Biological and Chemical Physics Commons^™

Towards An Understanding Of Pharmacologically Induced Intracellular Changes In Nicotinic Acetylcholine Receptors: A Fluorescence Microscopy Approach, Ashley M. Loe

Theses and Dissertations--Chemistry

Upregulation of nicotinic acetylcholine receptors (nAChRs) is a well-documented response to chronic nicotine exposure. Nicotinic acetylcholine receptors are pentameric ligand-gated ion channels consisting of alpha (α2-10) and beta (β2-4) subunits. Nicotine, an agonist of nAChRs, alters trafficking and assembly of some subtypes of nAChRs, leading to an increase in expression of high sensitivity receptors on the plasma membrane. These physiological changes in nAChRs are believed to contribute to nicotine addiction, although the mechanism of these processes has not been resolved. Recently, many studies have converged on the idea that nicotine induces upregulation by an intracellular mechanism. In this dissertation, expression …

A Novel Anthropomorphic Flow Phantom For The Quantitative Evaluation Of Prostate Dce-Mri Acquisition Techniques, Silvin Knight, Jacinta Browne, James Meaney, David Smith, Andrew Fagan

Articles

A novel anthropomorphic flow phantom device has been developed which can be used for quantitatively assessing the ability of MRI scanners to accurately measure signal / concentration time-intensity curves (CTCs) associated with dynamic contrast-enhanced (DCE) MRI. Modelling of the complex pharmacokinetics of contrast agents as they perfuse through the tumour capillary network has shown great promise for cancer diagnosis and therapy monitoring. However, clinical adoption has been hindered by methodological problems, resulting in a lack of consensus regarding the most appropriate acquisition and modelling methodology to use and a consequent wide discrepancy in published data. A heretofore overlooked source of …

Cluster Enhanced Nanopore Spectrometry, Amy Chavis

Theses and Dissertations

Nanopore sensing is a label-free method used to characterize water-soluble molecules. Recent work describes how Au₂₅(SG)₁₈ clusters improve the single molecule nanopore spectrometry (SMNS) technique when analyzing polyethylene glycol (PEG). This thesis will further study and optimize the enhancement effect resulting from a cluster’s presence. Additionally, a model describing the interaction between a cluster and PEG is developed to assist in understanding this mechanism of enhancement. This thesis will also discuss expanding the SMNS method to detect peptides, using Au₂₅(SG)₁₈ for enhancement, and adjusting solution conditions to improve the sensitivity of the SMNS system …

Development Of A Low-Cost Arduino-Based Sonde For Coastal Applications, Grant Lockridge, Brian Dzwonkowski, Reid Nelson, Sean P. Powers

University Faculty and Staff Publications

This project addresses the need for an expansion in the monitoring of marine environments by providing a detailed description of a low cost, robust, user friendly sonde, built on Arduino Mega 2560 (Mega) and Arduino Uno (Uno) platforms. The sonde can be made without specialized tools or training and can be easily modified to meet individual application requirements. The platform allows for internal logging of multiple parameters of which conductivity, temperature, and GPS position are demonstrated. Two design configurations for different coastal hydrographic applications are highlighted to show the robust and versatile nature of this sensor platform. The initial sonde …

Electropolymerized Layersas Selective Membranesin First Generation Uric Acid Biosensors, Kaiwen Chen, Grace E. Conway, Gregory A. Hamilton, Matthew L. Trawick, Michael C. Leopold

Chemistry Faculty Publications

Electropolymerized films that can serve as semi-permeable membranes and provide selectivity within a xerogel-based, 1^stgeneration biosensor assembly are explored in this study. Layered biosensing schemes of this nature rely primarily upon an electropolymerized ad-layer to supplement the xerogel and provide effective selectivity for detection of a targeted analyte. While effective electropolymers have been established for glucose sensing, the adaptation of the strategy to other analytes of clinical importance hinges upon the systematic evaluation of electropolymerized films to identify a selective film. Uric acid is a key species in the diagnosis/monitoring of a number of diseases and conditions. An …

