Physical Sciences and Mathematics Commons^™

Synthesis Of Bacterial Glycerophospholipids For Biomembrane Model Studies: A Means To Advanced Biofuels, Felix Adulley

Electronic Theses and Dissertations

To reduce reliance on fossil fuels, sustainable biofuels are being pursued, especially advanced biofuels like 1-butanol that have higher energy content and greater compatibility with existing infrastructure than ethanol. A persistent challenge is the yield-limiting toxicity of biofuels and process solvents, such as tetrahydrofuran, to the microbes that ferment biomass into biofuel. The cell membrane is a focal point of toxicity, and understanding how it interacts with fuels and solvents is key to improving yield. Phospholipid bilayers are the core of biomembranes, and model biomembranes of defined composition provide the ideal platform for biophysical studies. To this end, glycerophospholipids characteristic …

A Quantitative Visualization Tool For The Assessment Of Mammographic Risky Dense Tissue Types, Margaret R. Mccarthy

Electronic Theses and Dissertations

Breast cancer is the second most occurring cancer type and is ranked fifth in terms of mortality. X-ray mammography is the most common methodology of breast imaging and can show radiographic signs of cancer, such as masses and calcifcations. From these mammograms, radiologists can also assess breast density, which is a known cancer risk factor. However, since not all dense tissue is cancer-prone, we hypothesize that dense tissue can be segregated into healthy vs. risky subtypes. We propose that risky dense tissue is associated with tissue microenvironment disorganization, which can be quantified via a computational characterization of the whole breast …

Non-Destructive Imaging Of Phytosulfokine Trafficking In Plants Using Fiber-Optic Fluorescence Microscopy, Bernard Abakah

Electronic Theses and Dissertations

Plants secrete peptide ligands and use receptor signaling to respond to stress and control development. Understanding these phenomena is key to improving plant health and productivity for food, fiber, and energy applications. Phytosulfokine (PSK), a sulfated peptide hormone, regulates plant cell division, growth, and stress tolerance via specific phytosulfokine receptors (PSKRs). This study uses fiber-optic fluorescence microscopy to elucidate trafficking of PSK in live plants. The microscope features two-color optics and an objective lens connected to a 1-m coherent imaging fiber mounted on either a conventional upright microscope body or 5-axis positioning system (X–Y–Z plus pitch and yaw). PSK and …

Development Of Novel Cellular Assay Model And Therapeutic Deep Eutectic Solvents To Optimize The Activity Of Anticancer Agents, Nizam Uddin

Electronic Theses and Dissertations

Multidrug resistance (MDR) is the major burden behind chemotherapeutic treatment failure. It is the principal mechanism by which cancer cells evade chemotherapeutic treatment. As a result, aggressive cancer cells survive and continue uncontrolled cell division. Multidrug resistance affects survival rate of almost all types of cancer patients and death toll rises at an alarming rate. There are seven different mechanisms for evolving MDR. The most common mechanism in efflux activity of overexpressed ABC transporters. MRP1 is a prominent ABC transporter that pumps out a wide variety of anticancer drugs from the cells and thereby reduces intracellular drug concentrations and develops …

Post-Translational Modification Of Proteins Via Ambient Air Pollutants And Endogenous Reactive Species, Rachel Lauren Davey

Electronic Theses and Dissertations

Proteins can react with reactive oxygen species (ROS) and reactive nitrogen species (RNS) to form post-translational modifications (PTMs), which can affect protein structure and function. The formation of 3-nitrotyrosine (NTyr) and dityrosine (DiTyr) upon reaction of proteins with ROS/RNS are two common PTMs studied due to their stability and irreversibility, as well as their ability to enhance the allergenicity of pollen allergens upon formation. Many common techniques used to study the formation of these PTMs can reliably detect the PTMs but can only provide semi-quantitative information due to many assumptions and limitations. In Chapter 2 we present an analysis of …

Mechanistic Insights Into Mftr-Dependent Regulation Of The Redox Cofactor Mycofactocin, Aigera Mendauletova

Electronic Theses and Dissertations

Organic redox cofactors are essential for life. While classic flavins and nicotinamides are widely distributed across all domains of life, nature has also evolved niche cofactors in subsets of life domains. For example, in Actinobacteria, coenzyme F420 is commonly used in place of flavin mononucleotide in enzymes associated with carbon fixation and oxidation of secondary alcohols. The importance of niche cofactors has long been recognized however, detailed understanding about their biosynthesis and physiological uses has been lagging. One class of niche cofactors is derived from ribosomally synthesized and posttranslationally modified peptides (RiPPs). To achieve their mature form, the genetically …

