Biochemistry, Biophysics, and Structural Biology Commons^™

Investigating Mono-Driver Versus Multi-Driver Oncogenesis Via Alterations To Cell Signaling Pathways, Abygail Chapdelaine

Open Access Dissertations

The latest edition of Global Cancer Statistics released by the American Cancer Society reported approximately 20 million newly diagnosed cancer cases worldwide in 2022 with 9.7 million deaths. This ranks cancer as the second leading cause of death worldwide. For the majority of cancer patients, the standard treatment approach is chemotherapy and/or radiation therapy, and while this has been successful in some patients, a lack of specificity to cancer cells causes severe side-effects when these agents damage healthy cells. Despite extensive efforts that have gone into developing targeted cancer therapeutics that block functions specific to cancer, they have not been …

Temporal Dynamics Of Programmed Genome Rearrangement In Sea Lamprey Embryogenesis: A Deep Learning & Lightsheet Imaging Approach To Studying Early Developmental Transitions, Kasturi Rajandran

Theses and Dissertations--Biology

Programmed genome rearrangement (PGR) in the sea lamprey (Petromyzon marinus) leads to the elimination of ~0.5Gb (20%) of the germline genome during early embryogenesis, yet its timing relative to the maternal-to-zygotic transition (MZT) remains unclear. In this study, we imaged embryos cleared at 3-hour intervals (up to 72 hours post fertilization (hpf)) using high-resolution lightsheet fluorescence microscopy and a custom deep-learning image-analysis pipeline (~80% accuracy) to quantify nuclei and micronuclei counts. Micronuclei, which are the hallmarks of PGR first appear between 24 to 27hpf (vs ~36hpf previously reported) indicating PGR starts earlier than previously reported in the sea …

Extracellular Vesicles Released By All Patients Contain Hne-Adducted Proteins: Implications Of Collateral Damage, Jenni Ho, Suriyan Sukati, Tamara Taylor, Sherry Carter, Brittany Fuller, Amy Marmo, Caryn Sorge, John A. D'Orazio, D. Allan Butterfield, Subbarao Bondada, Heidi Weiss, Daret K. St. Clair, Luksana Chaiswing

Markey Cancer Center Faculty Publications

Off-target neuronal injury is a serious side-effect observed in cancer survivors. It has previously been shown that pediatric acute lymphoblastic leukemia (ALL) survivors have a decline in neurocognition compared to healthy age-matched counterparts. Elevated oxidative stress has been documented to be a mediator in off- target tissue damage in cancer survivors. Early detection of oxidative stress markers may provide an opportunity to prevent off-target tissue damage. Extracellular vesicles (EVs) have surfaced as a potential diagnostic tool due to molecular cargo they contain. We investigated the potential for EVs to be a sensitive indicator of oxidative stress and off-target tissue damage …

The Adiponectin-Pparγ Axis In Hepatic Stellate Cells Regulates Liver Fibrosis, Shangang Zhao, Qingzhang Zhu, Wang-Hsin Lee, Jan-Bernd Funcke, Zhuzhen Zhang, May-Yun Wang, Qian Lin, Bianca Field, Xue-Nan Sun, Guannan Li, Mbolle Ekane, Toshiharu Onodera, Na Li, Yi Zhu, Christine M. Kusminski, Terry D. Hinds Jr., Philipp E. Scherer

Markey Cancer Center Faculty Publications

Hepatic stellate cells (HSCs) are key drivers of local fibrosis. Adiponectin, conventionally thought of as an adipokine, is also expressed in quiescent HSCs. However, the impact of its local expression on the progression of liver fibrosis remains unclear. We recently generated a transgenic mouse line (Lrat-rtTA) that expresses the doxycycline-responsive transcriptional activator rtTA under the control of the HSC-specific lecithin retinol acyltransferase (Lrat) promoter, which enables us to specifically and inducibly overexpress or eliminate genes in these cells. The inducible elimination of HSCs protects mice from methionine/choline-deficient (MCD) diet-induced liver fibrosis, confirming their causal involvement in fibrosis development. We generated …

Urobilin Derived From Bilirubin Bioconversion Binds Albumin And May Interfere With Bilirubin Interacting With Albumin: Implications For Disease Pathology, Kevin I. Williams, Priyanka Suryadevara, Chang-Guo Zhan, Terry D. Hinds Jr., Zachary A. Kipp

