Biochemistry, Biophysics, and Structural Biology Commons^™

The Influence Of Myocardin Effector Genes On The Tgf-Beta Smad3 Signaling Pathway In Human Pleural Mesothelial Cells, Hema Chandra Hrushi Dusharla

Biotechnology Theses

Pleural Fibrosis (PF) involves excessive extracellular matrix (ECM) deposition, mainly by myofibroblasts, leading to pleural thickening and impaired lung function. Pleural mesothelial cells (PMCs) contribute via mesothelial and mesenchymal transition (MesoMT), triggered by cytokines like TGF-β. Our lab identified Myocardin (MyoCD), a transcriptional co-activator of cardiac and smooth muscle, is a master regulator of pleural fibrosis through interactions with serum response factor (SRF) and Smad2/3 transcription factors which initiate fibrosis signaling. RNA sequencing and qPCR analysis revealed that silencing MyoCD decreased the expression of CTNNB1, MDFI, and Tspan2. MDFI emerged as a potent candidate, as this gene affecting the expression …

Using The Safety Scissors: Dna Resection Regulation At Dna Double-Strand Breaks And Telomeres, Michael M, Soniat, Logan R. Myler

Department of Biochemistry and Molecular Biology Faculty Papers

DNA resection is a universal process in genome maintenance by which one strand of DNA is degraded, leaving the other strand intact. This sometimes highly processive process is critical for many forms of DNA damage repair, replication-coupled repair, meiotic recombination, and telomere maintenance. Therefore, resection must be tightly regulated to prevent genome instability and promote faithful and accurate repair. Here, we review what is known about how resection functions and how it is controlled, using DNA double-strand break repair and telomere maintenance as examples. We address how resection is regulated in three independent steps: resection initiation, long-range processing, and termination. …

A Cancer Education Needs Assessment: Informing Middle-Aged Female Patients About The Relationships Between Obesity And Women’S Health Concerns In The Reproductive System, Breast, And Endometrial Health, Batul Mirza

MUSC Theses and Dissertations

Obesity significantly impacts women’s health, particularly among middle-aged women, by increasing the risk of hormone-sensitive cancers such as breast, endometrial, and reproductive system cancers. This study examines the educational needs of this demographic group regarding obesity-related cancer risks and explores effective intervention strategies. Obesity-induced mechanisms – hormonal imbalances, chronic inflammation, and insulin resistance – drive cancer susceptibility, emphasizing the need for targeted health education. The study employs a qualitative design, which includes interviews with subject matter experts (SMEs) and surveys of middle-aged women. The goal is to assess awareness, perceived barriers, and preferred learning methods. Findings suggest that with many …

Identification Of Serum Exosome Proteins In Systemic Sclerosis With Interstitial Lung Disease By Aptamer Proteomics, Sonsoles Piera-Velazquez, Simon T. Dillon, Xuesong Gu, Towia A. Libermann, Sergio A. Jimenez

Jefferson Institute of Molecular Medicine Papers and Presentations

OBJECTIVE: A major unmet need for Systemic Sclerosis (SSc) clinical management is the absence of well validated biomarkers for early diagnosis of SSc-associated interstitial lung disease (SSc-ILD). The objective of this study was to identify proteins contained within serum exosomes that may serve as potential biomarkers to differentiate patients with Diffuse SSc without SSc-ILD from patients with Diffuse SSc with SSc-ILD employing aptamer-based proteomics.

METHODS: Serum exosomes were isolated from two cohorts of patients. The first cohort included 15 patients with Diffuse SSc without SSc-ILD and 14 patients with Diffuse SSc with SSc-ILD and the second cohort included 12 patients …

Computational And Imaging Approaches For Precision Characterization Of Bone, Cartilage, And Synovial Biomolecules., Rahul Kumar, Kyle Sporn, Vibhav Prabhakar, Ahab Alnemri, Akshay Khanna, Phani Paladugu, Chirag Gowda, Louis Clarkson, Nasif Zaman, Alireza Tavakkoli

