Biochemistry Commons^™

Abnormal Trafficking And Processing Of Multiple Matrix Metalloproteinases Drive Cartilage Defects In Congenital Disorders Of Glycosylation, Chia-Lun Wu

All Dissertations

Congenital Disorders of Glycosylation (CDG) are rare metabolic diseases caused by defects in glycosylation. Despite identification of over 200 CDG types, the mechanisms linking glycosylation defects to diverse clinical phenotypes remain unclear. This dissertation uses zebrafish models of PMM2-CDG and STT3-CDG to redefine CDG pathogenesis, shifting from a simple glycan deficiency model to one involving disrupted cellular spatial organization.

We identify a protease-dependent pathway underlying craniofacial cartilage defects. Specifically, defective proteolytic processing of N-cadherin, a key adhesion molecule in chondrogenesis, is a central driver of pathology. We further uncover an unconventional trafficking mechanism in which ER stress and altered secretory …

Mechanisms Of Bacterial Glucokinase Inactivation Through Site-Specific Lysine Modification And Chemical Inhibition, Joseph Robert Will Andrews

Graduate Theses and Dissertations

Glycolysis and related metabolic pathways are controlled by various post-translational modifications (PTMs) that affect enzyme activity and metabolic flow. In E. coli, glucokinase (GLK) sits at the crossroads of glycolysis and the pentose phosphate pathway and carries out the first committed step of glycolysis: ATP-dependent phosphorylation of glucose. While it's known that glucose binding causes GLK to close its domains, how phosphate binding, lysine modification, and small-molecule inhibitors regulate GLK's shape and function is still not fully understood. Here, I combine structural biochemistry and enzymology to figure out how phosphate binding, specific mutations, and chemical inhibitors affect E. coli GLK. …

A Novel Method Of Protein Purification Using Hedgehog Proteins As An Inducible, Self-Cleaving Tag, Antonia Kladias

Undergraduate Honors Theses

Because removing extraneous purification tag sequences from native proteins can be challenging and costly, there is demand for simple all-in-one techniques that directly furnish a tagless, functional protein-of-interest (POI). Current tagless purification systems are based on intein biochemistry; however, intein-based purification requires expensive, specialized resins and the POI often must be fused to the intein’s C-terminus. In this thesis, I present a novel approach for tagless POI purification in which the Drosophila melanogaster hedgehog protein catalytic domain (HhC) is repurposed as a small-molecule inducible, self-cleaving element dubbed Gtag. With Gtag, the POI is fused to the N-terminus of HhC/Gtag with …

Dried Water Treatment Residuals Might Be An Option To Reduce Soluble Reactive Phosphorus Release From Soils, Katie B. Mckay

Biological and Agricultural Engineering Undergraduate Honors Theses

Nonpoint source pollution from agricultural landscapes contributes to freshwater eutrophication, with legacy phosphorus (P) in soils potentially driving soluble reactive phosphorus (SRP) losses to surface waters. The objectives of this study were to evaluate SRP adsorption by dried water treatment residuals (WTRs) produced by Beaver Water District, quantify reductions in soil SRP release across increasing WTR application rates, and compare dried WTR performance to prior WTR studies.

Dried WTRs (~98% solids) were assessed using batch sorption experiments and soil core incubations. Phosphorus sorption was measured by mixing WTRs with CaCl₂ solutions containing increasing SRP concentrations and fitting results to …

Understanding The Role Of Toxs As A Bile Sensing Component Of The Toxrs Virulence Regulatory System In Vibrio Spp., Minje Kim

Dartmouth College Ph.D Dissertations

Pathogenic Vibrio bacteria, such as V. cholerae and V. parahaemolyticus, colonize in the human small intestine to cause severe gastrointestinal disease. During the infection, these bacteria encounter bile salts, antimicrobial cholesterol metabolites secreted into the intestine. Pathogenic Vibrio species have evolved to utilize bile salts as signals to regulate virulence. The signaling depends in part on ToxRS, a conserved co-component transmembrane transcription regulator. ToxRS consists of the transcription factor ToxR and its membrane-tethered binding partner ToxS. ToxS is required for ToxR stability and full transcriptional activity. Although bile salts are known to influence ToxRS-dependent virulence gene expression, the molecular …

Cleft Palate And The Coordination Of Wnt Signaling And Pax9 In Murine Palatogenesis, Landon Wyatt

Honors Theses

Cleft palate is a common craniofacial birth defect that arises when the molecular and morphogenetic events guiding secondary palate formation lose coordination during a narrow developmental window. In mice, successful palatogenesis requires the paired palatal shelves to grow vertically, elevate above the tongue, and fuse at the midline; disruption of any of these steps can result in clefting. Two important regulators of this process are canonical Wnt signaling and the transcription factor Pax9, both of which contribute to normal palatal mesenchymal growth and patterning during early development. This paper first examines whether altered Dkk1/Wnt signaling contributes to the Pax9-null palate …