Markey Cancer Center Faculty Publications

Background/Objectives: Bilirubin is a hydrophobic molecule that binds the carrier protein albumin for transport through systemic circulation. Bilirubin is cleared from the body through the liver and excreted into the intestines, where the microbiota modifies the chemical structure, forming urobilin, which can be reabsorbed into circulation by the hepatic portal vein. Urobilin has no known function. It is also unknown whether urobilin binds albumin for transport in circulation. We hypothesized that because of the likeness of their chemical structures, urobilin would also bind albumin like bilirubin does. Methods: First, we used in silico docking to predict if urobilin would bind …

Dissecting The Biophysical Mechanisms Of Oleate Hydratase Association With Membranes, William A. Lathram, Robert J. Neff, Ashley N. Zalla, James D. Brien, Vivekanandan Subramanian, Christopher D. Radka

Markey Cancer Center Faculty Publications

This study investigates the dynamics of oleate hydratase (OhyA), a bacterial flavoenzyme from Staphylococcus aureus, and its interactions with lipid membranes, focusing on the factors influencing membrane binding and oligomerization. OhyA catalyzes the hydration of unsaturated fatty acids, playing a key role in bacterial pathogenesis by neutralizing host antimicrobial fatty acids. OhyA binds the membrane bilayer to access membrane-embedded substrates for catalysis, and structural studies have revealed that OhyA forms oligomers on membrane surfaces, stabilized by both protein-protein and protein-lipid interactions. Using fluorescence correlation spectroscopy (FCS), we examined the effects of membrane curvature and lipid availability on OhyA binding to …

Cholesterol Modulation Of Bk Currents And Cerebral Artery Diameter Via Channel-Forming Alpha-Subunit, Elizabeth Schneider

Theses and Dissertations (ETD)

Voltage- and calcium-gated, large conductance potassium channels (BK; MaxiK) are ubiquitously expressed and subsequently mediate numerous physiological processes. Cholesterol is consumed in high amounts with the diet and accumulates in cellular membranes when plasma levels become elevated. Cholesterol is a known inhibitor of BK channels and is suspected of contribution to many pathophysiological issues via its interaction with these channels. However, the molecular mechanisms that drive cholesterol inhibition of BK channels remain largely unexplored. This dissertation hypothesized that cholesterol inhibits BK currents via binding to specific amino acid(s) of the channel-forming alpha subunit, and involving distinct modifications of channel gating. …

Conserved A-Rich Regions In The 3’ Utr Of Zika Virus Differentially Affect Viral Gene Expression, Kristen Kaytes

Electronic Theses & Dissertations (2024 - present)

Following its discovery in 1947, Zika virus garnered little attention in the global stage until a rapidly spreading epidemic brough the virus to the global stage in 2015. Continuous advances in research have begun to further the understanding of the molecular biology of Zika virus, however much is still unknown. Much of our understanding of the virus comes from cross reference to other viruses within the same family, such as Dengue virus and West Nile virus. A commonality of these viruses is that they resemble cellular mRNAs and have a single-stranded positive-sense RNA genome that contains a 5’-cap but lacks …

Development Of Dna Nanoswitches With Aptamer Based Detection For Thrombin, Camryn A. Beckles

Electronic Theses & Dissertations (2024 - present)

Bio-transducers are devices capable of converting the binding signals from molecular recognition events into readable signals for analytical detection. There is a need for modular bio-transducers that can specifically detect a wide range of analytes using a unified readout technique, as this approach could dramatically reduce costs of healthcare diagnostics and environmental monitoring.

To create such a modular transducer, the molecular recognition properties of aptamers will be used and integrated with the already established biosensing capabilities of DNA nanoswitches that reconfigure their shape in the presence of their target molecule. In this design, the detector strands of the nanoswitch will …

Modeling Functional Connectivity With Learning And Memory In A Mouse Model Of Alzheimer’S Disease, Lindsay Fadel, Elizabeth Hipskind, Steen E Pedersen, Jonathan Romero, Caitlyn Ortiz, Eric Shin, Md Abul Hassan Samee, Robia G Pautler

Faculty, Staff and Students Publications

Introduction: Functional connectivity (FC) is a metric of how different brain regions interact with each other. Although there have been some studies correlating learning and memory with FC, there have not yet been, to date, studies that use machine learning (ML) to explain how FC changes can be used to explain behavior not only in healthy mice, but also in mouse models of Alzheimer's Disease (AD). Here, we investigated changes in FC and their relationship to learning and memory in a mouse model of AD across disease progression.