Hydrogen Bond-Mediated Structural Order In Hydroxylated Bis-Mpa Dendritic Polymers: Experimental And Molecular Dynamics Simulation Study, Maliha N. Syed

Dissertations

Dendritic architectures are echoed throughout nature. While the significance of these pervasive patterns is not entirely clear, connections between their structures and physical properties are fascinating to contemplate. Particular interest has been paid to a family of synthetically manufactured and commercially available dendritic polymers based on 2,2-bis(hydroxymethyl) propionic acid (bis-MPA) as a monomer. Composed of two hydroxyls and a carboxyl group, bis-MPA based structures hydrogen bond (H-bond) profusely. Given the high concentration and unique spatial orientation of end-groups, as well as the multitude of carbonyl, ester, and ether interior H-bond acceptors, a set of distinct H-bond organizations may be observed …

The Relationship Of Childhood Stress To Adult Health And Mortality Among Individuals From Two U.S. Documented Skeletal Collections, Late 19Th To Early 20Th Centuries, Rhonda Coolidge

USF Tampa Graduate Theses and Dissertations

Although the association between social inequality and poor adult health is well established, the mechanisms by which inequality is translated into poor adult health are less clear. Increasingly, evidence suggests that many adult health problems and health disparities have their origins in early life; the developmental origins of health and disease (DOHaD) hypothesis provides an explanatory mechanism linking adverse early life conditions with permanent structural or functional changes that increase the risk for disease. This hypothesis is consistent with bioarchaeological research noting reduced lifespan among individuals exhibiting signs of childhood stress.

The principal aim of this dissertation is to contribute …

Investigating The Role Of Shape On The Biological Impact Of Gold Nanoparticles In Vitro, Furong Tian, Hugh Byrne, Joao Conde, Tobias Stoeger, Martin Clift,, Alan Casey, Pablo Del Pino, Beatriz Pelaz, Barbara Rothen-Rutishauser,, Giovani Estrada, Jesús De La Fuente

Articles

Aim: To investigate the influence of gold nanoparticle (GNP) geometry on the biochemical response of Calu-3 epithelial cells.

Materials and Methods: Spherical, triangular and hexagonal GNPs were used. The GNP-cell interaction was assessed via atomic absorption spectroscopy (AAS) and transmission electron microscopy (TEM). The biochemical impact of GNPs was determined over 72hrs at [0.0001-1mg/mL].

Results: At 1mg/mL, hexagonal GNPs reduced Calu-3 viability below 60%, showed increased reactive oxygen species production and higher expression of pro-apoptotic markers. A cell mass burden of 1:2:12 as well as number of GNPs per cell (2:1:3) was observed for spherical:triangular:hexagonal GNPs.

Conclusion:

These findings do …

Determination Of Nanoparticle Localisation Within Subcellular Organelles In Vitro Using Raman Spectroscopy, Esen Efeoglu, Mark Keating, Jennifer Mcintyre, Alan Casey, Hugh Byrne

Articles

Ease of sample preparation, narrow spectral bandwidth and minimal influence from water are features of Raman spectroscopy which make it a powerful, label-free way to study a wide range of biological structures and phenomena. In this context, given the concerns over their toxicology arising from their increased production and use, evaluation of nanoparticle uptake and localisation in biological systems and determination of the mechanisms of subcellular interaction and trafficking can provide long-term solutions for nanotoxicology, and potential strategies for nanomedicine. In this study, Raman spectroscopy is explored to monitor the sequential trafficking of nanoparticles through subcellular organelles in-vitro and to …

A Generalized Force-Modified Potential Energy Surface For Mechanochemical Simulations, Gopinath Subramanian, Nithin Mathew, Jeff Leiding

