Biochemistry, Biophysics, and Structural Biology Commons^™

The Epigenetic Impact Of Dietary Choline On Growth Outcomes Of Children Exposed To Gestational Diabetes Mellitus, Ismail Kadam

Dissertations, Theses, and Capstone Projects

Maternal insulin resistance and hyperglycemia lead to gestational diabetes mellitus (GDM) which can cause fetal hyperinsulinemia, ultimately leading to excessive fetal growth associated with macrosomia and increased adiposity at birth. Increased placental macronutrient transport and epigenetic changes in growth and metabolic genes affected by GDM contribute to fetal overgrowth and can result in complications such as overweight/obesity, insulin resistance/type 2 diabetes, cardiovascular disease risk factors, as well as cognitive impairment later in life. Choline, an essential nutrient, participates in lipid and energy metabolism by providing methyl groups for DNA methylation and thus may overcome the hypomethylation of growth and metabolic …

Voltage Set Points For Sodium Channel Inactivation: Intrinsic And Modulatory Mechanisms, Akshay Sharma

Dissertations, Theses, and Capstone Projects

During an action potential, voltage-gated sodium channels (VGSC) control sodium ion flow into the cytoplasm of cells by using membrane voltage to alter channel conformation. These membrane proteins exhibit three main functional conformations: closed, open, and fast-inactivated, with transitions between these states dependent on membrane voltage and kinetics. The channels open within 1 millisecond and swiftly transition from open to fast-inactivated within 1-2 milliseconds following membrane depolarization. Subsequent membrane repolarization resets the channels to the closed state. Notably, even at mildly depolarized potentials that preclude channel opening, VGSCs can undergo transitions between the closed and inactivated states, known as closed-state …

Newly Synthesized Pyroglutamate Amide And Its Neuroprotective Effect Against Neurotoxicity Induced Cell Death In Alzheimer's Disease, Nourelhouda Joutey Elamrani

Dissertations, Theses, and Capstone Projects

The neurodegenerative disorder is an umbrella term for a range of conditions that affects the neurons in the human brain causing neuronal cell death. The common pathway is the excitotoxicity, a phenomenon that describes the toxic actions of excitatory neurotransmitters, primarily glutamate, where the exacerbated or prolonged activation of glutamate receptors starts a cascade of neurotoxicity leading to the cell death. One of the most common neurodegenerative disorders is Alzheimer’s disease (AD), which represents 60 – 70% of cases and it ranked fourth cause of mortality in the USA. In Alzheimer’s disease, glutamate released from astrocytes and activates extrasynaptic N-methyl-D-aspartate …

Exploiting The Heavy Chain Glycans For The Improvement Of Radioimmunoconjugates, Cindy Rodriguez

Dissertations, Theses, and Capstone Projects

Radiolabeled antibodies have become indispensable tools in nuclear medicine. However, the natural roles of antibodies within the immune system mean that they have several intrinsic limitations as a platform for radiopharmaceuticals. A handful of recent preclinical studies suggest that binding by FcR and particularly FcyRI can affect the pharmacokinetic profiles of 89Zr-labeled radioimmunoconjugates. Fc receptors (FcR) are responsible for many of the interactions between immunoglobulins (IgG) and immune cells. In biomedicine, this interplay is critical to the activity of several types of immunotherapeutics; however, relatively little is known about how FcRs affect the in vivo performance of radiolabeled antibodies. Antibodies …

Understanding The Mystery Of R-Loops And Their Relationship To Nucleolar Stress, Kevin Shane

Master's Theses

Genomic instability is an increase in the likelihood of DNA mutations and genetic changes during cell division, a common feature in cancer cells. One cause of genomic instability comes from the aberrant formation of three-stranded nucleic acid structures called R-loops. R-loop form when an RNA strand hybridizes to its complementary strand of DNA, forming a stable RNA:DNA hybrid and displacing one free strand of DNA 1. Accumulation of unscheduled R-loops can lead to replication stress, fork collision, gene expression changes, and double-strand breaks that are underlying causes of genome instability and the development of many diseases, including cancer 2. Many …

