Biophysics Commons^™

Noncontact Diffuse Reflectance Spectroscopy Of Synovial Fluid Samples For Rapid Identification Of Infections, Erin E. Drewke, Robert L. Brand, Caroline G. Geels, Hanna K. Jensen, Kevin Wong, Jarret D. Sanders, Narasimhan Rajaram

Biomedical Engineering Faculty Publications and Presentations

Severe joint infections, such as septic arthritis, require rapid diagnostic testing of the synovial fluid aspirated from joints level so that a surgical team can be assembled quickly. We present a diffuse reflectance spectroscopy (DRS) system for noncontact determination of infection. Using a light-tight syringe holder and fiber optic probe, diffusely reflected light from 475 to 655 nm was acquired from 18 patient samples through the wall of a syringe in a noncontact and sterile manner. We determined the reflectance ratios at two different wavelengths—R ₄₉₀/R ₆₀₀ and R ₅₈₀/R ₆₀₀ and found statistically significant …

Uncovering The Contribution Of Desmoplakin Isoforms To Desmosome Structure And Function, Krishna Patel

All ETDs from UAB

UNCOVERING THE CONTRIBUTION OF DESMOPLAKIN ISOFORMS TO DESMOSOME STRUCTURE AND FUNCTION KRISHNA PATEL MULTIDISCIPLINARY BIOMEDICAL SCIENCE ABSTRACT Desmosomes are cell-cell junctions that maintain the integrity of tissues that experience significant mechanical stress, such as the skin and heart. Desmosomal plaque proteins are connected to the intermediate filaments by desmoplakin (DP), and genetic variants in DP are associated with several skin and heart pathologies, including erythrokeratodermia and arrhythmogenic cardiomyopathy. DP contains three domains: an N-terminal plakin head, a central rod, and an intermediate filament-binding C-terminal tail. Furthermore, DP has three splice isoforms (DPI, DPIa, and DPII) that differ only in the …

Elucidating The Nanoscale Architecture Of The Desmosome, William F. Dean

All ETDs from UAB

Desmosomes are intercellular anchoring junctions that are crucial for maintaining the mechanical integrity of tissues routinely subjected to large forces, such as epithelia and cardiac muscle. Adhesion in desmosomes is mediated by a specialized class of transmembrane glycoproteins known as the desmosomal cadherins (DCs). Defects in desmosomal adhesion are associated with severe disease of the heart and skin and are frequently linked to mutations in the DCs. It is therefore important to understand the relationship between DC architecture and desmosome function. Accordingly, several groups have attempted to elucidate DC architecture—primarily using electron tomography (ET). However, ET studies of the desmosome …

Macromolecular Crowding Effects On Enzymes That Display Non-Hyperbolic Kinetics, Kelsey A. Aldrich

Electronic Theses and Dissertations

Macromolecules occupy up to 30% of a cell's volume, yet the in vitro study of biological processes is almost exclusively performed in dilute solutions that fail to approximate the crowded interior of a cell. A growing body of literature has identified that macromolecular crowding has significant effects on a number of biochemical processes, including enzymatic activity. However, changes in kinetic parameters with increased macromolecule concentrations have only been determined for enzymes that follow hyperbolic Michaelis-Menten kinetics, despite the fact that over 25% of enzymes deviate from this model. Here, we perform the first characterization of macromolecular crowding effects on …

The Role Of Efflux Pump Inhibitor In Enhancing Antimicrobial Efficiency Of Silver Nanoparticles And Methylene Blue As An Effective Photodynamic Therapy Agent, Yaran Allamyradov

Masters Theses & Specialist Projects

Efflux pumps are critical active transport systems utilized by cells to expel toxic substances, including antibiotics and photosensitizer complexes, thereby contributing to antimicrobial resistance. Efflux pump inhibitors (EPIs), which are compounds that obstruct the transport of molecules through these pumps, play a pivotal role in enhancing the effectiveness of antimicrobial therapies against pathogens. This study investigates the effects of the EPI reserpine on the photodeactivation rate of pathogens when used in conjunction with silver nanoparticles (Ag NPs) and methylene blue (MB), a common photosensitizer.

Our research reveals that the application of reserpine, in combination with Ag NPs and MB, leads …

Structure-Function Relationships In Neurodegenerative And Infectious Diseases: Biophysical Characterization Of Rna Secondary Structures By Computational Techniques, Kendy Guarinoni

Electronic Theses and Dissertations

The research described in this dissertation focuses on the investigation of the structure and dynamics of regions of RNA implicated in two diseases: COVID-19 and amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). Both studies sought to create experimentally corroborated models that were used to characterize the structure and dynamics of the C9orf72 repeat expansion and the s2m region in coronaviruses, respectively and provided the foundation for future work. In our work involving the s2m region of SARS-CoV-2, the virus responsible for COVID-19, we determined that the homology modeling approach commonly used to derive atomistic structures when no coordinates are available yields a …

Characterizing Gsk3Β Interaction And Kinetics Via Isothermal Titration Calorimetry, W A Bhagya De Silva

