Biochemistry, Biophysics, and Structural Biology Commons^™

Characterizing Substituted Imidazolidinetriones As A Novel Class Of Pyruvate Carboxylase Inhibitors, Nicholas O. Schneider

Dissertations (1934 -)

Pyruvate carboxylase (PC) is implicated in a variety of diseases, including type-2 diabetes, cancer, and bacterial/viral infections. However, there are currently no molecular tools capable of precisely manipulating PC activity both in vitro and in vivo. This dissertation describes the identification and characterization of 1,3-disubstituted imidazolidinetriones as a novel class of potent, selective, and permeable allosteric inhibitors of Staphylococcus aureus PC. Based on kinetic, structural, and biophysical data, this class of inhibitors is hypothesized to bind at the noncatalytic “exo binding” site on PC. This exo binding site is reportedly important for catalysis, but it had not previously been considered …

Breast Cancer Molecular Subtype Classification According To Immunohistochemistry Markers And Its Association With Pathological Characteristics Among Women Attending Tertiary Hospitals In Tanzania, Allyzain Ismail, Sajida Panjwani, Neelam Ismail, Caroline Ngimba, Innocent Mosha, Philip Adebayo, Ally Mwanga, Ali Zehri, Aidan Njau, Ali Athar

Family Medicine, East Africa

Background: Breast cancer immunohistochemistry is a biological characteristic of the tumour which has a role to diagnose molecular subtype, prognosticate and guide treatment and is categorised into 4 subtypes. Data in Tanzania was lacking and was based off data extrapolated from studies in Western Africa thus hypothesizing that women of African ancestry predominately develop Triple Negative Breast Cancer (TNBC).

Methods: A retrospective cross-sectional study was carried out at two tertiary referral hospitals on participants who were recruited from the cancer registries from 2015 to 2022. Prevalence of each molecular subtype was determined and association between molecular subtype to demographic and …

The Anaerobic Rose Chamber (Arc): Novel Applications For Probing Clostridioides Difficile Dynamics, Tatiana Zvonareva

Chemistry & Biochemistry Theses & Dissertations

Clostridioides difficile infection (CDI) is an urgent public health threat with a high rate of recurrence and limited treatment options. Caused by the anaerobic intestinal pathogen C. difficile, this disease affects up to 500,000 Americans annually. Despite progress in our understanding of CDI pathophysiology, the lack of effective and accessible experimental platforms compatible with obligate anaerobe physiology hinders the advancement of treatment therapy. The application of in vivo models has been indispensable in understanding CDI pathophysiology, probing the complexity of the host response to the microbe, and establishing treatment protocols, and it continues to be essential in preclinical testing. …

Synthesis Of Drug-Like Molecules And Investigation Of Their Biological Activity, Duyen Nguyen '25, Sunny Nguyen '26, Jeffery A. Hansen

Annual Student Research Poster Session

This study examines the products derived from the ring-opening reactions of two novel epoxides—chlorobenzene epoxide and furan epoxide—highlighting their notable biological activity, particularly in the context of potential anticancer agents. One key finding: a synthesized stereoisomer of a hexylamine-derived β-amino alcohol exhibited a remarkably low LC50 value of 6.6 ppm in the Brine Shrimp Lethality Assay, significantly outperforming the other isomer compound’s LC50 value, at 13 ppm. This discovery underscores the critical role of stereochemistry in enhancing bioactivity, as evidenced by the distinct physical and chemical properties of the two hexylamine-derived isomers, including differences in appearance and solubility. Building on …

E-Textbook For Better Learning In Chemistry 120, Anh Vu '27, Jeffery A. Hansen

Annual Student Research Poster Session

Organic chemistry is a highly visual subject since organic compounds are 3D objects. For this reason, in order to fully understand the composition, properties, and chemistry of these compounds, it is essential to understand and visualize their 3D structures. Nevertheless, there is a frequent necessity to depict organic substances on 2D surfaces, such as paper, a computer screen, or a whiteboard. As a result, one of the biggest obstacles we will face is learning these molecules in a 2D format while maintaining an accurate understanding of 3D nature. The purpose of this e-textbook is to fully utilize the digital medium …

Inhibition Of Integrin Binding: Exploring Its Impact On Epidermal Cell Attachment, Erin R. Johnson '25, Colleen L. Doçi

Annual Student Research Poster Session

I worked with HaCaT cells, human epidermal cells that are sticky and like to attach to their surroundings in the skin. They have a surface protein called integrin, which interacts directly with collagen to induce cell attachment. I was particularly interested in interrupting this connection between integrin and collagen. I achieved this by using an inhibitory peptide that bound to the active site of integrin. This would allow me to calculate the cell attachment of HaCaT cells while in the presence of collagen. If we were able to target this treatment to tumor cells, we could help to stop them …