Diverse Origins Of Near-Identical Antifreeze Proteins In Unrelated Fish Lineages Provide Insights Into Evolutionary Mechanisms Of New Gene Birth And Protein Sequence Convergence, Nathan Rives, Vinita Lamba, C.H. Christina Cheng, Xuan Zhuang

Biological Sciences Faculty Publications and Presentations

Determining the origins of novel genes and the mechanisms driving the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. Recently evolved fish antifreeze proteins (AFPs) offer a unique opportunity to explore these processes, particularly the near-identical type I AFP (AFPI) found in four phylogenetically divergent fish taxa. This study tested the hypothesis of protein sequence convergence beyond functional convergence in three unrelated AFPI-bearing fish lineages. Through comprehensive comparative analyses of newly sequenced genomes of winter flounder and grubby sculpin, along with available high-quality genomes of cunner and 14 other related species, the study revealed that near-identical …

Noise Leads To The Perceived Increase In Evolutionary Rates Over Short Time Scales, Brian C. O'Meara, Jeremy M. Beaulieu

Biological Sciences Faculty Publications and Presentations

Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show …

Pm2.5 In The Respirable Air A Threat To Heart Health Investigating The Influence On Cardiovascular Performance And Unmasking The Potential Strategies For Cardio Protection, Bhavana Sivakumar

Theses and Dissertations

Air pollution, characterized by the presence of harmful substances in the atmosphere, represents a significant environmental and public health challenge impacting millions worldwide. The World Health Organization (WHO) reports that approximately 90% of the global population resides in regions where air pollution surpasses the recommended thresholds for healthy air quality. Within the realm of air pollution, the composition of particulate matter emerges as a pivotal consideration, particularly regarding PM2.5, comprising minute particles originating from diverse sources such as combustion processes, industrial operations, and natural phenomena like wildfires and dust storms. PM2.5 exhibit a range of chemical and physical attributes contingent …

Emerin Deficiency Drives Mcf7 Cells To An Invasive Phenotype, Emily Hansen, Christal Rolling, Matthew Wang, James M Holaska

Rowan-Virtua School of Osteopathic Medicine Departmental Research

During metastasis, cancer cells traverse the vasculature by squeezing through very small gaps in the endothelium. Thus, nuclei in metastatic cancer cells must become more malleable to move through these gaps. Our lab showed invasive breast cancer cells have 50% less emerin protein resulting in smaller, misshapen nuclei, and higher metastasis rates than non-cancerous controls. Thus, emerin deficiency was predicted to cause increased nuclear compliance, cell migration, and metastasis. We tested this hypothesis by downregulating emerin in noninvasive MCF7 cells and found emerin knockdown causes smaller, dysmorphic nuclei, resulting in increased impeded cell migration. Emerin reduction in invasive breast cancer …

Antimicrobial Studies Of Novel Pyrazole And Thiazole-Based Antibacterial Agents, Hansa Raj Kc

Student Theses and Dissertations

In recent years, the rise of antibiotic-resistant bacteria has become a global concern, resulting in fewer effective antibiotics. Several conventional antibacterial agents are ineffective against these, necessitating novel molecules with enhanced efficacy and diverse actions. We developed pyrazole and thiazole-based antibacterial agents and demonstrated that they have significant potency (minimum inhibitory concentration as low as 0.39 µg/mL) against antibiotic-resistant and susceptible bacteria, as well as promising anti-biofilm and anti-persister activity. In vivo toxicity tests on Caenorhabditis elegans showed no significant harm to this model host organism at low compound concentrations. These compounds rescued C. elegans from methicillin-resistant Staphylococcus aureus (MRSA) …

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 …

Unraveling The Role Of Hid-1: Insights Into Sgii Regulation, Breanna L. Sellers

Electronic Theses and Dissertations

The regulated secretory pathway is important for the secretion of hormones and neuropeptides from large dense core vesicles (LDCVs). Dysregulation of the biogenesis of LDCVs can result in metabolic and neurological diseases. Recent studies have suggested that the peripheral membrane protein HID-1 plays a role in the sorting and storage of granins which contribute to LDCV biogenesis. To further understand how HID-1 influences the regulation of granins, we investigated potential HID-1 interactors. We determined that while HID-1 is likely functioning in the same pathway as USP25, a deubiquitinating enzyme (DUB), the cause of reduced cellular SgII levels is likely not …

