Biophysics Commons^™

Stability Of Norwalk Virus Capsid Protein Interfaces Evaluated By In Silico Nanoindentation, Prakhar Bansal

University Scholar Projects

Studying the mechanical properties of viral capsids can give several insights into not only the lifecycle of the virus, but also into potential drug targets to thwart the progression of viral infection. Nanoindentation using an atomic force microscope is a useful technique for determining structural properties of small molecules and particles, and is commonly used to study viral capsids. This technique utilizes the probe of the microscope to push down on the capsid and record the forces along the indentation path. We ran this experiment in silico where we simulated the nanoindentation of Norwalk virus capsids using molecular dynamics. Running …

Influence Of Cholesterol On Single Arginine-Containing Transmembrane Helical Peptides, Jordana K. Thibado

Chemistry & Biochemistry Undergraduate Honors Theses

An essential component of animal cells, cholesterol exerts significant influence on the physical properties of the cell membrane and in turn, its constituents. One such category of constituents, the membrane proteins, are responsible for diverse and essential biological functions and often contain polar amino acids. Although sparse within the hydrophobic interior of lipid-bilayer membranes, polar amino acid residues are highly conserved and may play pivotal roles in determining specific structural and functional properties of key proteins. To gain greater understanding of the lipid membrane environment, and more broadly, cellular function, a model peptide framework termed “GWALP23” (acetyl-GGALWLALALAL¹²AL^{14 …}

A 'Tissue Model' To Study The Barrier Effects Of Living Tissues On The Reactive Species Generated By Surface Air Discharge, Tongtong He, Dingxin Liu, Han Xu, Zhichao Liu, Dehui Xu, Dong Li, Qiosong Li, Mingzhe Rong, Michael G. Kong

Bioelectrics Publications

Gelatin gels are used as surrogates of human tissues to study their barrier effects on incoming reactive oxygen and nitrogen species (RONS) generated by surface air discharge. The penetration depth of nitrite into gelatin gel is measured in real time during plasma treatment, and the permeabilities of nitrite, nitrate, O₃ and H₂O₂ through gelatin gel films are quantified by measuring their concentrations in the water underneath such films after plasma treatment. It is found that the penetration speed of nitrite increases linearly with the mass fraction of water in the gelatin gels, and the permeabilities of …

Affinity Cryo-Electron Microscopy: Methods Development And Applications, Guimei Yu

Open Access Dissertations

Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies. Although less concentrated and smaller amounts of samples are required for single particle cryo-EM compared to X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques holds great promise to tackle these challenging samples by combining the sample purification and freezing on TEM grids steps in cryo-EM grid preparation into a single step, revolutionize the grid preparation of cryo-EM, and extend single particle cryo-EM to a routine structural biology tool to characterize structures …

Thermal Analysis Of Borosilicate Glass For Its Biological Applications, Gregory Humble

Symposium of Student Scholars

Borosilicate glass doped with varying wt% of cerium oxide is investigated for biological applications. Thermal studies of each formulation were conducted using an SDT Q600 differential scanning calorimeter. 30mg samples of 350 - 425 μm particle size of each type of glass were heated to 1200°C in order to obtain the glass transition, crystallization, and melting temperatures. Samples were then heated to 900°C at several heating rates, ranging from 2°C/min to 100°C/min, then compared against each other as well as against an undoped borosilicate glass.

Synthesis And Characterization Of Nanoparticle-Coupled Proteins In Human Serum Albumin, Kyle M. Mahoney

Honors College Theses

Recently, cancer has become an ever-growing issue and has led to many researchers attempt to unravel the mystery of the disease. This research has led to a promising field of treatment: nanotechnology-coupled pharmaceuticals. Nanoparticles act as a whole unit when in conjugation with other molecules and add to the carrier molecule, most often proteins, benefits the nanoparticles themselves possess. One such carrier protein that can be conjugated with nanoparticles is Human Serum Albumin (HSA). Albumin is of interest in cancer research for two reasons: it is native to the human vasculature so it does not elicit immunological reactions, and it …

Preliminary Results On Organization On The Court, Physical And Technical Performance Of Brazilian Professional Futsal Players: Comparison Between Friendly Pre-Season And Official Match, Luiz Henrique Palucci Vieira, Sera N. Doğramaci, Ricardo Augusto Barbieri, Fabio Milioni, Felipe Arruda Moura, Vitor Luiz De Andrade, Guilherme Manna Cesar, Paulo Roberto Pereira Santiago

