Biochemistry, Biophysics, and Structural Biology Commons^™

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 …

Circuits With Broken Fibration Symmetries Perform Core Logic Computations In Biological Networks, Ian Leifer, Flaviano Morone, Saulo D. S. Reis, José S. Andrade Jr., Mariano Sigman, Hernán A. Makse

Publications and Research

We show that logic computational circuits in gene regulatory networks arise from a fibration symmetry breaking in the network structure. From this idea we implement a constructive procedure that reveals a hierarchy of genetic circuits, ubiquitous across species, that are surprising analogues to the emblematic circuits of solid-state electronics: starting from the transistor and progressing to ring oscillators, current-mirror circuits to toggle switches and flip-flops. These canonical variants serve fundamental operations of synchronization and clocks (in their symmetric states) and memory storage (in their broken symmetry states). These conclusions introduce a theoretically principled strategy to search for computational building blocks …

The Kinetic Signatures Of Antibody Binding To M. Genitalium Adhesin Protein Fragments, Margaret C. Lunn

Honors Projects

Mycoplasma genitalium is a sexually-transmitted bacterial pathogen that persists in patients by adherence to cells through matrix glycoproteins and evasion of host antibodies. The MgpB and MgpC adherence proteins consist of variable and conserved regions. Variable regions undergo antigenic variation to avoid specific antibodies. However, the C-terminus (MgpB-4a) does not vary, is highly immunogenic, and antibodies to this region inhibit attachment and promote bacterial killing in vitro. To better understand how M. genitalium avoids clearance by antibodies to MgpB-4a in vivo we used surface plasmon resonance (SPR) to measure kinetic values of binding events. Binding of polyclonal rabbit antibodies (3935 …

Analysis Of Biofilm Remediation Capacity For Octenyl Succinic Anhydride (Osa), A Bioactive Food Starch Modifier Compound, Matthew R. Borglin

Master's Theses

Matthew R. Borglin

This thesis demonstrates efficacy of Octenyl Succinic Anhydride (OSA), as a biofilm sanitizer. Biofilms allow bacteria to adhere to solid surfaces with the use of excreted polymeric compounds. For example, surfaces found in food production or processing facilities such as the interior of a raw milk holding tank, are some of the most susceptible to biofilm contamination. When present, biofilms can cause a variety of negative effects, which include; reduction of product shelf life, corrosion, and outbreaks of foodborne illnesses. The close association of biofilms with the majority of foodborne illness cases led the US Environmental Protection …

Dna Damage Recognition And Uvrb Loading By Uvra Within The Nucleotide Excision Repair Pathway, Silas Hartley

Dissertations, Theses, and Capstone Projects

Maintaining the cellular genome is paramount to survival by any organism. A mutated genome can have detrimental effects on different cellular processes, especially replication and transcription. Cells maintain their genome using different deoxyribonucleic acid (DNA) repair pathways. The nucleotide excision repair (NER) pathway has a unique capability of repairing the genome from several different mutations, deletions, and adducts. In bacteria, the NER pathway accomplishes repair through four important steps: damage recognition by UvrA, damage verification by UvrB, DNA incision by UvrC, and repair synthesis using various cellular machinery.

UvrA forms a head-to-head dimer (UvrA₂) with two ATPase sites …

Proton Pumping Mechanism In Cytochrome C Oxidase, Xiuhong Cai

Dissertations, Theses, and Capstone Projects

Cytochrome c Oxidase (CcO), is the terminal electron acceptor in the membrane bound aerobic respiratory chain. It reduces O₂ to water. The energy released by this reaction is stored by pumping protons from the high pH, N-side of the membrane to the low pH, P-side. The generated proton gradient provides the motive force for synthesis of ATP by the ATP synthase.

Building a proton gradient across the membrane requires that proton transport must occur along controllable proton pathways to prevent proton leakage to the N-side. It has been suggested that CcO function requires proton transfer channels in both the …

Modeling Single Microtubules As A Colloidal System To Measure The Harmonic Interactions Between Tubulin Dimers In Bovine Brain Derived Versus Cancer Cell Derived Microtubules, Arooj Aslam

Dissertations

The local properties of tubulin dimers dictate the properties of the larger microtubule assembly. In order to elucidate this connection, tubulin-tubulin interactions are be modeled as harmonic interactions to map the stiffness matrix along the length of the microtubule. The strength of the interactions are measured by imaging and tracking the movement of segments along the microtubule over time, and then performing a fourier transform to extract the natural vibrational frequencies. Using this method the first ever reported experimental phonon spectrum of the microtubule is reported. This method can also be applied to other biological materials, and opens new doors …

Effect Of Charged Lipids On The Ionization Behavior Of Glutamic Acid Containing Transmembrane Helices, Brooke Nunn

