Biochemistry Commons^™

Ion-Dna Interactions As A Key Determinant Of Uracil Dna Glycosylase Activity., Sharon N Greenwood, Alexis N Dispensa, Matthew Wang, Justin R Bauer, Timothy D Vaden, Zhiwei Liu, Brian P Weiser

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Because of their ubiquitous presence, ions interact with numerous macromolecules in the cell and affect critical biological processes. Here, we discuss how cations including Mg²⁺ alter the enzymatic activity of a DNA glycosylase by tuning its affinity for DNA. The response of uracil DNA glycosylase (UNG2) to Mg²⁺ ions in solution is biphasic and paradoxical, where low concentrations of the ion stimulate the enzyme, but high concentrations inhibit the enzyme. We analyzed this phenomenon by modeling experimental data with a statistical framework that we empirically derived to understand molecular systems that display biphasic behaviors. Parameters from our statistical …

Sequence Conservation Of Suppressor Of Ikk Epsilon Phosphorylation Sites, Kaydence M. Isaacs

Undergraduate Honors Theses

Suppressor of IKK epsilon (SIKE) is a protein that is implicated in immune response signaling pathways. SIKE interaction networks suggest roles in cell motility and macromolecular complexes mediating kinase/phosphatase activity. In this project, we aim to better understand the function of SIKE by analyzing amino acid sequences across different species. In human SIKE, viral infection leads to phosphorylation of SIKE at defined serine residues. Comparing SIKE sequences, and specifically these phosphorylation sites, allows us to discover its ancestral connections to innate immune function. This has particular applications in bridging the evolutionary gap between fungi and metazoa SIKE sequences. Multiple sequence …

The Effects Of Ataxin-1 Overexpression In The Central Nervous System On Specific Behavioral And Physiological Characteristics Of Drosophila Melanogaster, Sydney Davis

Theses and Dissertations

Spinocerebellar ataxia type 1 (SCA1) is a dominantly inherited neurodegenerative disease caused by a CAG repeat expansion in the ataxin-1 gene, which results in an abnormally long polyglutamine tract. Similarly, overexpression of wildtype Ataxin-1 (wt-Atx-1) in Drosophila melanogaster leads to neurodegeneration, reduced lifespan, and impaired negative geotaxis. Observations include disruptions in sleep-wake cycles, increased oxidative stress biomarkers (like protein carbonyls), and dysregulation of developmental genes such as armadillo (arm) and nemo kinase (nmo). Additionally, elevated expression of SUMOylation-related genes (Aos-1, Uba2, and dSmt3 or dSumo) and increased SUMO protein levels indicate enhanced SUMOylation in the brain. Quantitative analysis of neuronal …

Exploring Sexual Dimorphism In A Drosophila Melanogaster Model Of Spinocerebellar Ataxia Type 1, Madelyn Hunter

Theses and Dissertations

Neurodegenerative diseases affect over 36 million people and are characterized by loss of motor control, neuronal degradation, and behavioral changes. The most common of these diseases exhibit sexually dimorphic effects. In this study, Spinocerebellar ataxia type 1 (SCA1) was modeled in the Drosophila central nervous system using the yeast hybrid UAS/GAL4 system. Locomotor activity and clock gene expression was monitored for male and female SCA1 and control flies. Clock genes such as per, tim, Clk, and cyc were monitored over a 24-hour period using qRT-PCR, and distinct sexual dimorphism was detected in locomotor activity and in gene expression for SCA1 …

Chronic Inflammation: The Link Between A High Added Sugar Diet And Disease, Anna Collins

Senior Honors Theses

The modern diet includes many processed foods that contain added sugars, resulting in a significant increase in daily glucose and fructose consumption. Considering this, there is an increased effort to uncover the effects of excess sugar intake on the body’s health and metabolism. Strong evidence supports the connection between a high added sugar diet and the presence of chronic, low-grade inflammation due to cellular distress and metabolic dysfunction. Prolonged inflammatory responses are linked to tissue damage and the development of various metabolic diseases that are prevalent in modern society, such as obesity, fatty liver disease, cardiovascular disease, and type 2 …

Phosphomimetic Substitution Of Serine Residue Ser260 With Aspartate Suggests Regulation Of Activity Of Human Cytosolic Malate Dehydrogenase By Phosphorylation, Charles Pelagalli '25, Luke Tischio, Kathleen Cornely

Chemistry & Biochemistry Faculty Publications

Human cytosolic malate dehydrogenase (MDH1) is a key enzyme involved in the malate-aspartate shuttle of eukaryotic cells, and which catalyzes the reaction of oxaloacetate to malate. As MDH1 is responsible for maintaining redox homeostasis by regeneration of NAD+ for glycolysis, its regulation is of particular interest in pharmaceutical applications, specifically in treating cancer cells that proliferate quickly and hence rely greatly on glycolysis. While the regulation of MDH1 by the phosphorylation of key residues has been previously documented, work still remains in identifying the specific residues involved in regulation of the enzyme by phosphorylation. In this study, we used …

Apolipoprotein E4, Tauopathy, And Brain Injury: Molecular Insights Into Alzheimer's Disease Pathology, Nashanthea J. Roland