Athletic Performance Research

The main aim of this study was to verify possible differences between a friendly pre-season match (FM) and an official in-season match (OM) regarding physical, technical, and organizational performances of a professional Brazilian futsal team. Ten professional futsal athletes participated in this study. The matches were monitored with video cameras (30 Hz) and athlete trajectories obtained with automatic tracking. The values obtained for distance covered per minute, percentage of distance covered at moderate intensity, team coverage area, spread, passes, possessions, ball touches and successful passes per minute were greater for the OM than FM. On the contrary, percentage of distance …

Biophysical Studies Of The Allosteric Regulatory Mechanism Of Syk Tandem Sh2 Domains Interacting With Immunoreceptor Tyrosine-Based Activation Motifs, Chao Feng

Open Access Dissertations

The non-receptor spleen tyrosine kinase (Syk) is an important player in signal transduction from immunoreceptors to various downstream targets. It is widely expressed in both haematopoietic and epithelial cells. Syk disorder is closely related with many inflammatory and autoimmune diseases, as well as cancers.

Syk associates with immunoreceptors through its tandem SH2 domains (tSH2), which contain two SH2 domains connected by interdomain A. The association of Syk with immunoreceptors is regulated by Y130 phosphorylation in interdomain A. The unphosphorylated tSH2 can bind with the doubly phosphorylated immunoreceptor tyrosine-based activation motif (dp-ITAM) of the cytoplasmic domains of immunoreceptors with very high …

Learning The Abc's Of Ribose Transport Using Biophysical Methods, Satchal K. Erramilli

Open Access Dissertations

ATP-binding cassette transporters comprise a large superfamily of proteins that are involved in a variety of biological phenomenon, from bacterial metabolism to cellular homeostasis, antigen-presentation, and drug resistance. These proteins are implicated in a variety of clinically relevant phenomenon, including the human diseases cystic fibrosis, macular degeneration, and cancer. Understanding their structure-function can guide therapeutics and contribute to our overall understanding of these biological phenomena.

This study focuses on understanding the motor protein of the bacterial ribose ABC transporter in the context of transport. This complex is required for the uptake of the nucleotide precursor, ribose. Using biophysical methods, we …

Characterization Of Cu-Rich Aggregates In Neurogenic Niches Of The Rodent Brain By X-Ray Fluorescence Microscopy, Brendan T. Sullivan

Open Access Dissertations

Copper is an essential element in the brain playing several critical roles ranging from neurotransmitter synthesis to ATP production. As Cu is typically present in micromolar concentrations and has a spatially capricious distribution in the brain, determining concentrations has historically been challenging. X-ray fluorescence microscopy (XRF) offers excellent spatial resolution (down to 30~nm) and detection limits (sub parts per million), making it an excellent tool for analyzing metal distributions in the brain. Using XRF, it is demonstrated that Cu-rich aggregates with concentrations in the hundreds of millimolar are present in the subventricular zone of rats and mice. As the subventricular …

Biophysical Investigation Of Amyloid Formation And Their Prion-Like Self-Replication, Mentor Mulaj

USF Tampa Graduate Theses and Dissertations

Growth and deposition of amyloid fibrils, polymers of proteins with a cross beta-sheet structure, are associated with a significant number of human pathologies including Alzheimer’s disease, Parkinson’s disease, prion diseases, type II diabetes, and senile systematic or dialysis-related amyloidoses. The broader objective of my research is to identify the basic mechanisms regulating nucleation and growth of amyloid fibrils. There is increasing evidence that amyloid formation may proceed along at least two distinct assembly pathways for the formation of rigid fibrils. One pathway involves the nucleated polymerization of the characteristic rigid fibrils from partially denatured monomers and the other proceeds via …

The Interaction Between Eukaryotic Translation Initiation Factor Eif4g And 3’ Cap Independent Translation Element Of Barley Yellow Dwarf Virus Is Affected By Multiple Initiation Factors, Pei Zhao

Dissertations, Theses, and Capstone Projects

Barley Yellow Dwarf Virus (BYDV) lacks a 5’ (7-methyl guanosine) cap as well as a 3’poly A tail. Like many plant viruses, BYDV contains a cap independent translation element (CITE) in the 3’ untranslated region of the viral mRNA. BTE (Barley Yellow Dwarf Virus like cap-independent translation element) is one of the well characterized CITEs. BTE mediated translation primarily depends on eukaryotic initiation factor eIF4G. BTE binds to eIF4G; however, the details of BTE initiated translation are still unclear. Three eIF4G deletion mutants with different domain organization were used to investigate BTE interaction with eIF4G: eIF4G601-1196 is the eIF4G fragment …

Frontal Plane Comparison Between Drop Jump And Vertical Jump: Implications For The Assessment Of Acl Risk Of Injury, Guilherme Manna Cesar, Curtis L. Tomasevicz, Judith M. Burnfield

