Biochemistry 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 …

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. …

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 …

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 …

Identification Of A Serine Protease Involved In Spinosad Degradation In The Yellow Fever Mosquito, Aedes Aegypti, Hongxiao Yu, Caixia Peng, Zhaohui Chen, Jie Li, Yunqi Li, Xiaojing Zhu, Yuqi Huang, Linlong Jiang, Pablo Sobrado, Jianqiang Lan, Yingying Guo, Qian Han

Chemistry Faculty Research & Creative Works

Spinosad is a widely used insecticide effective in controlling Aedes aegypti populations, but the molecular mechanisms underlying resistance remain poorly understood. This study explores the role of a serine protease, AeaSP (AAEL002624), in the potential detoxification ability of spinosad. Our results showed the crude protein of Ae. aegypti degraded approximately 48% of spinosad in vitro within 1 h; based on our previous research, AeaSP was believed to be potentially involved in the degradation of spinosad. Subsequently, AeaSP was recombinantly expressed in vitro, and its enzymatic activity was tested using BAEE as a substrate, with a Michaelis constant (KM) of 0.88 …

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 …

Optimization Of Small-Scale Bioreactors For Increased Pdna Production And Yield, Laura M. Hills

Honors Theses and Capstones

No abstract provided.

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 …

Functional Characterization Of Vago In Black Tiger Shrimp Penaeus Monodon Ikk-Nf-Κb Signaling Pathway Against Viral Infection, Zittipong Nanakorn

Chulalongkorn University Theses and Dissertations (Chula ETD)

Cytokines serve as key regulators in innate antiviral defense. In crustaceans, research on cytokine-mediated immunity remains limited. A previous study in Penaeus monodon has demonstrated that PmVago proteins exhibit cytokine-like function by acting through the inhibitor of kappa B kinase-nuclear factor κB (IKK-NF-κB) cascade to defend against white spot syndrome virus (WSSV). In this study, five PmVago isoforms were identified, each showing differential transcriptional responses to pathogen challenges. Among them, PmVago1 and PmVago4 exhibited strong antiviral responses against WSSV infection. RNA interference of PmVago1 and PmVago4 increased shrimp susceptibility to WSSV infection with enhanced viral replication. Their suppression also disrupted …

Electrochemical Detection Of Prostate Cancer—Associated Mirna-141 Using A Low-Cost Disposable Biosensor, Alexander Hunt, Gymama Slaughter

Center for Bioelectronics Publications

Prostate cancer is the second leading cause of cancer-related deaths among men in the United States. The early detection of aggressive forms is critical. Current diagnostic methods, including PSA testing and biopsies, are invasive and often yield false results. MicroRNA-141 (miRNA-141) has emerged as a promising non-invasive biomarker due to its elevated levels in the urine of patients with metastatic prostate cancer. Here, a low-cost, paper-based electrochemical biosensor for the sensitive detection of miRNA-141 in synthetic urine is reported. The device employs inkjet-printed gold electrodes on photopaper, functionalized with thiolated single-stranded DNA-141 capture probes for specific target recognition. The biosensor …

Estrogen Receptor-Mediated Effects Of Resveratrol On Muscle Function, David Ayi-Bonte

Open Access Master's Theses

Artemis missions are set to send the next man and the first woman back to the moon and enable long-term missions on the lunar surface. However, exposure to lunar gravity has significant physiological effects characterized by loss of muscle mass, weakness and decreased bone density. Nutraceutical countermeasures such as Resveratrol (RSV), a naturally occurring polyphenol, have been identified as promising strategies to preserve musculoskeletal health; however, its pleiotropic effect hinders our ability to identify the primary cellular pathways through which it delivers its benefits. Furthermore, its efficacy in simulated lunar gravity is unknown. Based on the benefits observed with RSV …

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 …

Investigating The Lyoprotective Properties Of An Antifreeze Protein From A Broadleaf Desert Shrub, Alexzandria Sheppard

Honors Theses and Capstones

Lyophilization, or freeze-drying, is an important preservation method for protein-based products, such as protein pharmaceuticals. However, the process introduces both freezing and drying stresses that can harm proteins. Here, we have studied the efficacy of AnAFP, a dehydrin-like antifreeze protein isolated from the broadleaf desert shrub Ammopiptanthus nanus, in reducing enzyme damage during freeze-drying, or lyophilization. We have shown that AnAFP can protect the model enzyme lactate dehydrogenase (LDH) from both freezing and dehydration damages during lyophilization with similar or better efficacy than 10% w/v sucrose and superior to that of another known antifreeze protein.