Department of Medicine Faculty Papers

Abstract

Background/Objectives: Degenerative joint diseases (DJDs) involve intricate molecular disruptions within bone, cartilage, and synovial tissues, often preceding overt radiographic changes. These tissues exhibit complex biomolecular architectures and their degeneration leads to microstructural disorganization and inflammation that are challenging to detect with conventional imaging techniques. This review aims to synthesize recent advances in imaging, computational modeling, and sequencing technologies that enable high-resolution, non-invasive characterization of joint tissue health. Methods: We examined advanced modalities including high-resolution MRI (e.g., T1ρ, sodium MRI), quantitative and dual-energy CT (qCT, DECT), and ultrasound elastography, integrating them with radiomics, deep learning, and multi-scale modeling approaches. We …

Du Undergraduate Showcase Abstracts: Research, Scholarship, And Creative Works, Kabe Aberle, Nadia Kako, Kateri Mcrae, Brooke Agulnek, Sky Palmon, Yasmine Ramirez, Francisca Aguirre Beltran, Ashley Juarez, Bridget Kim, Tessa Appel, Sterling Kerr, Spencer Ingley, Gabe Meyer, Robin Tinghitella, Dale Broder, Lily Baeza, Chloe Beers, Julia Coakley, Whitney Kelsey, Sydney Gainforth, Gabi Wing, Audrey Martin, Aaliyah Amore Berry, Brooke Watley, Kiruthika Venkatesan, Rachel Bienstock, Annabella Brotherston, Madison Bryant, Mia Burgener, Emma P. Lieb, Rachel A. Johnson, Jennifer L. Hoffman, Kania Campbell, Kiena Campbell, Courtney Cassidy, Sage Krzyzkowski, Maddox Jones, Skylar Abookire, Luke Hawkins, Sunnah Yoon, Andrea Chu, Yan Qin, Nyah Cubbison, Brian Gearity, Daniel Mcintosh, Mariely Cruz, Edward Garrido, Grady Dionne, Nicole Doris, Lyndsie Salvagio, Ann-Charlotte Granholm-Bentley, Anna Dymov, Hannah Eckert, Gabrielle Welsh, Erica Larson, Charlie Ernst, Anna Zhou, Sarah Watamura, Larissa Fedorovich-Klein, Georgie Fields, Kimberly A. Guevara, Aven Mccall, Ben Peltier, Feruz Yahia, Patrick Flores, Jadyn Floyd, Sophia Forcier, J. Von R. Monteza, Peter Sokol-Hessner, Gwendolyn Geiger, Scott Nichols, Camryn Gunter, Kendal Hengst, Charlie Bednarz, Issy Garside, Addison Baker, Rachel Mina, Brooke Hermanson, Amanda Klingler, William Highfill, Sydney Jaques, Kerstin Lewey, Allison Grossery, Daniel Linseman, Ethan Lim, Jagger Livengood, Owen Mantelli, Gabby Pappas, Abby Mcdonald, Madeleine Dierking, Eve Miller, Emma Loeber, Anna Marlow, Michael Kerwin, Ella Mathews, Hillary Hamann, Khadija Mohamed, Vivian Nguyen, Gabri Notov, Ifunayachi Ogbonna-Ukuku, Sunil Kumar, Charles Baysah, Sarah Olson, Don Sullivan, Anna Paradiso, Jay Parrish, Mira Pronobis, Alisha Pravasi, Kerstin Haring, Diego Ramirez, Christopher Reardon, Juliana Ramirez, Casey Doherty, Ella Kestner, Teagan Weindel, Cate Billings, Pablo Torre-Walter, Lucy Rand, Samantha Reynolds, Mark Siemens, Khadeeja Rashid, Laine Satterlee, Piper Heilbronner, Lily Pound, Ben Whitehurst, Anna Respet, Lizzie Lesoing, Sydney Hertel, Aya Saad-Masri, Brooke Ballenger, Max Proske, Hannah Rosenberg, Ellia Nakahara, Sophia Espinoza, Ivan Woolhouse, Simon Ruland, Gorkem Er, Timothy Sweeny, Melaku Saketa, Michela Schenk, Maren Lynch, Madi Hamm, Grace Schroeder, Michelle Rozenman, Rana Seif, Jackson Hall, Marisela Simental, Daniel Paredes, Aaron Mena, Preston Spaan, Evelyn Stovin, David Andrew Swartz, Anh Tran, Daniel Pittman, Luke Farchione, Emily Boyer, Ukari Verner, Lacey Conrad, Jonathan Velotta, James Weiner, Jagger Gossett, Noah Sherry, Sam Proud, Ben Block, Avi Narayana, Zoey Weiss, Alyssa Wilson, Gabrielle Walsh, David Zonana, Keely Wright, Kena Riveria, Lillybelle Deer, Jena Doom, Elysia Davis, Isabelle Yaremenko, Caitlyn Young

DU Undergraduate Research Journal Archive

Abstracts from the DU Undergraduate Research Showcase.