Designing An Attachment Assay For Epidermal Cell-To-Cell Attachment, Tiala Ortega '26, Colleen L. Doçi

Annual Student Research Poster Session

Cell adhesion includes various processes and is essential in cell communication and regulation. The mechanical interactions between a cell and its extracellular matrix control the behavior and function of a cell. In this project, we are studying cell attachment in different ways. The epidermal monostrato layer is a vertical and horizontal interaction and is not accounted for in usual assay protocols so I wanted to investigate this by creating an assay including multiple cell layers, a monolayer and an attached layer, to further develop a protocol for optimal cell-to-cell attachment. I hypothesized that the number of cell attachments to the …

Comparison Of Two Disaccharides And Their Saccharide Components In Aot Reverse Micelles: Impacts Of D-Trehalose And D-Sucrose, Delaney Collier '25, Bridget L. Gourley, Nancy E. Levinger

Annual Student Research Poster Session

Reverse micelles, featuring an AOT surfactant with a polar head group and nonpolar tail, encapsulate a polar phase at the nanoscale. With water as the polar phase, the nanoconfined water pool interactions and water-interface interactions mimic biological nanoconfinement. Thus, we investigated the impact of osmolytes on AOT reverse micelles to explore the role they play in biological systems. We investigated two disaccharides, D-trehalose and D-sucrose, and their monosaccharide components, glucose+glucose and glucose+fructose. We chose these molecules for their biological significance and to allow us to investigate whether subtle structural changes in the osmolyte impacts the intermolecular interactions in confinement as …

A Comparative Analysis Of Urea Vs. Acetamide In Aot Reverse Micelles, Kate Walsh '26, Bridget Gourley, Nancy E. Levinger

Annual Student Research Poster Session

In our exploration of the interactions between water and amide osmolytes, we focused on the effects of urea and acetamide on the stability of reverse micelles (RMs) formed with Sodium Bis(2-ethylhexyl)sulfosuccinate (AOT) in isooctane. Water, with its unique polarity and its ability to facilitate hydrogen and proton transfer, played a crucial role in our study, as we aimed to uncover how these amides would influence micellar behaviour. Our results revealed a compelling contrast between urea and acetamide. Acetamide, with its lower polarity due to a methyl group substitution, demonstrated superior solubility and significantly reduced precipitate formation compared to urea. This …

Enzyme Encapsulation Within The Hk97 Virus-Like Particle: An Investigation Of Substrate Inhibition Kinetics Within A Confined And Crowded Environment, Joseph B. Lively

Chemistry Theses

Substrate inhibition is a paradoxical phenomenon observed in enzyme kinetics where increasing substrate concentrations lead to a marked decrease in the rates of enzyme-catalyzed reactions. Affecting an estimated 20% of studied enzymes, substrate inhibition poses significant challenges to the understanding of their function in essential biological processes and to their exploitation in industrial and therapeutic contexts. Studies show substrate inhibition to be a real limitation in vitro and rational conclusions have been drawn to explain the relevance of substrate inhibition in the self-regulation of biological pathways. However, there is currently no consensus on what role substrate inhibition plays in vivo …

"Deep Learning For Microscope Image Denoising", Nasreen Buhn, Sriya Adunur, Guy Hagen, Jonathan Ventura

College of Engineering Summer Undergraduate Research Program

In order to avoid damaging live cells, optical microscope imaging must be conducted under low-excitation light intensity and/or short exposure times, resulting in low signal-to-noise ratios (SNR). Deep learning methods offer an effective solution for removing microscope noise, utilizing algorithms that are able to reconstruct finer features in low SNR images. This research explores the denoising capability of several deep learning methods based on PSNR and SSIM. Tested methods include traditional approaches (BMED), supervised learning (CARE and Restormer), and unsupervised methods (Noise2Fast, N2V, SSD-Unsupervised, and SASSID). The Restormer model, which employs an encoder-decoder transformer architecture and progressive learning, stood out …

Considerations For Widespread Implementation Of Blood-Based Biomarkers Of Alzheimer's Disease, Michelle Mielke, Matthew Anderson, Wesson Ashford, Andreas Jeromin, Pei-Jung Lin, Allyson Rosen, Jamie Tyrone, Lawren Vandevrede, Deanna Willis, Zul Merali