Methods: We assessed the APP/PS1 mouse model of AD and wild-type controls …

Kinetic Model Of Glycolysis And Glutaminolysis Interplay Developed In Matlab Simbiology, Zohreh Mirveis, Hugh J. Byrne, Nitin Patil

Datasets

This dataset contains a kinetic model developed in MATLAB SimBiology to simulate the metabolic dynamics of glycolysis and glutaminolysis and their interconnection. The model was used in the study ‘Experimental and computational investigation of the kinetic evolution of the glutaminolysis pathway and its interplay with the glycolysis pathway’ (Mirveis et al., 2024). The dataset includes the original SimBiology project file together with the experimental data used for model training. These resources enable reproduction of the simulations reported in the publication and provide a reusable framework for further computational exploration of metabolic pathway kinetics.

Effects Of Starter Cultures On The Metabolite Profile, Antioxidant Activities, And Anti-Aging Properties Of Tapuy Lees, Edward Kevin B. Bragais, Paul Mark B. Medina

Biology Faculty Publications

The Philippine rice wine (tapuy) and tapuy lees making process utilizes bubod, the traditional starter culture. The bubod contains variable number and species of microorganisms and influences the physical and chemical properties of tapuy and tapuy lees, resulting in inconsistent quality products. Hence, improvement and standardization of local starter culture are significant. Here, we examined the effects of well-defined starter cultures (Rhizopus oryzae (RO), Mucor indicus (MI), and Saccharomyces cerevisiae (SC)) and bubod on the metabolite profile, antioxidant, and anti-aging activities of tapuy lees. Our results showed the presence of polyphenols (102.36 ± 2.84 to 173.92 …

Developing Novel Therapeutic Strategies For Mcrc With A Brafv600e Mutation, Mariah Geisen

Theses and Dissertations--Toxicology and Cancer Biology

Colorectal cancer (CRC) is the second leading cause of cancer death worldwide. The overall incidence rates of CRC have decreased in those over 50, but there is an increasing incidence rate in those under 50. Risk factors for CRC include diet, family history, and a sedentary lifestyle. Early detection of CRC is key to patient survival and treatment response. Localized CRC has a survival rate of 90% and allows for surgical resection and chemotherapy. The 5-year survival for metastatic CRC (mCRC) is significantly reduced to around 14%. Despite early detection, 50% of patients will develop metastasis after surgical resection and …

Swinging Lever Mechanism Of Myosin Directly Shown By Time-Resolved Cryo-Em, David P. Klebl, Sean N. Mcmillan, Cristina Risi, Eva Forgacs, Betty Virok, Jennifer L. Atherton, Sarah A. Harris, Michele Stofella, Donald A. Winkelmann, Frank Sobott, Vitold E. Galkin, Peter J. Knight, Stephen P. Muench, Charlotte A. Scarfi, Howard D. White

Department of Biomedical and Translational Sciences Faculty Publications

Myosins produce force and movement in cells through interactions with F-actin¹. Generation of movement is thought to arise through actin-catalysed conversion of myosin from an ATP-generated primed (pre-powerstroke) state to a post-powerstroke state, accompanied by myosin lever swing²,³. However, the initial, primed actomyosin state has never been observed, and the mechanism by which actin catalyses myosin ATPase activity is unclear. Here, to address these issues, we performed time-resolved cryogenic electron microscopy (cryo-EM)⁴ of a myosin-5 mutant having slow hydrolysis product release⁵,⁶. Primed actomyosin was predominantly captured 10 ms after …

Ciliary Arl14b In Vision, Alexis Breann Crockett

Graduate Theses, Dissertations, and Problem Reports (ETD)

