Biochemistry, Biophysics, and Structural Biology Commons^™

Gene Expression Of Anthocyanin Pigments In The California Native Plant Leptosiphon Parviflorus: Interactions Between Flower Color Morphology And Abiotic Stressors, Weston Gonor

Master's Theses

For plants to survive in harsh conditions imposed by abiotic stressors, they must develop mechanisms of adaptation. One of the common types of adaptation seen in plants is the production of anthocyanin pigments, which have been shown to protect plants from UV radiation, metabolic stress, and drought. In this study, we used the flower color polymorphic species Leptosiphon parviflorus to investigate the role of anthocyanin pigments in protecting plants from abiotic stress. To accomplish this, RNA samples were taken from flower, leaf and root tissue of different flower color morphs of Leptosiphon parviflorus (Polemoniaceae) grown in high magnesium and water …

Root Exudates: The Rhizospheric Frontier For Advancing Sustainable Plant Protection, Muhammad Rahil Afzal, Misbah Naz, Youbo Yu, Lisha Yan, Peiyi Wang, Janaki Mohotti, Gefei Hao, Jing-Jiang Zhou, Zhou Chen, Libo Zhang, Qian Wang

Faculty Publications

Root exudates (REs), a diverse array of bioactive metabolites secreted by plant roots in response to environmental stimuli, serve as key mediators of rhizosphere ecology and plant defense responses, offering a promising avenue for sustainable pest management and eco-friendly plant protection. While earlier reviews primarily focus on root exudates in the context of general rhizosphere dynamics and plant-microbial interactions, critical knowledge gaps persist in REs-plant-pest tripartite interactions, the mechanistic basis of REs-mediated plant defense, and their practical integration with integrated pest management (IPM) frameworks. This review provides a synthesis of the latest literature on the biochemical diversity and functions of …

Impact Of Varied Dietary Macronutrient Ratios On The Nutrition Status Of Swiss Albino Mice, Hellen Kinyi, Charles Kato, Gertrude Kiwanuka

Biomedical Sciences, East Africa

The nutrition status of an organism depends on the balance between nutrient intake and utilization. Malnutrition results not only from inadequate caloric intake but also from imbalanced macronutrient ratios, which can affect aging, metabolism, and health. While many studies focus on individual nutrients, this study used purified, isocaloric diets with varying macronutrient ratios to assess dietary effects on nutrition markers in Swiss albino mice.

Mice were randomized into 6 dietary groups, each containing 6 males and 6 females housed separately. Each group received an isocaloric diet with different carbohydrate, protein, and lipid ratios for 15 weeks. Animal weight, body mass …

Single Nuclei Transcriptomics Reveals Cellular Diversity In Tsc Subependymal Giant Cell Astrocytomas, Jennie C. Holmberg, Vijay Shankar, Rachel A. Lyman, Trudy F.C. Mackay, David M. Feliciano

Publications

Tuberous sclerosis complex (TSC) is a genetic disorder characterized by benign growths called hamartomas that are a significant cause of morbidity and mortality. Hamartomas are found along the neurocutaneous axis including along the brain’s ventricles near the boundaries of the striatum. They can be categorized by size and include small subependymal nodules (SENs) or larger subependymal giant cell astrocytomas (SEGAs). Here, we describe a quantitative analysis of SEGA cell identities based on single nuclei RNA sequencing. SEGAs contain several cell types. In contrast to unaffected samples, SEGAs have pronounced vasculature, more endothelial cells, increased perivascular macrophages, less myelination, and altered …

From Sequence To Allostery: How Amino Acid Differences Rewire Coupled Conformational Heterogeneity In The Ptp Enzyme Family, Shivani Sharma

Dissertations, Theses, and Capstone Projects

Protein Tyrosine Phosphatases (PTPs) are critical regulators of cellular signaling, and their activity is often modulated through allosteric mechanisms. Allostery is defined as a chemical or conformational change in one site of the protein due to a binding event at another site. Although several studies have investigated aspects of allostery in PTPs, the mechanistic foundations underlying allosteric regulation remain poorly understood. Despite a highly conserved catalytic domain across PTPs, regions with low or no conservation suggest potential "rewiring" of allosteric networks. This raises key questions about the universality versus individuality of allosteric mechanisms across the PTP family.

