Physical Sciences and Mathematics Commons^™

Cell Division Dynamics Of Escherichia Coli In Extreme Environments, Steven P. Murray

Graduate Theses and Dissertations

Life is remarkable in how resilient it can be. Many organism, classified as ex- tremophiles, can not only survive in extreme environments, but they can thrive in them. In the search for extraterrestrial life, the best candidates to harbor life exist with some kind of extreme condition. Europa, for example, is a favorite for the possibility of accommodating life as we know it within our solar system. Thought there is believed to be a liquid ocean under its icy surface, this habitat would be under immense pressures and high salinity. To best know where to look for extraterrestrial life, it …

The Binding Of The Micronutrient Transition Metals To The Alkylation Products Of Chemical Warfare Agent, Sulfur Mustard, And Thiols, Potentially Giving New Understanding To Physiological Effects Of Exposure And Increased Toxicity, Colin O'Donnell

Graduate Theses and Dissertations

Model compounds, 3,6,9-trithaiundecane-1,11-dicarboxylic acid (TTDPA), 2,5,8-trithianonane-1,9-dicarboxylic acid (TTDAA), and 1,11-diamide-3,6,9-trithiaundecane (TTDAce), closely related to the adducts formed by cysteine alkylation of the chemical weapon, sulfur mustard, were synthesized. It is shown that TTDPA forms complexes with key metal micronutrients: copper, nickel, cobalt, manganese, and zinc. Though the strength of binding to TTDPA varies, the complexes in many cases precipitate from solution. All metals produced a visible precipitate upon interaction with TTDPA under the conditions tested, however only Cu2+, Mn2+, and Zn2+ produced enough to be measured. The mass of formed precipitate seemed to peak at an equimolar ratio of TTDPA …

Using Molecular Dynamics Simulations To Decipher Mechanistic Details Of Biomolecular Processes Of Biology And Biotechnology Oriented Applications, Adithya Polasa

Graduate Theses and Dissertations

Researchers in chemistry and biology often utilize computer simulations, in conjunction with experimental data, to model and predict the structures, energies, kinetics, processes, and functions of the systems that are their focus of study, ranging from single molecules to whole viruses. Here, we use molecular dynamics (MD) techniques to gain a deeper understanding of biomolecular processes in biology and biotechnology-oriented applications. Using a mixture of equilibrium and non-equilibrium MD simulations, this work describes the insertion process of YidC at the atomic level. In order to better comprehend the insertion process, several docking models of YidC-Pf3 in the lipid bilayer were …

Examining The Expression Patterns Of Desulfotalea Psychrophila Dsrab Operon And Pit At Subfreezing Temperatures And Different Concentrations Of Sulfate Salts As A Model For Mars And Icy Worlds Survival And Colonization, Sergio Luis Mosquera Mora

Graduate Theses and Dissertations

Since ancient times, Humanity has been fascinated with the idea of what lies beyond the borders of our planet. Fortunately, the combined efforts of many nations have made it possible to send unmanned spacecraft to orbit planets located close to Earth. These missions have the principal goal to collect data that could help us understand the basic environmental conditions that persist on those planets, or for evidence of past or present life. Equally important, landers and rovers have been successfully deployed to start the in-situ exploration of many planets of the Solar System. Among them, Mars has been extensively studied …

Effects Of Localized Oxygen Production By Electrolysis On The First-Generation Glucose Sensor Response, Nandita Halder

Graduate Theses and Dissertations

Glucose sensors are very important for detecting blood glucose both in vitro and in vivo. First-generation glucose biosensors were based on the glucose oxidase (GOx) enzyme using molecular oxygen as the electron acceptor and therefore oxygen dependent. Unfortunately for in-vivo work, oxygen in the body is variable and limited. Alternative approaches to overcome the oxygen dependency came with their own limitations. The widely used and commercially available ex-vivo glucose test strip uses a mediator in place of oxygen to free it from oxygen dependency. The mediator-based technology, in most cases cannot be transferred to in vivo applications due to the …

Engineering Fluorescently Labeled Human Fibroblast Growth Factor One Mutants And Characterizing Their Photophysics Properties Towards Designing Fret Assays, Mamello Mohale

Graduate Theses and Dissertations

Human fibroblast growth factor one (hFGF1) belongs to a family of 22 FGF members produced by fibroblast cells. Cell signaling during physiological processes of angiogenesis and wound healing occurs when hFGF1 binds to its receptor (FGFR). However, when heterogenous homeostasis is not maintained, fibroblast cells exhibit excessive proliferation which can lead to a myriad of cancers. smFRET is an ultrasensitive distant dependent (1-10 nm) technique capable of resolving such heterogeneity in structural dynamics and binding affinities (Kd). Therefore, we successfully designed and characterized fluorescently labeled hFGF1 tracers which span the visible light region of the electromagnetic spectrum for use in …