Mechanistic Insights Into Enterolactone-Mediated Glut4-Dependent Glucose Uptake, Merritt Smith

Senior Honors Theses

Type 2 diabetes mellitus (T2D) is one of the leading causes of morbidity and mortality in the United States, with approximately 25% of healthcare expenditures directed toward its management and associated metabolic complications. In response to the urgent need for novel therapeutic strategies, recent research has focused on bioactive compounds derived from dietary sources. In light of that, we identified the plant lignan matairesinol (MA) and its gut-derived metabolite, enterolactone (ENL), as agents capable of enhancing glucose uptake in 3T3-L1 differentiated adipocytes. These results suggest that enterolactone may represent a promising dietary supplement for improving glycemic control in patients with …

Analysis Of Bacterial Virulence And Resistance In A Model Of Recurrent Uti, Rachel L. Proper

Undergraduate Honors Theses

Urinary tract infection (UTI) is a major women’s health issue, affecting approximately 40% of women during their lifetime. Formation of a biofilm by UTI-causing bacteria poses a major challenge in treatment, as the protection provided by the biofilm hinders both host defenses and antibiotic treatment. Failure to eradicate these infections causes them to become recurrent (rUTI). Previous research indicates that rUTI may be comorbid with a mutation in the SERPINE1 gene, which causes fibrin to accumulate within the body. Literature also indicates that fibrin provides a better scaffold for bacterial attachment and, subsequently, biofilm formation. In this work it was …

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 …

Pepper Spray Exposure And The Effect On Dna Profiling Of Blood, Brandon Schmakel

Honors Projects

Pepper spray is a common self defense tool used in both law enforcement and civilian settings, with the goal of incapacitating the sprayed individual. In real casework where pepper spray was used, a red-brown stain which tested positive presumptively for blood provided no DNA profile after further testing six months later. A previous graduate student, Emma Crawn, attempted to emulate these casework conditions and instead achieved a DNA profile with slight indications of inhibition or degradation. Further analysis of active pepper spray ingredients such as Oleoresin Capsicum (OC) and Chloroacetophenone (CN) reveals that there are observed reactions, such as oxidation, …

Establishment Of A Hek293t Cell Model System To Investigate Direct Intracellular Interactions Between Amyloid-Β (Aβ) And The Nlrp3 Inflammasome, Cristina Sinobas Pereira

Dissertations

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and the leading cause of dementia worldwide. While Amyloid-β (Aβ) aggregation is a defining pathological feature, increasing evidence highlights chronic neuroinflammation as a critical contributor to disease progression. Soluble Aβ assemblies can act as damage associated molecular patterns (DAMPs) including activation of the NLRP3 inflammasome, which links amyloid pathology to sustained inflammatory responses in the brain (Heneka et al., 2015; Nakanishi et al., 2018). However, the molecular mechanisms by which specific Aβ conformations influence inflammasome assembly remain incompletely understood.This study aimed to investigate whether distinct aggregation states of amyloid β42 (Aβ42) are …

Mitochondrial Dna Replication Is Regulated By Endoplasmic Reticulum-Mitochondrial Contact Sites, The Mitochondrial Calcium Uniporter, And Manganese, Amaia Lopez De Arbina, Angelica Zamudio-Ochoa, Mikel Muñoz-Oreja, Diego Perez-Rodriguez, Laura Mosqueira-Martín, Rebecca Lasalandra, Marina Villar-Fernandez, Uxoa Fernandez-Pelayo, Laura Rodriguez-Gomez, Seungtae Lee, Francisco Gil-Bea, Nerea Osinalde, Ainara Vallejo-Illaramendi, Dmitry Temiakov, Antonella Spinazzola, Ian Holt

Department of Biochemistry and Molecular Biology Faculty Papers

Mitochondrial DNA replication occurs at contact sites between the endoplasmic reticulum (ER) and mitochondria (ERMCS). Beyond the known role of the tubular ER protein RTN4, the factors regulating this process are poorly defined. Here, we show that repressing the ER protein ERLIN2 in human fibroblasts depletes ER-mitochondrial contact sites and inhibits mitochondrial DNA replication, as does silencing RTN4 or the ER-mitochondrial tether GRP75. GRP75 or RTN4 scarcity also decreases the level of the mitochondrial calcium uniporter (MCU), whose inhibition blocks mitochondrial DNA synthesis. Because ERMCS depletion did not diminish mitochondrial calcium, and MCU complex can transport manganese, we tested whether …