In this work, …

The Sonic Hedgehog Effector Smoothened Modulates Cholinergic Interneuron Activity, Physiology, And Striatum-Dependent Behaviors, Santiago Uribe-Cano

Dissertations, Theses, and Capstone Projects

The striatum is a central node in action selection and associative learning, integrating cortical, thalamic, and neuromodulatory input. Among its principal modulators, dopamine (DA) and acetylcholine (ACh) are known for their temporally coordinated yet mechanistically distinct influences on striatal output. However, the upstream signals that regulate their dynamic interplay, particularly within cholinergic interneurons (CINs)—the primary source of striatal ACh—remain incompletely characterized. This dissertation investigates the role of Smoothened (Smo), a G protein-coupled receptor (GPCR) effector of Sonic Hedgehog (Shh) signaling, in modulating ACh signaling dynamics in the striatum.

Building on evidence that midbrain DA neurons co-release Shh and that CINs …

Mechanistic Insights Into The Neuroprotective Effects Of The Antidepressant Agomelatine In Alzheimer's Disease, Grace Terry

Dissertations, Theses, and Capstone Projects

Alzheimer’s Disease (AD) is a complex neurodegenerative disease that has limited treatment options and no cure. AD is characterized by robust pathology including extracellular amyloid beta plaques, intracellular neurofibrillary tangles, neuronal and synaptic loss, neuroinflammation, and brain atrophy. AD presents with cognitive decline and memory loss but only years after neuropathology has started to accumulate. This robust pathology has made AD difficult to treat and highlights the need for therapeutics that modulate multiple pathways. Agomelatine (AGO) was selected by a high-throughput machine learning drug repurposing algorithm by our collaborator Dr. Lie Xie (Hunter College Dept. of Comp. Sci.) as having …

Investigating The Role Of Early Growth Response 1 (Egr1) Gene In Riluzole-Induced Apoptosis In Osteosarcoma, Syeda Maryam Azeem

Dissertations, Theses, and Capstone Projects

Osteosarcoma is a rare but aggressive bone malignancy most commonly affecting adolescents and young adults (AYA). With 5-year survival rate stagnating over the last four decades despite the advancements in multi-modal therapy, drug repurposing offers a rapid path to new osteosarcoma treatments. Recent studies suggest that Riluzole, a drug approved for amyotrophic lateral sclerosis (ALS), may be repurposed for osteosarcoma treatment due to its ability to slow tumor progression and induce apoptosis. Previously, we have shown that Riluzole increases reactive oxygen species (ROS), activating c-Abl, which phosphorylates YAP in the nucleus. YAP then forms a complex with p73 to enhance …

Development And Implementation Of Novel Mass Spectrometric Methods For Metabolism Studies In Drug Discoveries, Huifang Yao

Dissertations

The field of drug discovery has evolved significantly over the past few decades, with a growing emphasis on understanding the metabolic pathways and biotransformation processes that influence the pharmacokinetics and pharmacodynamics of drug candidates. Novel mass spectrometric methods have emerged as powerful tools in this domain, facilitating the comprehensive analysis of metabolic profiles and enabling the identification of metabolites with implications for safety, efficacy, and overall drug development. However, challenges remain in quantifying metabolic flux—an essential aspect of understanding drug action—particularly due to the limitations of traditional isotope kinetic assays, which often involve lengthy sample preparation and the use of …

Design And Development Of A Standalone Digital Holographic Microscope Employing Phase-Driven Reconstruction And Classification For Biomedical Imaging And Optical Diagnostics, Charlotte Kyeremah