Theses & Dissertations

Alzheimer’s disease (AD) is the world’s leading cause of dementia, characterized by progressive atrophy of the hippocampal and cortical brain regions, synapse damage and loss, and a buildup of senile plaques and neurofibrillary tangles composed of β-amyloid peptides and hyperphosphorylated tau, respectively. While age is the most significant risk factor for developing AD, apolipoprotein E4 (APOE4) is the strongest genetic risk factor for AD. Although it is known that APOE4 influences tau pathology, the molecular mechanisms by which APOE4 drives AD pathogenesis and progression remain unclear. In addition to intrinsic contributions to AD, there are many extrinsic factors that can …

Understanding The Role Of Sabp2-Interacting Proteins Sip432: A Premnaspirodiene Oxygenase Enzyme In Stress Signaling, Cristiana F. Martinez

Undergraduate Honors Theses

This study focuses on the characterization of a SABP2-interacting protein (SIP)-432. SIP432 is a putative premnaspirodiene oxygenase-like P450 enzyme. Premnaspirodiene is a 15-carbon compound that can be converted into antimicrobial compounds by a hydroxylation reaction. The interaction of SIP432 with SABP2, a critical component of salicylic acid-mediated plant immunity, implies a role for SIP432 in plant stress signaling. This study uses the T-DNA knockout mutant of Arabidopsis thaliana SIP432 (homolog of NtSIP432) to help understand its role in abiotic and biotic stress responses. Plants were subjected to abiotic and biotic stress to understand their role in stress response pathways. Gene …

A Comparative Analysis Of Small Nuclear Rna Sequences In Spinacia Oleracea, Arabidopsis Thaliana, And Homo Sapiens, Nhi T. Nguyen

2025 Spring Honors Capstone Projects - Archive

In eukaryotes, the structure and function of the Sm core and its associated small nuclear ribonucleoproteins (snRNPs) play a significant role in pre-mRNA splicing. These snRNPs exhibit a high degree of conservation. While plants also utilize alternative splicing, the conservation of plant snRNAs and other non-coding RNA such as snoRNA and scaRNA, which assemble the Sm core, remains largely unexplored. In this study, plant sequences were compared with human sequences using the multiple sequence alignment program Jalview to determine the conservation of snRNPs in other non-coding RNA. Sequences analysis showed that the Sm site in Spinacia oleracea and Arabidopsis thaliana …

Activity-Based Protein Profiling On Nucleophilic Amino Acid Residues With Pyrocarbonates, James Van Horn

Chemistry & Biochemistry Undergraduate Honors Theses

The complexity of the proteome requires strategies that efficiently characterize protein functions. Activity-Based Protein Profiling (ABPP) is a method that identifies enzyme activity by targeting key catalytic residues. This study focused on histidine, a residue involved in enzymatic catalysis, metal coordination, and protein-protein interactions. Despite its importance, histidine-specific chemical probes are limited due to its variable reactivity. This work developed and characterized a histidine-specific probe using a pyrocarbonate-based mechanism. Singleresidue assays confirmed selective reactivity of the probe with histidine over other nucleophilic amino acids. Further testing on enzymatic proteins and lysed cell proteomes showed that the probe modified histidine residues …

Novel Chloroviruses With Unique Glycans On Their Major Capsid Proteins, Cayden J. Homolka

Honors Program: Senior Projects (Public)

Chloroviruses, of the family Phycodnaviridae, are large, dsDNA viruses with a genome of 290 to 410 kb. These virus genomes are so large that they are classified as “giant viruses”. Within this genome, up to 16 tRNAs and 330 to 450 proteins are encoded. Among the massive amounts of genes and proteins are unique carbohydrate synthesis/metabolism genes, which are responsible for the glycosylation of chloroviruses major capsid proteins. In most viruses, these proteins are glycosylated by the host enzymes located in the endoplasmic reticulum. Instead, Chloroviruses encode their own glycosylation machinery; essentially decorating themselves. Furthermore, these chlorovirus glycans are unlike …

Structural Stability Of Fgf1-Fgf2 Dimer Established Via Salt Bridges With Mutation K296q, Ashleigh Letterman

Chemistry & Biochemistry Undergraduate Honors Theses

Fibroblast Growth Factors (FGFs) are a family of cell-signaling proteins. FGF, specifically the FGF-1 subfamily, which contains FGF-1 and FGF-2, is important in several biological functions such as wound healing, cell proliferation, and angiogenesis. FGF-1 has cell proliferation properties and FGF-2 has angiogenic properties. These FGFs have great potential for wound-healing therapy medications...

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Synthesis And Characterization Of 3,5 Trifluoromethyl Tpm With A Metal Carbonyl Complex, Emily P. Berkman

Undergraduate Honors Thesis Collection

Tris(pyrazolyl)methane (Tpm) ligands have a central carbon with 3 pyrazole rings attached. These were discovered in 1970 and have since been synthesized with many substituents on the rings. Based on the parent structure, my goal was to synthesize a fluorinated Tpm derivative. By adapting existing procedures, I have synthesized a Tpm derivative with trifluorinated methyl groups in the 3 and 5 positions of the pyrazole ring. The fluorinated ligand is expected to be electron withdrawing and exhibit interesting chemistry when bound to a metal center. Future directions of the project will be discussed.