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 …

Exploration Of A Relationship Between The Activities Of Trail And 4’-Trifluoromethoxychalcone., Abigail C. Ernst

Undergraduate Theses

Cancer is the overgrowth of dysregulated or mutated cells that affects 1 in 3 Americans. Chalcones are natural products with many possible derivatives, such as 4’-trifluromethoxychalcone (4TF), developed in Dr. Krzysiak’s lab, which exhibit anticancer activity against cancer cell lines. Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand (TRAIL) is a tumor surveillance cytokine that acts on two receptor types: death receptors and decoy receptors. One way cancer cells can become resistant to TRAIL is by upregulating decoy receptors and/or downregulating death receptors. In this study, MTS assays evaluated the potential relationship between TRAIL and 4TF that sensitizes A549 cells to TRAIL. The …

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 …

Quantitative Proteomics For The Investigation Of Phosphoprotein Phosphatase 1 And 3 Substrate Specificities, Galini Poimenidou

Dartmouth College Ph.D Dissertations

Reversible phosphorylation is a crucial post-translational modification (PTM) that modulates a variety of signaling pathways intracellularly, with aberrant protein phosphorylation being a hallmark of many human diseases. Kinases, which catalyze phosphorylation of their substrates, have been extensively studied in the context of the signaling pathways they regulate and their effects on cellular processes. In contrast, phosphoprotein phosphatases (PPPs), which catalyze the removal of phosphate groups from substrate proteins, have only recently come to the research spotlight. For a long time, protein phosphatases were deemed unspecific housekeeping enzymes, but they are now known to display exquisite substrate specificity. Phosphoprotein phosphatase 1 …

Mechanistic Insights Into E. Coli Recovery From Growth Arrest, Ahmed H. Hassan, Yuko Nakano, Howard Gamper, Isao Masuda, Ludmila Vesela, Matyas Pinkas, Sathya Narayanan Nagarajan, Jonathan Dworkin, Gregor Blaha, Ya-Ming Hou, Gabriel Demo

Department of Biochemistry and Molecular Biology Faculty Papers

Bacteria survive hostile conditions by shutting down protein synthesis, but how they restart growth remains poorly understood. Here, we use an E. coli ΔrimM strain, which exhibits a prolonged growth arrest, as a model to investigate how bacteria recover from this state and restore protein synthesis. RimM is a conserved ribosome maturation factor for the 3'-major (head) domain of the 16S rRNA within the bacterial 30S subunit. The loss of RimM causes a longer delay in recovery than other 30S maturation factors, including RbfA. Cryo-EM analysis of ΔrimM ribosomes suggests a delayed recruitment of ribosomal proteins to the 30S head …

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 …

Rna Interference Targeting Autocrine Motility Factor Receptor In Unfolded Protein Response In Acyrthosiphon Pisum, Micah A. Von Stroh, James Balthazor

SACAD: Scholarly Activities

Acyrthosiphon pisum, more commonly known as pea aphids, are a pest to many species of Fabaceae (legumes) mainly due to the species being prone to carrying Fabaceae diseases. Protection against A. pisum currently includes insecticides and natural predators, both of which bring potential negative effects to other organisms in the surrounding area. In this study, the use of RNA interference (RNAi) provides an alternative and species-specific elimination of A. pisum. The targeted proteins in this study, Autocrine Motility Factor Receptor, plays a role in removing misfolded proteins from the cells of A. Pisum and is encoded by the AMFR gene. …

Atp Architect - Development Of A Metabolism Boardgame, Selene J. Welch, Micah Burk, Brooklyn Gilchrist, Emma Haase, Timothy T. Jones

SACAD: Scholarly Activities

Traditional metabolism instruction often leaves students struggling with pathway interconnectedness and metabolite flux. To foster systems thinking, we are developing an educational board game where students manipulate tokens to navigate physiological constraints and achieve target energy goals. Grounded in Design-Based Research (DBR), the game undergoes iterative refinement based on player feedback. The design utilizes constructivism by allowing students to "fail safely" and revise strategies in real-time, while leveraging embodied cognition to externalize abstract flux into the physical trading of resource tokens.

