Digital Commons Network^™

Investigating The Stability Of Different Sizes Of Gold Nanoparticles In Physiological Environments And Different Gold Nanoclusters In Water., Narges Hajighasemi

Electronic Thesis and Dissertation Repository

Gold nanoparticles (AuNPs) have become promising candidates for various biomedical applications due to their unique physicochemical properties and biocompatibility. Nevertheless, the efficacy of AuNPs in these applications highly relies on their stability and ability to maintain their desired properties within the complex environment of the human body. This thesis investigates the stability and aggregation behavior of citrate-coated AuNPs in in-vitro physiological environments and nitrogen heterocyclic carbene (NHC)-coated gold nanoclusters (AuNCs) in water over time. Analytical techniques such as electrophoretic mobility, dynamic light scattering, and inductively coupled plasma mass spectrometry were employed. It was shown that cell media (in contrast to …

Integrating In Vitro And In Silico Approaches To Gain Insight Into The Mechanism Of Amyloid Fibrillogenesis, Marvin M. Bilog

Dissertations, Theses, and Capstone Projects

Amyloid fibril formation, the hallmark of numerous amyloid-related diseases, has been the subject of a vast number of scientific studies due to its pathological implications. Since the fibrillization process exhibits a certain level of intricacy, its investigation requires a multidisciplinary approach that integrates both experimental and computational methods. In vitro techniques involve biophysical assays and imaging tools for characterizing the structural and kinetic aspects of amyloid fibril formation. In parallel, in silico techniques offer programs for predicting atomistic details and behaviors of amyloidogenic proteins and peptides at the nanoscale level. Serum amyloid A (SAA), human islet amyloid polypeptide (hIAPP), and …

De-Fragmentation: Bridging Two Fragmented Communities Through Well Being In The West End Neighborhood, Mark Pinkney Jr

Bachelor of Architecture Theses - 5th Year

The intention of this thesis is to create a “Bridge” between two communities that are dealing with Physical and Social fragmentation. To address the issue of fragmentation, the design’s program will introduce 3 Well Being Programs. Physical Well Being, Intellectual Well Being, and Well Being through Sense of Community.

The West End community presents two forms for fragmentation Physical and Social. The specifically strives to create engagement between the older community in the West End historic neighborhood and younger community of the Atlanta University Students.

The 3 Well Being programs include on the Intellectual side a Trade school. The Physical …

Using Quantitative And Kinetic Proteomics To Explore Proteostasis, Nathan Raul Zuniga Pina

Theses and Dissertations

Every cell consists of carefully orchestrated biomolecules such as lipids, carbohydrates, and proteins. To maintain internal stability (homeostasis), cells maintain the right amount of these molecules at the right time and at the right place. This process is especially true for proteins since they are the foundation functional units within the cell. Proteins form structures and perform chemistry that bestows cells overarching functional roles. Cells maintain protein homeostasis (proteostasis) by modulating synthesis, folding, and degradation processes (turnover) to maintain the abundance levels for all proteins. This is the foundational kinetic model of proteostasis that is covered in this work, and …

A Privacy Safeguarding Framework For The Smart Grid, Gaurav Shivaji Wagh

Theses

The smart grid is an outcome of integrating communication technologies with traditional electrical systems. This enables the collection of granular metering data from the customer domain for providing grid and billing functionalities. However, the data collection process exposes the grid to various cyberattacks, posing a significant threat to customer privacy. This is a critical concern for the smart grid community and has hindered the global adoption of the smart grid technology. Although aggregation-based frameworks show promise for sharing metering data with the Electrical Service Provider while maintaining customer privacy, existing aggregation-based frameworks have several limitations. Some of these limitations include …

Diffusion-Driven Aggregation Of Particles In Quasi-2d Membranes, Oscar Gullickson Rausis

Physics

Many biological membranes can be modeled as two-dimensional (2D) viscous fluid sheets surrounded by three-dimensional (3D) fluids of different viscosity. Such membranes are dubbed quasi-2D as they exhibit properties of both 2D and 3D fluids. The Saffman length is a parameter that describes the energy exchange between the membrane and bulk fluids and controls the cross-over from 2D to 3D hydrodynamics. We aim to model diffusion-driven aggregation of particles embedded in a quasi-2D membrane. It is known that hydrodynamic interactions between solute particles significantly reduce their aggregation rate in 3D fluids. It is expected that in quasi-2D membranes the reduction …

