Biochemistry, Biophysics, and Structural Biology Commons^™

Geometric And Proximity Based Substrate Targeting By Cullin-Ring Ligases, Jerry Li

UNLV Theses, Dissertations, Professional Papers, and Capstones

Homeostasis, the process of maintaining stable biochemical and biophysical conditions, is a fundamental facet of cellular viability. Biochemical homeostasis is critical to support the biological functions that sustain living organisms. Protein ubiquitylation is one of the primary cellular pathways that regulate protein homeostasis and turnover. Ubiquitylation is initiated through the conjugation of a small globular protein known as ubiquitin, onto a given substrate. There exists a myriad of cellular fates that ubiquitylated proteins may undergo, but the most widely studied pathway is protein degradation, whereby a ubiquitylated protein substrate is shunted to a large macromolecular protease known as the proteasome, …

Deciphering The Crl Code: Novel Mechanisms Of Canonical And Non-Canonical Ubiquitylation, Nicholas Wayne Purser

UNLV Theses, Dissertations, Professional Papers, and Capstones

Protein degradation is a fundamental process required for maintaining cellular homeostasis in eukaryotic organisms. In humans, distinct cell types exhibit unique proteomic landscapes that are dynamically balanced by the continual synthesis and degradation of proteins. The timely removal of damaged, misfolded, or old proteins is essential to permit new protein synthesis and to ensure proper cellular function.

Central to this regulatory network is ubiquitylation, a highly conserved posttranslational modification system that governs protein stability and function across all eukaryotic cells. Through the covalent attachment of ubiquitin molecules to protein substrates, this system modulates a broad range of biological processes, including …

The Dynamic Interplay Between Monovalent Salts And Ribosomal Protein S1 In Regulating Rna G-Quadruplex Structure, Chloe M. Martin

Honors Theses

Many remarkable discoveries, especially in the last decade, have shown scientists just how important RNA is. In this study, the secondary structure of RNA, G-Quadruplexes, is the topic of interest and how they are affected by salts and S1 protein. To obtain the S1 protein it was transformed from E. Coli using a bacterial plasmid. The S1 protein was then purified from the bacteria through the use of many purification methods. The monovalent cationic salts used were LiCl and KCl which have different ionic radii size that contributes to the stability of RNA G-Quadruplexes. This stability was observed and affected …

Structural Basis Of Panx1 Permeation And Positive Modulation By Mefloquine, Yangyang Li, Zheng Ruan, Junuk Lee, Ian Orozco, Edward Zhou, Juan Du, Wei Lü

Department of Biochemistry and Molecular Biology Faculty Papers

Purinergic signaling relies on ATP release through exocytosis and large-pore channels. Large-pore channels permeate both small anions like chloride and large signaling molecules like ATP, but how this broad cargo selectivity is structurally controlled remains elusive. Here we investigate PANX1, a prototypical large-pore channel, and uncover structural plasticity at the extracellular entrance formed by seven tryptophan (W74) residues. The W74 sidechains are flexible, sampling conformations that range from a constricted state permissive only to chloride to a dilated state compatible with ATP. These states are coupled to variable cation-π interactions between W74 and arginine 75 (R75), suggesting a mechanism for …

Book Of Abstracts, Seton Hall University

2025 Augustine Undergraduate Research Symposium

No abstract provided.

You Have To Cut&Walk; Before You Can Cut&Run;: Regulation Of Gene Expression By The Vitamin D Receptor (Vdr) In The Annual Killifish, Austrofundulus Limnaeus, Rosalia Tanori

Dissertations and Theses

The annual killifish, Austrofundulus limnaeus, found in ephemeral ponds in South America, possesses a remarkable ability to survive extended periods without water and oxygen. This ability is associated with developmental dormancy known as diapause. Numerous genetic and environmental factors influence the entry into diapause and tolerance to environmental stress. Among these is vitamin D3 signaling mediated by the vitamin D receptor (VDR), which plays a crucial role in regulating entry into diapause and the continuous development of an embryo in a temperature-dependent manner. Vitamin D3 signaling influences a variety of physiological processes in vertebrates. While extensively characterized in mammalian …

