Biochemistry Commons^™

Spin-Label Probing Of Gp28 Elucidates Interactions With Lipid Vesicles Using Cw-Epr, Maxwell Sutherland, Binaya Baral, Gary Lorigan

ONU Student Research Colloquium

The phage protein gp28 is a bacterial membrane lysis protein that functions outside of currently understood canonical pathways for bacterial lysis. Primarily, lysis is done in conjunction with proteins called spanins, however about 15% of gram negative bacteria infecting phages have coding for spanins. This led to the discovery of the disruptins, a class of non-spanin outer membrane disrupting proteins which includes gp28 from the φKT phage. To understand the mechanism in which gp28 disrupts the outer membrane, we employ spin labeling of the protein in its synthesis and create samples of artificial membranes. Using electron paramagnetic resonance (EPR), we …

Optimizing Itpa R178c Assays Via Hplc, Jared J. Reisnouer, Wally D. Pines

2026 Symposium

Two of the major nucleotide bases in DNA and RNA (Adenine and Guanine) are derived from the purine Inosine Monophosphate (IMP). IMP may occasionally form the noncanonical nucleotide Inosine Triphosphate (ITP) within the cell and become incorporated into DNA during replication, leading to potentially lethal errors. To combat this, human cells produce the “housekeeping” enzyme Inosine Triphosphatase (ITPA) to revert ITP to IMP. A mutation of this protein that replaces the 178th amino acid Arginine with Cysteine (R178C) is associated with a fatal infantile encephalopathy. Previous assessments of enzyme-substrate binding and catalysis for ITPA variants have been run at a …

Assessment Of Total Cellular Protein Following Fatty Acid Treatment Using The Bca Assay, Carli B. Maguire

Create@State

Fatty acids can influence cellular metabolism and protein homeostasis, potentially altering total protein content within cell samples. Accurate quantification of total protein concentration is essential for standardization for further biochemical assays and ensuring reproducibility. In this study, adherent mammalian cells were treated with a defined fatty acid preparation under controlled culture conditions. Following treatment, whole-cell lysates were collected and total protein concentration was determined using the bicinchoninic acid (BCA) assay. The BCA assay is a colorimetric method based on the reduction of Cu²⁺ to Cu¹⁺ by peptide bonds under basic conditions, followed by formation of a purple-colored complex between bicinchoninic …

Evaluating The Impact Of K135t Mutation On Malate Dehydrogenase Kinetic Activity, Emily Frost, Kaitlyn Mello

Undergraduate Research Symposium (2026- )

Malate Dehydrogenase (MDH) is a key protein in the citric acid cycle; its dysregulation can have catastrophic impacts, such as neurological and metabolic disorders, and various cancers. MDH catalyzes the reversible oxidation-reduction reaction between malate and oxaloacetate, also reducing NAD+ to NADH in the process. The citric acid cycle is one of the central metabolic pathways, connecting to other essential pathways, such as amino acid and fatty acid biosynthesis, highlighting the importance of understanding how MDH works. A key site in MDH is the flexible loop region (amino acids 119-137), responsible for substrate binding, catalysis, and orientation. The flexibility of …

Proline To Serine Mutation In Flexible Loop Region Of Malate Dehydrogenase, Anna Molstad, Hannah Robertson

Undergraduate Research Symposium (2026- )

Malate Dehydrogenase (MDH) is an essential enzyme that converts malate to oxaloacetate using the reduction of NAD+ to NADH. In humans, MDH plays a role in energy metabolism by catalyzing a key step of the citric acid cycle, important for energy production. Other indirect roles for MDH include gluconeogenesis and reoxidizing NADH from fatty-acid β-oxidation. An important feature of MDH is a flexible loop region that can alter substrate binding and enzyme activity, but its role is not well understood. Our study investigated how Pro123 to Ser (P123S) mutation in the flexible loop region affects MDH function. We hypothesized that …

Evaluating Elisa-Based Domoic Acid Detection Methods In Fetal And Maternal Samples Of California Sea Lions (Zalophus Californianus), Deanie Woodruff, Emily Lickiss, Samuel Gardiner, Mia Gastile, Elizabeth Sandoval, Florybeth La Valle