Primary cilia are highly specialized organelles that regulate signaling, trafficking, and sensory perception across multiple tissues, including the retina. The small GTPase ADP Ribosylation Factor-Like Protein 13B (ARL13B) is an atypical ARF-family protein enriched in cilia. ARL13B acts as a guanine exchange factor (GEF) for another small GTPase ARF-like Protein 3 (ARL3). Mutations in ARL13B cause Joubert syndrome, a ciliopathy characterized by brain malformation, developmental delays, and retinal degeneration. Despite ARL13B’s known ciliary localization and clinical relevance, ARL13B’s precise functions in cilia remain poorly defined. This dissertation investigates the cilia-specific roles and GEF-specific roles of ARL13B in photoreceptors using two …

Ocean Acidification Mitigation: Potential Expansion Of Sav Restoration Strategy In The Chesapeake Bay, Cree N. Taylor

Undergraduate Research Posters

Zostera marina is a species of marine macrophyte that has been largely prioritized in past submerged aquatic vegetation (SAV) restoration initiatives within the Chesapeake Bay because of its 1) previous abundance, 2) demonstrated carbon burial abilities, and 3) observed ability for meadows of Z. marina to ameliorate low pH conditions. Due to the temperature variability and poor water quality associated with anthropogenic disturbances in the Chesapeake Bay, Z. Marina beds have experienced several die-off events with limited capacity for regrowth. This systematic review explored the possible benefits of focusing future SAV recovery initiatives on ensuring a diverse variety of SAV …

Analysis Of Differential Gene Expression In Androgen-Independent Clones Derived From The Mycap Pca Cell Line, Jessie L. Tignor, Melanie Sinanian, Richard Inho Joh, David Gewirtz, Jason Reed

Undergraduate Research Posters

Androgen deprivation therapy (ADT) is a primary treatment strategy for prostate cancer (PCa), yet many tumors eventually develop androgen independence, leading to treatment resistance. To investigate the molecular changes underlying this transition, we analyzed differential gene expression in four androgen-independent (AI) clones derived from the Myc-CaP prostate cancer cell line using RNA sequencing. Gene expression profiles were compared to the parental Myc-CaP line, and differentially expressed genes (DEGs) were identified using DESeq2 and edgeR. The AI clones exhibited significant downregulation of senescence-associated genes, including Ezh2 and lamin B1, suggesting a loss of senescence-related chromatin repression. Additionally, upregulation of Wnt pathway …

Nature, Nurture, And Serial Murder: A Biocriminological Analysis Of Jeffrey Dahmer And Aileen Wuornos, Dori W. Jal

Honors Thesis

In recent years, there has been an increase in public fascination with serial killers, however current criminological explanations continue to focus on social and psychological factors, lacking commentary on potential biological implications. This thesis addresses a gap in the literature by examining how biological processes, specifically epigenetic, neurobiological, and endocrinological mechanisms, interact with environmental stressors to shape serial homicidal behavior. The goal is to determine whether serial murder can be more effectively understood through a biosocial framework that integrates biological vulnerability with lived experience, rather than relying on singular explanatory models.

Using a qualitative multiple-case study methodology, this research analyzes …

Bacteria-Engineered Vesicles For Cancer Immunotherapy: From Immunomodulation In Vitro To Anti-Tumor Effects In Melanoma Models, Lan Li

Theses and Dissertations--Chemistry

Bacterial vesicles hold immense potential in various biomedical fields. Among these, outer membrane vesicles (OMVs) produced by Gram-negative bacteria are the most extensively studied. While the exact mechanism of OMV production remains unclear, numerous environmental factors have been shown to influence both their yield and composition. In this study, we investigated the effect of three different antimicrobial families on OMV production by E. coli. Interestingly, antimicrobials within the same family did not provide the same effects on OMV yield, suggesting that OMV production may not directly correlate with the antimicrobial mechanism of action. OMVs have demonstrated tumor-inhibitory activity in multiple …

Raman Spectroscopy For Rapid Quantification Of Macronutrients In Heirloom Beans, K. Chandler Williams

Graduate Theses, Dissertations, and Problem Reports (ETD)