Investigation Of Early Complex Formation Of Huntingtin Protein With And Without Lipids, Alyssa R. Stonebraker

Graduate Theses, Dissertations, and Problem Reports

Huntington’s disease (HD) is a fatal neurodegenerative disease caused by the expansion of the polyglutamine (polyQ) domain of the huntingtin protein (htt). The expansion of the polyQ domain beyond a threshold of approximately 35 repeats triggers complex toxic aggregation mechanisms and results in altered interactions between htt and lipid membranes. Many factors modulate these processes. One such modulator includes sequences flanking the polyQ domain, most notably the first 17 amino acids at the N-terminus of the protein (Nt17), and environmental factors including the presence of membranous structures. Nt17 has the propensity to form an amphipathic a-helix in the presence of …

Small Heat Shock Protein 27 And Its Role In Human Disease, Bianka Andrea Holguin

Open Access Theses & Dissertations

Small heat shock protein 27 (Hsp27) is a ubiquitously expressed molecular chaperone with roles in many physiological processes. As an ATP-independent molecular chaperone, Hsp27 protects substrates from irreversible aggregation and holds them in a folding competent state for later recycling into the proteome. Hsp27 proteins form dimers that are assembled into large oligomeric complexes. Phosphorylation of Hsp27 dissembles the oligomers into chaperone active dimers. Several missense mutations of Hsp27 are causative for the neurodegenerative disorders Charcot-Marie-Tooth disease 2F and distal Hereditary Motor Neuropathy IIB. Here I show that the oligomerization and chaperoning ability of Hsp27 are altered by the Hsp27 …

Optimizing Virus Prefiltration For Biopharmaceutical Manufacturing, Solomon Isu

Graduate Theses and Dissertations

Virus filters are single-use devices that use a size-based separation process. In virus filters, contaminating virus particles are retained while the therapeutic molecules pass through the membrane pores. Virus filters are an essential component of the overall virus clearance strategy. Sections 1 and 2 of this dissertation provide an introduction and extensive review of monoclonal antibody (mAb) process development, where virus filtration is pivotal. In section 3, prefiltration studies were performed with an industrially relevant IgG1 type mAb using adsorptive and size-exclusion-based prefilters with different mechanisms of action. This mAb has an isoelectric point range of 7.1 to 8.0 and …

The Importance Of Protein Context In Spinocerebellar Ataxia Type 3, Sean Luis Johnson

Wayne State University Dissertations

Spinocerebellar Ataxia Type 3 (SCA3) is a member of the family of polyglutamine (polyQ) neurodegenerative disorders that includes Huntington's Disease and several other SCAs. SCA3, the most common dominant ataxia in the world, is caused by polyQ tract expansion in the protein, ataxin-3. How SCA3 occurs and how to treat it remain unresolved issues. The primary culprit of toxicity in all polyQ diseases is the glutamine repeat: its abnormal expansion leads to neuronal dysfunction and death. With that said, there is indisputable evidence that the way polyQ-dependent toxicity presents—areas impacted, cellular processes perturbed—is predicated in large part on regions outside …

The Ecological Role Of Cassiopea In Shallow Mangrove Habitats, David Marcel Durieux

USF Tampa Graduate Theses and Dissertations

Upside-down jellyfish, Cassiopea sp., can be locally abundant in shallow mangrove habitats throughout the tropics and subtropics. Unlike other jellyfish, Cassiopea sp. are epibenthic. Due to this unique lifestyle and their ability to achieve high population densities, an understanding is needed of their ecological impacts both individually and in aggregations, particularly given that Cassiopea sp. ranges are expanding poleward due to global climate change. We quantified the fluid flow produced by Cassiopea sp. feeding currents and found that an average-sized Cassiopea sp. can transport over 200 l/h of water in the vertical excurrent jet of their feeding current. Populations of …

Accelerating Aggregation Efficiency: Using Postgres As A Cache With Mongodb, Mason Q. Porter-Brown