Seaver College Research And Scholarly Achievement Symposium

Harmful algal blooms produced by the diatom Pseudo-nitzschia regularly expose marine mammals along the California coast to domoic acid (DA), a neurotoxin that bioaccumulates in marine food webs. In California sea lions (Zalophus californianus), domoic acid exposure is associated with seizures, hippocampal injury, and maternal-fetal transfer of the toxin that can result in abortion. Bloom events have led to large numbers of stranded sea lions along the California coast. Although some clinical and neurological effects of domoic acid toxicosis have been documented, especially with regard to the hippocampus, there is limited understanding of how domoic acid concentrations fluctuate over the …

Identification Of Covalent Catechin Adducts Of Enoyl-Acp Reductase (Fabi) From E. Coli Using Mass Spectrometry, Francisco G. Atwi, P. M. Joyner, Rustin Ghidari

Seaver College Research And Scholarly Achievement Symposium

Enoyl-ACP reductase (FabI), an enzyme which is inhibited by catechin, is essential for lipid biosynthesis in bacteria (E. coli). Another FabI inhibitor, triclosan, has strong antibacterial effects,1 but overuse can be detrimental to the environment. Flavonoids, a class of dietary compounds, are known to have potent inhibitory effects on FabI and other kinases.2,3,4 Adducts form as a result of the biochemical reaction between flavonoids and cysteine, a modification which can be verified by m/z shifts on the mass spectra.5 Samples of E. coli protein with overexpressed FabI are utilized: the wild type with ordinary primary structure, and mutant type lacking …

Asphalt Pavement Rejuvenation Investigated By Nuclear Magnetic Resonance Relaxometry, Catherine Skaggs

Miners Solving for Tomorrow Research Conference

Asphalt is a relatively inexpensive material commonly used for road pavements; however, asphalt ages from exposure to oxygen and UV radiation, leading to loss of elasticity, which leads to cracks and potholes. To slow or reverse asphalt aging, pavement preservation treatments are in use. It’s unclear whether these treatments truly rejuvenate the pavement structure or merely offer a short-term benefit. Nuclear Magnetic Resonance (NMR) relaxometry is an analytical technique that uses the recovery of excited nuclear magnetization as a parameter to gain insights into molecular environments. Recovery-time distributions gathered from asphalt materials show differences between regular and rejuvenated asphalt samples, …

Recombinant Gelonin: Purification And Functional Validation For Electroporation-Assisted Delivery, Eleni Zivla, Giedrė Šilkūnienė, Andrei G. Pakhomov, Mantas Šilkūnas, Olga N. Pakhomova

Knowledge and Creativity Expo

Type I ribosome-inactivating proteins, such as gelonin, are enzymatically potent toxins but are effectively non-toxic under physiological conditions because they are unable to cross the plasma membrane[1]. Pulsed electric fields (PEF) overcome this delivery barrier by transiently permeabilizing the plasma membrane, allowing direct cytosolic entry. This enhances gelonin cytotoxicity by several thousand-fold, highlighting gelonin’s potential as an electrochemotherapy candidate[2]. Here, we present a recombinant gelonin (rGel) expression platform in E. coli with HPLC-based purification that enables reproducible protein production and structure-guided engineering.

The mature gelonin sequence (residues 47–297) was cloned into pET-32a(+) with an N-terminally fused Trx-6×His tag and TEV …

Have You Had Your Vitamins Today? Development Of An Lc-Ms/Ms Method With A 100% Aqueous Gradient To Simultaneously Measure B Vitamins In Plasma From Study Participants In A “Greens” Nutritional Supplement Clinical Trial, Kennedy Brothers, Abigail Davis, Anna Losher, Yusra Ahmed, Sora Ghanem, Matthew J. Vergne

Student Scholar Symposium

This study assessed the absorption of key micronutrients from the multi-ingredient supplement using a novel developed LC-MS/MS method capable of analyzing B vitamins in a single run.

The study a randomized, double-blind, placebo-controlled crossover trial with 16 healthy participants (8 males, 8 females) to measure plasma nutrient appearance over 8 hours after supplement consumption. Serial blood samples were collected pre-consumption and at specified intervals post-ingestion. The novel LC-MS/MS method simultaneously quantified biotin, nicotinamide, pyridoxine, riboflavin, and thiamin in blood samples.

