Biochemistry, Biophysics, and Structural Biology Commons^™

Flux Crystal Growth Of Potassium Lanthanide Double Vanadates With Lanthanide-Dependent Coordination Number Variance, Hunter B. Tisdale, Hans Conrad Zur Loye

Faculty Publications

A series of potassium rare earth double vanadates is presented. Single crystals of double vanadates with stoichiometry K₃Ln(VO₄)₂ (Ln = La, Pr, Nd, and Sm) and crystallizing in the glaserite structure type were synthesized via a molten alkali chloride/fluoride flux reaction. Different structures were observed depending on the constituent rare earth: K₃La(VO₄)₂ crystallizes in an as-of-yet unreported modification of the typical glaserite structure in the space group P2₁/c, likely due to its larger ionic size that results in an increase in the lanthanide coordination number …

The Chemistry Of Red Lipstick: The Impact Red Lipstick Has On Society, Lilliana Weldeslassie

Electronic Theses & Dissertations (2024 - present)

Cosmetic chemistry is deeply embedded in everyday life, shaping the products people use from morning to night. Among these, red lipstick stands out as a formulation that blends complex chemistry with a cultural meaning. This thesis examines the scientific foundations of red lipstick through its chemical composition, pigment structure, toxicological history, analytical methods, and evolving sustainability practices. Historically, red lipsticks relied on high-risk ingredients such as lead, mercury, and other toxic metals, reflecting an era before chemical safety and regulatory oversight were incorporated.²¹ Modern formulations have established safer synthetic dyes, natural waxes, plant-based oils, and stabilizers created to optimize …

Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit

Electronic Theses & Dissertations (2024 - present)

The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.

In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …

Photo And Spatial Control Of Rna Structures And Functions: Exploring Positional Effects And Photo-Responsiveness Of Azobenzene Modified Nucleotides, Jinxi Du

Electronic Theses & Dissertations (2024 - present)

RNA molecules perform many important biological functions by forming complex three-dimensional structures stabilized by base pairing, tertiary interactions, and metal ion coordination. Because RNA function depends strongly on its structure, methods that allow reversible control of RNA conformation and activity are important for understanding RNA behavior and for potential therapeutic applications. However, achieving reversible and site-specific control of RNA structure, especially at the single-nucleotide level, remains challenging. In this dissertation, I developed and applied azobenzene-modified nucleotides as a chemical tool to enable optical and spatial control of RNA structure and function.

The first part of this dissertation focuses on establishing …

Advancing Lipidomics Through Fluoroalcohol-Induced Multiphase Fractionation And Orthogonal Lc×Lc–Ms Detection, Md Al Amin

Chemistry & Biochemistry Dissertations

Comprehensive characterization of the lipidome remains a significant analytical challenge due to the immense structural diversity, wide dynamic range, and complex physicochemical continuum of lipid species. Conventional extraction methods, such as those by Bligh–Dyer and Folch, and one-dimensional liquid chromatography (1D-LC) often fail to resolve this complexity, leading to chromatographic overlap, severe ion suppression, and limited coverage of low-abundance or highly hydrophobic species. This dissertation addresses these bottlenecks by establishing a separation-driven analytical framework that integrates novel fluoroalcohol-induced multiphase systems (FAiTPS) with orthogonal multidimensional liquid chromatography–mass spectrometry (LC×LC–MS).

The core of this research is the development and physicochemical characterization of …

Exploring The Limitations Of Substrate Scope In Dimethylallyltryptophan Synthases, Evan T. Miller

Theses and Dissertations--Pharmacy

Natural products (NPs), are the largest source of bioactive compounds in Nature, and are essential to the treatment of human disease. Nearly 50% of drugs approved for use from 1981 to 2019 owe some aspect of their development to NPs, either in terms of their structure, pharmacophore, or mechanism of action. However, NPs are difficult to structurally optimize. Chemoenzymatic methods for NP derivatization have been increasingly seen as practical alternatives to traditional synthetic methods. Prenyltransferases (PTs) are involved in the primary and secondary metabolism of plants, bacteria, and fungi, and they are key enzymes in the biosynthesis of many clinically …

Recirculated Submarine Groundwater Discharge Dominates Nutrient Inputs And Enhances Eutrophication Risk In A Coastal Lagoon, Júlia Rodriguez-Puig, Clara Ruiz-González, Marc Diego-Feliu, Irene Alorda-Montiel, Aaron Alorda-Kleinglass, Daniel Romano-Gude, Andrea G. Bravo, Júlia Dordal-Soriano, Javier Gilabert, Sophia Bergeler, Celine Lavergne, Gemma Casas, Marisol Manzano, Jordi Garcia-Orellana, Valentí Rodellas