Quantification of macronutrients in food requires a large investment in facilities and instrumentation as well as ongoing expenses of labor, reagents, and hazardous waste disposal. These costs pose a significant barrier to determining macronutrient quantities in the thousands of uncharacterized landrace and heirloom crops and discourage traditional crop breeding projects from ensuring that their selected crops maintain desirable macronutrient profiles in addition to target agronomic traits. Our objective was to test whether a hand-held Raman spectrometer—a technology which has found use in plant disease diagnostics but remains largely overlooked in nutrient quantification-- could provide a feasible means for quantifying the …

Redox Control In A Fused Electron Transfer Flavoprotein From A Thermophilic Archaeon And Expanded Significance Of A Hydrogen Bond From A Conserved Histidine Residue That Contributes To Flavin Redox Tuning And Activation For Covalent Modification, Debarati Das

Theses and Dissertations--Chemistry

In absence of O₂ as terminal electron acceptors in anaerobic bacteria and archaea, carbohydrate metabolism is 15 times less efficient compared to aerobic energy metabolism resulting in energy deficit conditions. Despite their meager resources these anaerobes were able to generate H₂ and a chemiosmotic potential able to drive energy demanding reactions such as CO₂ or N₂ fixation. These observations raised concerns as production of high energy reductants (H₂) from mediocre fuels (NADH) defied the laws of thermodynamics.

In 2008, a known mechanism “electron bifurcation” but with flavins as redox mediators instead of quinones was …

Expanding The Vibrating Sharp-Edge Spray Ionization Toolkit For Oligonucleotide Characterization, Sultan Mahmud

Graduate Theses, Dissertations, and Problem Reports (ETD)

A gentle or soft Ionization process is a critical component in native mass spectrometry (MS) to lift the biomolecules from the bulk solution into the gas phase environment of the mass spectrometer preserving their shape, topology and non-covalent interactions. Electrospray ionization (ESI) facilitates structural preservation of proteins, nucleic acids and their complexes and as a result it has been extensively used in native MS. However, in negative ion mode, ESI is somewhat limited in sensitivity due to corona discharge effect resulting from the requirement of a high amount of voltage. This often disrupts the ESI process and may not preserve …

Development And In Vitro Evaluation Of Novel Near-Ir Fluorescent Sensors For Egfr Kinase, Haniyeh Jadidi

Graduate Research Theses & Dissertations

This thesis presents the in vitro evaluation of a novel near-infrared (NIR) fluorescent small-molecule probe AB-139 that selectively binds to epidermal growth factor receptor (EGFR) kinase and operates through a turn-on fluorescence mechanism. The sensor addresses several limitations associated with conventional protein-based probes by offering small-molecule specificity, tunable modularity, deep-tissue imaging potential, and reduced background noise. AB-139 comprises four key components: A Zn-phthalocyanine fluorophore that serves as the NIR emission reporter; hydrophilic triethylene glycol chains that enhance aqueous solubility and reduce aggregation; cationic quaternary ammonium groups that facilitate cellular permeability; and a gefitinib-derived recognition anchor that targets the intracellular ATP-binding …

Investigating Rna Dysfunction Of Inherited Neuromuscular And Neurodevelopmental Disease, Jacob H. Schroader

Electronic Theses & Dissertations (2024 - present)

ITPase deficiency is a rare but fatal, autosomal recessive enzyme deficiency involving encephalopathy, microcephaly, congenital cataracts, hypotonia, developmental delay, and dilated cardiomyopathy. Within a decade since the original description of the severe form in humans, there are huge gaps in the field regarding the underlying molecular mechanisms driving pathogenesis resulting from ITPase deficiency. Past studies have focused on characterization of the organism level ITPase-deficient phenotype, but the molecular and cellular characterization remains to be fully described. Due to the biochemical function and established biological role of the ITPase enzyme, investigation into the consequences of inosine accumulation and misincorporation into RNA …

Interfacing Neural Models: Biocompatibility And Fabrication Of A Flexible, Self-Folding Microelectrode Array, Fernando A. Pesantez Torres

Electronic Theses & Dissertations (2024 - present)

Neurodegenerative diseases pose a formidable challenge in modern medicine, necessitating the development of advanced research tools that can elucidate their complex pathophysiology. Recent advancements in neurodegenerative disease research have led to the development of three-dimensional (3D) neurodegenerative organoids using human induced pluripotent stem cells (hiPSCs). These organoids closely mimic human brain architecture and functionality, providing a valuable tool for understanding complex diseases. Additionally, the ability to generate and study brain organoids consistently and in large quantities holds potential for a controlled in vitro setting and high-throughput drug screening. However, these models are complex systems requiring specialized maintenance, analysis, and manipulation …