Graduate Doctoral Dissertations

Access to advanced biomedical imaging technologies remains a significant challenge in resource-limited settings, especially for early disease detection and monitoring of diseases such as malaria, HIV, and other blood-borne diseases. Although point-of-care (POC) devices have gained popularity in global health, many rely on antibody-based tests, lateral flow strips, or optical readouts that often lack quantitative capabilities, sensitivity to early infections, or versatility in different diagnostic targets. In addition, these systems are typically dependent on disposable reagents or manual interpretation, which limits their effectiveness in remote areas. Digital Holographic Microscopy (DHM) presents a promising alternative as a label-free imaging method capable …

Role Of Nucleic Acids As Chaperones In Protein Folding, Zijue Huang

Electronic Theses and Dissertations

Many proteins have slow folding times in vitro that are physiologically untenable. To combat this challenge, ATP-dependent chaperonins are thought to possess the unique ability to catalyze protein folding. Performing quantitative model selection using protein folding and unfolding data, we here show that short nucleic acids containing Gquadruplex (G4) structure can also catalyze protein folding. Performing the experiments as a function of temperature demonstrates that the G4 reshapes the underlying driving forces of protein folding. To understand the structural basis of this catalytic activity, we introduce NMR method to solve the structures, at base-level resolution, of a multiconformer G4 with …

Centrosomal And Non-Centrosomal Microtubule Networks Coordinate To Drive Nuclear Dynamics In Developing Epithelium, Rashmi Budhathoki

Electronic Theses and Dissertations

The morphogenesis of developing tissues relies on extensive cellular rearrangements in shape, position, and identity. A key process in reshaping tissues is cell intercalation-driven elongation, where epithelial cells align and intercalate along a common axis. Typically, analyses focus on how peripheral cortical forces influence cell shape changes. Less attention is given to how inhomogeneities in internal structures, particularly the nucleus, impact cell shaping. Here, we examine how pulsed contractile and extension dynamics interact with the nucleus in elongating Drosophila embryos. Our data show that tightly packed nuclei in apical layers hinder tissue remodeling/oscillatory behaviors. We identify two mechanisms for resolving …

Enhancing Cataract Surgery Outcomes: Optimal Use Of Pre- And Post-Operative Eye Drops, Keith Skolnick M.D., Anu Valiaveedu

Mako: NSU Undergraduate Student Journal

Many preoperative and postoperative cataract patients struggle with comprehending the use of prescription medication as directed. Language barriers and low health literacy levels are major factors contributing to improper use of prescriptions. To increase patients comprehension, the Fort Lauderdale Eye Institute employed an educational intervention consisting of a live presentation and an instructional video. Results found that 44% of patients were hesitant to ask questions to clinical staff, 32% felt overwhelmed, and nearly 70% lacked confidence in using their prescribed eye drops. Following the intervention, 91% of patients reported increased confidence in their medications, and most indicated that the video …

3d Bioprinting On Electrospun Nanofibrous Scaffolds To Fabricate Myocardial Patches, Muthu Parkkavi S

Theses and Dissertations

Tissue-engineered three-dimensional (3D) myocardial patches offer superior and innovative treatment strategy for myocardial infarction (MI). Among the various scaffold fabrication techniques, electrospinning and 3D bioprinting have received great attention due to their ability to recreate native cardiac tissue mimetic characteristics. Despite several advantages, electrospun nanofibers have limitations in cell delivery due to random cell seeding, while bioprinting faces challenges in creating hydrogel constructs with ideal mechanical properties capable of supporting cardiac contraction/relaxation cycle. Hence in this work, hybrid myocardial patches were developed by converging electrospinning and bioprinting techniques.