Biochemical Characterization Of Small Molecule Inhibitor Binding On A Ras Related Gtpase And Its Effector Interactions, Djamali Muhoza

Graduate Theses and Dissertations

The Ras superfamily of GTPases has 167 proteins that are involved in various cellular processes such as proliferation, transformation, migration, and inhibition of cell death. Mutations, abnormal expression, and function of these proteins are observed in many diseases, including several forms of cancer. Even though these GTPases were among the first discovered oncogenes, no successful Ras drug candidate has successfully passed clinical trials. Drugs targeting these proteins have failed mainly because of the complexity of their regulation, their high affinity to GTP, and their structure’s dynamic nature. Recently, novel promising targeting approaches have renewed interest in the Ras drug discovery …

Elucidating Collagen Degradation Synergy Between Col G And Col H From Hathewaya (Clostridium) Histolytica And Identifying Novel Structural Features In Hpt And Rec Domains From Vars Histidine Kinase In V. Alginolyticus, Perry Caviness

Graduate Theses and Dissertations

In this research the mechanisms by which Hathewaya (Clostridia) histolytica collagenases are secreted and work together to degrade collagens are investigated. While H. histolytica collagenases Col G and Col H have similar multi-domain structures the difference in number of and orientation of the domains hint that the two target different regions in collagen. Study small angle x-ray scattering (SAXS) was used to give a low-resolution envelope of full-length Col G and Col H and Col G/Col H non-catalytic domains bound to a collagen-like peptide (mini-collagen). SAXS derived envelopes along with structural information was used to tease out the mechanisms by …

Structural Analysis Of The Multifunctional Spoiie Regulatory Protein Of Clostridioides Difficile., Blythe Emily Bunkers

Graduate Theses and Dissertations

Clostridioides (formally Clostridium) difficile is a medically relevant pathogen pertinent to infectious disease research. C. difficile is distinctly known for its ability to produce two toxins, enterotoxin A and cytotoxin B, and the propensity to colonize the mammalian gastrointestinal tract. It is known that metabolism is tightly correlated with sporulation in endospore producers such as C. difficile, but an interesting and novel regulatory relationship found by the Ivey lab has yet to be understood. The relationship explored in this study is observed between the sporulation factor, SpoIIE, which represses expression of an ABC peptide transporter, app. In this study, two …

Phenotypic Switching Of Bacterial Cells In Extreme Environments, Sudip Nepal

Graduate Theses and Dissertations

A large number of terrestrial microbial lives thrive in extremes of environmental conditions, including extremes of pressure, temperature, salinity, pH, and a combination of them. For example, all the marine biomass thrive at high hydrostatic pressure depending on depth. The temperature in the ocean can be very high near the hydrothermal vents and salinity and pH depends on the composition of salt in the surrounding areas. On the surface, hot springs, lakes and geysers provide high temperature conditions, while many places are permafrost regions with subzero temperatures. There is an emerging body of work on the viability, genomics, and metagenomics …

Probing Of Carbohydrate-Protein Interactions Using Galactonoamidine Inhibitors, Jessica B. Pickens

Graduate Theses and Dissertations

Glycoside hydrolases are ubiquitous and one of the most catalytically proficient enzymes known, and thus understanding their mechanisms are crucial. Most research has focused on the interaction of the glycon of substrates and their inhibitors within the active site of glycoside hydrolases. The inhibitors employed to probe these interactions generally had small aglycons (i.e. a hydrogen atom, amidines, small aliphatic groups, or benzyl groups). Here, the interactions of the aglycon with glycoside hydrolases are examined by probing the active sites with a library of 25 galactonoamidines. The studies described in this dissertation aim to increase the understanding of stabilization of …

Rotational Tuning Of Transmembrane Helix Properties Based On The Precise Placements Of Aromatic And Charged Residues, Matthew J. Mckay

Graduate Theses and Dissertations

Designed model transmembrane peptides and oriented 2H and 15N solid-state nuclear magnetic resonance (NMR) spectroscopy were used to analyze how simple sequence modifications can influence peptide structure, behavior and dynamics as well as for determining the pKa of glutamic acid at the membrane interface. The GW5,19ALP23 (acetyl-GGALW(LA)6LWLAGA-amide) peptide framework adopts a well-defined tilted orientation in lipid bilayers (DLPC, DMPC and DOPC) and undergoes low amounts of dynamic motion. The sequence was initially modified by moving the Trp residues outwards to positions 4 and 20. This new sequence GW4,20ALP23 (acetyl-GGAW(AL)7AWAGA-amide) displays high amounts of signal averaging of NMR observables caused by …