Modulatory Effects Of Deacetylated Sialic Acids (A Sugar Residue) In Nk-Mediated Cytotoxicity And Targeted Therapy By Receptor Tyrosine Kinase Inhibitors, Mathias Tawiah Anim

Electronic Theses and Dissertations

The complex nature of the biology of cancer is still an unraveling science, yielding several biomarkers that have served as molecular targets for detection and treatment of the disease. How sugars, glycans, play a role has remained relatively uninvestigated. Sialic acid (Sia), a sugar residue on the surface of cells, has been identified as a hallmark of cancer and its progression. Sialic acid can be highly functionalized, but we became interested in acetylated Sias. This functional group is modulated by Sialate O- acetylesterase (encoded by the gene SIAE) and Sialate O-acetyltransferase (encoded by CASD1), enzymes that play a crucial role …

Biophysical Insights Into Peptide And Alcohol Perturbations On Biomimetic Membranes, Michael Hai Nguen

Electronic Theses and Dissertations

Biological membranes exist in every domain of life. Life exists due to the presence of these special structures for which we take for granted. They are composed of fatty lipids and workhorse proteins and act as the premier interface of biological processes. Due to the sheer quantity and complexity within their thin boundary, studying their actions and properties pose challenges to researchers. As a result, simplified biomembrane mimics are employed regularly. We will use several types of biomembrane mimics to understand fundamental properties of membranes. In the present thesis, we also attempt to move beyond the canonical structure-based theories upon …

Quantum Computations And Molecular Dynamics Simulations: From The Fundamentals Of Antimicrobial Resistance To Neurological Diseases, Angel Tamez

Electronic Theses and Dissertations

Biophysical phenomena are modeled using a combination of quantum and classical methods to interpret and supplement three distinct and diverse problems in this dissertation. In the first project, decarboxylation reactions are ubiquitous across chemical and biological disciplines, yet the origin of non-catalytic solvent effects remains elusive. Specific solvent structure and energetics have not been well described for the monoanion of malonate, nor corrected from the gas-phase charge-assisted intramolecular hydrogen bond model known as “pseudochair”. In the aqueous phase, a low-lying energy conformer known as the “orthogonal conformation” is computed to be preferred by a three-water cluster of hydrogen bonding over …

Next-Generation Sequencing Shows Increasing Temperatures Affect Stream Fungal Communities, Regan Hodgson

Electronic Theses and Dissertations

Under climate change predictions, surface air temperature is expected to continue to rise and will likely affect functioning of stream ecosystems and microbial communities. Aquatic hyphomycetes are key fungal decomposers of plant litter in headwater streams controlling carbon, energy, and nutrient flows to higher trophic levels. This project addressed the effects of temperature on stream fungal communities in two recently conducted experiments (microcosm and streamside channel studies) using Illumina sequencing. The objectives were to determine (1) if temperature affects community structure of stream fungi based on relative abundances of ITS2 rDNA sequences, (2) if the effects of temperature on aquatic …

A Computational Model Of The Line-1 Retrotransposon Life Cycle And Visualization Of Metabolic Networks In 3-Dimensions., Michael D. Martin

Electronic Theses and Dissertations

Computational modeling of metabolic reactions and cellular systems is evolving as a tool for quantitative prediction of metabolic parameters and reaction pathway analysis. In this work, the basics of computational cell biology are presented as well as a summary of physical processes within the cell, and the algorithmic methods used to find time dependent solutions. Protein-protein and enzyme-substrate interactions are mathematically represented via mass action kinetics to construct sets of linear differential equations that describe reaction rates and formation of protein complexes. Using mass action methods, examples of reaction networks and their solutions are presented within the Virtual Cell simulation …

Lipophilic Probes For Cellular Ethylene Detection, Morgan R. Brown

Electronic Theses and Dissertations

The structure of ethylene is simple, yet its biological effects are significant. When considering its role in biology it is almost exclusively regarded as a plant hormone. Research on ethylene from plants was progressed by several advancements in analytical instrumentation, from its discovery to elucidation of its signaling pathway. There is currently limited understanding of ethylene’s role in mammals, but evidence suggests that it may be a biomarker for oxidative stress! Additional tools and technology are crucial to study this surprising and important signaling role in mammals. Our group has developed molecular ethylene probes as a strategy to detect ethylene …

Elucidating Mechanisms For S-Nitrosoglutathione Reductase Activity And Control In Plants Using O-Aminobenzoyl-S-Nitrosoglutathione And A Novel Photo-Sensitive Probe, Leslie Ventimiglia

