Biochemistry, Biophysics, and Structural Biology Commons^™

Identifying The Constituents Of Pyrolysis Oil Using Supercritical Fluid Chromatography- Fraction Collection (Sfc-Fc) And Gas Chromatography- Mass Spectrometry/Vacuum Ultraviolet Spectroscopy (Gc-Ms/Vuv), Sadid Morshed

2025 Fall Honors Capstones Projects - Archive

Plastic waste continues to accumulate as production increases and disposal methods remain insufficient. Even with recycling programs in place, much of the discarded plastic still ends up in landfills or waterways, eventually breaking down into harmful microplastics. One promising solution is the conversion of plastic waste into pyrolysis oil, which can also serve as an alternative feedstock for chemicals. Pyrolysis oil is produced by heating plastics to approximately 800 °C in the absence of oxygen, resulting in a complex mixture of hydrocarbons that includes paraffins, isoparaffins, olefins, naphthenes, and aromatics. Analyzing the amount of oxygen, nitrogen, and sulfur in these …

Cdh-3/Cadherin, Yap-1/Yap And Egl-44/Tead Promote Syx-2/Syntaxin And Eff-1 Fusogen-Mediated Phagosome Closure, Alec Whited, Aladin Elkhalil, Ginger Clark, Piya Ghose

Biology Theses - Archive

Physical interactions between cells, such as cell-cell junctions, can profoundly impact cell fate. A vital cell fate for normal development and homeostasis is programmed cell death. Cells fated to die must be efficiently cleared away via phagocytosis, and defects are associated with a variety of diseased states. Whether cell-cell physical associations affect programmed cell elimination has not been well-explored. Here we describe, in vivo, a cell-cell adhesion-driven signaling pathway that ensures compartment-specific cell clearance during development. We previously described the specialized cell death program “Compartmentalized Cell Elimination” (CCE) in the C. elegans embryo. During CCE, the tail-spike cell (TSC), a …

Resveratrol Exerts Anti-Inflammatory Effects On Human Thp-1 Macrophages, Valeria B. Martinez

Chemistry & Biochemistry Theses - Archive

Inflammation is a natural biological response to harmful stimuli. It initiates a series of reactions that prompt defensive and curative mechanisms, ridding the body of offending agents and healing remaining injuries. Inflammation involves the intricate communication between cells, requiring complex signaling that mediates various pathways. This acute form of inflammation is vital for our survival, promoting a myriad of mechanisms that function to defend and heal. However, if this inflammatory response is not resolved, it results in a prolonged condition referred to as chronic inflammation. This persistent inflammatory state is incredibly harmful, damaging the host's healthy cells, tissues, and organs. …

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 …

The Role Of Sodium Butyrate As An Inflammatory Regulator And Its Effect On Long Noncoding Rnas In Neuroinflammation, Angel Covarrubias

Chemistry & Biochemistry Theses - Archive

Inflammation is a crucial homeostatic process that contributes to both the elimination of foreign invaders and tissue repair. Inflammation at sites of tissue injury or infection is initiated by the detection of a harmful stimulus, triggering vital inflammatory immune signaling pathways and a cascade of cytokines and inflammatory mediators. The dysregulation of this process, however, can result in inappropriate inflammatory responses manifesting in tissue damage and compromised cell function. Dysregulation of the inflammatory response is seen frequently in many human diseases such as Diabetes, Cancer, cardiovascular disease, and neurodegenerative diseases.

In the context of the Central Nervous system, inflammation is …

Characterizing And Targeting The Non-Catalytic Functions Of Phosphatase Of Regenerating Liver 3 (Prl-3) In Oncogenesis And Cancer Progression, Jeffery T. Jolly

Theses and Dissertations--Molecular and Cellular Biochemistry

Phosphatase of Regenerating Liver 3 (PRL-3) is frequently upregulated in various cancers and is associated with poor patient prognosis. Although traditionally studied for its phosphatase activity, PRL-3 also interacts with the CNNM family of magnesium transporters through its catalytic site, and these two functions are mutually exclusive at any given time. Most previous studies relied on a commonly used PRL-3 mutation that disrupts both phosphatase activity and CNNM binding, making it challenging to determine which function drives its oncogenic effects. To address this gap in the field, I utilized a panel of PRL-3 mutants that selectively disrupt either phosphatase activity …