OES Faculty Publications

Submarine groundwater discharge (SGD) is a widely recognized pathway for nutrient transport to coastal systems. Prior studies overlook the unique biogeochemical signatures of different SGD pathways, neglecting their differences in biogeochemical transformations and spatiotemporal factors. Here, we present an integrated assessment of nutrient delivery through three SGD pathways (fresh SGD, long‐scale recirculated SGD, and short‐scale porewater exchange), alongside surface water inputs, to evaluate their seasonality and impact on nutrient dynamics in a coastal lagoon. We conducted five field surveys in March, July, and November 2021, July 2024, and March 2025 in the Mar Menor lagoon, an ecosystem facing severe ecological …

Biochemical Investigations Of F420-Dependent Glucose-6-Phosphate Dehydrogenase From Cryptosporangium Arvum, Sarah T. Al-Noubani

2026 Spring Honors Capstones Projects

F₄₂₀-dependent glucose-6-phosphate dehydrogenase (FGD) catalyzes the conversion of glucose-6-phosphate to 6-phosphogluconolactone using the deazaflavin, Cofactor F₄₂₀. FGD from Mycobacterium tuberculosis has been investigated due to its health relevance to prodrug activation. More recently, FGD from Cryptosporangium arvum (Cryar- FGD) has been investigated due to its broader substrate specificity toward multiple sugar phosphates. Kinetic and NMR studies have shown that Cryar-FGD has dual catalytic activity as a dehydrogenase and isomerase. Further investigations are being conducted on Cryar-FGD to characterize key residues involved in catalysis.

To investigate the catalytically active residues of Cryar-FGD, …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk, Yasir A. Alshehry, Matthew S. Halquist Phd, Sandro R.P. Da Rocha Phd

Graduate Research Posters

Background

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance …

Characterization Of Phytoplankton-Excreted Metabolites Mediating Carbon Flux Through The Surface Ocean, Yuting Zhu, Hanna S. Anderson, Eli Salcedo, Samuel E. Miller, Krista Longnecker, Melissa C. Kido Soule, Sheean T. Haley, Gretchen J. Swarr, Rogier Braakman, Sonya T. Dyhrman, Elizabeth B. Kujawinski

Chemistry & Biochemistry Faculty Publications

The marine labile dissolved organic carbon (DOC) pool is a dynamic reservoir of thousands of molecules that cycles approximately one-quarter of Earth’s primary production within days to weeks. After excretion by phytoplankton and other microbes, metabolites are rapidly consumed, resulting in low standing concentrations (picomolar to low nanomolar). Despite the decades-long search for labile DOC sources and molecular identities, marine phytoplankton exometabolomes are not well characterized, largely due to difficulties in measuring small polar molecules in saline water. Here, we profiled the exometabolomes of six axenic phytoplankton species representing key functional groups including a diatom (Thalassiosira pseudonana CCMP1335), a …

Overview And Methods Of Molecular Paleontology: A Review, Shelby Touchstone

Williams Honors College, Honors Research Projects

Molecular paleontology—the study of ancient biomolecules preserved in fossils and sediments, including ancient DNA, lipids, and proteins—has motivated researchers since the 1950s, inspiring both scientific inquiry and broader cultural imagination. Think Jurassic Park. This honors thesis presents a comprehensive review of the history, current state, and methods of the field of molecular paleontology. Drawing on peer-reviewed literature and scholarly resources accessed through databases such as EBSCO and Bierce library, this review examines key techniques such as Next Generation Sequencing and amino acid racemization and will go over limitations and controversies in the field. It will also explore potential new …

An Investigation Into The Potential Role Of Thioester Bonds In Prebiotic Atp Synthesis, Adam J. Ruf

Williams Honors College, Honors Research Projects

In this project I will attempt to show a potential prebiotic pathway for the synthesis of ATP. This pathway involves the use of thioester bond containing molecules, as derivatives of these bonds have been shown to exhibit enzyme-like catalytic properties. Nuclear magnetic resonance spectroscopy will be utilized to characterize each step of the pathway to ensure it is successful.

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk

Theses and Dissertations

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance quality …

A Major Update And Improved Validation Functionality In The Mwtab Python Library And The Metabolomics Workbench File Status Website, P. Travis Thompson, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, updating its mwTab and JSON deposition text file formats and its web-based infrastructure. However, the growth of MW has been exponential since its inception in 2013 and continues to be exponential, with the number of datasets hosted on the repository increasing by 50% since April 2024. As part of regular maintenance to keep up with changes to …

31p Solution Nmr Investigation Of Abasic Dna, Clarissa R. Krimmel

Graduate Theses/Dissertations

Base excision repair (BER) mechanisms fix single base lesions in DNA, such as T:G mismatches. During the base excision repair mechanism, an abasic site (AP site) is formed as an intermediate. AP sites are unstable and highly mutagenic; they can stop DNA replication. This research investigates how the conformational properties of abasic sites in DNA affect the binding recognition of enzymes involved in DNA repair mechanisms, including BER. Three different abasic sequences are being analyzed for this research project. A second project looks at the effects of a naturally occurring purine derivative, hypoxanthine, on the DNA backbone. These hypoxanthine lesions …

Preliminary Analysis Of Soil Volatile Organic Compounds As Soil Health Indicators, Thorne Taul