Faculty Publications

We describe the modifications that a spatially varying external load produces on a Born-Oppenheimer potential energy surface (PES) by calculating static quantities of interest. The effects of the external loads are exemplified using electronic structure calculations (at the HF/6-31G- level) of two different molecules: ethane and hexahydro-1,3,5-trinitro-s-triazine (RDX). The calculated transition states and Hessian matrices of stationary points show that spatially varying external loads shift the stationary points and modify the curvature of the PES, thereby affecting the harmonic transition rates by altering both the energy barrier as well as the prefactor. The harmonic spectra of both molecules are blueshifted …

Ionic Driven Embedment Of Hyaluronic Acid Coated Liposomes In Polyelectrolyte Multilayer Films For Local Therapeutic Delivery, Stephen L. Hayward, David M. Francis, Matthew J. Sis, Srivatsan Kidambi

Papers in Biomolecular Engineering

The ability to control the spatial distribution and temporal release of a therapeutic remains a central challenge for biomedical research. Here, we report the development and optimization of a novel substrate mediated therapeutic delivery system comprising of hyaluronic acid covalently functionalized liposomes (HALNPs) embedded into polyelectrolyte multilayer (PEM) platform via ionic stabilization. The PEM platform was constructed from sequential deposition of Poly-LLysine (PLL) and Poly(Sodium styrene sulfonate) (SPS) “(PLL/SPS)_4.5” followed by adsorption of anionic HALNPs. An adsorption affinity assay and saturation curve illustrated the preferential HALNP deposition density for precise therapeutic loading. (PLL/SPS)_2.5 capping layer on top …

Vibrational Spectroscopic Studies To Elucidate The Structure Of Water At Biological Interfaces, Bahar Bahrani, Luke O'Neill, Hugh Byrne

Articles

In biological systems, water takes up to 80% of the volume inside a cell. This water solubilizes the biological macromolecules such as the DNA, proteins and lipids. Recent advancements have shown that the water at the interface of a lipid membrane is structured, as five layers of structured water have been found at this solvent cage. Steady state Raman spectroscopy of water in lipids was performed in an attempt to elucidate the structure of water at the biological interface. Deuterium oxide (heavy water) was employed to hydrate lipid biomolecules. The heavier deuterium atom shifts the molecular vibrations and renders them …

Combination Treatment With Conjugated Linoleic Acid And Nitrite Protects Against Myocaridal Infarction., Natia Qipshidze Kelm

Electronic Theses and Dissertations

According to the CDC, the most common type of heart disease is coronary artery disease, which frequently leads to myocardial infarction (MI). Therapeutic approaches to lessen the resulting cardiovascular injury associated with MI are limited. Recently, the management paradigm for cardiac injury has entered the molecular era and microRNAs (miRNAs) have been shown to act as negative regulators of gene expression by inhibiting mRNA translation and/or stimulating mRNA degradation. A single miRNA can modulate physiological or disease phenotypes by regulating whole functional systems. Importantly, miRNAs can regulate cardiac function, thereby modulating heart muscle contraction, heart growth and morphogenesis. MicroRNA-499 (miRNA-499) …

A Lego® Brewster Angle Microscope For Quantitative Monolayer Film Analysis, Nicholas Benz

Physics

In order to study single-molecule thick films and their phase behavior we built a Brewster Angle Microscope (BAM). BAM’s are inherently expensive due to their accuracy and precision. We built a fully functional BAM using Lego® Mindstorm® kits for the fraction of the price of a commercial BAM. And by utilizing the 10µm patented Lego® tolerance, comparable accuracy was attained. The BAM was mounted to a Langmuir-trough and will be used for laboratory experiments for optics and physical chemistry along with research on lung surfactant and on liquid crystals.