Characterization Of The Erv41-Erv46 Complex As A Retrograde Receptor For Misfolded Secretory Proteins, John Andrew Fuesler

Dartmouth College Ph.D Dissertations

The Endoplasmic Reticulum (ER), the site of secretory protein biosynthesis

provides a favorable environment to promote polypeptide folding, protein

oligomerization and export. Although the ER contains many chaperones and other

factors that assist in protein folding, this process is error prone. Eukaryotes have

evolved protein quality control checkpoints to maintain homeostasis in the secretory

pathway, however these processes are imperfect and may result in proteotoxicity

when toxic levels or aggregates of proteins arise. Mutations in proteins involved in

trafficking in the early secretory pathway are closely associated with disease states.

Therefore, it is of great interest to further understand how …

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 …

Traction Force Microscopy Using An Epifluorescence Microscope: Experimental Considerations And Caveats, Zaria Booth, Mazen Mezher, Rudra Patel, Venkat Maruthamuthu

Mechanical & Aerospace Engineering Faculty Publications

Forces exerted by cells due to their internal contractility play fundamental roles in a host of processes, including adhesion, migration, survival and differentiation. Traction force microscopy (TFM) enables the determination of forces exerted by cells or cell collectives on their environment, which is typically taken to be an extra-cellular matrix (ECM)-coated substrate. Sample preparation for TFM involves the plating of cells onto an environment embedded with fiducial markers. The imaging of these fiducial markers in the presence and absence of the cells then enables calculation of the displacement of localized regions of the environment, and, consequently, the spatial distribution of …

Transient Transmembrane-Electrostatically Localized Protons And Transmembrane Potential In A Laser Flashed Bacteriorhodopsin Purple Membrane Open Flat Sheet - Summary, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The transmembrane-electrostatically localized protons/cations charges (TELCs, also known as TELPs) model may serve as a unified framework to explain a wide range of bioenergetic phenomena. Transient transmembrane-electrostatically localized protons (TELPs) and transmembrane potential in a laser flash-energized bacteriorhodopsin (bR) purple membrane (PM) open flat sheet are now better analyzed. Under the Heberle et al. (1994) experimental conditions, the number of bR molecules is now calculated to be 8200 per PM open flat sheet with a diameter of 600 nm. With a single-turnover laser flash intensity of 3 mJ/cm² to photoexcite 10% of the bR molecules, the laser flash-induced peak TELCs …

Molecular Interactions Between The Shellfish Pathogen Vibrio Coralliilyticus Re22 And The Probiont Phaeobacter Inhibens S4sm, Jessica Coppersmith

Open Access Dissertations

Oyster larvae aquaculture is an important industry, both economically and environmentally, helping to create sustainable food systems by supplying seed oysters to farms, and also to restoration projects aimed at building coastal resilience and improving water quality by rejuvenating wild populations. However, oyster larvae are highly susceptible to rapid mortality events, crashes, which can seriously impact the industry. One source of these crashes in hatchery systems is vibriosis, caused by pathogenic species of Vibrio bacteria that are ubiquitous in temperate coastal waters, and with rising surface water temperatures their prevalence and virulence are increasing. To prevent these larval crashes from …

Durable Oxyfluoride Waste Forms For Salt Wastes From Molten Salt Reactors, Alevtina A. Maksimova, Jake W. Amoroso, Matthew Page, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

Molten salt reactors (MSRs) are promising technology to replace traditional light and heavy water reactors in the near future. Waste management for MSRs, however, remains a pressing concern that needs to be resolved prior to realizing deployment of MSRs. Specifically, the generated salt waste needs to be safely sequestered, a task made difficult by the high solubility of the salt waste that can cause the release of radionuclides into the environment. This work demonstrates a new approach to immobilize multiple fluoride salts into a single waste form by converting highly-soluble fluorides to durable and stable oxyfluorides. Notably, we report a …

Racial Health Disparities Among Pregnant Women Of Color In New York City: Biological And Systemic Impacts, Kaylin Peña

Pitzer Senior Theses

Racial Health Disparities Among Pregnant Women of Color in New York City: Biological and Systemic Impacts