UNLV Theses, Dissertations, Professional Papers, and Capstones

Glycogen synthase kinase 3β (GSK3β) is a multifunctional serine/threonine kinase involved in several key signaling pathways, including glycogen metabolism, WNT/β-catenin, and Hedgehog signaling. Hyperactivity of GSK3β has been linked to Alzheimer’s disease, bipolar disorder, type II diabetes, and some cancers. Therefore, GSK3β is of interest as a target for therapeutics. Lithium ion (Li+) is a classical inhibitor of GSK3β. Structurally similar beryllium ion (Be2+) is ~1000-fold more potent. Lithium and beryllium have demonstrated pathway-specific and cell type-specific inhibition of GSK3β, prompting an investigation into the inhibitory mechanisms and thermodynamic characteristics of the metal-enzyme interaction.Isothermal titration calorimetry (ITC) is a label-free …

Defining A Dynamic Architecture Of Protein Tyrosine Phosphatases, Colin L. Welsh

MUSC Theses and Dissertations

Protein tyrosine phosphatases (PTPs), a critical class of signaling enzymes, are principally responsible for balancing the actions of kinases through the dephosphorylation of tyrosine residues on substrate proteins. As such, this family is involved in myriad pathways and individual members are able to perform both oncogenic and tumor-suppressing roles. However, while clinical success has been achieved in targeting kinases, PTPs have remained therapeutically challenging. Orthosteric inhibition is limited in PTPs due to their highly conserved fold, leading to off-target effects, and their highly charged active site, requiring highly polar molecules with poor bioavailability. These challenges posit the allosteric inhibition of …

Structural Analysis Of Dj-1 Glyoxalase Activity By Mix-And-Inject Serial Synchrotron Crystallography, Coleman Dolamore

Department of Biochemistry: Dissertations, Theses, and Student Research

Observing enzyme structures while they are catalyzing a reaction has been a major goal of both enzymology and structural biology for decades. With the advent of time-resolved serial X-ray crystallography using X-ray free electron lasers (XFELs) and synchrotron sources, enzyme reactions can be monitored in real time in crystallo. Here, we use two different approaches to study related enzymes involved in methylglyoxal detoxification. For human DJ-1, we used pink beam mix-and-inject serial crystallography (MISC) at the Advanced Photon Source (BioCARS 14-ID) to probe the controversial mechanism of DJ-1’s action on methylglyoxal by using serial Laue diffraction. The high flux …

Investigation Of Self-Assembly Of Hen Egg White Lysozyme Fibrils, Nabila Bushra

USF Tampa Graduate Theses and Dissertations

Amyloid proteins are a large group of proteins that tend to aggregate and form insoluble fibrils with a characteristic cross-β sheet structure. Intriguingly, this process of “amyloid formation” has been simultaneously linked to devastating human diseases called amyloidoses, ranging from Alzheimer’s Disease, cardiac amyloidoses to type II diabetes, as well as functional biological responses such as hormone storage and sperm quality control. Amyloid fibrils have also attracted significant attention for their unique mechanical, chemical, and optical characteristics, establishing them as promising tough biomaterials. The urgent need to find treatments for Alzheimer’s disease, and the demand for safe and renewable biomaterials …

Single-Molecule Orientation Imaging Reveals The Nano-Architecture Of Amyloid Fibrils Undergoing Growth And Decay, Brian Sun, Tianben Ding, Weiyan Zhou, Tara S. Porter, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Amyloid-beta (Aβ42) aggregates are characteristic Alzheimer’s disease signatures, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational “wobble” of Nile blue (NB) molecules transiently binding to Aβ42 fibrils. We correlate fibril architectures measured by SMOLM with their growth and decay over the course of 5 to 20 min visualized by single-molecule localization microscopy (SMLM). We discover that stable Aβ42 fibrils tend to be well-ordered and signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order …

Modeling Hydroxide In Classical Proton Hopping Simulations And Amyloid Beta Membrane Pores, Ankita Dutta

Dissertations, Theses, and Capstone Projects

H3O+ and OH- ions display anomalously large diffusion coefficients, a property that is often attributed to their ability to perform structural diffusion which allow these ions to move through aqueous solutions by sequential proton transfers, also known as ‘Grotthuss hopping’. A rearrangement of the local solvation structure is known to be the prerequisite for proton transfer events via these ions. Studying this phenomenon using classical molecular dynamics simulations that do not allow bond rearrangements poses significant obstacles. Here we use a Monte Carlo augmented classical Molecular Dynamics method called the MOBHY algorithm which allows instantaneous changes in protonation states in …

Assessing The Pre- And Post-Synaptic Effects Of Opioids On Inspiratory Rhythmogenesis, Jingzhi Zhao, Diego Morandi Zerpa

Biology and Medicine Through Mathematics Conference

No abstract provided.