Asymmetric Synthesis Of The C29-C34 Moiety Of Fragment A Of The Antascomicin B & Thermal Azole Based Claisen Rearrangements, Dharma Theja Nannapaneni

Graduate Theses and Dissertations

The dissertation describes asymmetric synthesis towards C29-C34 moiety of fragment A of the Antascomicin B and Thermal azole based Claisen rearrangements. In chapter 1, we describes asymmetric synthesis towards C29-C34 moiety of fragment A of the Antascomicin B. The non-immunosuppressant Rapamycin, Ascomycin, and Tacrolimus (FK506), strongly binds with FKBP12, the ligand FKBP12 complexes responsible for immunosuppressive activity. Antascomicin B structurally related to Rapamycin, Ascomycin, and Tacrolimus (FK506), binds strongly to FKBP12, yet does not shown immunosuppressive activity. The ligand FKBP12 binding complexes shown to have potent neuroprotective and neurogenerative properties in mouse models of Parkinson’s disease. The linear synthesis of …

Characterization Of Bacteriorhodopsin And Halorhodopsin Reconstituted In Lipid Bilayer Membranes, Joel Domkam Kamwa

Graduate Theses and Dissertations

Motivated to produce electricity with photon activated ion pumps, the main purpose of this work was to characterize the photosynthetic membrane proteins bacteriorhodopsin (proton pump) and halorhodopsin (chloride pump). The proteins were re-suspended in lipid bilayers. For this work, an experimental set-up was built which included: chambers for lipid bilayer formation and characterization, lasers for ion pump activation, and an AxoPatch electrophysiology system for small photocurrent measurement. Lipid bilayer membranes were formed using mostly folding method: folding two monolayers together. The membranes were characterized by their resistance, capacitance, and generated photocurrent. Photocurrent was generated upon illumination of lipid-protein membranes with …

Detection Of Survival And Proliferation Of Sulfate Reducers Under Simulated Martian Atmospheric And Soil Conditions, Sergio Mosquera Mora

Graduate Theses and Dissertations

Numerous studies have tried to determine the survivability and proliferation of microorganisms under simulated Martian conditions. Furthermore, most of them have been focused on the ability of these microbes to cope with high brines’ salt (NaCl) concentrations inherent of the Martian surface. However, there are not studies related to the ability of bacteria to survive on subsurface environments that have increasing concentrations of sulfate compounds. For this research, a group of microorganisms known as sulfate-reducing bacteria or simply sulfate reducers were chosen due to their ability to use sulfate compounds as terminal electron acceptors to produce metabolic energy, their tolerance …

A Numerical Study Of The Interaction Between One Dimensional Carbyne Chain And Single Stranded Dna, Zeina Salman

Graduate Theses and Dissertations

resolution at the single nucleotide level when developing DNA sequencers. The purpose of this research was to numerically study the electrical properties associated with the interaction between 1D carbon chain, known as carbyne, and ssDNA. First, the electrical properties of the carbyne chain were calculated. Second, the electrical properties of the carbyne chain were calculated in the presence of different ssDNA bases. Analyzing the differences between the two cases led to determining the effects of these different bases on the electrical properties. The numerical simulation approach conducted in this research was based on the first-principle simulation. The first-principle simulation was …

Influence Of Histidine Residues, Ph And Charge Interactions On Membrane-Spanning Peptides, Ashley N. Henderson

Graduate Theses and Dissertations

Designed transmembrane peptides were employed for investigations of histidine residues within the hydrophobic environment of the lipid bilayer by means of oriented solid-state deuterium NMR spectroscopy. Using the model peptide GWALP23 sequence (GGALW(LA)6LWLAGA) as a host framework, the effects of single and double histidine mutations were explored. Replacement of leucine residue 12 to polar neutral histidine had little influence on the peptide average orientation, however under strongly acidic pH conditions in DOPC bilayers, the histidine becomes positively charged (pKa 2.5) and the GWALP23-H12 peptide exits the membrane and adopts a surface-bound orientation. Conversely, mutation of leucine 14 to neutral histidine …

Interactions In The Cpsrp Dependent Targeting Of Light Harvesting Chlorophyll Binding Protein To The Thylakoid Membrane, Rory Henderson