Abstract

This thesis aims to explore how racial health disparities, underrepresentation in gynecology, and socioeconomic barriers contribute to adverse pregnancy outcomes among women of color in New York City. Through an interdisciplinary approach that combines resources from medical anthropology and human biology, this research will examine the biological implications of chronic stress, specifically HPA axis dysregulation, and its role in maternal health outcomes. With the idea of intersectionality, as conceptualized by Kimberlé Crenshaw, the study analyzes the various effects of systemic inequities and social …

The Relevance Of Dnajb1 Protein Dimerization Against The Human Neurodegenerative Diseases, Erina Kotreli, Trang Le, Szymon Ciesielski

Dean's Leadership Council Library Research Prize

All biological functions in living organisms depend on the activity of proteins, long molecules that must twist and fold into specific shapes to become functional. A subset of proteins known as molecular chaperones is essential for maintaining cellular health by assisting other proteins in folding correctly and refolding those damaged by stress. When proteins misfold and clump together, they can form toxic aggregates linked to many neurodegenerative diseases, including Alzheimer’s disease (AD), one of the leading causes of death in the United States. In AD, these protein aggregates form organized, elongated structures referred to as amyloid-like fibrils, which damage neurons …

Organic Geochemical Evidence For Life In Archean Rocks Identified By Pyrolysis-Gc-Ms And Supervised Machine Learning, Michael L. Wong, Anirudh Prabhu, Conel O'D. Alexander, H. James Cleaves Ii, George D. Cody, Grethe Hystad, Marko Bermanec, Wouter Bleeker, C. Kevin Boyce, Andrea Corpolongo, Andrew D. Czaja, Souvik Das, Robert R. Gaines, Daniel D. Gregory, John A. Jaszczak, Emmanuelle J. Javaux, Jaganmoy Jodder, Andrew H. Knoll, Martin Van Kranendonk, Katie M. Maloney, Nora Noffke, Robert Rainbird, Emersyn Slaughter, Eva E. Stüeken, Roger E. Summons, Frances Westall, Jasmina Wiemann, Shuhai Xiao, Robert M. Hazen

OES Faculty Publications

Throughout Earth’s history, organic molecules from both abiogenic and biogenic sources have been buried in sedimentary rocks. Most of these organic molecules have been significantly altered by geologic processes through deep time. Nonetheless, the nature and distribution of those ancient fragmentary organic remains have the potential to reveal diagnostic biomolecular information after billions of years of burial. Here, we analyzed 406 fossil, modern biological, meteoritic, and synthetic samples using pyrolysis gas chromatography and mass spectrometry. We explored these analytical data via supervised machine-learning methods to discriminate samples of biogenic vs. abiogenic origin, plant vs. animal phylogenetic affinity, and photosynthetic vs. …

Development And Application Of Enhanced Sampling Techniques For Investigating Protein Interactions And Drug Discovery, Timothy Hasse

Wayne State University Dissertations

Understanding the dynamics of protein–protein and protein–ligand interactions is critical for elucidating biological function and guiding drug discovery. However, many such processes involve rare events and high energy barriers that are difficult to capture with conventional molecular dynamics (MD). Enhanced sampling techniques extend the reach of MD, enabling access to biologically relevant transitions and thermodynamic properties. In the first project, Gaussian accelerated MD (GaMD) was used to study the MEIG1–PACRG complex, a key regulator of sperm flagellar assembly. Simulations of wildtype and mutant MEIG1 (W50A, Y68A) revealed mutation-specific disruptions to the binding interface and identified druggable pockets, particularly on PACRG. …

Creation Of A Dual-Fluorescence Reporter System To Assay Mirna Regulation Of Apobec3a, Tolulope D. Ajayi

All Graduate Theses, Dissertations, and Other Capstone Projects

MicroRNAs have an important role in regulating gene expression, including regulating the transcripts of the APOBEC3 family of cytidine deaminases. The APOBEC3 family is part of the immune defense against viral infection but has also been implicated in cancer progression. The hypothesis for this thesis is that specific miRNAs could be identified that regulate APOBEC3A (A3A) expression. I used molecular cloning and confocal microscopy to evaluate the miRNA-mediated silencing of A3A. A commercially available vector, psiCHECK-2, can be used to assay microRNA (miRNA) activity on specific targets. Molecular cloning was performed to modify the psiCHECK-2 Dual luciferase system (Renilla and …

Ubiquitin, Cavitand, And Nmr: 15n-1h Hsqc Analysis Of Cavitand Binding Domains On Ubiquitin, Grant Stucky