Brain and Mind Institute

Diagnosing Alzheimer's disease (AD) poses significant challenges to health care, often resulting in delayed or inadequate patient care. The clinical integration of blood-based biomarkers (BBMs) for AD holds promise in enabling early detection of pathology and timely intervention. However, several critical considerations, such as the lack of consistent guidelines for assessing cognition, limited understanding of BBM test characteristics, insufficient evidence on BBM performance across diverse populations, and the ethical management of test results, must be addressed for widespread clinical implementation of BBMs in the United States. The Global CEO Initiative on Alzheimer's Disease BBM Workgroup convened to address these challenges …

Recommendations For Clinical Implementation Of Blood-Based Biomarkers For Alzheimer's Disease, Michelle Mielke, Matthew Anderson, Wesson Ashford, Andreas Jeromin, Pei-Jung Lin, Allyson Rosen, Jamie Tyrone, Lawren Vandevrede, Deanna Willis, Zul Merali, Chinedu Momoh

Brain and Mind Institute

Blood-based biomarkers (BBM) for Alzheimer's disease (AD) are being increasingly used in clinical practice to support an AD diagnosis. In contrast to traditional diagnostic modalities, such as amyloid positron emission tomography and cerebrospinal fluid biomarkers, BBMs offer a more accessible and lower cost alternative for AD biomarker testing. Their unique scalability addresses the anticipated surge in demand for biomarker testing with the emergence of disease-modifying treatments (DMTs) that require confirmation of amyloid pathology. To facilitate the uptake of BBMs in clinical practice, The Global CEO Initiative on Alzheimer's Disease convened a BBM Workgroup to provide recommendations for two clinical implementational …

Investigating Neurite Outgrowth Influenced By Breast Cancer Progression Using In Vitro Models Of Collagen I Hydrogels, Emma Waskom '27, Nikolas Ala-Kokko, Younghye Song

Annual Student Research Poster Session

Through the use of vitro modeling of tumor progression, using collagen I hydrogels and progressing cell lines, a demonstration of the interactions between breast cancer cells and nerve cells can be investigated. With these models, our goal is to compare the measurement of outgrowth of nerve cells through the use of supplemented NGF and co cultures of breast cancer cells. Human MCF-CA1a.cl1, -AneoT, and -10A, adipose-derived stem cells (ASCs), and rat PC-12 cells, were all passaged from 2D cultures and cultured in a collagen I hydrogen at a cell density of 250,000 cells/ml of media. Collagen hydrogels were then made …

Knockdown Of Ketohexokinase Versus Inhibition Of Its Kinase Activity Exert Divergent Effects On Fructose Metabolism, Se-Hyung Park, Taghreed Fadhul, Lindsey R. Conroy, Harrison A. Clarke, Ramon Sun, Kristina Wallenius, Jeremie Boucher, Gavin O'Mahony, Alessandro Boianelli, Marie Persson, Sunhee Jung, Cholsoon Jang, Analia S. Loria, Genesee J. Martinez, Zachary A. Kipp, Evelyn A. Bates, Terry D. Hinds Jr., Senad Divanovic, Samir Softic

Markey Cancer Center Faculty Publications

Excessive fructose intake is a risk factor for the development of obesity and its complications. Targeting ketohexokinase (KHK), the first enzyme of fructose metabolism, has been investigated for the management of metabolic dysfunction–associated steatotic liver disease (MASLD). We compared the effects of systemic, small molecule inhibitor of KHK enzymatic activity with hepatocyte-specific, N-acetylgalactosamine siRNA–mediated knockdown of KHK in mice on an HFD. We measured KHK enzymatic activity, extensively quantified glycogen accumulation, performed RNA-Seq analysis, and enumerated hepatic metabolites using mass spectrometry. Both KHK siRNA and KHK inhibitor led to an improvement in liver steatosis; however, via substantially different mechanisms, KHK …

Predicting The Pathway Involvement Of All Pathway And Associated Compound Entries Defined In The Kyoto Encyclopedia Of Genes And Genomes, Erik D. Huckvale, Hunter Moseley

Markey Cancer Center Faculty Publications

Background/Objectives: Predicting the biochemical pathway involvement of a compound could facilitate the interpretation of biological and biomedical research. Prior prediction approaches have largely focused on metabolism, training machine learning models to solely predict based on metabolic pathways. However, there are many other types of pathways in cells and organisms that are of interest to biologists. Methods: While several publications have made use of the metabolites and metabolic pathways available in the Kyoto Encyclopedia of Genes and Genomes (KEGG), we downloaded all the compound entries with pathway annotations available in the KEGG. From these data, we constructed a dataset where each …