Electronic Theses and Dissertations

S-nitrosoglutathione reductase, (GSNOR) is widely accepted as the master regulator of stress through NO signaling and protein S-nitrosylation. GSNOR mediates stress response through the catalysis of its principal substrate S-nitrosoglutathione (GSNO). The instigation of various stressors in plants cause observable changes in plant phenotype, which are associated with changes in GSNOR activity. There are no current methods for measuring GSNOR activity directly in living plants. In this paper, a previously developed fluorogenic pseudo-substrate for human GSNOR, OAbz-GSNO, was applied to the Solanum lycopersicum plant model. OAbz-GSNO was identified as a promising novel pseudo- substrate to study changes …

Biomimetic Synthesis Of Palladium Nanoparticles For Catalytic Application, Emily A. Groover

Electronic Theses and Dissertations

The synthesis of palladium nanoparticles (Pd NPs) using materials-directed peptides is a novel, nontoxic approach which exerts a high level of control over the particle size and shape. This biomimetic technique is environmentally benign, featuring nonhazardous ligands and ambient conditions. Nanoparticles are extremely reactive catalysts, boasting a large surface-to-volume ratio when compared to their bulk counterparts. The rational design of these nanoparticles using peptides has been very successful in aqueous environments, but no research has been done to apply it in organic systems. As such, the biomimetic synthesis of Pd NPs in an organic system is here investigated, with ethanol …

Investigating Spatiotemporal Kinetics, Dynamics, And Mechanism Of Exosome Release, Anarkali Mahmood

Electronic Theses and Dissertations

Exosomes are small lipid-based vesicles that can carry biomolecules from one cell to another. While exosomes are crucial to maintain homeostasis in healthy cells, they are exploited by unhealthy cells to aid disease progression. Exosomes likely facilitate disease progression via the transfer of disease-causing biomolecules from unhealthy to healthy cells. Exosomes are generated in Multivesicular endosomes (MVEs) and are then secreted into the extracellular space to travel to other cells. Despite being a crucial step, very little is known about exosomes release mechanism and dynamics. To further our understanding of exosomes, specifically their secretion, my work has focused on investigating …

Structure And Mechanics Of Biomembrane Mimics In The Presence Of Vitamin E, Mitchell Dipasquale

Electronic Theses and Dissertations

Over the course of this dissertation, the fundamental behaviours and interactions between various analogs of vitamin E and biologically-relevant membranes will be explored. These analogs include the biologically active form, α-tocopherol; the most naturally abundant form γ-tocopherol; an oxidized product, α-tocopheryl quinone; and the synthetic stabile form, vitamin E acetate.

Beginning in Chapter 1, a foundation in membrane biophysics is established from a historical progression of the field. The importance of biomembranes is argued and a deep connection is established between structure and function. Key structural features of lipid assemblies, and role of lipid composition is defined, and with the …

Characterization Of Cyclopropyl Synthases Involved In The Maturation Of Ribosomally Synthesized And Posttranslationally Modified Peptides, Yi Lien

Electronic Theses and Dissertations

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of natural products with significant human health implications. RiPPs are synthesized from a genetically encoded precursor peptide that undergoes significant modifications by maturing enzymes, or maturases. Recently, radical-S-adenosylmethionine (rSAM) enzymes have emerged as an important family of RiPP maturases. rSAM enzymes have been shown to install ether, thioether, and carbon-carbon bonds on the precursor peptide. These modifications usually define the backbone structure of the mature RiPP. This thesis describes the characterization of a novel RiPP modification catalyzed by the radical S-adenosylmethionine enzyme TigE. TigE belongs to the TIG biosynthetic …

Computationally Modeling Dynamic Biological Systems, Katherine Jarvis

Electronic Theses and Dissertations

Modeling biological systems furthers our understanding of dynamic relationships and helps us make predictions of the unknown properties of the system. The simple interplay between individual species in a dynamic environment over time can be modeled by equation-based modeling or agent- based modeling (ABM). Equation based modeling describes the change in species quantity using ordinary differential equations (ODE) and is dependent on the quantity of other species in the system as well as a predetermined rates of change. Unfortunately, this method of modeling does not model each individual agent in each species over time so individual dynamics are assumed to …

Investigations Of Elastin Recoil On Molecular And Macroscopic Levels., Nour Mohammad Jamhawi