Electrospinning of PLCL:PEOz (B73, 7:3 blend of poly-L-lactide-co-ε-caprolactone (PLCL) and polyethyl oxazoline …

Effect Of Osmolytes On The Interplay Of Water Protein And Dna In Ecori Dna Recognition Using Molecular Dynamics Simulations, Aathithya D

Theses and Dissertations

EcoRI is a type II restriction endonuclease that has been widely used as a model system to study protein-DNA interaction owing to its high degree of specificity. This enzyme does not recognize even a single basepair change in its recognition sequence, (GAATTC)2, under normal conditions. However, in the presence of osmolytes, such as glycerol and DMSO, the specificity of EcoRI is slightly relaxed and recognizes sequences that differ from its cognate sequence in the first basepair position. This relaxed specificity has been attributed to the dehydration of the EcoRI-DNA which presumably results in tighter complex formation and subsequent catalysis. However, …

Empowering Science With The World's First High Accuracy And High Throughput Functional Assay, Christopher Giacoletto

UNLV Theses, Dissertations, Professional Papers, and Capstones

Understanding the functional consequences of genetic mutations remains a central challenge in modern biology, with far-reaching implications for human health and disease. While early systematic methods like alanine scanning and phage display provided foundational insights into protein structure and function, the emergence of high-throughput approaches—such as Multiplexed Assays of Variant Effect (MAVEs)—and predictive tools powered by artificial intelligence have vastly expanded our ability to profile mutational landscapes. However, these methods are often constrained by trade-offs between accuracy, scalability, and biological relevance.This dissertation presents the development and application of the GigaAssay, the world’s first high-throughput functional assay capable of delivering both …

Claudin-1-Mediated Signaling And Therapy Resistance In Colorectal Cancer: From Mechanism To Translation, Mark W. Primeaux

Theses & Dissertations

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality, with metastatic cases showing poor response to chemotherapy due to both intrinsic and acquired therapy resistance. Claudin-1 (CLDN1), a tight junction protein, is overexpressed and mislocalized outside of tight junctions in CRC, where it contributes to an aggressive, metastatic phenotype. Although this causal relationship has been well established, the mechanisms by which CLDN1 promotes tumor progression were unclear due to its lack of intrinsic enzymatic activity. This dissertation investigates the molecular mechanisms through which CLDN1 drives oncogenic signaling, its role in therapy resistance, and its translational potential as both a …

Development Of Emerin Mrna Lipid Nanoparticles To Rescue Myogenic Differentiation., Nicholas Marano, Liza Elif Guner, Rachel S Riley, James M Holaska

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Emery-Dreifuss muscular dystrophy 1 (EDMD1) arises from mutations in EMD. Most EDMD1 patients lack detectable emerin expression. They experience symptoms such as skeletal muscle wasting, joint contractures, and cardiac conduction defects. Currently, physicians rely on treating patient symptoms without addressing the underlying cause-lack of functional emerin protein. Thus, there is a need for therapeutic approaches that restore emerin protein expression to improve patient outcomes. One way would be to deliver emerin mRNA or protein directly to affected tissues to restore tissue homeostasis. Here, we evaluated the utility of lipid nanoparticles (LNPs) to deliver emerin mRNA to diseased cells. LNPs …

Computational Investigation Of The Structural And Electronic Effects Of Phenyl, Alkyl, And Halogen Fully Substituted Acenes, Emily A A Jarvis, Viraj Jain, Georgia Grace Tully, Peter W. Jarvis

Chemistry and Biochemistry Faculty Works

Acenes are a class of polycyclic aromatic hydrocarbons that may hold promise as organic semiconductors (OSCs) in solar cells and electronic devices. Their instability and poor solubility present challenges that may be improved by replacing the hydrogens with phenyl, halogen or alkyl substituents to sterically induce a helical twist to these otherwise planar molecules. This twisted structure also impacts the optical properties of these molecules. We employ time-dependent density functional theory (TD DFT) to investigate acenes spanning from naphthalene to heptacene. We focus on the structural and electronic effects of fully substituting these molecular backbones to create seven distinct substituent …

Growth Of Cylindrical Micelles And Their Use To Prepare Porous Materials With Tailored Dimensions And Alignment, Mengxue Zhang, Xiaomeng Li, Chuanbing Tang, Morgan Stefik