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, …

Dendrimer Nanogels With Built-In Free Radical Scavenging Enable Efficient Topical Delivery Of A Hydrophilic Antioxidant To Restore Lens Redox Balance For Cataract Treatment, Lin Qi, Huari Kou, Anna Chernatynskaya, Da Huang, Vimalin Jeyalatha Mani, Humeyra Karacal, Nuran Ercal, Hu Yang

Chemistry Faculty Research & Creative Works

Cataract is a leading cause of vision impairment worldwide and are primarily caused by oxidative stress that damages and aggregates lens proteins, leading to lens opacification. However, the eye's anatomical barriers limit the penetration and bioavailability of antioxidant therapies. To address this challenge, a dendrimer-based nanogel with a built-in reactive oxygen species (ROS)-scavenging capability developed by us was employed to deliver the antioxidant N-acetylcysteine (NAC) to the lens. NAC was loaded into a generation-5 PEGylated poly(amidoamine) dendrimer (G5-PEG-TK, termed the GPT) nanogel. The resulting NAC-GPT was characterized for its ROS-scavenging activity, bioavailability, and corneal permeability. The efficacy of NAC-GPT was …

G-Quadruplex Dna-Driven Genomic Instability Under Ber Loss, Addison Belick, Claryssa Gutierrez, Joslynn Rosas, Andrea Vargas

Posters - 2026

Base Excision Repair (BER) is a cellular tool that can repair damaged DNA (Hindi et al., 2022, Cellular and Molecular Life Sciences). G-quadruplexes (G4s) are unique 4-stranded structures in DNA or RNA that are rich in guanine (Gray et al., 2023, Nat. Chem. Biol). The purpose of this study is to understand whether BER contributes to the removal of G4s in DNA. This will determine if the BER-deficient yeast is more sensitive to treatment with G4-binding drugs than the BER-proficient yeast. We will replace the APN1 gene in the yeast genome with the URA3 gene, because the wild type yeast …

Synthesis Of Copper-Phenanthroline Complexes: A Solvothermal-Compatible Approach For The Exploration Of Metal Complexes, Yunping Zhoujin, Michael Anim Safo, Navindra Keerthisinghe, Mark D. Smith, Sophya Garashchuk, Hans Conrad Zur Loye

Faculty Publications

Inorganic–organic hybrid materials have been widely investigated for their applications in catalysis, optics, magnetism, and biomedicine. Copper halide complexes are of particular interest due to their structural diversity and physicochemical properties. Conventional crystal growth approaches, such as slow evaporation and hydro(solvo)thermal synthesis, typically require extended reaction times and often favor thermodynamically stable phases. In this study, we prepared ten copper-phenanthroline halide (X = Cl, Br, and I) complexes using both traditional hydrothermal reactions and microwave-assisted hydrothermal methods and obtained [CuI(C₁₂H₈N₂)₂][I₃], [C₁₂H₉N₂][CuI₂]·(H_{2 …}

Improving Cannabis Sativa's Phytoremediation Capabilities Of Forever Chemicals Through Microbial Inoculations, Tyler S. Jolin

All NMU Master's Theses

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants that pose ecological and human health risks due to their resistance to degradation and potential for bioaccumulation. Phytoremediation has emerged as a potential strategy for mitigating PFAS contamination, and plant-microbe interactions may influence contaminant uptake and transport within plant systems. These studies investigated microbial inoculation methods and examined whether Bacillus subtilis could influence the uptake and distribution of perfluorooctane sulfonate (PFOS) in hydroponically grown hemp (Cannabis sativa L.). Plant height and stem diameter growth rates and biomass accumulation were compared across treatments with and without PFOS exposure and microbial inoculation. PFOS …

Increased Backbone Rigidity Of Artificial Transcription Factors, Jasmine Glover, Emma Otey, Joanna K. Kwao, Nicholas Truex

Senior Theses

Programming DNA-binding proteins is an effective strategy for developing therapeutics that regulate gene expression. These proteins can directly bind to DNA to activate or repress transcription of specific genes. Zinc finger proteins are a class of DNA-binding proteins commonly found in eukaryotic organisms. Their DNA-binding function is derived from unique amino acid sequences within each domain that recognizes specific nucleotides, allowing each finger to selectively recognize three DNA base pairs. Adjoining of multiple domains in tandem allows recognition of a specific DNA sequence. Artificial transcription factors can be made of multiple zinc finger domains arranged in tandem and engineered to …

Investigating The Endogenous & Synthetic Estrogens To The Three Estrogen Receptor Subtypes Of Teleost Fish, Ann Cyril

Posters - 2026

Estrogen and the estrogen receptors are important biological and physiological processes. The various types of estrogen include estrone, estradiol and estriol. Estradiol’s main function is to maintain the reproductive system. Estrone’s main function is to develop the female's reproductive functions. Estriol’s main function is to aid the female's sexual developments but is on the weaker side. The fish, Atlantic Croaker, has three different estrogen receptors: ERα, ERβa, and ERβb. Based on the estrogen receptors, it appears that their binding affinities do differ in strength. Each estrogen receptor has different amino acids involved that could contribute to the difference in their …