Measuring Charge Carrier Mobility In Graphene, Christina A. Harmon

Senior Theses

This research reports measurements of electron mobility in Graphene Field Effect Transistors (GFET), gated with liquid. Mobility is a quantity describing how easily charge carriers move through a material. GFET biosensors have the greatest sensitivity when the mobility is high; therefore, increasing mobility should improve sensitivity of these and similar devices. An optimal method was established for preparing samples and taking measurements of a liquid-gate device. Sheet conductivity was measured using van der Pauw geometry and carrier density was determined from measurements of the liquid-gate capacitance. It is shown that mobility improves after the graphene surface is cleaned by an …

Characterization Of Low Density Intracranial Lesions Using Dual-Energy Computed To Mography, Jessica L. Nute

Dissertations and Theses (Open Access)

Calcific and hemorrhagic foci of susceptibility are frequently encountered on routine brain MR studies. Both etiologies cause variations in local magnetic field strength, leading to dark regions on the MR images that cannot be classified. Single-energy CT (SECT) can be used to identify lesions with attenuation over 100 HU as calcific, however lesions with lower attenuation cannot be reliably identified. While calcific lesions are unlikely to cause harm, hemorrhagic lesions carry a risk of subsequent intracranial bleeding; as such, identification of hemorrhage is vital in preventing the inappropriate use of anticoagulant medications in patients with hemorrhagic lesions.

Given there currently …

Development, Validation, And Application Of Analytical Methods For Characterizing Adsorbed Protein Orientation, Conformation, And Bioactivity, Aby Thyparambil

All Dissertations

The structure and bioactivity of adsorbed proteins are tightly interrelated and play a key role in their interaction with the surrounding environment. These factors are of critical importance in many biotechnological applications. However, because the bioactive state of an adsorbed protein is a function of the orientation, conformation, and accessibility of its bioactive site(s), the isolated determination of just one or two of these factors will typically not be sufficient to understand the structure-function relationships of the adsorbed layer. Rather a combination of methods is needed to address each of these factors in a synergistic manner to provide a complementary …

Quantitative Analysis Of Single-Molecule Force Spectroscopy On Folded Chromatin Fibers, He Meng, Kurt Andresen, John Van Noort

Physics and Astronomy Faculty Publications

Single-molecule techniques allow for picoNewton manipulation and nanometer accuracy measurements of single chromatin fibers. However, the complexity of the data, the heterogeneity of the composition of individual fibers and the relatively large fluctuations in extension of the fibers complicate a structural interpretation of such force-extension curves. Here we introduce a statistical mechanics model that quantitatively describes the extension of individual fibers in response to force on a per nucleosome basis. Four nucleosome conformations can be distinguished when pulling a chromatin fiber apart. A novel, transient conformation is introduced that coexists with single wrapped nucleosomes between 3 and 7 pN. Comparison …

Biophysical Interaction Between Nanoparticles And Biomolecules, Slaven Radic

All Dissertations

In the last two decades nanotechnology market has undergone remarkable growth. Breakthroughs in nanomaterial synthesis increased diverse nanomaterials production and subsequently their application. Owing to its large surface to volume ratio and remarkable physical properties not seen in the bulk materials, nanoparticles are finding emerging use in industry and medicine. Hence, it is expectable that at some point these nanomaterials will end up released into the environment and interact with bio systems. The purpose of this dissertation is to elicit implications of nanomaterial transformation once it gets inside biological milieu.

Spectropathology For The Next Generation: Quo Vadis?, Hugh Byrne, Malgorzata Baranska, Gerwin J. Pupples, Nick Stone, Bayden Wood, Kathleen M. Gough, Peter Lasch, Phil Heraud, Josep Sulé-Suso, Ganesh Sockalingum

Articles

Although the potential of vibrational spectroscopy for biomedical applications has been well demonstrated, translation into clinical practice has been relatively slow. This Editorial assesses the challenges facing the field and the potential way forward. While many technological challenges have been addressed to date, considerable effort is still required to gain acceptance of the techniques among the medical community, standardise protocols, extend to a clinically relevant scale, and ultimately assess the health economics underlying clinical deployment. National and international research networks can contribute much to technology development and standardisation. Ultimately, large-scale funding is required to engage in clinical trials and instrument …