Biochemistry, Biophysics, and Structural Biology Commons^™

Evaluation Of Flt3 Inhibition With Quizartinib During Busulfan Conditioning For Hematopoietic Stem Cell Transplantation, Catherine Jankovic

Biochemistry and Molecular Biology

Hematopoietic stem cell transplantation (HSCT) is one of the only curative therapy options for many hematologic malignancies. HSCT relies on effective conditioning regimens to deplete host hematopoietic cells and enable donor engraftment. The alkylating agent Busulfan is widely used in myeloablative conditioning strategies due to its potent cytotoxic effects on hematopoietic cells and ability to clear the bone marrow. However, optimization of conditioning strategies remains an important area of investigation to improve transplant outcomes and reduce toxicity. Preliminary studies have shown that the FLT3 inhibitor Quizartinib synergizes with some chemotherapeutic agents, suggesting that targeted inhibitors may enhance conventional conditioning regimens. …

Analysis Of Developmental Cardiogenic Processes Mediated By Fox And Zinc-Finger Transcription Factors, Rajnandani Katariya

All-Inclusive List of Electronic Theses and Dissertations

Cardiogenesis is a highly choreographed biological process requiring the precise integration of gene regulatory networks to govern cell division, fate determination, and spatial positioning. Disruptions in these mechanisms lead to congenital heart defects (CHDs), which affect approximately 1% of live births globally. Due to the evolutionary conservation of cardiac signaling pathways and the structural homologies between the Drosophila dorsal vessel and the early vertebrate heart tube, Drosophila melanogaster serves as a powerful model for dissecting the fundamental mechanisms of heart development. This dissertation investigates the molecular orchestration of cardiac development, specifically focusing on the roles of the transcription factors Jumu …

Reconstruction Of Fox Transcription Factor-Regulated Subnetworks Mediating Cardiac Progenitor Cell Divisions, Md Rezaul Hasan

All-Inclusive List of Electronic Theses and Dissertations

Congenital heart disease (CHD) is the most common congenital anomaly worldwide, affecting approximately 1% of live births, corresponding to 1.35 million infants born with CHD each year, and remains a leading cause of infant mortality; therefore, it is urgent to understand the genetic and molecular mechanisms underlying CHD for advancing early diagnosis and treatment. Because many aspects of the Drosophila heart formation are highly reminiscent of vertebrate heart development, Drosophila melanogaster serves as a simple yet powerful model system for studying cardiac development and CHD. While at least eight Forkhead box (Fox) transcription factors (TFs) are required for proper cardiac …

Analysis Of The Effects Of Astaxanthin On Human Colorectal Cancer Cells, Kara A. Walters

Theses/Capstones/Creative Projects

Astaxanthin (AXT) is an antioxidant carotenoid that is produced by the microalgae Haemococcus pluvialis. This supplement is best known for its potential health benefits including anti-inflammatory, antitumor, immunomodulatory, anticancer and antidiabetic activities. Astaxanthin is marketed as an oral dietary supplement and is widely used in the nutraceutical industry as well as a coloring agent in the food industry. Since Astaxanthin has been increasingly popular as a dietary supplement, cytotoxicity is relevant to consumer exposure. Obtaining the IC50, the concentration that inhibits 50% of cell growth, is important to find how Astaxanthin may interact with cancer, and this can be found …

Developing A Protocol For Non-Cellular Transplantation Of Donor Mitochondria Into Recipient Cells, Andrew Parton

Honors Theses

Tumor innervation has emerged as a critical feature of cancer progression, with increased nerve density correlating with enhanced aggressiveness, metastatic dissemination, and poor clinical outcome. However, the functional contribution of neurons to tumor biology remains incompletely defined. We recently identified the intercellular transfer of mitochondria from neurons to cancer cells as a mechanism that promotes tumor progression. We therefore hypothesized that disruption of this transfer could attenuate tumor aggressivity. To directly investigate this process, we developed an approach to isolate mitochondria from donor cells and transplant them into recipient cancer cells independently of canonical cell-cell interactions. Transferred mitochondria were tracked …

Understanding Tlr3 Immune Response Activation In Cryptosporidium Parvum And Cryspovirus Pathogenesis, Surayya Hudayberganova

Biochemistry and Molecular Biology

Cryptosporidiosis is a serious gastrointestinal illness caused by a protozoan parasite known as Cryptosporidium. It is particularly dangerous for malnourished children and those with compromised immune systems. My research focuses on the Toll-like receptor 3 (TLR3) response to the Cryptosporidium parvum infection, specifically in the presence of the parasite’s viral mutualist named cryspovirus (CSpV1). Results using research methodologies like ELISA and RT-qPCR have indicated that TLR3 expression increases during the infection process of Cryptosporidium parvum (C. parvum). Furthermore, one intriguing observation concluded during this study suggests that administering the TLR3-specific inhibitor CU-CPT4a to infected cells drastically decreased this activation. This …

Genome-Wide Phenotypic Characterization Of Mycobacteriophage Mercurio, Tyler Downs

