s2m region in coronaviruses, respectively and provided the foundation for future work. In our work involving the s2m region of SARS-CoV-2, the virus responsible for COVID-19, we determined that the homology modeling approach commonly used to derive atomistic structures when no coordinates are available yields a …

Performance And Enhanced Efficiency Induced By Cold Plasma On Sapo-34 Membranes For Co2 And Ch4 Mixtures, Fnu Gorky, Vashanti Storr, Grace Jones, Apolo Nambo, Jacek B. Jasinski, Maria L. Carreon

Chemical Engineering Faculty Publications and Presentations

In this study, we investigate the influence of cold-plasma-induced enhanced performance and efficiency of SAPO-34 membranes in the separation of CO₂ and CH₄ mixtures. Placing the herein presented research in a broader context, we aim to address the question of whether cold plasma can significantly impact the membrane performance. We subjected SAPO-34 membranes to plasma mild disturbances and analyzed their performance in separating CO₂ and CH₄. Our findings reveal a notable enhancement in membrane efficiency and sustained performance when exposed to cold plasma. The pulsed plasma separation displayed improved structural integrity, and the experimental results …

Developing A Comprehensive Genome-Scale Metabolic Model For The Arabidopsis Thaliana Root System, Lohani Esterhuizen

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Arabidopsis thaliana (Arabidopsis) is the most well-established model plant to date. Being the first plant to have its genome mapped, studies on Arabidopsis have provided insurmountable insights into the physiological and biochemical nature of plants. Methods that allow us to computationally study the metabolism of organisms include the use of genome-scale metabolic models (GEMs). Despite its popularity, no GEM currently maps the metabolic activity in the root system of Arabidopsis, which is the first organ to face and respond to stress conditions in the soil. This work aims to develop and implement a comprehensive GEM of the Arabidopsis root system …

Unveiling The Intercompartmental Signaling Axis: Mitochondrial To Er Stress Response (Mersr) And Its Impact On Proteostasis, Jeson Li

Dissertations and Theses (Open Access)

Maintaining protein homeostasis is essential for cellular health. During times of protein stress, cells deploy unique defense mechanisms to achieve resolution. Our previous research uncovered a cross-compartmental Mitochondrial to Cytosolic Stress Response (MCSR), a unique stress response activated by the perturbation of mitochondrial proteostasis, which ultimately results in the improvement of proteostasis in the cytosol. Here, we found that this signaling axis also influences the unfolded protein response of the endoplasmic reticulum (UPRER), suggesting the presence of a Mitochondria to ER Stress Response (MERSR). During MERSR, the IRE1 branch of UPRER is inhibited, introducing a previously unknown regulatory component of …

A Data-Driven Discovery System For Studying Extracellular Microrna Sorting And Rna-Protein Interactions, Sasan Azizian

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Interactions between microRNAs (miRNAs) and RNA-binding proteins (RBPs) are pivotal in miRNA-mediated sorting, yet the molecular mechanisms underlying these interactions remain largely understudied. Few miRNA-binding proteins have been verified, typically requiring extensive laboratory work. This study introduces DeepMiRBP, a novel hybrid deep learning model designed to predict microRNA-binding proteins. The model integrates Bidirectional Long Short-Term Memory (Bi-LSTM) networks with attention mechanisms, transfer learning, and cosine similarity to offer a robust computational approach for inferring miRNA-protein interactions.

DeepMiRBP is implemented through two distinct architectures. The first architecture employs a Y-shaped model that uses Bi-LSTM networks and transfer learning to extract contextual …

Role Of The Malate Dehydrogenase-Citrate Synthase Metabolon In Metabolic Flux Regulation, Joy John Omini

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The TCA cycle enzymes- malate dehydrogenase (MDH) and citrate synthase (CS)- interact to transfer oxaloacetate from the active site of MDH to the active site of CS, through an electropositive channel. The MDH-CS metabolon is highly conserved across different domains of life, and it has been associated with many advantages. Some of these advantages include protecting oxaloacetate from competing enzymes like aspartate aminotransferase, allowing the thermodynamically unfavorable MDH forward reaction to occur and increasing the local concentration of oxaloacetate within the active site of CS. These advantages and conservativeness of the MDH-CS metabolon indicate that it is highly important to …

Elucidating The Roles Of Septin Proteins In Thermotolerance And Cell Wall Integrity In Cryptococcus Neoformans, Stephani S. Martinez Barrera

All Dissertations

Cryptococcus neoformans is a globally distributed fungal pathogen responsible for causing cryptococcal meningitis in immunocompromised individuals. This pathogenic yeast must adapt to changes in temperature upon entering the human host. Septin proteins are conserved filament-forming GTPases that assemble as higher-order complexes at the cell cortex to support cytokinesis and morphogenesis in fungal and animal cells. In C. neoformans, four septin homologs (Cdc3, Cdc10, Cdc11, and Cdc12) assemble at the mother-bud neck, contributing to cytokinesis through poorly understood mechanisms. C. neoformans strains lacking the septins Cdc3 or Cdc12 are viable at 25°C, but fail to proliferate at 37°C, and are …

How Local Interactions Give Rise To Large-Scale Conformational Changes In Proteins: A Molecular Dynamics Study, Shadi A. Badiee