Site-Specific Modification Of Antibodies Utilizing Microbial Transglutaminase For Improved Immunoassay Performance, Emily Beitello

Theses and Dissertations

Immobilization strategies used for fixing antibodies to solid phase surfaces significantly contribute to the antigen capture capacity and influences the performance and sensitivity of immunoassays. Traditional methodologies result in the random orientation and/or the weak attachment of immobilized antibodies. Different formats of immunoassays scope in applicability to many fields of research and everyday use. Improving the efficiency of immobilizing antibodies in immunoassays is a beneficial endeavor to increase assay sensitivity. Here, we investigated the use of enzyme-mediated conjugation of antibodies to facilitate a highly oriented immobilization. Microbial transglutaminase (mTG) catalyzes the covalent bond formation between a plethora of primary amine …

Open Path Spectroscopic Detection Of The Hydroxyl Radical: A Comparison Between Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas) And Bbceas Coupled With A Fabry-Pérot Interferometer (Bbceas-Fp), Callum Flowerday, Ryan Thalman, Matthew C. Asplund, Samuel A. Badstubner, Adam K. Cook, Philip Lundrigan, Jaron C. Hansen

ScholarsArchive Data

Data collected by the BBCEAS and BBCEAS-FP instruments described in the paper "Open Path Spectroscopic Detection of the Hydroxyl Radical: A Comparison Between Broadband Cavity-Enhanced Absorption Spectroscopy (BBCEAS) and BBCEAS coupled with a Fabry-Pérot Interferometer (BBCEAS-FP)"

Microbial And Plant Biodiversity In Appalachian Agroecosystems And Their Implications For Soil Health, Kinsey Reed Close

Graduate Theses, Dissertations, and Problem Reports (ETD)

The sustainability of agricultural landscapes depends on understanding the complex interactions between plants, soil, and microbes. In Appalachia, a region shaped by complex terrain and long histories of human and ecological interaction, small family farms produce hay, livestock, and row crops. These agroecosystems, though often treated as “artificial” by many ecologists, have the potential to support both food production and biodiversity conservation if managed with an understanding of ecological complexity. This dissertation examines how plant and microbial diversity interact with soil and management to influence nutrient cycling, soil health, and long-term resilience in Appalachian agricultural systems. A literature review revealed …

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 …

Investigations Of Proteins Including Yellow Thermal Protein, Blue Thermal Protein, Lactoperoxidase, And Thyroid Peroxidase, Cammi Dargatz

Graduate Theses/Dissertations

This research investigated four different proteins: yellow thermal protein (YTP), blue thermal protein (BTP), lactoperoxidase (LPO), and thyroid peroxidase (TPO). YTP and BTP were both engineered from the extremely stable and non-aggregative thermal green protein (TGP) by mutating one residue each to obtain proteins with shifted spectra while preserving the stability properties observed in TGP. Site-directed mutagenesis (SDM) was utilized to construct YTP by mutating a histidine at residue 197 to a tyrosine (H197Y) and BTP by mutating a tyrosine at residue 67 to a histidine (Y67H). These proteins were expressed in E. Coli and purified with nickel and diethylaminoethyl …

Development Of Cyan And Blue Thermostable Fluorescent Proteins: Characterization And Structural Analysis, Acacia J. Jurkowski

Graduate Theses/Dissertations

Fluorescent proteins are commonly used as cell markers in living organisms. Modifications by mutation can be used to improve the qualities of these proteins including fluorescence, thermostability, pH stability, and chemical stability. The goal of this project is to use mutagenesis to improve the fluorescence of thermostable cyan and blue proteins derived from the thermal green protein (TGP). The first cyan protein developed by the DeVore lab (CTP 0.0) shifted the fluorescence to cyan but decreased the quantum yield (Φ_F) to 0.056. Further mutations were incorporated to increase the quantum yield through incorporating hydrogen bonding interactions to the …

Human Serum Albumin Interaction With Organochlorine Pesticides, D. S. Sanford, R. Yadav, A. Mishra

Journal of the Arkansas Academy of Science

Human serum albumin (HSA) is the most abundant blood plasma protein and plays a crucial role in drug transport and physiological homeostasis. HSA has a highly flexible structure consisting of three domains, each with multiple binding sites lined with hydrophobic and hydrophilic residues. The structural properties of HSA make it a robust reservoir and receptor for various endogenous and exogenous compounds, including therapeutic drugs. Organochlorine pesticides (OCPs) are a subclass of pesticides characterized by their chlorine content. Once widely used, these compounds remain persistent in the environment and biological systems despite regulatory restrictions in many developed countries. The strong ligand-binding …

Long-Term Antibacterial Efficacy Of Silver (I) Cyanoximates Against Streptococcus Mutans Ua159 Biofilm Growth, Tiffany A. Rojas