Departmental Honors & Graduate Capstone Projects

Bacteriophages, or phages, are being piloted as a supplemental or alternative therapeutic to antibiotics against drug-resistant Mycobacterium pathogens, such as M. tuberculosis, which pose a global public health crisis.  Characterizing bacteriophage genomes can provide insights into efficacy in phage therapy before implementation or elucidate new targets to manipulate bacterial growth.  Overexpression of individual phage genes is useful to study a gene product’s function independent of others.  Here, the results of phage Mercurio plasmid library overexpression in plate-based assays are described.  Mercurio infects nonpathogenic Mycobacterium smegmatis and is genetically related to bacteriophages infecting pathogenic Mycobacterium species.  Eleven gene products of …

Phenotypic Contribution And Regulation Of Vibrio Parahaemolyticus Cold-Shock Protein Homologue Vp1889, Oleg Borisovich Ermolinsky

Theses and Dissertations

Vibrio parahaemolyticus is the primary causative agent of a form of gastroenteritis called vibriosis commonly acquired from ingestion of raw and undercooked seafood. The primary mitigation of seafood-borne illnesses is immediate storage on ice following catch, which inhibits bacterial metabolism and replication. Mesophilic bacteria such as V. parahaemolyticus induce expression of cold-shock proteins in a process named the cold shock response, which facilitates survival at low temperatures. V. parahaemolyticus bears 3 homologues of the major Escherichia coli cold-shock protein CspA, an RNA chaperone. Induction of E. coli CspA at low temperatures depends on autogenous modulation by its mRNA structure, which …

Membrane Organization Of Rheb And Rhoa: Roles In Function And Allosteric Druggability, Chase M. Hutchins

Dissertations and Theses (Open Access)

Small GTPases of the Ras superfamily are membrane-bound molecular switches that regulate nearly all major cellular processes, and their dysregulation drives cancers, neurological disorders, and metabolic diseases. While anchored to cellular membranes, the catalytic domains of small GTPases undergo orientation dynamics, adopting distinct configurations that can occlude or expose effector-binding surfaces and modulate signaling output. These dynamics have been characterized in the Ras oncoproteins, but whether they extend across the superfamily and influence allosteric druggability has remained unknown.

In this dissertation, I address these questions through Rheb and RhoA, two small GTPases with complementary differences in subfamily lineage, membrane localization, …

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 …

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 …

Characterization Of Snrk1 Signaling In Rice Growth, Reproduction, And Stress Responses Using Phenotypic And Omics Analysis, Maria Clara Faria-Bates

Graduate Theses and Dissertations

SnRK1 is an evolutionarily conserved protein kinase belonging to the SNF1/AMPK family that is composed of a catalytic subunit (α) and two regulatory subunits (β and βγ), and it has a major role in adjusting growth in response to the energy status. SnRK1 phosphorylates and alters the activities of enzymes involved in metabolism and regulates gene expression by altering the activity of chromatin-remodeling enzymes or transcription factors. Rice contains three functional paralogs of SnRK1α: OsSnRK1αA (Os05g0530500), OsSnRK1αB (Os8g0484600), and OsSnRK1αC (Os03g0289100). Although SnRK1 is known to play a central role in plant growth and stress responses, the functional specialization of …

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 …

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, …

The Pam-1 Aminopeptidase Does Not Protect Against Ptl-1 Mediated Neurodegeneration In C. Elegans., Ethan E. Schuff

Honors College Theses

Debilitating neurodegenerative conditions are increasingly prevalent in our aging population, yet treatment options remain limited. Though neurodegenerative diseases vary in pathophysiology and clinical manifestations, these diseases are related to one another in that many involve misfolded proteins. Tau is a member of the microtubule-stabilizing MAPT/MAP2/MAP4 family, and misfolded tau proteins form the neurotoxic aggregates called neurofibrillary tangles (NFTs) found in the brains of patients with Alzheimer's disease and other neurodegenerative diseases. Designing a study to elucidate the neurotoxic role of tau is difficult because other MAPs may have compensatory mechanisms which confound study data. Caenorhabditis elegans (C. elegans) …

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 …

Maternal Inflammation Alters Nuclear And Mitochondrial Dna Methylation Patterns In Neonatal Brain Monocytes, Andrew Ebenezer, Jonathan Hicks, Brooke Hollander, Alexander Hone, Mona Batish, Robert Akins, Adam Marsh, Elizabeth Wright-Jin

Department of Medicine Faculty Papers

Neonatal hypoxic ischemic encephalopathy (HIE) is a common birth complication that can cause death or lifelong disabling conditions like cerebral palsy, epilepsy, and autism. It is well established that maternal infection and inflammation are significant risk factors for HIE but reasons for this increase in neurological risk to the offspring remain unknown. Inflammation or infection are associated with epigenetic changes and may contribute to the increased risk of neurodevelopmental disability in exposed offspring. Here, we analyzed and compared DNA methylation patterns in brain monocytes isolated from control, maternal immune activation (MIA), and an inflammation sensitized HIE (IS-HIE) CF-1 mouse model …