Graduate Theses and Dissertations

Proteins are dynamic entities that undergo conformational changes essential for their biological functions. These structural changes often correspond with chemical events such as lipid interactions or environmental changes like protonation or acidification. Understanding the complex relationship between these chemical perturbations and the resultant mechanical responses is crucial for elucidating protein mechanisms. This dissertation investigates the chemo-mechanical coupling in the conformational dynamics of the bacterial ABC transporter Sav1866 and the impact of protonation on the Influenza virus hemagglutinin HA0. Using molecular dynamics simulations, we explore the conformational landscapes of Sav1866 and HA0. Our study examines how varying lipid compositions affect the …

Investigation Of The Microbiome Of A Recirculating Aquaculture System (Ras) For Crassostrea Virginica Larvae, Isabelle Townsend

Master's Theses

Recirculating Aquaculture Systems (RAS) offer control over physicochemical and biological factors impacting aquaculture success. One understudied facet of RASs is the water microbiome. Oyster larval microbiomes are shaped by their aquatic microbiomes. Understanding the dynamics of and the factors shaping RAS microbiome may provide insights to how the microbiome can be a tool for optimizing larval production. This study’s goals were to investigate the microbiome stability of a RAS rearing oyster larvae across time and space, determine impacts of larval presence on the microbiome, and examine connections between larvae production outcomes and microbiome stability. Water samples were collected weekly from …

Characterizing Gsk3Β Interaction And Kinetics Via Isothermal Titration Calorimetry, W A Bhagya De Silva

UNLV Theses, Dissertations, Professional Papers, and Capstones

Glycogen synthase kinase 3β (GSK3β) is a multifunctional serine/threonine kinase involved in several key signaling pathways, including glycogen metabolism, WNT/β-catenin, and Hedgehog signaling. Hyperactivity of GSK3β has been linked to Alzheimer’s disease, bipolar disorder, type II diabetes, and some cancers. Therefore, GSK3β is of interest as a target for therapeutics. Lithium ion (Li+) is a classical inhibitor of GSK3β. Structurally similar beryllium ion (Be2+) is ~1000-fold more potent. Lithium and beryllium have demonstrated pathway-specific and cell type-specific inhibition of GSK3β, prompting an investigation into the inhibitory mechanisms and thermodynamic characteristics of the metal-enzyme interaction.Isothermal titration calorimetry (ITC) is a label-free …

Cigarette Smoke-Induced Epithelial-To-Mesenchymal Transition: Insights Into Cellular Mechanisms And Signaling Pathways, Sarah Mohammed Alqithami, Amrita Machwe, David K. Orren

Markey Cancer Center Faculty Publications

This review delves into the molecular complexities underpinning the epithelial-to-mesenchymal transition (EMT) induced by cigarette smoke (CS) in human bronchial epithelial cells (HBECs). The complex interplay of pathways, including those related to WNT//β-catenin, TGF-β/SMAD, hypoxia, oxidative stress, PI3K/Akt, and NF-κB, plays a central role in mediating this transition. While these findings significantly broaden our understanding of CS-induced EMT, the research reviewed herein leans heavily on 2D cell cultures, highlighting a research gap. Furthermore, the review identifies a stark omission of genetic and epigenetic factors in recent studies. Despite these shortcomings, the findings furnish a consolidated foundation not only for the …

Cryo-Em Reconstruction Of Oleate Hydratase Bound To A Phospholipid Membrane Bilayer, Michael L. Oldham, M. Zuhaib Qayyum, Ravi C. Kalathur, Charles O. Rock, Christopher D. Radka

Markey Cancer Center Faculty Publications

Oleate hydratase (OhyA) is a bacterial peripheral membrane protein that catalyzes FAD-dependent water addition to membrane bilayer-embedded unsaturated fatty acids. The opportunistic pathogen Staphylococcus aureus uses OhyA to counteract the innate immune system and support colonization. Many Gram-positive and Gram-negative bacteria in the microbiome also encode OhyA. OhyA is a dimeric flavoenzyme whose carboxy terminus is identified as the membrane binding domain; however, understanding how OhyA binds to cellular membranes is not complete until the membrane-bound structure has been elucidated. All available OhyA structures depict the solution state of the protein outside its functional environment. Here, we employ liposomes to …

Nsd3::Nutm1 Fusion Sarcoma Mimicking Malignant Peripheral Nerve Sheath Tumor With Prolonged Survival, Jing Di, Ali M. Alhaidary, Chi Wang, Jinge Liu, Sainan Wei, Joseph Valentino, Therese J. Bocklage

Markey Cancer Center Faculty Publications

Nuclear Protein in Testis (NUT)-rearranged tumors comprise predominantly NUT car- cinoma but also include certain lymphomas, leukemias, skin appendage tumors, and sarcomas. Although histologically diverse, all are genetically identified by oncogenic rearrangement in the NUTM1 gene. Many fusion partners occur, and NSD3 is NUT carcinoma’s third most common partner. Herein, we present a case of a 26-year-old man with an NSD3::NUTM1 fusion sarcoma. The patient presented at the age of 13 months with a scalp nodule. Over the next 24 years, he experienced five local recurrences and ultimately expired of a rapidly progressive recurrence. His treatment included surgical resections, radiation, …