Graduate Theses, Dissertations, and Problem Reports (ETD)

Over the past decade, soil health (SH) has gained popularity due to the novelty of sustainable soil use related to human wellbeing. Soil health describes the overall quality of soil and its capacity to function over time. As interest in SH grows, researchers continue to explore new soil health indicators that can improve knowledge on how soil health is assessed and managed. Some indicators directly reflect soil health status, and some indirectly relate to processes and functions occurring within the soil. Volatile organic compounds (VOCs) are naturally occurring compounds that play a role in multiple soil processes. They are associated …

Understanding The Fidelity And Specificity Of Dna Polymerase I, Bill R. Miller Iii, Andrew V. Yeager, Jake A. Collins, Alexis Blake, Elise Tate, Carol A. Parish, Eugene Y. Wu

Chemistry Faculty Publications

High-fidelity DNA polymerases employ complex mechanisms to catalyze template-dependent DNA synthesis while quickly discarding mismatches. Atomic-level structural details about short-lived states during nucleotide discrimination are necessary to gain insight into the kinetic checkpoints that contribute to fidelity. We performed microsecond molecular dynamics simulations of DNA polymerase I, large fragment, from Bacillus stearothermophilus (Bacillus fragment, or BF) in complex with a template guanine and a mismatched thymidine triphosphate to observe the early events in the process of selection against a mismatch. Although the nucleobases formed a wobble base pair early, the mismatched pair was blocked from fully entering the active site …

Developing A Tool To Measure Resistance To Sustainable Food Choices: A Pilot Study In Ireland And The Netherlands, Kate Flanagan, Bart Sinteur, Patricia J. Bulsing, John M. Kearney

SURE Journal: Science Undergraduate Research Experience Journal

Consumer uptake of a sustainable diet is critical for addressing environmental challenges and promoting public health. Understanding why consumers resist adopting sustainable eating habits can inform targeted interventions and policies. This pilot study examines whether a newly developed scale can effectively detect consumer resistance to a sustainable diet. Currently, there is a lack of research on a tool to measure consumer resistance to a sustainable diet, highlighting the need for a reliable instrument.

The aim of this study is to develop a scale, based on existing literature, to measure consumer resistance to a sustainable diet. Additionally, the study aims to …

Editorial-Sure Journal Volume 7, Issue 2, Geraldine M. Dowling, Eva Campion, Sinead Loughran, Ariane Perez-Gavilan, Josephine Treacy

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Energetics And Kinetics Of Alkali Ion Exchange In Analcime, Jinyi Liu, An T. Ta, R. Seaton Ullberg, Jean Wilfried Hounfodji, Michael Badawi, Hans Conrad Zur Loye, Simon R. Phillpot

Faculty Publications

We employ density functional theory calculations to investigate the energetics and diffusion mechanisms of alkali metal ions (Na⁺, K⁺, Rb⁺, and Cs⁺) within the analcime framework. While Na⁺preferentially adsorbs at the center of the 8-member ring, DFT calculations show that larger ions, such as Cs⁺, occupy the center of the cage due to steric constraints. The computed exchange energies indicate that exchange of Na⁺by Cs⁺is thermodynamically favorable. Migration energy barriers, determined using the climbing image nudged elastic band method, show that Na⁺is …

Self-Assembling Rna Nanostructures Are Highly Sensitive To Environmental Conditions, Jordan Aposhian, Surya Pratap S. Deopa, Scott Horowitz, Joseph D. Yesselman

Chemistry and Biochemistry: Faculty Scholarship

Recent developments in RNA nanotechnology have led to an increase in the design of specific, higher-order RNA structures, which will ultimately be used in drug delivery and immunomodulation applications. As researchers create RNA nanostructures with the intention of making them a standard tool in molecular biologists' toolkits, further investigation is required into the robustness of RNA designs. Primarily, in what different molecular contexts are the designed and intended nanostructures stable? In this work, we show that RNA nanostructure self-assembly is highly sensitive to environmental conditions by using second-order right-angle light scattering. While a test RNA hexagonal grid nanostructure forms correctly …

Design, Synthesis And Biological Activities Of N-Substituted Phthalimide Derivative, Beaula Mangundah

Honors Theses

Phthalimides are a group of compounds among bicyclic non-aromatic nitrogen heterocycles that have gained recognition for their bioactivity across various fields, notably anti-cancer, anti-microbial, anti-oxidant, and anti-inflammatory. This study discusses the synthesis of a novel phthalimide derivative and provides an analysis of its biological activity. It was conducted through a Boric acid Imide synthesis and yielded a successful derivative using hexylamine. The product was evaluated in vitro for antimicrobial, anticoagulant, and anti-inflammatory properties using Kirby-Bauer disk diffusion, clotting time, hemolysis inhibition, and protein denaturation assays. It showed mild anticoagulant and anti-inflammatory activity.

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, …

Book Of Abstracts, Seton Hall University

2025 Augustine Undergraduate Research Symposium

No abstract provided.

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% …

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 …

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 …