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 …

Soft Sets Extensions: Innovating Healthcare Claims Analysis, Daniela Gifu, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

In the dynamic arena of healthcare research, where the complexities of data often rival the intricacies of biological systems, the ability to model and analyze such multifaceted datasets is crucial. This comprehensive review delves into the evolution and application of Soft Sets and their extensions, including HyperSoft Sets, SuperHyperSoft Sets, IndetermSoft Sets, IndetermHyperSoft Sets, and TreeSoft Sets, in healthcare claims data analysis.

Molecular Docking, Pharmacological Profiling, And Molecular Dynamics Simulation Of Potential Antihyperuricemic Agent From Secondary Metabolites Of Dillenia Philippinensis Rolfe (Dilleniaceae), Louie Rince C. Suyo, John P. Paulin, Nicole Clarence Louise L. Gapaz, Markus Brent S. Arevalo, Vince Tyrell P. Yongco, Librado A. Santiago

Karbala International Journal of Modern Science

Crystal accumulation in the joints due to increased serum uric acid (sUA) may lead to an inflammatory condition called gout. Increased sUA is caused by the excessive reabsorption of the urate anion transporter-1 (URAT-1). Therefore, URAT-1 inhibition will promote uric acid excretion and reduce the risk of having gout. Dillenia philippinensis Rolfe, often known as katmon, is an endemic plant in the Philippines with bioactive compounds associated with several therapeutic benefits. The present study represents the first scientific inquiry into the antihyperuricemic potential of compounds isolated from D. philippinensis. This study aimed to assess the interaction of URAT-1 with …

Structural Basis For Substrate Binding And Selection By Human Mitochondrial Rna Polymerase, Karl Herbine, Ashok Nayak, Dmitry Temiakov

Department of Biochemistry and Molecular Biology Faculty Papers

The mechanism by which RNAP selects cognate substrates and discriminates between deoxy and ribonucleotides is of fundamental importance to the fidelity of transcription. Here, we present cryo-EM structures of human mitochondrial transcription elongation complexes that reveal substrate ATP bound in Entry and Insertion Sites. In the Entry Site, the substrate binds along the O helix of the fingers domain of mtRNAP but does not interact with the templating DNA base. Interactions between RNAP and the triphosphate moiety of the NTP in the Entry Site ensure discrimination against nucleosides and their diphosphate and monophosphate derivatives but not against non-cognate rNTPs and …

Informatics-Based Discovery Of New Natural Products, Their Biosynthesis, And Their Biological Roles, Ethan Older

Theses and Dissertations

In this work, genome mining and biosynthetic knowledge are applied for the discovery of new natural products, their biosynthetic pathways, and their promising biological activities and roles through the development of two unique new informatics-based approaches.

In chapter one, an overview of microbial natural product biological functions and biosynthesis is provided. The use of bioinformatics leveraging microbial natural product biosynthetic knowledge is also introduced. This chapter highlights the importance and need for developing innovative approaches to accessing microbial natural products, a vastly untapped source of new molecules with promising biological activities.

In chapter two, a correlational network linking the gene-encoded …

Absolute Quantification Of Human Myosin And Titin Isoforms In Disease By A Mass Spectrometry Approach, Nitha Aima Muntu

Master's Theses

Heart failure (HF) is the leading cause of death worldwide and produces an immense economic burden. Dilated cardiomyopathy (DCM), characterized by contractile weakness and chamber dilation, is a significant cause of HF. The sarcomeric proteins play a crucial role in regulating the contractile properties of the heart. As the primary motor protein, the expression of cardiac myosin isoforms (α-MHC and β-MHC) dictates the performance and cardiac energy utilization of the sarcomere. Titin is the giant spring protein in the sarcomere, and titin isoform expression impacts the passive stiffness of the myocardium. Small changes in the α-MHC/β-MHC and titin isoform ratios …