Positive Allosteric Modulation Of Glun1/Glun3 Nmda Receptors, Mia Ruth Johns

Graduate Student Theses, Dissertations, & Professional Papers

N-methyl-D-aspartate (NMDA) receptors are ionotropic glutamate receptors that mediate excitatory neurotransmission in the central nervous system (CNS) where they play critical roles in normal and pathological brain functions and neurodevelopment. While the glutamate/glycineactivated GluN2-containing NMDA receptors (GluN1/GluN2) have been extensively studied, the physiological roles and pharmacology of glycine-activated GluN3-containing receptors (GluN1/GluN3) remain less understood. Although GluN1/GluN3 receptors exhibit unique functional properties and play distinct roles in neuronal development and synapse maturation, studies of their precise roles in neurophysiology and circuit function are impeded by limited availability of GluN3-selective pharmacological tools. This study describes UCM-A86, a novel GluN3-selective positive allosteric …

Combining Esm Models With Experimentally Derived Structural Stability To Identify Functional Missense Mutations, Rucha Deo

Master's Projects

Missense mutations can impact protein function and structure, yet their effects on protein function are difficult to predict. In this study, I compared two deep learning models, ESM1v and ESM1b, by evaluating their mutation predictions against experimental structural stability data. ESM1v showed a stronger correlation with experimental structural stability scores compared to ESM1b. A sigmoid curve was fitted to explore this relationship further. Over 100,000 mutations were identified where experimental stability differed significantly from model predictions. Many mutations that remained structurally stable experimentally but were predicted as harmful by the ESM models were frequently found at known functional sites. Structural …

The Importance Of Solution Studies For The Structural Characterization Of The Enterovirus 5' Cloverleaf, Morgan G. Daniels, Meagan E. Werner, Xiaobing Zuo, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Enteroviruses initiate genomic replication via a highly conserved mechanism that is controlled by an RNA platform, also known as the 5' cloverleaf (5'CL). Here, we present a biophysical analysis of the 5'CL conformation of three enterovirus serotypes under various ionic conditions, utilizing CD spectroscopy, size-exclusion chromatography, and small-angle X-ray scattering. In general, a tendency toward a smaller monomeric hydrodynamic radius in the presence of salts was observed, but the exact structural signature of each 5'CL varied depending upon the serotype. Rhinovirus B14 (RVB14) exhibited at least two monomeric conformations and a low propensity for dimerization, while poliovirus 1 (PV1) showed …

Characterization Of Lipids In Tenebrio Molitor Larvae And Pupae Under Various Extraction Methods, Nariman A. Ktil

Graduate Theses, Dissertations, and Problem Reports (ETD)

Tenebrio molitor, or the yellow mealworm is an edible insect widely recognized and consumed for its rich nutritional value. Mealworms are known for their flexible nature of adapting to various environmental conditions and being able to thrive under harsh conditions and low-value wastes. In this paper, our main goal was to investigate the mealworm’s ability to grow and develop while being reared on apple pomace, the biowaste from apple production, and the effect it would have on its nutritional value specifically its lipid profile. Then these reared insects were used for oil extraction and analyzing their fatty acid profiles. …

An Investigation Into How The Prostate And Androgens Mediate Greater Levels Of Uric Acid In Males Compared To Females, Rachel D. King

Graduate Theses, Dissertations, and Problem Reports (ETD)

Chronic elevated circulating uric acid (UA) levels (hyperuricemia) are associated with gout as well as cardiovascular, metabolic, and renal dysfunction. Men have greater mean circulating UA levels than women and are more likely to exhibit hyperuricemia. This may be partly driven by the hormonal regulation of renal UA transporters; however, a direct link between hormones and UA production has not been established. Production of UA is catalyzed by xanthine oxidoreductase (XOR / XDH), which is ubiquitously expressed but has the greatest specific activity in the liver. Interestingly, an extensive gout genome-wide association study (GWAS) recently revealed a robust genetic …