Honors Program Theses

Streptococcus mutans is the primary causative agent of dental caries due to its ability to form resilient multispecies biofilms. These biofilms promote acid production and degradation of the protective layers of the tooth, making biofilm formation a target for novel treatments. Silver(I) cyanoximates are of interest as alternatives to traditional antimicrobials and antibiotics due to the high UV and heat resistivity as well as poor solubility of the cyanoxime ligand paired with the well-established antimicrobial silver ion. Previous research has shown that silver(I) cyanoximates can effectively inhibit S. mutans biofilm formation after 24 hours in vitro. This study aimed to …

Target Cell-Associated Cd47 Suppresses Nadph Oxidase Activity In Macrophages During Antibody Dependent Cellular Phagocytosis, Seuly Akter

Electronic Theses and Dissertations

CD47-SIRPα signaling is a well-known immune checkpoint that suppresses macrophage-mediated antibody-dependent cellular phagocytosis (ADCP). In this study, we explored how CD47 influences reactive oxygen species (ROS) production driven by Fcγ receptor (FcγR) signaling. Our results show that macrophages produce significantly more ROS when encountering IgG coated target cells lacking CD47.Polarization with IFNγ further amplified this effect. ThusCD47-SIRPα interactions limit phagocytosis and suppress oxidative ROS production by macrophages. We found that CD47 blockade and IFNγ stimulation enhanced ADCP through distinct mechanisms. CD47 blockade removed the inhibitory "don't eat me" signal supporting ADCP and ADROS. Similarly, IFNγ enhances ADCP by upregulating FcγRI …

Bridging The Gap Between Structural And Cellular Biology: Insight Into The Organization Of Glycolytic Enzymes In Cells, Heather Hansen

Graduate Theses, Dissertations, and Problem Reports (ETD)

Glycolytic enzymes are spatially organized in the cytoplasm, and are shown to localize with cellular structures such as the plasma membrane, F-actin, mitochondria, or associate independently within the cytosol. The assembly of these enzymes is hypothesized to regulate pathway flux to meet the energetic needs of the cell. However, it is unclear whether all of these assemblies have the same mechanism of formation or function in the cell. We investigated the role of glycolytic enzyme assemblies in cells, using the glycolytic “gatekeeper” enzyme phosphofructokinase-1 (PFK1). PFK1 is extensively regulated by multiple mechanisms, including over 20 allosteric ligands, post translational modifications, …

Probing The 10-23 Dnazyme Catalytic Core: Insights From Structural And Mechanistic Studies, Evan Rhyse Cramer

Graduate Theses, Dissertations, and Problem Reports (ETD)

The 10-23 DNAzyme is a catalytically active DNA oligonucleotide capable of cleaving RNA at purine-pyrimidine junctions in the presence of divalent metal ions, most notably magnesium. Despite its promise as a programmable RNA knockdown tool, its clinical and biotechnical utility has been hampered by limited structural characterization, low catalytic efficiency under physiological conditions, and poor understanding of its in-cell activity. This dissertation presents a comprehensive framework for the structural and functional analysis of DNAzymes using the 10-23 DNAzyme as a model system. In the absence of high-resolution structures, we first employed detailed in vitro biochemical assays to map essential residues …

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 …

Green Chelation Strategy For Deashing Of Algal Biomass, Agyare Asante, George Daramola, Ryan W. Davis, Sandeep Kumar

Civil & Environmental Engineering Faculty Publications

This study investigated a green chelation strategy for deashing algal biomass using nitrilotriacetic acid (NTA) and deionized water (DI) to enhance its suitability for biofuel and bioproduct applications. Solid-state algal turf scrubber (SS ATS), green algal turf scrubber (ATS), and Scenedesmus were analyzed, with Scenedesmus selected for detailed evaluation due to its high ash removal efficiency. The objective was to optimize a purification process that minimizes ash and heavy metal content while preserving biochemical integrity. Algal biomass underwent sequential washing with DI, NTA, and NTA+DI under varying temperatures (90-130 °C). Analytical techniques including Fourier Transform Infrared (FTIR) spectroscopy, Inductively Coupled …

Environmentally Friendly Chelation For Enhanced Algal Biomass Deashing, Agyare Asante, George Daramola, Ryan W. Davis, Sandeep Kumar

Civil & Environmental Engineering Faculty Publications

High ash content in algal biomass limits its suitability for biofuel production by reducing combustion efficiency and increasing fouling. This study presents a green deashing strategy using nitrilotriacetic acid (NTA) and deionized (DI) water to purify Scenedesmus algae, which was selected for its high ash removal potential. The optimized sequential treatment (DI, NTA chelation, and DI+NTA treatment at 90–130 °C) achieved up to 83.07% ash removal, reducing ash content from 15.2% to 3.8%. Elevated temperatures enhanced the removal of calcium, magnesium, and potassium, while heavy metals like lead and copper were reduced below detection limits. CHN analysis confirmed minimal …

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. …