Faculty Publications

Materials with cylindrical pores are optimal for electrochemical devices and filtration due to their straight paths with minimal tortuosity when aligned. Polymer templates have led to many individual cylindrical architectures however the independent tailoring of pore and wall dimensions has remained elusive. Here short cylindrical micelle templates (PEO-b-PS) with glassy cores enabled the fabrication of sample series with constant cylindrical pore diameter (∼63 nm) and tailored wall thickness (TiO₂, ∼45–100 nm). This ShortCyl series (aspect ratio 4.25) had modest alignment that was attributed to the low free-energy cost for misalignment. Though the plasticized micelles (DCM present) …

Long Intergenic Non-Coding Rna 00511 (Linc00511) Genetic Variations And Haplotype Implication For Colorectal Cancer Susceptibility And Prognosis, Eman Fouad Sanad, Ahmad Abd El Hady, Mohamed Ali, Shorouk Eldash, Nermeen H. Elmorshedy, Farah Ayman, Hams M. Khattab, Amr Maher, Hadeel Ashree, Mahitab Abdelhady, Mazen Mohamed, Ahmed Adel, Sajed Khalil, Omar Alyan, Ahmed Samir, Alhassan A. Bakr, Nadia Hamdy

Pharmacy

Long intergenic non-coding RNA 00,511 (LINC00511) is considered an oncogene for various cancers. However, the association between LINC00511 single nucleotide polymorphisms (SNPs) and colorectal cancer (CRC) remains unclear. Our study aims to study whether LINC00511 SNPs could predict CRC susceptibility or prognosis, an important step-toward precision-health, based on an Egyptian CRC patient cohort. A total of 200 CRC patients and 200 cancer-free controls were genotyped for three LINC00511 SNPs − rs9906859, rs1558535, and rs17780195 using qRT-PCR. Studied SNPs were in strong linkage disequilibrium and moderately correlated in all groups. Genotype association concerning tumor stage, revealed rs1558535 AT and rs17780195 AG …

An Rna Modification Prevents Extended Codon-Anticodon Interactions From Facilitating +1 Frameshifting, Evelyn M. Kimbrough, Ha An Nguyen, Haixing Li, Jacob M. Mattingly, Nevette A. Bailey, Wei Ning, Howard Gamper, Ya-Ming Hou, Ruben L. Gonzalez, Christine M. Dunham

Department of Biochemistry and Molecular Biology Faculty Papers

RNA post-transcriptional modifications act by stabilizing the functional conformations of RNA. While their role in messenger RNA (mRNA) decoding is well established, it is less clear how transfer RNA (tRNA) modifications outside the anticodon contribute to tRNA stability and accurate protein synthesis. Absence of such modifications causes translation errors, including mRNA frameshifting. By integrating single-molecule fluorescence resonance energy transfer and cryogenic electron microscopy, we demonstrate that the N1-methylguanosine (m1G) modification at position 37 of Escherichia coli tRNAProL is necessary and sufficient for modulating the conformational energy of this tRNA on the ribosome so as to suppress +1 frameshifting otherwise induced …

Development Of A Cure In Principles Of Cell And Molecular Biology, Heather Seitz

Sabbatical Projects

This project presentation highlights the work done during sabbatical to develop an authentic research experience into BIOL135 Principles of Cell and Molecular Biology. The sabbatical allowed for development time but further work was done to measure impact and outcomes for future implementation.

Effect Of Histidine Tag On The Enzymatic Activity Of Pseudolysin And Its Interaction With The Streptomyces Metalloprotease Inhibitor (Smpi) Protein, Adewale Adeboye Adewole

Electronic Theses and Dissertations

Pseudolysin (PLN) protein is a major virulent factor in Pseudomonas aeruginosa infection. PLN belongs to the family of zinc-dependent metalloproteases. It is naturally inhibited by a smaller protein called streptomyces metalloprotease inhibitor (SMPI), secreted by Streptomyces nigrescens. Previous and current studies demonstrate that the interaction between PLN and SMPI offers unique mechanistic insights for drug development against infections caused by P. aeruginosa. This study investigated the effect of N-terminal Histidine (His) tag on the enzymatic activity of PLN and its interaction with SMPI. His-tagged PLN and SMPI proteins were expressed in bacteria and purified by affinity chromatography …

Unwrapping The Cube Visual Essay, Arthur L. Loeb, C. Todd Stewart

Loeb Design Science: Documents

A visual and conceptual essay illustrating the many faces and properties of the cube.