CMC Senior Theses

Ubiquitin and its derivatives through side chain modification are present in many of the degradation pathways for proteins found in neurodegenerative diseases. A non-toxic method for determining the amount of these proteins could have biosensing applications, but the binding domains of such proteins are not well characterized. ¹⁵N-¹H HSQC analysis of ubiquitin’s interactions with different concentrations of a small negatively charged host molecule called cavitand provides insight into the binding interactions with side chains on the protein such as lysine and arginine. This is done comparing the HSQC spectra of different concentrations of cavitand and ubiquitin to …

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 …

The Effect Of Polyethylene Glycol Surface Density Of Dense Brush Gold Nanoparticles On Insulin Fibrillation, Ethan Patrick Grier

Graduate Theses/Dissertations

The development of various neurodegenerative diseases such as Parkinson’s disease and Alzheimer’s disease has been linked to the fibrillation of various proteins within the brain. Parkinson’s disease is specifically linked to the fibrillation of α-Synuclein. During the fibrillation process, the proteins take the form of oligomers, and exposure to these oligomers has been linked to various cytotoxic and neurotoxic effects. Once the fibrillation process is complete, the fibrils made have been shown to be much less toxic than the oligomer stage. This fibrillation process is thermodynamically favorable and is largely irreversible, so one course of action for treatment of these …

Reversible Degradation Of Peptidoglycan By Lytic Transglycosylases, Aaron Devereaux

Theses and Dissertations (Comprehensive)

Antimicrobial resistance continues to be a burden on the global healthcare system with an estimated cost of billions of dollars and millions of deaths each year. Recently, there has been little to no development on new antibiotics to treat bacterial infection, and any that are developed become resisted to within a few years. Both Gram-positive and Gram-negative bacteria contain a mesh-like layer called peptidoglycan (PG) that surrounds their cells providing strength, cell shape, and protection from their environments. This layer is a polymer of N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) connected via a b-1,4-glycosidic bond, with each strand being cross-linked …

Impact Of Membrane Lipid Composition On The Structure And Function Of Uncoupling Proteins 1 And 2 From Arabidopsis Thaliana (Atucp1 And Atucp2), Elizabeth Silva

Theses and Dissertations (Comprehensive)

A proton gradient across the inner mitochondrial membrane (IMM) is required for the synthesis of adenosine triphosphate (ATP) via ATP synthase. In other words, generation of the proton gradient is coupled to the synthesis of ATP. Interestingly, uncoupling proteins (UCPs), also located in the IMM, dissipate the proton gradient, meaning that the gradient is not efficiently used for the production of ATP.¹ The mechanism of proton transport activity of UCPs has been hypothesized and widely debated for the past 20 years to also reduce oxidative stress by reducing the production of reactive oxygen species (ROS).² The majority of …

Characterizing The Targeting Of Toc159 Receptors To The Chloroplast Outer Envelope Membrane And Their Role In The Assembly Of Distinct Toc Complexes, Michael Fish

Theses and Dissertations (Comprehensive)

Global agriculture and food security face challenges from climate change, population growth, and other human-driven pressures. Enhancing our understanding of plant biology, particularly chloroplast function, is critical for improving crop yield and stress resilience. As the sites of photosynthesis and key regulators of plant responses to environmental cues, chloroplasts depend on the precise import of thousands of nuclear-encoded proteins to maintain their biogenesis and function. While much is known about the core translocon components in the chloroplast outer envelope membrane that form the TOC complex, the mechanisms underlying their targeting, assembly, and regulation remain incompletely understood.

Plastids, including chloroplasts, evolved …

Characterization Of P38alpha And Nitric Oxide Synthase 3 Binding, Gillyan M. Jewett

Master's Theses

P38alpha is a member of the mitogen activated protein kinase (MAPK) family. This family is important for mediating signal transduction pathways through phosphorylation of downstream substrates. Previous work has described the ability of p38alpha to bind and phosphorylate nitric oxide synthase 3 (NOS3) at two sites, the autoinhibitory loop (AI) at S600 and the N-terminal MAPK binding site (NtMAP) at S114. P38alpha has two substrate binding domains, the common docking groove (CD-groove) and a hydrophobic pocket (DEF) that are important in binding and phosphorylating various substrates specific to each pocket. Utilizing biolayer interferometry, this work describes the importance of both …