Purification Of Uranium Tetrafluoride Using Ammonium Bifluoride, Kyle R. Foster, Juliano Schorne-Pinto, Ronald E. Booth, Annabelle Husek, Mina Aziziha, Hunter B. Tisdale, Bernie W.N. Fitzpatrick, Hans Conrad Zur Loye, Markus H.A. Piro, Theodore M. Besmann

Faculty Publications

A method of purification for UF₄ utilizing NH₄HF₂ was investigated to remove oxygen and hydrate impurities from the salt. The original salt exhibited a melting point at 915–920 °C, which corresponds to the eutectic temperature of the UF4-UO2 system, showing clear signs of oxygen contamination. To purify the salt, an air-tight reaction vessel inside an argon glovebox was used to react UF4/NH4HF2 mixtures at elevated temperatures under a continuous flow of inert gas. The process yielded a significantly purer UF4 salt as confirmed via inert gas fusion, X-ray diffraction, differential scanning calorimetry and inductively coupled plasma-optical …

Crystal Growth, Thermal, Optical, Magnetic And Electrochemical Properties Of Mo2Ta2O11, Md Abdullah Al Muhit, Alevtina A. Maksimova, Sean C. Wechsler, Habiba Binte Kashem, Gopabandhu Panigrahi, Gregory Morrison, Morgan Stefik, Hans Conrad Zur Loye

Faculty Publications

Single crystals of the transition metal oxide Mo2Ta2O11 were grown for the first time using molten flux synthesis. The compound crystalizes in the trigonal space group R 3‾m (no. 166) with lattice parameters a = b = 5.6267(1) Å and c = 25.1424(6) Å and a unit cell volume of 689.36(3) ų. The structure of Mo2Ta2O11 is composed of alternating layers of TaO6 octahedra and MoO4 tetrahedra connected via corner-sharing. CaH2 was used to achieve a partial low temperature reduction of Mo2Ta2O11. The electrochemical lithiation of polycrystalline Mo2Ta2O11 was also investigated for the first time. Mo2Ta2O11 underwent a …

Biocomputing Approach To Modeling And Modulating Calcium Signaling, Sehee Sun

School of Computing: Dissertations, Theses, and Student Research

Biocomputing is an emerging field that seeks to perform computational tasks using biological substrates and processes. Unlike conventional computing systems based on silicon hardware, biocomputing leverages the parallelism, energy efficiency, and complex dynamics of living systems. Among various cellular mechanisms, calcium (Ca2+) signaling stands out as a central regulator of diverse biological functions, offering a promising basis for programmable logic and control in living cells.

This thesis introduces a novel framework for modeling and modulating Ca2+ dynamics using biologically inspired Boolean logic circuits. Specifically, we propose the Ca2+ Boolean Logic (CaBL) model, in which Ca2+ fluxes and interactions are abstracted …

Elucidating The Role Of Mir-10a/B In The Wound Healing Process In Larval Zebrafish, Jacquelyn E. Jacobs

All NMU Master's Theses

This study explores the regulatory role of microRNA-10 (miR-10) in larval zebrafish caudal fin regeneration, a model with broad implications for the future of regenerative medicine. Building on prior research from the lab, which indicated that miR-10 knockdown impairs regeneration, we verified this finding through rescue experiments, assessed its influence on healing projections, and examined its role in the innate immune response during the wound healing process. To address these questions, we employed a multi-faceted approach, including timed matings, microinjections, immunohistochemistry, fixed sample microscopy, and live imaging. Our results show that the experimental introduction of exogenous miR-10 can rescue the …

Oxytocin As A Possible Vegf Inhibitor For Treatment Of Diabetic Retinopathy, Daira Yepez