Chemistry & Biochemistry Undergraduate Honors Theses

Transmembrane proteins make up critical components of living cells. Protein function can be greatly impacted by the charged state of its respective components, the side chains of amino acid residues. Thus far, in the lipid membrane, little is known about the properties of residues such as glutamic acid. To explore these properties, I have included glutamic acid in a suitable model peptide-lipid system for fundamental biophysical experiments. Within the system, I have placed a glutamic acid residue instead of leucine in the L14 position of the helical hydrophobic peptide GWALP23 (acetyl-GGALWLALALALAL¹⁴ALALWLAGA-amide). Substitutions of glutamine and aspartic acid serve …

Functional Analysis Of A Critical Glycine (Glycine 12) In Beta-Type Connexins Of Human Skin, Rasheed Bailey

Biology Theses

At least five beta-type connexins are expressed in various layers of the skin (Cx26, Cx30, Cx30.3, Cx31, and Cx32) and all include a glycine residue at position 12. Glycine12 (G12) is located about halfway through the cytoplasmic amino terminus and has been the focus of several studies related to connexin diseases and gap junction channel structure. The importance of this residue is evident in the severity and diversity of diseases associated with amino acid substitutions at G12 including hereditary forms of skin disease, deafness and neuropathy. This study uses bioinformatic analysis in combination with mutational analysis and electrophysiology to better …

Effect Of Ph And Lipid Composition On Membrane-Spanning Helices With Glutamic Acid Examined By Solid-State Nmr, Kelsey Marr

Chemistry & Biochemistry Undergraduate Honors Theses

Transmembrane proteins constitute about 30% of the proteins in a mammalian cell and are involved in major biological processes. The dynamic properties of membrane proteins and the ionization states of particular side chains are important for biological function. The biophysical properties of membrane proteins nevertheless can be difficult to decode, particularly for glutamic acid in the lipid environment of cell membranes. To study the ionization of glutamic acid in transmembrane peptides, guest glutamic acid residues were substituted into the well-defined model helix of GWALP23 (acetyl-GGAL4WLALALALALAL16ALWLAGA-amide). These guest residues were placed at position L16 or L4 and specific 2H-labeled alanine residues …

Analyzing Change-Of-Direction And The Laterally Resisted Split Squat: Incorporating A Lateral Vector Into The Single Leg Squat, Derek Maddy

Boise State University Theses and Dissertations

Improving change of direction (COD) with the use of strength training has led to mixed results. To date, the modified single leg squat (MSLS) and the bilateral squat (BS) have been successfully used to improve COD, with equal improvement. COD is primarily performed at a 45-75° frontal plane angle; however, the MSLS and BS are performed at a 90° frontal plane angle. Based on the force vector theory, it is proposed that a more mechanically similar strength training exercise, the Laterally Resisted Split Squat (LRSS), be used. The purpose of this study is to compare COD with the LRSS, MSLS, …

Investigating The Interactions Between Individual Calmodulin And Hiv-1 Protein Domains, Riley K. Kendall, Jerry Larue

Student Scholar Symposium Abstracts and Posters

The World Health Organization found that 37.9 million people were living with HIV by the end of 2018. HIV is a virus that weakens the immune system through viral replication and the destruction of CD4⁺ T-cells, which are white blood cells that detect infection and make antibodies. A cure for HIV has not yet been discovered. HIV-1 contains a Gag polyprotein which regulates the stages of viral replication. Previous studies suggest that the myristoyl group of a matrix protein peptide found on the Gag polyprotein, MA, forms a complex with a calcium-binding, multifunctional regulatory protein called Calmodulin (CaM). CaM …

Computational Molecular Docking Models And Design Of Diarylpentanoids For The Androgen Receptor, Jarett Guillow

Computational and Data Sciences (MS) Theses

The androgen receptor (AR) is a member of the nuclear receptor protein family that, upon binding to its natural ligand dihydrotestosterone (DHT) in the cytoplasm, translocates to the nucleus and exerts nuclear transcription factor activity to drive gene expression related to normal prostate development. AR signaling becomes overactive during the development and progression of prostate cancer through different mechanisms, including over-expression and mutation of the AR. Therefore, the AR is a prominent molecular target in the clinical management of prostate cancer. However, all therapeutic modalities targeting the AR, including androgen ablation therapy and AR block suffer from transient efficacy and …

Characterization Of Beryllium Ion Complexation In The Presence Of Biological Buffers Using Isothermal Titration Calorimetry, Guillermo Alexander Ramirez