Electronic Theses and Dissertations

Elastin is one of the most hydrophobic proteins, and it is extremely flexible when hydrated. The driving force for recoil is the decrease in entropy of the protein and/or the hydrating solvent. This dissertation is a study of both mechanisms. Following an introduction (Chapter 1), Chapters 2 and 3 investigate the recoil mechanism on the molecular level in the hydrating solvent and in the protein, respectively. Chapter 4 examines macroscopic properties of recoil by thermomechanics. Conclusions are discussed in Chapter 5. Using double quantum NMR, the deuterated water ordering at the elastin surface was studied quantitatively as a function of …

Simulation Of The Interaction Between Striated Muscle Unc-45 And Transcription Factor Gata-4, Drake Alexander Duncan

Electronic Theses and Dissertations

Striated Muscle UNC-45, also known as UNC-45b, is an important protein that acts as a chaperone for myosin in cardiac and skeletal muscles, binding to myosin at its C-terminal UCS domain and regulating its assembly into thick filaments and sarcomeric structures. The UCS domain contains a large loop that is believed to be the first point of interaction between myosin and UNC-45b. GATA-4 is an essential transcription factor that facilitates transcription of several genes in cardiac development, particularly alpha-heavy chain myosin in heart tissue. Recently, studies have shown that there is interaction of GATA-4 with UNC-45b and that GATA-4 binds …

Modeling Disorder In Proteins Yields Insights Into The Evolution Of Stability And Function, Jonathan Huihui

Electronic Theses and Dissertations

The central dogma of molecular biology dictates that a DNA sequence codes for an RNA sequence, which in turn codes for a sequence of amino acids that comprises a protein. Proteins are responsible with performing myriad functions within living organisms and most proteins require a folded structure in order to perform their function. The protein's structure is the direct link from sequence to function. This is known as the sequence - structure - function paradigm. However, this does not mean that the unfolded state is unimportant. In order to properly model the stability of the folded state, one needs to …

Validation Of A Deployable Proteomic Assay For The Serological Screening Of Sexual Assault Samples, Catherine O'Sullivan Brown

Electronic Theses and Dissertations

Protein mass spectrometry (MS) has emerged as a technique to supplant traditional serological tests for body fluid identification. It was hypothesized that proteomic techniques would surpass the sensitivity and specificity of traditional serological techniques. An automated workflow coupled with protein MS has been developed for the confirmatory identification of five biological fluids. A developmental validation was completed, assessing parameters such as reproducibility, sensitivity, ion suppression, and limit of detection. Implementation was determined through tandem sample processing by MS, traditional serological tests, and standard DNA profiling methods. The MS approach offered superior detection limits while also providing true confirmatory results, producing …

Therapeutic Immunoglobulin G Surface Mobility Promotes Antibody-Dependent Cellular Phagocytosis By Arp2/3 And Syk Mediated Rearrangement Of Fcγ Receptors, Seongwan Jo

Electronic Theses and Dissertations

Therapeutic antibodies are rapidly growing class of drugs for treating cancers and immunological disorders by targeting specific antigens or blocking certain pathway to inhibit the tumor growth. In cancer immunotherapy, it was found that Fcγ receptor (FcγR) in immune cells play an important role in antibody dependent cell toxicity against tumor cells. Therefore, understanding FcγR activation mechanism, which requires ligation with immunoglobulin (IgG), is crucial to enhance potency of therapeutic antibodies. One crucial immune responses triggered upon FcγR ligation with IgG is phagocytosis which indicates clearing targets by engulfment. It is known that FcγRs form microclusters which gets rearranged during …

Live Cell Super-Resolution Microscopy Quanitifies An Interaction Between Influenza Hemagglutinin And Phosphatidylinositol 4,5-Bisphosphate, Jaqulin N. Wallace

Electronic Theses and Dissertations

Influenza virus, colloquially known as the flu, is an acute respiratory disease that infects several millions of individuals each year in the U.S. and kills tens of thousands of those infected. Yearly viral vaccines are widely available, however, due to the virus’s high mutation rate, their efficacy varies greatly. Due to the variability in vaccine efficiency against seasonal influenza, and the potential for even more pathogenic versions of influenza to emerge at any time, there is a high demand for a universal treatment option.