Upregulation Of Fatty Acid Synthase Increases Activity Of Β-Catenin And Expression Of Notum To Enhance Stem-Like Properties Of Colorectal Cancer Cells, Courtney O. Kelson, Josiane Weber Tessmann, Mariah E. Geisen, Daheng He, Chi Wang, Tianyan Gao, B. Mark Evers, Yekaterina Y. Zaytseva

Markey Cancer Center Faculty Publications

Dysregulated fatty acid metabolism is an attractive therapeutic target for colorectal cancer (CRC). We previously reported that fatty acid synthase (FASN), a key enzyme of de novo synthesis, promotes the initiation and progression of CRC. However, the mechanisms of how upregulation of FASN promotes the initiation and progression of CRC are not completely understood. Here, using Apc/VillinCre and ApcMin mouse models, we show that upregulation of FASN is associated with an increase in activity of β-catenin and expression of multiple stem cell markers, including Notum. Genetic and pharmacological downregulation of FASN in mouse adenoma organoids decreases the activation of β-catenin …

Multivalent Protein-Nucleic Acid Interactions Probed By Composition-Gradient Multiangle Light Scattering, Josephine C Ferreon, Natee Kongchan, Phoebe S Tsoi, Kyoung-Jae Choi, Sophia Kenrick, Joel Neilson, Allan Chris M Ferreon

Faculty, Staff and Students Publications

Many RNA-binding proteins, such as TDP-43 or CELF1, interact multivalently with nucleic acid repetitive elements. The molecular stoichiometry of protein to nucleic acid is often difficult to assess, particularly by standard electrophoretic mobility shift assays (EMSAs). Here, we investigate the use of composition-gradient multiangle light scattering (CG-MALS) for quantifying binding affinity and stoichiometry for two RNA-binding proteins with their nucleic acid partners of varied sequence and length: TDP43's N-terminal RNA recognition motifs with both TG/GU-repeat ssDNA and ssRNA, respectively, and CELF1's two N-terminal RNA recognition motifs with (TG/UGUU/GU) repeats and an experimentally defined cognate GU-rich element (GRE). Our CG-MALS data …

Metabolic Crossroads: Gaba Synthesis In Trichomonas Vaginalis Infection, Yesha Dhruv

Biochemistry and Molecular Biology

This study examines the gamma-aminobutyric acid (GABA) synthesis pathway in Trichomonas vaginalis infection of human HCT-8 cells, focusing on key enzymatic processes in glutamate conversion to GABA and metabolic adaptations. The hypothesis tested was that T. vaginalis modulates GABA metabolism to enhance host cell invasion and adaptation. Infection time-point studies, RNA sequencing, and aldehyde dehydrogenase (ALDH) assays were conducted. Comparisons between T. vaginalis strains Casu 2 and Casu 2/MOZ 2 revealed distinct infection dynamics. Casu 2 rapidly attached and replicated within an hour, peaking at 24 hours, while Casu 2/MOZ 2 exhibited delayed replication, peaking at 48 to 72 hours, …

Integrated Safety And Efficacy Analyses Of Phase 3 Trials Of A Microbiome Therapeutic For Recurrent Cdi, Colleen S Kraft, Matthew Sims, Michael Silverman, Thomas J Louie, Paul Feuerstadt, Edward S Huang, Sahil Khanna, Charles S Berenson, Elaine E L Wang, Stuart H Cohen, Louis Korman, Christine Lee, Colleen R Kelly, Alberto Odio, Paul P Cook, Bret Lashner, Mayur Ramesh, Princy Kumar, Ananya De, Asli Memisoglu, David A Lombardi, Brooke R Hasson, Barbara H Mcgovern, Lisa Von Moltke, Darrell S Pardi, Ecospor Iii And Ecospor Iv Investigators

Faculty, Staff and Students Publications

INTRODUCTION: Recurrent Clostridioides difficile infection (rCDI) often occurs after standard-of-care antibiotics. VOWST oral spores (VOS, previously SER-109), an FDA-approved orally administered microbiome therapeutic, is indicated to prevent rCDI following antibiotics for rCDI.

OBJECTIVE, DESIGN, AND PATIENTS: To evaluate safety and efficacy of VOS from two phase 3 trials, (randomized, placebo-controlled [ECOSPOR III: NCT03183128] and open-label, single arm [ECOSPOR IV: NCT03183141]) of 349 adults with rCDI and prevalent comorbidities.

METHODS: VOS or placebo [ECOSPOR III only] (4 capsules once daily for 3 days). Integrated analysis of treatment-emergent adverse events (TEAEs) collected through week 8; serious TEAEs and TEAEs of special interest …