Disulfide-Cleavable Linkers In Antibody-Drug Conjugates For Targeted Cancer Therapy, Emily Hwang

Undergraduate Honors Thesis Collection

This project aims to discover a way to improve the safety of and reduce adverse side effects of disulfide-linked antibody-drug conjugates. Disulfide-cleavable linkers for antibody-drug conjugates function by exploiting the differential concentrations of dominant thiol species in the blood plasma and in the cytosol of malignant cells. This project aimed to identify a relationship between the stability of disulfide cleavable linkers in the blood plasma and disulfide linker structure, to prevent premature release of the cytotoxic drug. Three disulfide linker analogs with varying carbon chain lengths were synthesized through reaction with 2,2’-dipyridyl disulfide. Each analog was conjugated to a fluorescent …

Cultural Health Benefits And Challenges Of Food Preparation And Consumption: A Comparative Study Of The United States, Italy, And Norway, Natalie G. Link

Undergraduate Honors Thesis Collection

This study aims to investigate the cultural health benefits and challenges associated with food preparation and consumption in the United States, Italy, and Norway, with a particular focus on citizens in lower socioeconomic levels. By examining the dietary habits, social structures, and health outcomes in these three countries, this research aims to uncover broader insights into the health status and well-being of their respective populations. The study will employ secondary data analysis approach examining existing research on cultural practices and social support systems. The findings of this research will contribute to a deeper understanding of the complex interplay between food …

Semiconductors In Space: Data Analysis Of Microgravity's Impact On Crystal Formation, Keegan Jo Jackson

Undergraduate Honors Thesis Collection

Comprehensive data analysis on crystal growth in microgravity is a requisite to inform understanding of prior work. Our research constructed and analyzed a database containing data gathered from research focusing on semiconductors grown in microgravity. Data curation spanned multiple decades, countries, and semiconductor materials. All relevant reported information was recorded in the database, notably data regarding the metrics used to determine the impact space had on crystal growth: size, structure, uniformity, and performance. After data cleaning and data processing, the database was organized and readied for analysis. Data analysis was performed using RStudio and SciKit-learn. RStudio was employed for data …

Linking The Past And The Future: Understanding How Pollutants Cause Corrosion During An Oddy Test, Kylie Blair Blake

Undergraduate Honors Thesis Collection

Artifacts and artwork continue to tell a story long after a time or culture has disappeared. Preventive art conservation science involves careful and responsible management of the objects entrusted in the care of the museum staff to ensure environmental and display conditions do not cause damage so future generations can observe and learn about past cultures. An accelerated metal corrosion test, the Oddy test, has been used to help determine the suitability of display and storage materials. The Oddy test is subjective, so newer methods are being developed involving the use of gas chromatography and mass spectrometry to identify specific …

A New Transition Metal Borate, Co6(B24O39(Oh)6(H2O) 6·2.21h2O, Synthesized Via A Mild Hydrothermal Synthesis, Alevtina Maksimova, Patrick Belt, Nilah Whitfield, Mark D. Smith, Gopabandhu Panigrahi, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

A new transition metal borate hydrate, Co₆B₂₄O₃₉(OH)₆(H₂O)₆·2.21H₂O, was synthesized via a mild hydrothermal method using boric acid as the melt. The compound crystallizes in the trigonal space group P 3‾ with lattice parameters a = b = 13.17840(10) Å, c = 12.3287(2) Å, and a unit cell volume of 1854.27(4) ų (Z = 2). This borate hydrate crystallizes in a new structure type comprised of layers containing [BO3] trigonal planar units and [BO4] tetrahedra that are linked by CoO6 and Co(OH)2(H2O)4 octahedra via corner-sharing. The …

Innovation Scholars Program, Lauren Voll, Olivia Latour, Owen Montreuil, Kaennae Mortimer

Celebrating Scholarship and Creativity Day (2018-)

The innovations scholar program spans roughly five months and included two trips to Mayo Clinic Rochester. The team of four undergraduate students and an MBA student worked with Mayo Clinic ventures to assess the viability of a few patents. The project included a 40-page comprehensive paper as well as a 30-minute presentation. The specific details are protected under an NDA agreement however our key takeaways are shared on the poster.

Antiproliferative Effects Of Salvia On Breast Cancers., Allison C. Portaro

College of Arts & Sciences Senior Theses

Breast cancer is the most common cancer diagnosed in female adults, with 2.3 million new cases worldwide in 2020. Plants have been used in traditional medicine and are a potential source of pharmaceuticals. One example is the large Lamiaceae (mint) family. The Salvia genus, commonly known as the sages, is the largest genus in Lamiaceae with almost 900 known species. Salvia lyrata (lyre-leaved sage) has a history of Native American medicinal use to treat cancers and other ailments resulting in this plant being referred to as ‘cancer weed.’ Extracts were produced from the leaves of S. lyrata, S. lyrata …