Influenza virus hijacks a variety of host cell components in order to replicate. The glycoprotein hemagglutinin …

Quantification Of Interactions Between Influenza Hemagglutinin And Host Cell Phosphoinositides By Super-Resolution Microscopy, Matthew T. Parent

Electronic Theses and Dissertations

The influenza viral membrane protein hemagglutinin (HA) forms dense nanoscale clusters on host cell plasma membranes (PM), but the mechanisms that direct HA clustering are not well understood. Previous studies have observed HA associated with actin rich regions of the PM, but there are no known direct interactions between HA and actin. Phosphatidylinositol 4,5-biphosphate (PIP2) is a signaling lipid in the PM which can regulate the actin cytoskeleton, and actin comets initiated by PIP2 are known to be exploited by HA to reach the PM of infected cells. PIP2 is also used by other viruses, such as HIV and Ebola, …

Scavenger Hunt: The Search For Sulfur Mustard-Neutralizing Compound In 2-Chloroethyl Ethyl Sulfide (Cees) Treated Human Keratinocyte (Hacat) Epithelial Cells, Tanner Diemer

Electronic Theses and Dissertations

Sulfur mustard is a highly toxic and dangerous vesicant that has been utilized as a chemical warfare agent (CWA) since World War I. Despite its extensive history, an effective antidote to sulfur mustard exposure still does not exist. With detectable levels of unreacted sulfur mustard lasting days after initial contact, a window of opportunity exists to administer a “scavenger” to affected individual immediately and in the days following exposure in hopes of reducing harm by neutralizing unreacted sulfur mustard. For this strategy to be effectively implemented, it is essential to identify a candidate compound with excellent affinity towards sulfur mustard …

Quantification Of Dynamic Epithelial Sheet Architecture In Botryllus Schlosseri Using 2-D & 3-D Image Analysis, Roopa Madhu

Electronic Theses and Dissertations

Epithelial tubules form critical structures in various body tissues; how- ever, since they are difficult to access experimentally, their architecture and dynamics are not well understood. Here we examine the dynamic remodeling of epithelial tubes in vivo using a novel and uniquely accessible model system: the extracorporeal vasculature of Botryllus schlosseri (sea squirt). In Botryllus, massive retraction of blood vessels can be triggered without loss of barrier function, through (i) disrupting collagen crosslinking in the basement membrane using β-aminopropionitrile (BAPN); or (ii) disrupting the integrin pathway through inhibition of focal adhesion kinase (FAK). We performed stereographic projections of 3-dimensional …

Examining Artifacts Of The Watershed Segmentation, Emily Jo Armitage

Electronic Theses and Dissertations

The watershed segmentation is an algorithm used to systematically track cell intercalary behaviors during germ band extension of the Drosophila embryo. Neighboring cells share a contracting vertical interface, called a T1, which continues contracting to a single point, a T2, and extending in the horizontal direction to create what is called a T3 interface (Fig. 1). Additionally, higher order vertices called rosettes occur when five or more cells meet at a common vertex. Simulated T2 events demonstrate that cell angle and not noise level in the image contributes to the incorrect detection of artifactual T1s in more acute angled cells …

Tumor-Targeted Conjugated Polymer Nanoparticles With Encapsulated Iron And Its Biomedical Application For In Vitro Killing Of Melanoma Cell Lines Through Ferroptosis Assisted Chemodynamic Therapy (Cdt), Khalaf Jasim

Electronic Theses and Dissertations

Melanoma represents one of the most aggressive and lethal forms of skin cancer, with annually rising incidences throughout the world. Although chemotherapy modalities remain the mainstay of treatment, the therapeutic potential of chemotherapy typically is hampered by multidrug resistance (MDR) and nonspecific drug distribution that causes side-effects. To surmount such limitations, novel nanoformulations of low band-gap poly ({4,8-bis [(2-ethylhexyl) oxy] benzo [1,2-b:4,5-b?] dithiophene-2,6-diyl}{3-fluoro-2-[(2-ethylhexyl) carbonyl] thieno [3,4-b] thiophenediyl}) (PTB7) and poly [2,1,3-benzothiadiazole- 4,7- diyl [4,4-bis (2-ethylhexyl)- 4H-cyclopenta [2,1-b:3,4-b'] dithiophene-2,6-diyl]] (PCPDTBT) were fabricated by a reprecipitation method. These conjugated polymer nanoparticles were functionalized with the polypeptide endothelin-3 (EDN3-CPNPs) to target melanoma. The …

Wetland Biogeochemical Responses To Predicted Climate Change Scenarios, Angela R. Shaffer

Electronic Theses and Dissertations

Wetlands are one of the world's largest known carbon sinks while comprising only a small amount of the Earth's surface. However, the amount of carbon sequestered by wetlands is shrinking as droughts and human disturbance increases. Carbon in wetlands is stored through the contrast of decomposition and sedimentation of organic matter and absorption of CO₂ from the atmosphere by soil microbes. Understanding how changing hydrological regimes and increased wildfires will affect wetland soil and microbial processes is important in the face of predicted climate change for future wetland conservation practices. Specifically, I seek to understand the response of southeastern …