Results:The LC-MS/MS method had a range of 0.1 ng/mL to 1000 ng/mL and it proved to be robust and …

Structural Basis Of A Class Ii Ribonucleotide Reductase Found If Mycobacterium Tuberculosis, Leah Jacob

Student Scholar Symposium

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a leading global health challenge, particularly due to its ability to enter a dormant, drug-tolerant state that enables long-term persistence within the host. Just before dormancy, Mtb replicates its entire genome creating DNA precursors for when the infection reactivates. Ribonucleotide reductases (RNRs) play a critical role in bacterial survival by catalyzing the conversion of ribonucleotides into deoxyribonucleotides, a necessary step for DNA replication and repair. The class II RNR, NrdZ, has been implicated in facilitating Mtb persistence under hypoxic stress conditions, yet its structural and mechanistic function remains largely uncharacterized. …

From Venom To Medicine: Harnessing Animal Toxins For Drug Discovery, Christine Vega, Ying Jia

Research Colloquium

Background: Drug development research has long focused on synthesizing novel therapeutics while overlooking isolation from naturally available sources such as animal venoms. Recently, the discovery of the therapeutic effects of highly bioavailable animal venom caused the field of venom research to soar in popularity. Animal venom serves as a natural, sophisticated tool optimized over millions of years by evolution with the ability to bind to ion channels such as nAChRs, non-specific ligand-gated ion channels distributed throughout the human nervous system. However, purifying individual venom toxins from crude venom is challenging due to its availability. Therefore, synthesizing large quantities of venom …

Antioxidant Properties Of Phytochemicals In Watercress And Mint Extracts In Serum Albumin, Perla Tovar

Undergraduate Research Conference

Hypothesis: Phytochemicals present in mint and watercress help stabilize protein under oxidative stress. Main Objective: Analyze the interaction of HSA with different phytochemicals present in mint extract.

The Fractography Of Bone: Impact Of Flat Bone And The Story It Tells, Abigail Hoffmeister, Chase Freeman, Brandon Mendoza, Nathaniel Fitch, Annie Markarian, Jack Tran, Joshua Lau, Nicholas Tran

Seaver College Research And Scholarly Achievement Symposium

Fractography as a method for fracture analysis has been applied widely to materials that range from glass to ceramics and polymers of varying compositions. Very limited research has been done, however, to apply this knowledge of fractography and fracture patterns to bone. With the goal of telling the story of how a bone was broken, this research focuses on observing known patterns of fracture in polymers, and applying these patterns to bone. For the purposes of this research, porcine scapulae were acquired, dissected from surrounding tissue, and broken using a standardized weight drop at varying heights. The fractured bone was …

Diets And Environmental Impacts - Generational Outlook, Aspen Hopper, Melanie Jex

Student Research Symposium

How different diets impact the environment: Are we aware?

Determining The Kinetic Basis Of Crispr-Cas12a2 Function, Sobita Kunwar, Thomson Hallmark, Dylan Keiser, Bronson Naegle, Sudeshna Manna, Aaron Thomas, Chase L. Beisel

Student Research Symposium

CRISPR- Cas (Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR associated) systems are bacterial adaptive immune systems that protect bacteria against mobile genetic elements such as viruses and plasmids^1,2.

Solving The Structure Of An Ancestral Protein Tyrosine Phosphatase, Natalie Turcsanski, Edna Armah

Student Research Symposium

Protein tyrosine phosphatases (PTPs) regulate cell signaling by removing phosphate groups from tyrosine residues. Malfunction of these enzymes can lead to diseases such as diabetes and cancer. A conserved feature among PTPs is the catalytic acid loop, essential for phosphate removal. Computational analysis of PTP structures revealed that ancestral PTPs have considerable variation in conformations of this loop, sparking interest in their further study. The Asgard group, identified as ancestral to eukaryotic PTPs, was successfully expressed and purified under optimized conditions. Current efforts focus on optimizing crystallization to obtain larger crystals for structural analysis. This project will investigate the allosteric …

Determining The Function Of Type Iv-B Crispr-Cas Systems, Eric Jenkins, Brendon Guinn

Student Research Symposium

CRISPR-Cas systems are a diverse group of prokaryotic adaptive immune systems that defend against Mobile Genetic Elements (MGEs) such as bacteriophages and plasmids. CRISPR-associated (Cas) proteins bind to guide RNAs (crRNAs) transcribed from a DNA repeat array (CRISPR array) containing spacers complementary to MGEs. Upon infection by a MGE, the Cas protein-crRNA complex binds to the target sequence in the invaders genome and cleaves the nucleic acid.