Development Of A Physiologically Based Pharmacokinetic (Pbpk) Model And Evaluation Of Antioxidant Capacity For Polypodium Leucotomos Extract, Christopher L. Basel

Doctoral Dissertations and Projects

The purpose of this study was to develop an equation to calculate the approximate concentration of active components in orally administered Polypodium leucotomos fern extract (PLE) and to develop physiologically based pharmacokinetic (PBPK) models for an active component of PLE or its metabolite to address the need for human pharmacokinetics (PK). Model differences based on ethnic groups were also investigated. This was a quantitative study using secondary data. It has been estimated that skin cancers account for approximately 40% of all human cancers and that approximately 13,000 people will die of skin cancer in 2024. People with darker skin experience …

Advancing Single-Molecule Nanopore Sensing: From Protein Conformation And Metal Binding To Dna Transport Via Hybrid Nanostructures, Matthew J. Odonohue

Multidisciplinary Studies Theses and Dissertations

This dissertation presents the development and application of solid-state and hybrid nanopore platforms for single-molecule analysis of biomolecular interactions. First, a silicon nitride nanopore was employed to characterize the conformational states of the transferrin receptor (TfR), enabling discrimination between its monomeric and dimeric forms, as well as from its ligand, human serum transferrin (hSTf), despite their similar molecular weights. In a separate study, the same nanopore configuration was used to track the real-time binding of titanium ions to transferrin, demonstrating single-molecule sensitivity to metal-induced conformational changes. A hybrid microtubule–solid-state nanopore (MT–SSN) was then engineered, repurposing microtubules as electrostatically anchored conduits …

Novel Nanomaterials For Developing Bone Scaffolds And Tissue Regeneration, Nazim Uddin Emon, Lu Zhang, Shelby Dawn Osborne, Mark Allen Lanoue, Yan Huang, Z. Ryan Tian

Cell and Molecular Biology Faculty Publications and Presentations

Nanotechnologies bring a rapid paradigm shift in hard and soft bone tissue regeneration (BTR) through unprecedented control over the nanoscale structures and chemistry of biocompatible materials to regenerate the intricate architecture and functional adaptability of bone. This review focuses on the transformative analyses and prospects of current and next-generation nanomaterials in designing bioactive bone scaffolds, emphasizing hierarchical architecture, mechanical resilience, and regenerative precision. Mainly, this review elucidated the innovative findings, new capabilities, unmet challenges, and possible future opportunities associated with biocompatible inorganic ceramics (e.g., phosphates, metallic oxides) and the United States Food and Drug Administration (USFDA) approved synthetic polymers, including …

Cultivation Of Botryococcus Braunii For The Production Of Hydrocarbons Suitable For Fuel Use, Bryan C. Carroll

All Theses

Energy security, rural poverty, and climate change are pressing issues of our time. Biofuels provide a solution to these issues, with a focus on sustainable aviation fuel, SAF, due to compatibility with aircraft infrastructure and energy density. This research aims to review and produce knowledge about a specific microalga, Botryococcus braunii, for its potential for SAF. First a literature review on the process was conducted followed by an experimental study on the impact of aqueous media and inorganic carbon its growth and hydrocarbon content. The literature review found the process consists of cultivation followed by lipid extraction or hydrothermal …

Yizhi Sun: Profile Of The Newest Chbc Faculty Member., Danna Jaimes-Fajardo, Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

Presents the research profile of Yizhi Sun, Assistant Professor, Chemistry and Biochemistry department. It highlights his research interests, education, and impact of his research.