Engineered Multifunctional Drug-Loaded Dendrimer Nanoparticles For Glaucoma: Triple Mechanism Via Antioxidant Activity, Iron Chelation, And Enhanced Ocular Transport, Burhan Ates, Ashish Trital, Vimalin Jeyalatha Mani, Lei Xu, Jonathan Kenlee, Nuran Ercal, Hu Yang

Chemistry Faculty Research & Creative Works

In this study, we developed multifunctional nanoparticles based on polyamidoamine (PAMAM) dendrimers functionalized with caffeic acid (CA) and poly (ethylene glycol) maleimide (PEGM) for the topical delivery of hydrophobic antiglaucoma drugs brimonidine (BM) and betaxolol (BX). The PAMAM-CA and PAMAM-CA-PEGM conjugates exhibited antioxidant and iron-chelating activities in a dose-dependent manner. BM- and BX-loaded dendrimer nanoparticles produced using a multi-inlet vortex mixer showed uniform spherical morphology (∼80 nm by TEM) and hydrated sizes of ∼135-144 nm by DLS. Both nano formulations demonstrated high cytocompatibility with human corneal epithelial cells and were nonirritant in the HET-CAM assay, with PEGM further improving cytocompatibility. …

Buffer Vs. Swabs: Efficacy Of Carrier Nucleic Acids In Robotic Extractions, Shawn Cecil

Honors Projects

This study compared the efficiency of two carrier nucleic acid methods, specifically using salmon sperm DNA (spDNA), in robotic solid-phase extractions of cotton swab samples. Robotic extractions reduce processing time and workload but result in substantially lower DNA recovery than manual organic extraction. This research tested 10 µg of spDNA being added to the lysis buffer or pre-treating the swabs with it before DNA was added. Both methods showed a significant increase in recovery compared to extractions with no carrier. In the buffer extractions, recovery ranged from 69.4% to 117.5% and the swabs being pre-treated ranged from 84.2% to 125.8% …

Investigating Factors That Affect Total Ige Antibody Levels Of A Canine Population In Louisville, Ky, Iris N. Gillespie

Undergraduate Theses

Canine atopic dermatitis (CAD) is a genetically predisposed condition that causes inflammatory and pruritic (itchy) skin reactions in response to environmental and food allergens. The main purpose of this study is to determine if there is a correlation between pollen counts and total canine IgE antibody levels of dogs living in Louisville, KY. Additionally, data is analyzed to look for trends documented in previous studies related to the impacts of sex, age, and allergic symptoms on total IgE count. In collaboration with the Downtown Animal Hospital, blood samples were drawn from 16 dogs at one point in February (when pollen …

Grapes Cure Cancer: My First Molecular Docking Analysis Of Resveratrol Binding To Anti-Apoptotic Protein Bcl-2: In Silico, Sydni Ann Kolokoltsev, Vishwas Joshi

Publications and Research

B-cell lymphoma 2 (BCL-2) is an anti-apoptotic protein frequently overexpressed in cancer, enabling tumor cells to evade programmed death. Resveratrol, a grape-derived polyphenol, has reported anticancer properties. Here we performed in silico docking of resveratrol to human BCL-2 using AutoDock Vina. The best-ranked pose exhibited a predicted binding free energy of 8.0 kcal/mol and formed at least one short hydrogen bond (~1.8 Å) with pocket residues. These results support further evaluation of resveratrol as a potential modulator of BCL-2-mediated apoptosis.

Unsaturated Fatty Acid Oil-Based Microdroplets: A Promising Novel Class Of Microdroplets, Ramiz S. Alejilat

Seton Hall University Dissertations and Theses (ETDs)

Droplet-based microfluidics has rapidly advanced numerous fields, including chemistry, biology, materials science, medicine, food science, and cosmetics. In these systems, fluorocarbon oil combined with fluorinated surfactants is the preferred medium for fluid encapsulation, offering exceptional stability and biocompatibility essential for sensitive biological and chemical processes. However, growing concerns about the environmental and biological risks associated with fluorinated chemicals have prompted a search for alternatives.

