Biochemistry, Biophysics, and Structural Biology Commons^™

Institutional And Individual Approaches To Change In Undergraduate Stem Education: Two Framework Analyses, Stephanie B. Feola

USF Tampa Graduate Theses and Dissertations

The overarching goal of this dissertation is to examine institutional change initiatives in STEM and to understand the impact of engaging with a specific change strategy on a biochemistry educator’s instructional practice. Institutional change initiatives involve executing an intentional strategy to influence teaching practices within a specific institution. This research investigates NSF-funded change initiatives at three public research universities that were focused on encouraging the adoption of evidenced-based instructional practices (EBIPs) by STEM faculty. As part of an effort to understand how the three institutions approached this task, framework analysis was performed using the initiative’s annual reports to NSF. Further …

Flow Visualization And Aerosol Characterization Of Respiratory Jets Exhaled From A Mannequin Simulator, Sindhu Reddy Mutra

USF Tampa Graduate Theses and Dissertations

It is important to understand the airborne transmission of infectious diseases due to the COVID-19 pandemic. Physical experiments were conducted to understand the dispersion of aerosols emitted from a mannequin simulator replicating human tidal breathing through the nose and mouth with and without a protective face mask in an enclosed space. Flow patterns are observed via high-speed visualization, and the concentration and size distribution of the particles is measured as a function of distance from the mannequin using an optical particle sizer. Masks were shown to effectively reduce the horizontal dispersion of aerosol for both mouth and nose breathing. Further, …

Data-Driven Modeling Of The Causes And Effects Of Interneuronal Dysfunction In Alzheimer’S Disease And Dravet Syndrome, Carlos Perez

USF Tampa Graduate Theses and Dissertations

One of the defining features of Alzheimer’s disease (AD) is the increased cleavage of the amyloid precursor protein (APP), causing abnormally high levels of the aggregation form of amyloid beta (Aβ ). Many studies have shown that both AD patients and AD mice models exhibit abnormal network activity, including hypersynchronous excitatory neuron behavior, altered brain rhythms, and in some instances epileptic seizures when exposed to high levels of Aβ In particular, strong experimental evidence suggests that it is the small globular amyloid oligomers (gOs) and curvilinear fibrils (CFs) rather than the more stable, late stage rigid fibrils (RFs) that cause …

Origins Of Amyloid Oligomers And Novel Approaches For Their Detection, Jeremy Barton

USF Tampa Graduate Theses and Dissertations

Alzheimer’s disease, type II diabetes, and other amyloid diseases are known to be associated with the formation of amyloid aggregates. It has been thoroughly researched whether amyloid fibrils or oligomers are the main culprit for these diseases, and recent evidence has connected oligomers as the most disease relevant aggregate species. However, many difficulties have arose in confirming this hypothesis. Techniques for oligomer detection are often limited in their sensitivity, and in many cases are unable to distinguish oligomers from rigid fibrils. Additionally, the role oligomer splay in fibril assembly is still unclear, and has led to the belief that different …

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 …

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 …

Constituent Partitioning Consensus Docking Models And Application In Drug Discovery, Rainer Metcalf

USF Tampa Graduate Theses and Dissertations

This work expounds on some of the current computational tools and programs available and the best practices associated with their use. A high-level introduction, intended for both novices and the semi-experienced, focusing on the more common programs used in scientific literature is the scope of this topic. Both classical and quantum techniques are described. Classical methodologies include Molecular Dynamics, Monte Carlo, energy minimization methods, molecular docking, low-mode, and homology modeling. Quantum chemistry techniques are also discussed encompassing Hartree-Fock, Post-Hartree-Fock theories, and Density Functional Theory along with associated basis sets.

Along with established methodologies, novel theoretical methods are introduced for furthering …

Amyloid Protein Aggregation And Associated Toxicity, Chamani A. Niyangoda

USF Tampa Graduate Theses and Dissertations

Amyloidosis is a group of diseases in which amyloid fibrils accumulate and deposit into plaques and intracellular inclusions which lead to disruption of the tissue architecture and function. Most of the amyloid diseases are incurable due to a lack of understanding of the amyloid formation, as well as associated toxicity. My research work is focused on three different aspects of amyloid aggregation.

The aim of the first project is to investigate the potential use of deep-blue autofluorescence (dbAF) as an intrinsic optical probe to study amyloid self-assembly. This novel fluorescence signal is excited at the long wavelength edge of the …

The Modified Synchronization Modulation Technique Revealed Mechanisms Of Na,K-Atpase, Pengfei Liang

USF Tampa Graduate Theses and Dissertations

The Na/K pumps are essential for living system and widely expressed in all eukaryotic cell membranes. By actively transporting sodium ions out of and potassium ions into the plasma membrane, Na/K pumps creates both an electrical and a chemical gradient across the plasma membrane, which are crucial for maintaining membrane potential, cell volume, and secondary active transporting of other solutes, etc.

Previously, oscillating electric field with a frequency close to the mean physiological turnover rate was used to synchronize and modulate the Na/K pump molecules. Results showed that the turnover rate of Na/K pumps can be accelerated by folds. However, …

Analyzing The Effects Of Ca2+ Dynamics On Mitochondrial Function In Health And Disease, Patrick Toglia

USF Tampa Graduate Theses and Dissertations

Mitochondria plays a crucial role in cells by maintaining energy metabolism and directing cell death mechanisms by buffering calcium (Ca²⁺ )from cytosol. Therefore, the Ca²⁺ overload of mitochondria due to the upregulated cytosolic Ca²⁺ , observed in many neurological disorders is hypothesized to be a key pathway leading to mitochondrial dysfunction and cell death. In particular, Ca²⁺ homeostasis disruptions due to Alzheimer’ s disease (AD)-causing presenilins (PS1/PS2) and oligomeric forms of β-amyloid peptides Aβ commonly found in AD patients are presumed to cause detrimental effects on the mitochondria and its ability to function properly. We begin …

Investigations Into The Non-Mevalonate Isoprenoid Biosynthesis Pathway's First Two Enzymes Utilizing Hybrid Qm/Mm Techniques, Justin K. White

USF Tampa Graduate Theses and Dissertations

Molecular drug design begins with the identication of a problem to solve. This work identies the growing resistance among human pathogens to current treatments. Once the problem is identied and understood, solutions must be proposed. This one is straight forward, we need new antimicrobial drugs. More specically, we need to identify novel targets to inhibit. A large portion of antibiotics focus on disruption of macromolecular production while only a few target metabolic systems. Finally, you need to propose solutions based on the information gathered. In order to avoid existing resistance, it is important to avoid the macromolecular route and focus …

Thermodynamic And Kinetic Aspects Of Hen Egg White Lysozyme Amyloid Assembly, Tatiana Miti

USF Tampa Graduate Theses and Dissertations

Deposition of protein fibers with a characteristic cross-β sheet structure is the molecular marker associated with human disorders ranging from Alzheimer's disease to type II diabetes and spongiform encephalopathy. Given the large number of non-disease related proteins and peptides that have been shown to form amyloid fibrils in vitro, it has been suggested that amyloid fibril formation represents a generic protein phase transition. In the last two decades it has become clear that the same protein/peptide can assemble into distinct morphologically and structurally amyloid aggregates depending on the solution conditions. Moreover, recent studies have shown that the early stage, oligomeric …