Rwanda's Natural Remedies: A Fresh Look At The Fight Against Malaria, Leandre Nsabimana Ndisanze

Pomona Senior Theses

Malaria remains one of the most devastating parasitic diseases globally, disproportionately affecting sub-Saharan Africa, where Rwanda continues to face high transmission rates and rising resistance to conventional interventions. Despite decades of control efforts, the emergence of drug-resistant Plasmodium falciparum and insecticide-resistant Anopheles mosquitoes threatens to reverse recent gains. This research responds to the urgent need for sustainable and culturally relevant alternatives by exploring the therapeutic potential of Rwandan traditional medicinal plants. These indigenous remedies, long used by local healers, offer an underexplored reservoir of bioactive compounds that may provide the basis for novel antimalarial drugs.

The central hypothesis of this …

Extended Inter-Laboratory Characterization Of The New Coastal Seawater Dissolved Organic Matter Reference Material Trm-0522, Alexander J. Craig, Lydia Babcock-Adams, Maxime C. Bridoux, Charlotte Brun, Juliana D'Andrilli, Aleksandar I. Goranov, Patrick G. Hatcher, Oliver Lechtenfeld, Hang Li, Rebecca Matos, Garrett Mckay, Amy M. Mckenna, Madelyn Miller, Sasha Wagner, Margot E. White, Alexander Zherebker, Jeffrey A. Hawkes

Chemistry & Biochemistry Faculty Publications

Dissolved organic matter (DOM) reference materials are critical to ensuring reliable comparability of measurements across experiments and between labs. TRM-0522, isolated in 2022 from 45 m deep seawater off of Sweden’s west coast, fills the niche of a previously unavailable coastal marine DOM reference material. After its isolation, we detailed a limited number of metrics for TRM-0522, initially disclosing Orbitrap high-resolution mass spectrometry, nuclear magnetic resonance, carbon proportion, absorbance, and fluorescence data. With TRM-0522 becoming more widely used, a variety of labs have generated different metrics that help to characterize and define the chemical properties of this coastal reference material. …

From Biophysics To Cellular Function: Neural Telcs-Membrane-Anions Capacitor Transmembrane Potential, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Based on the transmembrane-electrostatically localized protons/cations charges (TELCs) theory, neural transmembrane potential including both resting and action potential is now well elucidated as the voltage contributed by the TELCs-membrane-anions capacitor biophysics in a neuron. Accordingly, neural transmembrane potential has an inverse relationship with TELCs surface density, which may represent a substantial progress in bettering the fundamental understanding of neuroscience. In this article, I will present a review on the latest development of the TELCs neural transmembrane potential theory and address Silverstein’s interesting arguments regarding the TELCs model that may constitute a complementary development to both the Hodgkin-Huxley classic cable theory …

Experimental Demonstration And Study Of Transmembrane-Electrostatically Localized Protons Prevail, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

In this review in relation to some interesting arguments from Silverstein, it is now reaffirmed that the experimental demonstration of transmembrane-electrostatically localized protons (TELPs) was successfully accomplished through 1) using an aluminum film as a TELPs sensor in a biomimetic anode water-membrane-water cathode system, 2) analyzing the water-electrolysis current curve, and 3) measuring bulk liquid phase pH. Formation of induced TELPs was subsequently discovered in an anode water-membrane-water-membrane-water cathode system. The discovery of induced TELPs enabled clean experimental tests on the cation-TELPs exchange process by using sodium bicarbonate or potassium bicarbonate solution in the central liquid chamber. The sodium/TELPs exchange …

Systematic Review Of Immunohistochemistry Protocols, Arpitha Parthasarathy

Pitzer Senior Theses

Immunohistochemistry (IHC) is an essential technique in biological research that allows for the visualization and localization of proteins within tissue samples. This systematic review analyzes the most effective, efficient and reproducible protocols for IHC. It focuses on three critical steps: freezing, cryosectioning, and staining of skeletal muscle tissues in mice models. A total of 41, 44, and 48 articles on freezing, cryosectioning, and staining techniques, respectively, were analyzed, from reputable sources in biology like PubMed and Web of Science. Results showed the following. For freezing, the use of isopentane combined with liquid nitrogen appeared to be the best method, minimizing …