First-In-Class Peptide Molecules Targeting The Mien1 Cancer Signaling Pathway, For Which No Inhibitors Have Been Identified To Date., Amit Tripathi, Jamboor K. Vishwanatha

Research Symposium

Background: Migration and Invasion Enhancer 1 (MIEN1) is a critical oncogene that drives cancer cell migration, invasion, and epithelial-to-mesenchymal transition (EMT) in various cancers. MIEN1 overexpression is linked to aggressive tumor progression and poor prognosis. Despite its established role in cancer biology, targeted therapeutic options remain unexplored. This study aimed to identify and characterize first-in-class therapeutic molecules targeting the MIEN1 signaling pathway to inhibit cancer progression.

Methods: To develop novel bio-active peptides, we leveraged conserved immunoreceptor tyrosine-based activation motif (ITAM) and prenylation motifs within the MIEN1 protein sequence. Using rational peptide design, we identified and synthesized bioactive peptides, namely LA3IK …

Transcription Factor Binding And Discovery Of Novel Gene In The Opportunistic Human Pathogen, Pseudomonas Aeruginosa, Alaina Westee

Symposium of Student Scholars

Pseudomonas aeruginosa (PA) is a gram-negative, ubiquitously-found bacterium that primarily causes nosocomial, or hospital-borne, infections within immunocompromised patients. Therefore, it has been deemed a critical priority pathogen by the World Health Organization (WHO) and the Center for Disease Control (CDC), generating a need for research on its fundamental biology. The Van Dyke laboratory focuses on proteins called transcription factors, which promote or repress gene expression to regulate an organism’s functioning. We are specifically studying the cadmium-responsive transcription factor, CadR, due to the importance of metals in virulence and the lack of information on PA’s response to metal fluctuations. We intend …

In-Silico Modeling And Characterization Of Kcc2 Protein Interaction With A Small Molecule Direct Agonist Identifies Potential Binding Sites For Modulating Behaviors Associated With Substances Of Abuse, William Hai Dang Ho, Alfred Amendolara, Kenyon Mitchell, Jaden Miner, Ruth Northcott, Braxton Bingham, Andrew J. Payne

Annual Research Symposium

Purpose

KCC2 is a potassium-chloride cotransporter that plays a critical role in neuronal function by regulating GABAergic signaling via chloride gradients. Maintaining this concentration gradient is crucial for balancing excitation and inhibition in the brain. While KCC2 dysregulation has been implicated in epilepsy and seizures, recent studies suggest that KCC2 inhibition results in phenotypes mirroring those seen in chronic opioid dependence. As such, increasing evidence support KCC2 being a potential therapeutic target for modulating behaviors associated with substances of abuse. Currently, only a few direct small molecule agonists against KCC2 have been reported, and no definitive active site on the …

Probing The Stability Of Designed Protein, Axel Irianni, Shuvo Chakraborty, Maral Afshinpour

SDSU Data Science Symposium

Naturally occurring proteins have evolved to perform specific biochemical functions, and their amino acid sequences are optimized for those functions rather than for stability. Enhancing protein stability without compromising its function is highly desirable for biotechnological applications, such as vaccine design. Computational protein design algorithms offer a solution by making targeted amino acid changes to the native protein sequence, potentially enhancing stability without the need for the lengthy, labor-intensive, and costly experimental processes typically involved in stabilizing proteins. There are various categories of computational protein design algorithms, and it remains unclear which approach is the most effective. In this study, …

Exploring Biosignatures And Biogeochemical Processes In Lanzarote Lava Tubes: Implications For Martian Analog Research, Vera Palma, Ana Z. Miller, Francesco Sauro, Bogdan P. Onac, José M. De La Rosa, Sara Gutiérrez-Patricio, Beatriz Cubero, José A. Gonzalez-Perez, Jesus Martínez-Frías, A Teresa Caldeira

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Exploring Pristine Microbial Ecosystems From The Uninhabited Volcanic Selvagens Islands, Pedro N. Jiménez-Morillo, Sara Gutiérrez-Patricio, Vera Palma, Ana Teresa Caldeira, Nicasio Tomás Jiménez-Morillo, Ana Z. Miller

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Improving The Drug Antipyrine: Synthesis Of N2-Aryl Analogs Through Oxidation Of Dihydroantipyrines, Eli Mans