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 …

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 …

Biophysical Insights Into A Cryptic, Hydrophobic Binding Site On Pcna, Alexis Dispensa

Theses and Dissertations

Proteins are dynamic molecules whose functional landscapes extend beyond static structural representations. Transient cryptic pockets (buried cavities that emerge through protein motion) represent underexplored targets for allosteric regulation and drug discovery. General anesthetics are small, lipophilic, weakly polar molecules that are well suited to partition into such hydrophobic sites. In this work, environment-sensitive fluorescence, photoaffinity labeling, mass spectrometry, mutational analysis, and microsecond molecular dynamics simulations were integrated to discover and characterize a cryptic, highly apolar binding site within the hydrophobic core of human proliferating cell nuclear antigen (PCNA), a central scaffold in DNA replication and repair. Using the solvatochromic fluorescent …

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 …

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 …

Studying The Role Of Combitional Flavonoids Against Toxicity Of Chemothrapeutic Drugs In Human Fibroblast Cells, Hussain Al Zouabi

Thesis/ Dissertation Defenses

Chemotherapy remains the primary treatment strategy for cancers; however, its clinical efficacy is often limited by severe toxic effects resulting in normal cells. The study investigated the protective potential of the flavonoids epigallocatechin-3-O-gallate (EGCG) and quercetin, used in combination, against chemotherapy-induced toxicity in human fibroblast F-180 cells. Cells were exposed to three commonly used chemotherapeutic agents, doxorubicin, cisplatin, and etoposide, in the presence or absence of EGCG and quercetin at concentrations of 25 and 50 μM. cells viability was assessed using the MTT assay, while oxidative stress and antioxidant capacity were evaluated by intracellular reactive oxygen species (ROS) and total …

Protocol For Inducing Focal Striatal Stroke In Mice Using Photothrombosis, Bridget R. Boyle, Eileen Collyer, Andrea P. Berghella, Elena Blanco-Suarez

Department of Neuroscience Faculty Papers

Here, we present a protocol for inducing focal striatal stroke in mice using photothrombosis. We describe steps for photothrombotic striatal surgery, magnetic resonance imaging, open field behavioral assessment of stroke-induced motor deficits, and post-stroke monitoring. We then detail procedures for tissue collection and immunofluorescence. This protocol provides a standardized approach for consistently modeling striatal stroke in mice, enabling mechanistic studies and preclinical therapeutic testing.

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 …

Effects Of Mycoplasma Pneumoniae Cards Toxin On Lung Fibroblast Function, Shuri Magdalene

Posters - 2026

Mycoplasma pneumoniae is a common respiratory pathogen whose virulence depends largely on the community-acquired respiratory distress syndrome (CARDS) toxin, a 591-amino-acid ADP-ribosylating protein¹. CARDS toxin induces immune responses²˒³, causes vacuolation in lung epithelial cells, and contributes to the inflammatory and pathological features of pneumonia. IMR-90 fibroblasts. IMR-90 cells are human fetal lung fibroblasts widely used to study responses to inflammatory signals, extracellular matrix production, and lung injury or repair. Rationale. Fibroblasts are key drivers of tissue remodeling and fibrosis during lung injury. Defining how CARDS toxin influences fibroblast programs in inflammation, cell-cycle control, and matrix remodeling²˒³ will clarify how M. …

Evaluating The Effects Of Akt Knockdown And Everolimus Treatment On Ewing Sarcoma, Arisha Arif, Alfie Barcenez, Nicole Vanegas-Riddick

Posters - 2026

The purpose of this study is to use the gene AKT1, due to the interest in AKT1’s role in cancer cell proliferation, and the drug Everolimus, to determine if combined targeted therapy works as a more efficient therapeutic approach. We hypothesize that the knockdown of AKT1 will increase the sensitivity of Ewing sarcoma cells to Everolimus, resulting in reduced proliferation and/or survival compared to drug treatment alone. This would suggest that AKT1 normally protects cells from drug-induced stress. Ewing Sarcoma has been connected to chromosomal translocations and most common in pediatric patients. It is most often treated with chemotherapy and …

Sirna Knockdown Of Rptor Alters Gene Expression In Ewing Sarcoma Cells, Sergio Cipriano, David Leavitt, Michael Oliva, Liam Valdez

Posters - 2026

Ewing sarcoma is a highly aggressive cancer that primarily affects children and young adults. Although treatment options exist, many patients do not respond effectively, showing the need for improved targeted therapies¹. RPTOR is a key in mTORC1 complex which regulates cell growth, proliferation, and survival². LY2874455 is a selective pan-FGFR inhibitor that targets growth factor signaling pathways involved in tumor progression³, and FGFR signaling interacts with pathways such as mTOR, making it a potential target for combination therapies. We hypothesized that silencing RPTOR in Ewing sarcoma cells would disrupt mTOR signaling and alter expression of genes linked to cell survival …