UNLV Theses, Dissertations, Professional Papers, and Capstones

Be2+ ion is a biologically active metal that is capable of binding to proteins and has been shown to affect various cellular processes. When treated with Be2+, certain cancer cells display cytostatic effects. GSK3β is a regulatory kinase involved in the β-catenin pathway that may be involved in producing these cytostatic effects when Be2+ binds to it. In order to determine binding parameters between Be2+ and GSK3β, isothermal titration calorimetry (ITC) can be utilized. However, titrations at physiological pH cannot be carried out due to Be2+ unique speciation at neutral pH ranges. Significant precipitation occurs at pH 6 and higher …

Stereotactic Radiosurgery Implementation At Utah Valley Hospital, Ryan Sharp

UNLV Theses, Dissertations, Professional Papers, and Capstones

Utah Valley Hospital (UVH) implemented a stereotactic radiosurgery (SRS) program as an additional line of service. SRS as defined by the American College of Radiology is radiation therapy delivered via stereotactic guidance with approximately 1 mm targeting accuracy to intracranial targets in 1-5 fractions. Effectively implementing the SRS program at UVH requires the adoption and implementation of hardware and software technologies, a review of the clinical workflow with appropriate quality assurance tests, and the assessment of additional technologies that will further enhance the capabilities of the program. The scope of this work is to include a comprehensive writeup of the …

Characterization Of Avidin And Case9 Single Protein Molecules By A Solid-State Nanopore Device, Haopeng Li

Graduate Theses and Dissertations

The shape and charge of a protein play significant roles in protein dynamics in the biological system of humans and animals. Characterizing and quantifying the shape and charge of a protein at the single-molecule level remains a challenge. Solid-state nanopores made of silicon nitride (SiNx) have emerged as novel platforms for biosensing such as diagnostics for single-molecule detection and DNA sequencing. SSN detection is based on measuring the variations in ionic conductance as charged biomolecules translocate through nanometer-sized channels driven by an external voltage applied across the membrane. In this paper, we observe the translocation of asymmetric cylindrical structure CRISPR-Cas9 …

The Role Of Conformational Dynamics In Isocyanide Hydratase Catalysis, Medhanjali Dasgupta

Department of Biochemistry: Dissertations, Theses, and Student Research

Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site electrostatic environment. Although a vast number of enzymes rely on cysteine modification for function, precisely how altered structural and electrostatic states of cysteine affect protein dynamics, which in turn, affects catalysis, remains poorly understood.

Here we use X-ray crystallography, computer simulations, site directed mutagenesis and enzyme kinetics to characterize how covalent modification of the active site cysteine residue in the enzyme, isocyanide hydratase (ICH), affects the protein …

Study Of The Therapeutic Effects Of Synchronization-Modulation Of The Na/K Pump On Muscle Fatigue, Jason E. Mast

USF Tampa Graduate Theses and Dissertations

It has been shown that by applying a specially designed oscillating external electric field to a cell membrane that the membrane's sodium/potassium pumps can be synchronized to all work at the same rate. Then by slowly increasing the electric field's frequency the pumps' turnover rate can also be increased. By increasing the pumps' turnover rate, the sodium and potassium concentration gradients can be increased, this type of stimulation is called synchronization-modulation. There are three generations of the synchronization-modulation waveform each with different utilities. In particular, the third generation of synchronization-modulation has the ability to use the energy of the external …

Allosteric Control Of Proteins: New Methods And Mechanisms, Nalvi Duro

USF Tampa Graduate Theses and Dissertations

Allostery describes the phenomenon where perturbations in one region of a protein affect protein behavior in another non-overlapping region. Considerable efforts made over decades to understand the molecular basis of allostery, yet an overarching theory that can predict signaling pathways and contributions from chemical components is still lacking. In fact, molecular details in even the most well-studied of model systems, PDZ domains and GPCRs, remain unclear. In this dissertation I use molecular simulation methods to understand the role of allostery in the regulated entry of paramyxovirus into host cells, and also develop a new method to determine time-dependent signaling pathways …

Impedance Analysis Of Tissues In Nspef Treatment For Cancer Therapy, Edwin Ayobami Oshin

Biomedical Engineering Theses & Dissertations

Nanosecond pulsed electric field (nsPEF) for cancer therapy is characterized by applications of high voltage pulses with low pulsed energy to induce non-thermal effects on tissues such as tumor ablation. It nonthermally treats tissues via electroporation. Electroporation is the increase in permeabilization of a cell membrane due to the application of high pulsed electric field. The objective of this study was to investigate the effect of nsPEF on tissue by monitoring the tissue’s impedance in real-time. Potato slices (both untreated and electroporated), and tumors extracted from female BALBc mice were studied. 100ns, 1-10kV pulses were applied to the tissues using …

Fibration Symmetries Uncover The Building Blocks Of Biological Networks, Flaviano Morone, Ian Leifer, Hernán A. Makse