Graduate Theses and Dissertations

Targeting of proteins is a critical component of cellular function. A universally conserved targeting system of the cytosol utilizes a signal recognition particle (SRP) to target many proteins contranslationally to the endoplasmic reticulum in eukaryotes or the inner membrane in prokaryotes. A homologous SRP system exists in the chloroplast that delivers light harvesting chlorophyll binding proteins (LHCP) to they thylakoid membrane. The chloroplast SRP (cpSRP) is a heterodimer composed of a novel 43 kDa subunit and a 54 kDa subunit homologous to a component of the SRP system, SRP54. Many details regarding the interactions between the proteins of the cpSRP …

Bioorthogonal Reactions: Synthesis And Evaluation Of Different Ligands In Copper Catalyzed Azide-Alkyne1,3-Dipolar Cycloaddition (Cuaac), Zainab Abdullah Almansaf

Graduate Theses and Dissertations

The Copper CatalyzedAzide-Alkyne1,3-Dipolar Cycloaddition (CuAAC) reaction has unique features that qualify it to be one of the best click reactions. Its applications have been shown in different aspects and for multiple purposes. The oxidative degradation of biological systems (labile proteins and live cells) is, however, generally recognized as the major problem when using this reaction in living systems. Reactive oxidation species can be easily produced in the presence of copper(II), ascorbate and air, and this is the main cause of toxicity. However, the uses of ligands have shown a major impact on reducing copper toxicity, protecting Cu(I) from the redox …

Heparin-Peptide Interactions, Jacqueline Anastasia Morris

Graduate Theses and Dissertations

Heparin is a polydispersed sulfated molecule that is part of the family called glycosaminoglycans found in the extracellular matrix and cell surfaces. This molecule is extremely important for the activation of proteins and protein-receptor interactions that are responsible for downstream cell signaling pathways. Heparin has been isolated from porcine intestine and used as an anticoagulant for the prevention of embolisms, heart thrombosis, and clotting during heart surgeries. This so-called miracle drug was in use until 2008, when isolated batches were found to be contaminated with other glycosaminoglycans similar to heparin. From 2008, there has been a dire need for a …

Investigation Of The Interaction Of Dimeric Ruthenium Complexes With Cytochrome B5, Christopher Dain Rupar

Graduate Theses and Dissertations

Photoreactive complexes to study the kinetics of electron transfer of proteins have been in use for a long time. It has always been speculated that complexes bind near the heme or the electron transfer reaction would not occur. But it is unkown exactly how the complex interacts with the protein. The structural, thermodynamic, and kinetic properties of rat liver microsomal cytochrome b5 were investigated when bound to ruthenium dimer complexes. Heteronuclear Single Quantum Coherence studies support a dynamic binding model of a dimer Ru complex bound near the protein’s heme involving residues H39, E44, G42, V61, G62, and H63. The …

Mechanism Of Rapid Electron Transfer Reactions Involving Cytochrome Bc1, Cytochrome C And Cytochrome Oxidase, Jeremy Erik Durchman

Graduate Theses and Dissertations

Electron transfer between mitochondrial proteins complexes represents the primary means by which living things acquire the requisite energy for survival. The coupling of electron transfer to proton translocation creates an electrochemical gradient that drives the synthesis of highly energetic compounds such as ATP. The purpose of these studies is to measure rates of electron transfer and elucidate the important governing factors in the redox events involving cytochrome bc1, cytochrome c and cytochrome oxidase. Using rapid initiation of redox events triggered by laser flash excitation of ruthenium compounds, and strategically monitoring unique spectral properties of these proteins in the visible region …

Designing Fret Assays To Study Electrostatic Interactions Pertaining To The Binding Of Intrinsically Disordered Proteins, Ashley Ann Howard

Graduate Theses and Dissertations

Fibroblast growth factor receptor plays a major role in several biological processes. Without FGFR, a human cannot live. FGFR is involved in cell differentiation and wound healing. Of course, if FGFR signaling becomes unregulated, it causes severe distress in the body. Several cancers are contributed to high signaling levels, as well as developmental conditions like rickets and Kallmann’s syndrome. FGFR is thought to undergo an auto-inhibition (or self-regulatory) process in order to try to facilitate regulation. The exact method of this inhibition is currently unknown, but is proposed to involve the unstructured acid box region of FGFR. We developed a …

Mirror Buckling Transitions In Freestanding Graphene Membranes Induced Through Scanning Tunneling Microscopy, James Kevin Schoelz