This study is the first to explore the use of unsaturated fatty acids derived from emu oil for microdroplet formation. We characterized droplet formation based on flow rates and the presence non-fluorinated surfactant at a certain …

The Triangular Interaction Between Dietary Polyphenols, Gut Microbiota, And Metabolic Syndrome, Emily Bayliss

Senior Honors Theses

Type 2 diabetes mellitus (T2DM) is a growing global health concern characterized by peripheral insulin resistance as well as impaired insulin secretion from pancreatic β-cells. Emerging evidence suggests that the gut microbiome, specifically gut dysbiosis, an imbalance in the gut microbiome, is a critical modulator of the pathophysiology of T2DM. Dietary polyphenols, a diverse group of bioactive compounds that are abundant in plant-based foods, have recently gained attention for their potential to attenuate metabolic disorders through their antioxidant and anti-inflammatory properties as well as through modulating the composition and activity of gut microbes, thereby attenuating dysbiosis. However, the diabetic state …

Molecular Pathway Dysregulation In Chronic Liver Disease: Metabolic And Mechanotransductive Drivers Of Hepatic Pathophysiology, Samantha Harvat

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

Metabolic dysfunction–associated steatotic liver disease (MASLD) represents a rapidly growing cause of chronic liver injury, yet the molecular interactions linking metabolic stress, inflammation, fibrosis, and hepatocellular carcinoma (HCC) remain incompletely defined. This thesis integrates transcriptomic analyses across multiple GEO datasets to identify coordinated metabolic, inflammatory, and mechanotransductive pathways that collectively drive disease progression.

Analysis of human liver biopsy datasets (GSE126848 and GSE89632) revealed consistent suppression of glycolysis, β-oxidation, and oxidative phosphorylation across MASLD and MASH samples, accompanied by modest compensatory TCA cycle activation. These alterations reflect impaired metabolic flexibility, mitochondrial stress, and increased ROS susceptibility. Concurrently, cytokine-network enrichment demonstrated activation …

Dendrimer Gel Nanoparticles With Dual-Targeting Of Upar And Ribonucleotide Reductase R2 Influence Necrosis, Apoptosis, And Cell Cycle Arrest In Triple-Negative Breast Cancer, Hsin Yin Chuang, Yue-Wern Huang, Hu Yang

Biological Sciences Faculty Research & Creative Works

Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with limited treatment options due to the absence of estrogen (ER), progesterone (PR), and human epidermal growth factor receptor 2 (HER2) receptors. We previously developed highly adaptable polyamidoamine (PAMAM) dendrimer-based gel nanoparticles (GDP-uPA/GTI) with dual-targeting capabilities against urokinase-type plasminogen activator receptor (uPAR) and ribonucleotide reductase R2 (R2) to achieve selective antitumor effects. In this study, we investigated the underlying mechanisms of GDP-uPA/GTI-induced tumor inhibition. In vivo, GDP-uPA/GTI significantly downregulated R2 expression and activated caspase 8 and caspase 3, indicating caspase-dependent apoptosis. Histological evaluation of major organs revealed no observable toxicity. …

Flux Crystal Growth Of A Series Of Calcium Rare Earth Silicate Chlorides Calnsio4Cl (Ln = Pr, Nd, Sm, Eu, Gd, And Tb): Mixed Anion Materials With A Spodiosite-Type Structure, Maria Goncalves, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

A series of calcium rare earth silicate chlorides, CaLnSiO4Cl (Ln = Pr, Nd, Sm, Eu, Gd, and Tb), was obtained as single crystals from flux crystal growth. The structures were determined by single crystal X-ray diffraction and were found to be related to the spodiosite/Wagnerite mineral structure, Ca2PO4F. The obtained compositions are variations of the spodiosite structure that result from two simultaneous elemental substitutions. Replacing one calcium for one rare earth element and the simultaneous replacement of one VO4³⁻ or PO4³⁻ with one SiO4⁴⁻. CaEuSiO4Cl was found to luminesce, and its photoluminescence spectrum is reported.