Senior Projects Fall 2021

For decades now relational databases, namely SQL, have been the industry standard. However, recently MongoDB and other NoSQL databases have been growing in popularity due to their flexibility and scalability. SQL still has the upper hand in a variety of areas, including data consistency, advanced and established analytics functions, and efficient “JOIN” functions. This project focuses on MongoDB’s shortcomings when it comes to replicating “JOIN” operations using MongoDB’s aggregate functions. “JOIN” operations refer to the action of comparing data from one or more collections of data and joining similar data together in order to analyze and draw statistics from the …

Interactions Of The Nlrp3 Inflammasome Complex, Nyasha Makoni

Dissertations

The innate immune system is the first line of defense in response to invasion by pathogens. One of the major pathways in the innate immune system involves a three-protein complex known as the NLRP3 inflammasome. This complex comprises of NLRP3, ASC, and procaspase-1. In response to stimuli, the inflammasome assembles to activate caspase-1 which subsequently facilitates production of interleukin-1β (IL-1β), an inflammatory cytokine. The NLRP3 inflammasome has been implicated in a variety of inflammatory disorders including Alzheimer’s disease (AD). Amyloid beta (Aβ) is the protein that causes AD and Aβ deposits in the brain activate microglia resulting in chronic inflammation. …

Opto-Fluidic Manipulation Of Microparticles And Related Applications, Hao Wang

USF Tampa Graduate Theses and Dissertations

Contemporary biomedical technologies introduce many new instruments that are important for diagnosis and treatment of the patients. Instrument that can do rapid detection of bacterial infections, and further direct medical practitioner to prescribe optimal antibiotics is highly desirable. But unfortunately, this instrument is not available yet. Ideally, this instrument has to be portable to be used at point-of-care. This means it has to be small and inexpensive, but still highly accurate. Another critical requirement for the instrument is that the test results have to be available promptly. Because in case of such complications of bacterial infections as sepsis, each additional …

Aggregated Reverse Time Transfer, Brandon Smith

Master's Theses and Capstones

Monitoring mechanisms are a critical component of the security and maintenance of high precision timing networks. Any and all guarantees of determinism and correctness are invalidated if a synchronous network malfunctions or is compromised by an attacker. Existing mechanisms allow for a comprehensive view of the distribution of time throughout a network, but they do not scale to large networks. I propose a new method called aggregated reverse time transfer (ARTT), which redefines the existing mechanisms to include a new aggregation scheme that serves the dual purpose of distributed data summarization and anomaly detection for networks of any size. With …

Efficient Forward-Secure And Compact Signatures For The Internet Of Things (Iot), Efe Ulas Akay Seyitoglu

USF Tampa Graduate Theses and Dissertations

In the modern Internet of Things (IoT) applications, the system entities collect security-sensitive information that must be cryptographically protected. In particular, authentication and integrity, as foundational security services, are essential for any IoT applications. Digital signatures provide both authentication and integrity to these applications. Nevertheless, once an IoT device is compromised, its signature private key is leaked to an adversary. Forward-secure digital signatures mitigate the impact of such key compromises by incorporating a key-evolving mechanism into the authentication process. However, existing forward-secure signatures suffer from large signature/key sizes, heavy computational overhead, and some prominent variants that can only sign a …

Aggregation Behavior In The Bed Bug, Cimex Lectularius L., Paul D. Baker

Theses and Dissertations--Entomology

The bed bug, Cimex lectularius L., is a common household pest that feeds on the blood of its human hosts. Unlike many other hematophagic arthropods, bed bugs have not demonstrated the ability to vector disease; yet its presence in a household often leads to fear and anxiety amongst its human host victims. Bed bugs spend the majority of their time aggregating in enclosed and hidden locations, making it difficult to detect and eradicate them. One of the significant mediators of aggregation behavior is an aggregation pheromone. The pheromone has been identified to be six chemical compounds, five volatile compounds that …

Characterization Of The Dimerization And Salt Dependent Aggregation Of The Als-Linked Protein Tdp-43, Elizabeth Ehrhardt

Electronic Theses and Dissertations

Trans-active response (TAR) DNA-binding protein 43 (TDP-43) is essential for RNA processing but can also form toxic cytoplasmic inclusions in neurons of patients with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RNA-binding has been shown to have the potential to decrease or inhibit the aggregation of TDP-43, indicating that supplying RNA therapeutics may be a solution to treat these neurodegenerative disorders. However, the mechanism of aggregation, transitioning from TDP-43’s native dimeric state to small oligomers to toxic aggregates, is still relatively unknown. This needs to be established before determining how to target and disrupt this aggregation. Using GFP-TDP-43, …