Publications and Research

A major ambition of systems science is to uncover the building blocks of any biological network to decipher how cellular function emerges from their interactions. Here, we introduce a graph representation of the information flow in these networks as a set of input trees, one for each node, which contains all pathways along which information can be transmitted in the network. In this representation, we find remarkable symmetries in the input trees that deconstruct the network into functional building blocks called fibers. Nodes in a fiber have isomorphic input trees and thus process equivalent dynamics and synchronize their activity. Each …

Development And Application Of Computational Models For Biochemical Systems, Fiona L. Kearns

USF Tampa Graduate Theses and Dissertations

Chemistry is the study of matter and its transformations. Computational chemistry uses computer models to study chemistry in all its intricate complexity. In this thesis I hope to accessibly introduce fundamental concepts central for computational chemistry including quantum mechanics, molecular mechanics, and multiscale modeling. I then present several works which I have conducted throughout my graduate career employing many different computational methods. The investigations described here can be summarized as follows. Chapter 2.1 modeling proteins involved in crustacean molting, and identifying possible inhibitors to this molting. Chapter 2.2 modeling d-fructose bound to synthetic saccharide receptors with hopes of improving saccharide …

Evaluation Of Optimal Technique For Left Breast Irradiation, Amitpal Singh Saini

USF Tampa Graduate Theses and Dissertations

Numerous studies have indicated that radiation therapy reduces the risk of the local recurrence of breast cancer in several cases and that it has increased the overall survival rate. Although radiation therapy is beneficial for the treatment of breast cancer, it is known to increase the risk of both radiation toxicity and secondary breast cancer. In left-sided breast cancer, radiation therapy treatment often leads to the heart and its components—such as the left ventricle and left anterior descending artery—being exposed to high doses of radiation because of the proximity of the heart to the left breast, resulting in cardiac complications …

Advanced Computational Methodologies To Study Binding Free Energies Of Biomolecular Complexes, Rajat Kumar Pal

Dissertations, Theses, and Capstone Projects

Molecular recognition is the basis of biological mechanisms and is a key element to consider while formulating effective and safe drugs. Pharmaceutical drugs are designed so as to bind a target protein even at very low concentrations to alter the diseased conditions without interfering with normal biological processes. In a rational drug design process, this is achieved by acquiring information about the chemical structure and the physical and chemical properties of the target protein receptor to gain insights on how changing the chemical composition of the substrate drug could affect the protein-drug interaction and binding affinities. Computational models are used …

Case 34: Kinetics Of Alkaline Phosphatase, Dr. Kathleen Cornely

Chemistry & Biochemistry Case Studies

Kinetic studies are carried out using the alkaline phosphatase, an enzyme that has an important role in skeletal mineralization.

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 …

Quantification Of Mitochondrial Zinc Homeostasis And Analysis Of Zinc And Polyamine-Mediated Axonal Trafficking, Dylan Hunt Fudge

Electronic Theses and Dissertations

The zinc ion is an important emerging signaling molecule for biological processes. In this work we engineered improved zinc sensors based on our previously developed fluorescent sensor GZnP1 to provide sensors with a higher fluorescent readout, faster kinetics, and a superior sensitivity to zinc. We utilized these zinc sensors and further developed the sensors to answer questions pertaining to biological zinc. We showed the labile zinc concentration in the mitochondrial matrix was less than 1 pM while the labile zinc concentration in the cytosol and mitochondrial IMS were comparable (~100 pM) across four different cell lines. Using these zinc sensors …

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 …

Cellular And Organismal Ramifications Of De Novo Purine Synthesis Dysregulation, Randall Craig Mazzarino

Electronic Theses and Dissertations

Purines are a class of nitrogenous bases and are essential small molecules to life. Purines are used within the cell as genetic information carriers, energy currency, signaling molecules, and cofactors for multiple processes. They are formed through de novo and salvage pathways found in cells across the phylogenetic tree. The substrates of enzymes within de novo purine synthesis are known to influence other processes within the cell, such as energy homeostasis. In humans, de novo purine synthesis disorders are rare, with around 100 people identified. These patients exhibit a range of phenotypes, with varying degrees of mental retardation, seizure activity, …

Single-Lipid Sorting And Dynamics At Nanoscale Membrane Curvatures: The Effects Of Fluorescence Labeling, Composition, Phase, And Temperature, Xinxin Woodward

Wayne State University Dissertations

Nanoscale membrane curvature on cell plasma membrane assists in the spatial organization and domain formation that are critical for life of eukaryotic cells. Lipids and proteins can sense, be sorted by, and generate both functional domains and membrane curvature. Reveal the relationship between membrane curvature, phase separation, and single-molecule behavior is a key to understanding fundamental processes, such as phagocytosis initiation, cell signaling, and membrane budding. Single lipid dynamic and sorting on engineered membrane curvature is studied to understand the effects of fluorescence labeling, composition, phase separation, and temperature. Single particle tracking was used to find radial averaged diffusion at …