Investigating The Oncogenic Role Of Nkx3.1 In Prostate Cancer, Audris Budreika

Master's Theses

Prostate cancer is a unique disease in that it is fueled by androgen receptor (AR) signaling. In the clinic, AR signaling is disrupted by removing androgens via chemical castration and employing AR-antagonists such as enzalutamide. Unfortunately, these therapies are short-lived, resistance sets in, and tumors evolve to a form of the disease called castration-resistant prostate cancer (CRPC). At this stage, therapeutic options are virtually exhausted and palliative care is pursued. There is a growing need to characterize other molecular players that cooperate with AR or play a unique role in CRPC on their own. One such potential candidate is the …

Quantification Of Immunometabolite Derived Protein Modifications During Mitochondrial Metabolic Stress, Justin Hunter Cox

Theses and Dissertations

The immunometabolite itaconate accumulates during lipopolysaccharide (LPS) stimulation of macrophages and microglia. Itaconate non-enzymatically reacts with cysteine residues to generate 2,3-dicarboxypropylcysteine (2,3-DCP), referred to as protein dicarboxypropylation. The tricarboxylic acid (TCA) cycle metabolite fumarate non-enzymatically reacts with the amino acid cysteine to form S-(2-succino)-cysteine (2SC), resulting in irreversible protein succination. Since fumarate and itaconate levels dynamically change in activated immune cells, the levels of both 2SC and 2,3-DCP reflect the abundance of these metabolites and their capacity to modify protein structure and function. I generated esters of 2SC and 2,3-DCP from protein hydrolysates and used stable isotope dilution liquid chromatography-tandem …

Design Of An Artificial Transcription Factor For Inducing Potent Interferon-Γ Signals, Ashley King

Theses and Dissertations

Cytokines are small immune signaling proteins responsible for cellular communication and their levels are tightly regulated throughout immune recognition and defense. Interferon gamma is a key cytokine responsible for upregulation of antigen presentation and supports the differentiation of pro-inflammatory effector cells. Due to its role in regulation, excess interferon gamma is cleared from the body limiting the success of interferon gamma immunotherapies. This study reports the design and validation of an artificial transcription factor (ATF) that induces endogenous interferon gamma expression. The transcription factor contains zinc finger proteins to recognize the interferon gamma gene and an activation domain to promote …

Characterizing The Role Of The Escherchia Coli Monothiol Glutaredoxin, Grxd, As An Iron-Sulfur Cluster Carrier Protein, Claire Elizabeth Fisher

Theses and Dissertations

Iron-sulfur (Fe-S) clusters are important cofactors with a primary role of electron transport that are required by proteins involved in wide range of biological pathways such as respiration, photosynthesis, and DNA repair. In Escherichia coli (E. coli), the assembly and transfer of these clusters to their target apo-protein is a highly coordinated process encoded by the multiprotein systems iscRSUAhscBAfdx and sufABCDSE operons. These clusters are assembled on a scaffold protein, where they are then transferred to a carrier protein that will deliver the cluster to the target apo-protein. The Isc and Suf systems contain their own carrier proteins IscA …

Investigation Of P27 Tumor Suppressor Gene (Cdkn1b) Polymorphisms In Dogs With Malignant Mammary Tumors, Gizem Kırmızıoğlu, Iraz Akış

The Thai Journal of Veterinary Medicine

Mammary tumors are the most common neoplasm in dogs, with a high mortality rate. The development of canine mammary tumors (CMT) is multifactorial, but different incidence rates between breeds suggest the effects of genetic risk factors. Many CMT-associated candidate genes were reported, mainly involved in cell cycle control. This study aims to investigate p27 tumor suppressor gene polymorphisms in dogs with mammary tumors and analyze the association between variations and CMTs. For this purpose, case and control groups were formed from 22 dogs diagnosed with malignant mammary tumors and 10 dogs with healthy mammary glands. The whole canine p27 gene …

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 …

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 …

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. …

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. …

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 …