The Interactions Of Centromeric Nucleosomes Elucidated By Atomic Force Microscopy, Shaun Filliaux

Theses & Dissertations

Nucleosomes are the fundamental unit of compaction for DNA in the genome. These positively charged proteins have two main types of nucleosomes: canonical (H3 containing) and centromere (CENP-A containing). The compacting of DNA allows for DNA to fit into the nucleus of cells, but creates a barrier for DNA accessibility for operations such as replication or transcription. Centromeric chromatin is a subset of chromatin structure and governs chromosome segregation. Compared to the bulk chromosome, centromeres are composed of H3 and CENP-A nucleosomes in which H3 histones is replaced by its homolog CENP-A histone. This results in nucleosomes with different structures, …

Intrinsically Disordered Proteins And Their Role In Biomolecular Condensates, Danielle Latham

All Dissertations

Proteins are biomacromolecules responsible for the functions of life. While classically proteins are thought to be well structured in order to perform a specific function, 50% of proteins within Eukaryotic cells contain intrinsically disordered regions (IDRs), regions with no well-defined structure. IDRs are often used for cell signaling, responding to external factors such as temperature changes or the presence of small molecules. To understand how IDRs can function without structure, it is important to understand the dynamics of such systems. Understanding IDR intramolecular and intermolecular interactions will shed light on IDR dynamics. Intramolecular interactions are first explored using fluorescence spectroscopy …

Assessing Nordihydroguaiaretic Acid Properties And Its Potential Therapeutic Effect For Glioblastoma, Jose Arturo Guerrero

Open Access Theses & Dissertations

This study employs a combination of theoretical and experimental analysis to spectroscopically investigate the biomechanistic structure relationship and therapeutic effects of the Nordihydroguaiaretic Acid (NDGA) chemical derived from the Larrea Tridentata plant. These relationships are crucial for understanding NDGA's efficacy in disease prevention, treatment, and potential toxicological effects. While the medicinal and antiviral properties of the NDGA have been studied extensively, there remains a gap in optically identifying and reporting its structural changes. The current research successfully reveals evident trends in NDGA's vibrational signatures, particularly highlighting the absence of the Raman feature at 780 〖cm〗^(-1) as indicative of a fully …

An Investigation Into The Structural Features That Control Factor Xiii Stability And Substrate Specificity., Rameesa Darul Amne Syed Mohammed

Electronic Theses and Dissertations

Factor XIII (FXIII) is a transglutaminase enzyme with multiple physiological roles that is found in plasma and cells of bone marrow origin. The catalytic A subunit (FXIII-A) is made of an N-terminal activation peptide (AP), β-sandwich, catalytic core, and two β-barrel domains. FXIII crosslinks the sidechains of glutamine (Q) and lysine (K) residues across plasmatic and cellular substrates. Because of its involvement in clot stabilization and determining fibrin clot size, FXIII-A is regarded as a target for developing new anticoagulants with minimal bleeding risks. However, the FXIII-A structural features that control its stability and substrate specificity largely remain unknown. Plasma …

Coomassie Brilliant Blue Dye As A Method For Analyzing Fracture Markings In Bone, Abigail Hoffmeister, David Harutunyan, Matthew Aizawa, Everett Baker, Brandon Mendoza, Chase Freeman, Siran Iskanian

Seaver College Research And Scholarly Achievement Symposium

Coomassie Brilliant Blue Dye is a dye commonly used to stain proteins. Because of its ability to adhere to proteins, this research has focused on perfecting a method of dyeing a fractured flat bone in order to most accurately observe and analyze fracture markings within the trabecular layer. Stereoscopic microscopy was the chosen technique of analysis for this research because of its proven effectiveness in glass and ceramic fractography to observe varying depths. In order to most effectively apply stereoscopic microscopy to this research, the following variables were manipulated to maximize color contrast in the trabecular layer in order to …

Development Of An Integrated Workflow For Nucleosome Modeling And Simulations, Ran Sun

Doctoral Dissertations

Nucleosomes are the building blocks of eukaryotic genomes and thus fundamental to to all genetic processes. Any protein or drug that binds DNA must either cooperate or compete with nucleosomes. Given that a nucleosome contains 147 base pairs of DNA, there are approximately 4^147 or 10^88 possible sequences for a single nucleosome. Exhaustive studies are not possible. However, genome wide association studies can identify individual nucleosomes of interest to a specific mechanism, and today's supercomputers enable comparative simulation studies of 10s to 100s of nucleosomes. The goal of this thesis is to develop and present and end-to-end workflow that serves …

Identification Of Regulatory Elements In The Untranslated Regions Of Streptolysin S Associated Gene A Messenger Rna From Group A Streptococcus, Cameron R. Carroll, Sara G. Nibar, Alexis S. Brown, Lauren R. Angello, Gabriela C. Pérez-Alvarado, Brian M. Lee

Journal of the South Carolina Academy of Science

Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a human pathogen associated with a variety of diseases such as strep throat, scarlet fever, toxic shock syndrome, and necrotizing fasciitis. One of the virulence factors released by GAS during an invasive infection is a cytotoxic peptide, streptolysin S (SLS), which inhibits the immune response to necrotizing fasciitis. The streptolysin S associated gene A product, SagA, is modified to produce SLS. Thesag operon includes sagA and the genes required for enzyme-mediated post-translational modifications of SagA and the export of SLS. The sagA gene is contained within the pleiotropic …