Water Circulation Beneath A Hovering Suas For Water Quality Monitoring Applications, Erin E. Hackett, Boone Fleenor, Jensine C. Coggin, Duvall Dickerson-Evans, Nikolaos Vitzilaios, Whitney E. Schuler, Paige K. Williams, Michael L. Myrick

Faculty Publications

Water quality has traditionally been measured via in situ sensors and satellites. The latter has limited applicability for smaller inland water bodies, while the former requires significant logistics, labor, and expense for routine sampling, and reactive/spurious sampling is often not feasible as a result (e.g., sampling pre-/post-storm). Consequently, small uncrewed aircraft system-based (sUAS-based) sampling has emerged as a potential solution to bridge these sampling gaps and challenges. But sampling from an sUAS is complicated by the need to pump water from depth, rather than suspending a sensor from the sUAS, due to concern over sampling sUAS-impacted waters. Here, we measure …

Thermodynamic Assessment Of The Li, Na, K, Cs | F, I Reciprocal Salt For Msr Applications, Clara M. Dixon, Mina Aziziha, Amir Mofrad, Jorge Paz Soldan Palma, Ronald E. Booth, Aiswarya Padinhare Manissery, Jack A. Wilson, Hans Conrad Zur Loye, Hunter B. Tisdale, Juliano Schorne-Pinto, Theodore M. Besmann

Faculty Publications

Gibbs energy models necessary to describe the thermochemical behavior of cesium and iodine in molten FLiNaK (46.5LiF-11.5NaF-42KF mol%), a proposed molten salt reactor coolant and fuel solvent, have been developed as they are of concern due to their high radiotoxicity and volatility. The six constituent pseudo-binary systems LiI-CsI, LiI-KI, LiI-NaI, NaI-KI, KI-CsI and NaI-CsI were evaluated using available phase equilibria and mixing enthalpy measurements. The models for the ternary reciprocal salt systems Li,Cs|F,I, Li,K|F,I, Li,Na|F,I, Na,K|F,I, Na,Cs|F,I and K,Cs|F,I were obtained by interpolation of the optimized pseudo-binary systems and parameters fit as necessary based on observed behavior. The additive (common …

Functional Characterization Of The Hssb1 K94q Mutation, Isaiah Singleton

All Theses

Genome stability depends on precise DNA repair pathways such as homologous recombination (HR), where human single-stranded DNA-binding protein 1 (hSSB1) stabilizes single-stranded DNA (ssDNA) intermediates and recruits repair complexes. Post-translational modifications, including acetylation, are known to regulate hSSB1 activity, but their molecular effects remain poorly defined. This study examined the role of lysine 94 (K94) acetylation using a glutamine substitution mutant (K94Q) that mimics the acetylated state. Recombinant hSSB1 wild type (WT) and hSSB1_K94Q were expressed in Escherichia coli and purified using Ni–NTA affinity chromatography. Biochemical analyses, including electrophoretic mobility shift assays (EMSA), single-strand annealing assays, and displacement loop …

Evaluating The Effectiveness Of An Air Purification System In Reducing Bacterial Chondronecrosis With Osteomyelitis Lameness In Broiler Chickens, Abdulaziz Ali Alqahtani

Graduate Theses and Dissertations

Bacterial chondronecrosis with osteomyelitis (BCO) is the primary cause of lameness in commercial broiler production and has a profound impact on animal welfare and cost-effectiveness. The purpose of this experiment was to examine the effect of an air purification system on mitigating BCO lameness in broiler chickens. One thousand eight hundred broiler chicks were reared in two side-by-side research barns. Eight air filtration units were installed in one building, and none in the other. Treatment groups in both houses included positive control birds on wire flooring to induce BCO, as well as negative control, feed additive, vaccination, and a combination …

Exploring The Growth Dynamics Of Streptococcus Mutans In Diverse Environmental Conditions, Vanessa Escudero

Theses and Dissertations

Dental caries, a prevalent oral health issue, is primarily associated with the growth of Streptococcus mutans, a Gram-positive bacterium that grows under various oral environments. The primary objective of this study was to evaluate the impact of different beverages and mechanical cleaning on the growth of S. mutans, which plays a crucial role in tooth decay. Using a nano-spectrophotometer we analyzed bacterial growth by constructing growth curves under different conditions, including exposure to cranberry juice, Hawaiian juice, and mechanical brushing.

The study was designed to mimic real-world oral conditions by testing S. mutans in four distinct environments. First, we established …