Contemporary Problems In Aerosol Aggregation And Gelation, Pai Liu

McKelvey School of Engineering Theses & Dissertations

Aggregation of nanoparticles in aerosols is a fundamental phenomenon with important implications to diverse fields ranging from material synthesis to pollutant control. The past few decades have witnessed extensive research on investigating the structure and growth mechanism of aerosol aggregates with sizes spanning across several orders of magnitude. This dissertation focuses on some contemporary problems that remain unaddressed in this topical area. Aerosol aggregates in sub-micron regimes, which are formed via the irreversible collision and aggregation of solid nanoparticle monomers, are fractal-like in their morphology. A mathematical description of this seemingly random structure dates to the seminal works by Forest …

Aggregation Services And Songwriter Independence, Saxon John Paul Ahern

Capstone Projects and Master's Theses

Digital download aggregation services are the modern songwriter’s greatest ally and independent record labels’ newest competition. Digital download aggregators like CDBaby, Distrokid, Tunecore, and Awal have made releasing an album for online distribution far easier than before. Many aggregators are affordable and also provide many services to the songwriter that historically involved employing additional middlemen.

Like distribution, the mastering stage of production has evolved. Mastering music can now be done through online services independently and on a very tight budget. Automated mastering services like LANDR and iZotope will be briefly discussed in section three, as well as additional options for …

Modeling And Simulations Of Peptoids, Pu Du

LSU Doctoral Dissertations

Polypeptoids, or poly-N-substituted glycines, are a class of sequence defined polymers that are structural mimics of polypeptides. Polypeptoids currently have received a growing interest due to their improved thermal stability, larger chemical diversity, and easier synthetic pathways as compared to peptides. Their lack of backbone hydrogen bonding and stereochemistry coupled with their easily tunability make them an ideal prototypical model system to study the effect of secondary/non-covalent interactions on self-assembly in solution. In order to develop a molecular level understanding of the effect of secondary interactions on polypeptoid self-assembly, systematic studies were carried out using molecular dynamics simulations on several …

Use Of Anodic Stripping Voltammetry To Study The Size-Selective Electrophoretic Deposition And Aggregation-Dependent Oxidation Of Metal Nanoparticles., Stacy L. Allen

Electronic Theses and Dissertations

This dissertation describes how anodic stripping voltammetry (ASV) was used to study size-controlled electrophoretic deposition (EPD) and the aggregation-dependent oxidation properties of citrate-stabilized Au nanoparticles (NPs). EPD of citrate-coated Au NPs occurs in the presence of hydroquinone (HQ) onto indium-tin-oxide-coated glass electrodes (glass/ITO) at potentials positive of the HQ oxidation potential. HQ oxidation produces protons at the electrode surface, which serve to neutralize the citrate molecules that electrostatically stabilize the Au NPs. Neutralization leads to the loss of stabilization and deposition onto the electrode. EPD in the presence of ferrocyanide, a non-proton-producing molecule, at oxidation potentials resulted in no deposition …

Virus Adsorption To Colloids In Water: Interactions Between Bacteriophage Ms2, Kaolinite, And Fiberglass, Ashlee N. Ellis

Theses and Dissertations

Virus adsorption to colloidal particles is an important issue in the water quality community, and it is a particularly important issue for conventional wastewater treatment plants that accept biohazardous waste. Colloids impact the transport of viruses in engineered treatment systems, and they also provide protection against oxidants and other destructive mechanisms. This study evaluated the adsorption of bacteriophage MS2 to colloidal suspensions of kaolinite (KAO) and fiberglass (FG). A series of laboratory batch tests were carried out over a range of experimental conditions to determine kinetic rate constants and characterize bond strength, and computational experiments were done to assess both …

Characterization Of A Phosphomimetic Mutant Of The Als Associated Protein Tdp-43, Nicole Toro