Student Academic Conference

Idiopathic Pulmonary Fibrosis (IPF) is a progressive and fatal lung disease that affects thousands of people worldwide. Current drugs are used in clinical settings to treat IPF but these drugs have low efficacy and a high monetary costs. The molecule antipyrine has been identified by colleagues at Mayo Clinic as an early-stage drug candidate for treatment for IPF. The Jasperse group is synthesizing analogs of antipyrine to create a drug library for improved IPF treatment. A novel three step process via a silyl enol ether intermediate has been developed to convert a C-C bond to a C=C bond between C4-C5 …

Hgs-3 The Influence Of A Tandem Cycling Program In The Community On Physical And Functional Health, Therapeutic Bonds, And Quality Of Life For Individuals And Care Partners Coping With Parkinson’S Disease, Leila Djerdjour, Jennifer L. Trilk

SC Upstate Research Symposium

Purpose Statement: Several studies have shown that aerobic exercise can have a positive impact on alleviating symptoms experienced by individuals with Parkinson's disease (PD). Despite this evidence, the potential benefits of exercise for both PD patients and their care partners (PD dyad) remain unexplored. This research project investigates the effectiveness, therapeutic collaborations, and physical outcomes of a virtual reality (VR) tandem cycling program specifically designed for PD dyads.

Methods: Following approval from the Prisma Health Institutional Review Board, individuals with PD were identified and screened by clinical neurologists. The pre-testing measures for PD dyads (N=9) included emotional and cognitive status …

A Comparison Of In Vitro Studies Between Cobalt(Iii) And Copper(Ii) Complexes With Thiosemicarbazone Ligands To Treat Triple Negative Breast Cancer, Duaa R. Alajroush, Chloe B. Smith, Brittney F. Anderson, Ifeoluwa T. Oyeyemi, Stephen J. Beebe, Alvin A. Holder

Undergraduate Research Symposium

Triple negative breast cancer (TNBC) is one of the most aggressive forms of breast cancer, and disproportionately affects African American women. TNBC cells lack the common hormone receptors that many pre-existing cancer treatments target. Fortunately, metal-based complexes with thiosemicarbazone ligands have gained significant attention for their potential as anti-cancer agents. Cobalt(III) complex ([Co(phen)2(MeATSC)](NO3)3•1.5H2O•C2H5OH]) and Copper(II) complex ([Cu(acetylethTSC)Cl]Cl•0.25C2H5OH) specifically have properties of high toxicity, which can contribute to decreased cancer cell activity. The effects of these complexes are currently being investigated on cancerous and non-cancerous breast cell lines. The cytotoxic effect of the cobalt(lll) complex and the copper(ll) complex was analyzed …

Coomassie Brilliant Blue Dye As A Method For Analyzing Fracture Markings In Bone, Abigail Hoffmeister, David Harutunyan, Matthew Aizawa, Everett Baker, Brandon Mendoza, Chase Freeman, Siran Iskanian

Seaver College Research And Scholarly Achievement Symposium

Coomassie Brilliant Blue Dye is a dye commonly used to stain proteins. Because of its ability to adhere to proteins, this research has focused on perfecting a method of dyeing a fractured flat bone in order to most accurately observe and analyze fracture markings within the trabecular layer. Stereoscopic microscopy was the chosen technique of analysis for this research because of its proven effectiveness in glass and ceramic fractography to observe varying depths. In order to most effectively apply stereoscopic microscopy to this research, the following variables were manipulated to maximize color contrast in the trabecular layer in order to …

Evaluation Of Ergosterol And Its Metabolites As Lxr Agonists And Their Anticancer Potential In Colon Cancer, Yogain Taank, Navneet Agnihotri

Research Symposium

Purpose: Aberrant cholesterol homeostasis is a well-recognized hallmark of cancer and implicated in metastasis and chemotherapeutic resistance, the two major causes of cancer associated mortality. Liver X receptors (LXRs) are the key transcription factors that induce cholesterol efflux via enhancing the expression of ABCA1 and ABCG1.

Methods: Molecular docking and dynamic simulation studies were done to assess the binding affinity and stability of the receptor ligand complexes. Activation of LXRs was evaluated using the luciferase reporter assay. qRT-PCR and western blotting was done to analyse the mRNA and protein expression of cholesterol homeostasis genes. Flow cytometric analysis was carried out …

Long Non-Coding Rna As A Potential Diagnostic Tool In Coronary Artery Diseases - A Systematic Review, Arthi Sri A.S, Vishnu Priya Veeraraghavan

Annual Research Symposium

POSTER - SYSTEMATIC REVIEW - LONG NON CODING RNAS AS DIAGNOSTIC MARKER FOR CAD