Theses and Dissertations

Diabetic retinopathy (DR) is a major complication of diabetes and a leading cause of vision loss largely driven by the overexpression of vascular endothelial growth factor (VEGF), which promotes neovascularization and vascular permeability in the retina. Current treatments, primarily anti-VEGF injections, inhibit the effects of VEGF once it has been secreted but can be ineffective in a certain subset of patients. Recent studies suggest that oxytocin (OXT), a neuropeptide mainly known for its roles in reproduction and social bonding, may downregulate VEGF expression. This study aimed to investigate whether OXT influences VEGF secretion in the human retinal pigment epithelial (RPE) …

L-Quebrachitol Modulates The Anti-Convulsant Effects Of Carbamazepine Possibly Through Voltage-Gated Sodium Channel Blocking Mechanism In Chicks: In Vivo And In Silico Studies, Asifa Asrafi, Mohammad Aslam, Ali G. Alkhathami, Md. Sakib Hossain, Imam Hossen Rakib, Md. Sakib Al Hasan, Feroz Khan Nun, Md. Faisal Amin, Muhammad Torequl Islam

School of Integrative Biological & Chemical Sciences Faculty Publications

Introduction: L-Quebrachitol (LQB), a naturally occurring bioactive compound, exhibits anti-inflammatory, anti-oxidant, anti-cancer, and anti-diabetic properties. However, its therapeutic potential in convulsant management remains largely unexplored. The objective of this study was to investigate the anticonvulsant effects of LQB in an In Vivo model and to examine its molecular interactions via In Silico docking simulations.

Methods: In the In Vivo study, pentylenetetrazol (PTZ) was administered intraperitoneally (i.p.) at 80 mg/kg to induce convulsions, and the test animals were treated orally with three doses of LQB (1, 5, and 10 mg/kg), with carbamazepine (CBZ) at 80 mg/kg as a standard drug.

Results: …

Using Radium Isotopes To Compare Nutrient Inputs Via Submarine Groundwater Discharge To Offshore Export On The West Florida Shelf, Andrew L. Lindgren

OES Theses and Dissertations

Radium isotopes have been used to trace submarine groundwater discharge (SGD) and associated nutrient and metal inputs into the coastal ocean. They have also been used to estimate rates of diffusive mixing and export fluxes of dissolved constituents offshore. However, use of both approaches in tandem to determine the fate of groundwater inputs after they enter the coastal ocean is still relatively unexplored. Radium isotopes and nutrients were measured in two cross-shelf cruises on the West Florida Shelf in different seasons and in quarterly sampling of offshore wells. Through 226Ra mass balance and 223Ra-derived diffusive mixing rates, inputs of nutrients …

Investigating The Role Of Metallothioneins In Fungal Iron Homeostasis, David Eap

Theses and Dissertations

The pathogenic fungi Aspergillus fumigatus requires metals to survive and infect humans, but metal overload can be detrimental. Metallothioneins (MTs) are small, cysteine-rich proteins that alleviate metal toxicity by binding excess metals (typically Zn or Cu) for storage or delivery. A recent report indicates that the Fe-S cluster binding glutaredoxin GrxD and the putative Cu-MT CmtA were interacting under high iron conditions in A. fumigatus. We hypothesize that this MT may have a role in binding iron or Fe-S clusters under iron overload conditions to prevent iron toxicity. We also aim to characterize this new MT by determining its …

Cytidine Triphosphate Specifically Modulates Parb-Mediated Dna Compaction: Insights From Single-Molecule Analysis And Parb C-Terminal Lysine Mutagenesis, Lois Akosua Serwaa

Theses and Dissertations

ParB is a central player in bacterial chromosome segregation, and cytidine triphosphate (CTP) is known to modulate its DNA compaction activity. This study explored whether CTP’s regulatory effect is due to specific molecular interactions beyond its known CTP-binding pocket. Using single-molecule flow-stretching and TIRF microscopy, we showed that CTP significantly reduces DNA compaction by wild-type Bacillus subtilis ParB, while ATP has no effect, supporting the hypothesis that CTP acts through specific recognition rather than general charge. CTP’s modulatory effect persisted across C-terminal domain (CTD) lysine mutants. Compaction was reduced in wild-type and K255A but abolished in K252A and K259A. The …

From Differentiation To Disease: Cyclin C Directly Coordinates Transcription And Mitochondrial Dynamics, Alicia Campbell