Electronic Theses and Dissertations

Trans-activation response (TAR) DNA-binding protein 43 (TDP-43) is a natively dimeric 414-residue protein that is encoded by the human TARDBP gene that has important implications in the pathogenesis of the neurodegenerative disorders ALS, FTD, and CTE. TDP-43 has been found hyperphosphorylated and ubiquitinated in the aggregates of the affected neurons of these diseases. The discovery of the presence of TDP-43 positive inclusions in brain matter of patients with CTE has made repetitive brain injury a possible environmental stimulus for aggregation in TDP-43 proteinopathies. We expand upon the hypothesis that TDP-43 readily aggregates under agitation conditions and that the addition of …

Development Of A Hek293 Cell Line To Show Inhibition Of Tau Aggregation, Justin Ray Shady

Electronic Theses and Dissertations

Intracellular deposition of aggregated tau is the hallmark of several different tauopathies, the most widespread of these being Alzheimer's disease. Tau is a highly soluble, intrinsically disordered, microtubule associated protein. Tau's native function is to stabilize microtubule formation in the axons of neurons. Post translational modification such as hyperphosphorylation as well as several familial mutations allow tau to nucleate and form fibrils. These fibrils can recruit healthy monomers onto their ends in a fashion described as template-assisted growth. Tau has 6 isoforms that vary by the inclusion or exclusion of two N-terminal repeats and the inclusion or exclusion of the …

Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman

Electronic Theses and Dissertations

Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation. This …

Computational Insights Into The Structures, Mechanisms, And Chemical Properties Of Metal Complexes, Enzymes, And Bio-Molecules, Thomas J. Paul

Open Access Dissertations

In this thesis, we have focus on the following three projects: (1) the inhibition of amyloid beta aggregation, (2) structural and mechanical properties of amyloid peptides, and (3) complex biological systems of molecular recognition pertaining to hydrolysis. In the first project, we have looked at the inhibition of early and late forms of Aß peptides using heparin derived disaccharides, small molecules, and a Rhenium centered photoluminescence probe. We have determined and characterized the most relevant binding sites of these complexes to both the monomeric and fibrillar forms of the Aß peptide. Currently, the aggregation of biomolecules has been implicated in …

Molecular Mechanism Of Early Amyloid Self-Assembly Revealed By Computational Modeling, Mohtadin Hashemi

Theses & Dissertations

Protein misfolding followed by the formation of aggregates, is an early step in the cascade of conformational changes in a protein that underlie the development of several neurodegenerative diseases, including Alzheimer’s and Parkinson’s diseases. Efforts aimed at understanding this process have produced little clarity and the mechanism remains elusive.

Here, we demonstrate that the hairpin fold, a structure found in the early folding intermediates of amyloid b, induces morphological and stability changes in the aggregates of Aβ(14-23) peptide. We structurally characterized the interactions of monomer and hairpin using extended molecular dynamics (MD) simulations, which revealed a novel intercalated type complex. …

Investigating Initial Interactions Between Silver Nanoparticles And Wastewater, Casey Gibson

Biological and Agricultural Engineering Undergraduate Honors Theses

The use of nanoparticles (NPs) has increased exponentially in the last 15-20 years, especially in the consumer market. NPs are currently found in over 1800 commercial products, including cosmetics, clothing, packaging, and toys. As a result, NPs can enter the environment via wastewater (WW) streams, leading to new challenges in WW treatment. This study focuses on the initial fate of silver nanoparticles (AgNPs) in WW. The AgNP interaction including aggregation and dissolution in both synthetic and real WW were studied. Real WW was collected from the primary-clarifier, secondary-clarifier, and effluent WW streams at two local WW treatment plants (Westside and …

A Mechanistic Understanding Of Self-Propagating Amyloid-Β Oligomer Conformations In Alzheimer Disease, Dexter Nathanael Dean

Dissertations

Alzheimer disease (AD) is a fatal neurodegenerative disorder characterized by the widespread deposition of proteinaceous plaques abundant in amyloid-β (Aβ) aggregates. Although the plaques mainly contain high molecular weight, insoluble Aβ fibrils, the low molecular weight soluble aggregates called oligomers have been shown as the primary toxic species responsible for synaptic dysfunction and neuronal loss in AD. The process of aggregation is nucleation-dependent, but also highly stochastic and inhomogeneous resulting in biophysically diverse assemblies. Recent advances in the field indicate a potential correlation between the phenotypic diversity observed in AD subtypes and aggregate polymorphism. Therefore, understanding the molecular mechanisms which …