Graduate Theses and Dissertations

Graphene has the ability to provide for a technological revolution. First isolated and characterized in 2004, this material shows promise in the field of flexible electronics. The electronic properties of graphene can be tuned by controlling the shape of the membrane. Of particular interest in this endeavor are the thermal ripples in graphene membranes. Years of theoretical work by such luminaries as Lev Landau, Rudolf Peierls, David Mermin and Herbert Wagner have established that 2D crystals should not be thermodynamically stable. Experimental research on thin films has supported this finding. Yet graphene exists, and freestanding graphene films have been grown …

Distinguishing Macrophage Activation States By Mass Spectrometry, Matthias Manfred Knust

Graduate Theses and Dissertations

Macrophages are versatile and highly adaptive cells that are involved in a wide range of physiological processes including host defense, homeostasis or regeneration, as well as pathogenesis. They react to their microenvironment, assuming various roles based on chemical and/or physical cues, and can reversibly shift between these so-called activation states. Concurrently, the technique of immunohistochemistry is used to gain spatial information on activated macrophages on tissue sections. The aim of this work was to find mass spectral biomarkers that allow the differentiation of activation states, and establish conditions that can be used in imaging mass spectrometry (IMS) experiments to investigate …

Photoelectric Characterization Of Bacteriorhodopsin Reconstituted In Lipid Bilayer Membrane, Joel Kamwa

Graduate Theses and Dissertations

The objective of this work was to conduct basic research in biologically inspired energy conversion solutions. A photosynthetic protein (Bacteriorhodopsin) was reconstituted in a bi-layer membrane. Then, when a laser beam was shined on the membrane, the photon energy was used by the protein to pump protons across the membrane. The translocation of protons across the membrane was measured as photocurrent. For this purpose, a system was built to characterize the lipid bilayer membranes and to measure the photocurrent. The lipid bilayer membrane was characterized by its capacitance and resistance. A picoampere photocurrent was observed when Bacteriorhodopsin protein was present …

Measuring The Role Of Inhibition In Auditory Discrimination In Mice, Tazima Nur

Graduate Theses and Dissertations

Understanding how inhibitory neurons affect sensory information processing in the cerebral cortex is an ongoing goal of both neuroscience and statistical physics research. In this master's thesis research project, an experimental system has been designed and built for studying how auditory dynamic range depends on inhibitory neurons, based on observations of mouse behavior. In this thesis, firstly, the topic of inhibition and information processing has been introduced. Then two papers related to inhibition and dynamic range has been reviewed in detail. One of the papers is an experimental work that analyzes the affect of inhibition on dynamic range. The other …

Atom-Based Geometrical Fingerprinting Of Conformal Two-Dimensional Materials, Mehrshad Mehboudi

Graduate Theses and Dissertations

The shape of two-dimensional materials plays a significant role on their chemical and physical properties. Two-dimensional materials are basic meshes that are formed by mesh points (vertices) given by atomic positions, and connecting lines (edges) between points given by chemical bonds. Therefore the study of local shape and geometry of two-dimensional materials is a fundamental prerequisite to investigate physical and chemical properties. Hereby the use of discrete geometry to discuss the shape of two-dimensional materials is initiated.

The local geometry of a surface embodied in 3D space is determined using four invariant numbers from the metric and curvature tensors which …

Monodentate, Bidentate And Photocrosslinkable Thiol Ligands For Improving Aqueous Biocompatible Quantum Dots, Hiroko Takeuchi

Graduate Theses and Dissertations

Water-soluble Quantum Dots (QDs) are highly sensitive fluorescent probes that are often used to study biological species. One of the most common ways to render QDs water-soluble for such applications is to apply hydrophilic thiolated ligands to the QD surface. However, these ligands are labile and can be easily exchanged on the QD surface, which can severely limit their application. As one way to overcome this limitation while maintaining a small colloidal size of QDs, we developed a method to stabilize hydrophilic thiolated ligands on the surface of QDs through the formation of a crosslinked shell using a photocrosslinking approach. …

Interactions Between Ions And Lysenin Nanochannels And Their Potential Applications As Biosensors, Radwan Awwad Al Faouri

Graduate Theses and Dissertations

Lysenin is classified as a pore-forming toxin protein that is isolated from the earthworm Eisenia fetida and consists of 297 amino acids [1]. Lysenin inserts large conducting pores (3.0-4.7 nm in diameter) into artificial membranes (BLM) which include sphingomyelin. These pores (channels) are open and oriented upon insertion into the bilayer lipid membrane. Lysenin channels gate at positive voltages (voltage-induced gating), but not at negative voltages. Lysenin pores also exhibit activity modulation in response to changes in ionic strength and pH, indicating that electrostatic interaction is responsible for Lysenin conductance activities. In this line of inquiries, and by modulating Lysenin …