Theses and Dissertations

Organelle crosstalk is essential for coordinating cellular responses to various external cues, including stress and differentiation. Two key organelles, the nucleus and mitochondria, engage in extensive crosstalk to manage responses to a range of environmental and developmental signals. Complex processes such as stem cell differentiation and neuronal development rely on organelle crosstalk. Both processes integrate changes in gene expression with cytosolic and organellar remodeling. However, it remains unclear how these two complex processes are coordinated to achieve the desired outcome. This project concentrates on cyclin C (CCNC), a component of the Mediator Kinase Module (MKM), and its role in directly …

A Customizable Ligand-Conjugate System For Investigation And Detection Of Ghrelin O-Acyltransferase, Amber Ford

Dissertations - ALL

Ghrelin is a 28 amino acid peptide hormone responsible for a variety of physiological functions. Ghrelin signals these functions via its cognate receptor, GHSR, after an essential post translational modification which acylates its third serine. The acylation of ghrelin is facilitated by the enzyme ghrelin O-acyltransferase (GOAT) for which ghrelin is the only known substrate. Canonically, GOAT acylates ghrelin in the endoplasmic reticulum before it is further processed and secreted in circulation. Recent studies, however, have detected GOAT in the cytoplasm, plasma membrane, and in circulation in extracellular vesicles. Furthermore, GOAT has been identified as a potential prostate cancer (PCa) …

Synthesis Of Carboxymethyl Cellulose From Nypa Fruticans For Coating Metformin On Zn-Based Metal-Organic Framework Nanohybrid As A Bionanocomposite Drug Delivery System, Delviani Delviani, Viola Giary Rizkillah Maharani, Putri Nur Shadrina, Tri Warni, Regina Wan Azizah, Indra Lasmana Tarigan, Madyawati Latief

Makara Journal of Science

Diabetes is a common and rapidly spreading disease that affects 6.6% of the world’s population. Metformin hydrochloride (HCl) is an effective oral pharmacological treatment for type 2 diabetes mellitus (T2DM) patients because of its capability to reduce glucose levels and the risk of hypoglycaemia. However, gastrointestinal sensitivities to this drug can cause diarrhoea, nausea, vomiting and stomach ache. An alternative is controlled release technology by coating metformin with carboxymethyl cellulose (CMC) and zinc-metal-organic framework (Zn-MOF) through the encapsulation method. Therefore, this study aimed to coat metformin formulations using CMC in a Zn-MOF to control release into the body and minimise …

Microscopic Nucleic Acid-To-Protein Ratio: A Label-Free Approach For Pancreatic Cancer Detection, Sky Gao, Keerthi Priya Jangili, Alfred Akinlalu, Emmanuel Ogberefor, Tommy Gao, Kalpana Devaraj, Dali Sun

Electrical and Computer Engineering: Faculty Scholarship

Accurate and timely diagnosis remains a major clinical challenge, hindered by the limitations of conventional histopathological methods, which often rely on labor-intensive staining protocols and subjective interpretation by specialized pathologists. These methods can fail to capture the full molecular and phenotypic heterogeneity of tumors, leading to increased diagnostic time, cost, and variability. To overcome these challenges, we developed a novel label-free ultraviolet (UV) microscopic imaging technique that exploits the intrinsic optical absorption properties of cellular nucleic acids and proteins. By modifying standard brightfield microscopes, our approach quantitatively measures the nucleic acid-to-protein ratio (NPr), enabling high-resolution visualization and discrimination between malignant …

Photo-Crosslinked Persistent Micelle Templates With Near Universal Solvent Compatibility, Coby S. Collins, Mengxue Zhang, Cj Strurgill, Christian X. Ruff, Bryce Melton, Morgan Stefik

Faculty Publications

The controlled preparation of porous nanomaterials from block polymer templates is important for diverse applications from energy devices to optical coatings and sorbents. The architectural dimensions determine the overall performance for many of these applications, however the independent control of these dimensions has remained limited to a narrow range of solvent conditions for kinetically trapped (“persistent”) micelle templates. Polymers with a photo-reactive chemistry are shown to enable cross-linked micelle templates that universally remain persistent under diverse solvent conditions. Specifically, poly(poly(ethylene glycol methacrylate))-b-poly(butyl methacrylate-co-coumarin methacrylate) (OBC) was prepared by RAFT polymerization and the resulting micelles were crosslinked …