Athletic Performance Research

The potential to use the vertical jump (VJ) to assess both athletic performance and risk of anterior cruciate ligament (ACL) injury could have widespread clinical implications since VJ is broadly used in high school, university, and professional sport settings. Although drop jump (DJ) and VJ observationally exhibit similar lower extremity mechanics, the extent to which VJ can also be used as screening tool for ACL injury risk has not been assessed. This study evaluated whether individuals exhibit similar knee joint frontal plane kinematic and kinetic patterns when performing VJs compared with DJs. Twenty-eight female collegiate athletes performed DJs and VJs. …

Weight Control Practices Of Division I National Collegiate Athletic Association Athletes, Patrick B. Wilson, Leilani Madrigal, Judith M. Burnfield

Athletic Performance Research

Objectives: Altering body weight can have substantial effects on an athlete’s performance and well-being. Limited information is available describing the weight control practices of Division I National Collegiate Athletic Association (NCAA) athletes.

Methods: Weight control practices data from 188 (138 male and 50 female; 18-23 y) Division I NCAA athletes were analyzed as a part of this cross-sectional, retrospective study. Participants completed questionnaires on weight control practices and weight control nutrition knowledge at the end of their season and were classified into weight-sensitive and less weight-sensitive sports.

Results: A higher proportion of females attempted to lose weight than males among …

Heart And Sole: The Functional Role Of Fast-Skeletal Myosin Binding Protein-C In Cardiac And Skeletal Muscle, Brian Leei Lin

Dissertations

The goal of my dissertation was to compare and contrast the function of all three major isoforms of Myosin Binding Protein-C (MyBP-C): slow-skeletal, fast-skeletal, and cardiac (ssMyBP-C, fsMyBP-C, and cMyBP-C, respectively), with a focus on the least characterized isoform, fsMyBP-C. Using a variety of ex vivo, in vitro, and in silico methods, my research demonstrated that the N-terminal region of all MyBP-C isoforms bind to actin and shift tropomyosin, thus activating the thin filament during contraction. Furthermore, each isoform differentially activated the thin filament over isoform-specific ranges of Ca2+: slow-skeletal activates at low Ca2+, fast-skeletal activates at higher Ca2+, and …

A Mechanistic Study Of An Ipsc Model For Leigh’S Disease Caused By Mtdna Mutataion (8993 T>G), John P. Galdun

Theses and Dissertations

Mitochondrial diseases encompass a broad range of devastating disorders that typically affect tissues with high-energy requirements. These disorders have been difficult to diagnose and research because of the complexity of mitochondrial genetics, and the large variability seen among patient populations. We have devised and carried out a mechanistic study to generate a cell based model for Leigh’s disease caused by mitochondrial DNA mutation 8993 T>G. Leigh’s disease is a multi-organ system disorder that depends heavily on the mutation burden seen within various tissues. Using new reprogramming and sequencing technologies, we were able to show that Leigh’s disease patient fibroblasts …

Functional Effects Of Calcium Regulation Of Thin Filaments At Single Particle Resolution, Christopher Solis-Ocampo

Electronic Theses and Dissertations

Heart disease is the leading cause of death in the United States. Understanding heart function at the molecular level is critical for developing of more effective treatments. In the cardiac muscle, the thin filament is composed by troponin (Tn), tropomyosin (Tm), and F-actin. It provides Ca2+-dependent regulation of contraction by modulating myosin attachment and force generation in a cooperative scheme. However, this mechanism remains unclear. To understand thin filament activation, we studied the binding and functional properties of Tn and Tm to F-actin at single particle resolution by employing fluorescence image colocalization, in vitro motility assays, and Förster resonance energy …

A Dielectric Rod Antenna For Picosecond Pulse Stimulation Of Neurological Tissue, Ross A. Petrella, Karl H. Schoenbach, Shu Xiao

Bioelectrics Publications

A dielectrically loaded wideband rod antenna has been studied as a pulse delivery system to subcutaneous tissues. Simulation results applying 100-ps electrical pulse show that it allows us to generate a critical electric field for biological effects, such as brain stimulation, in the range of several centimeters. In order to reach the critical electric field for biological effects, which is similar to 20 kV/cm, at a depth of 2 cm, the input voltage needs to be 175 kV. The electric field spot size in the brain at this position is similar to 1 cm(2). Experimental studies in free space with …

Bayesian Signal Detection And Source Separation In Simulated Brain Computer Interface Systems, Muhammad Asim Mubeen

Legacy Theses & Dissertations (2009 - 2024)

The problems of signal detection and source separation are important in many fields of science and engineering. In many cases, a target signal needs to be detected in real time and is contaminated by noise. Sometimes the level of noise is on the order of the signal itself. The real time detection of a target signal is of key importance in problems such as the brain computer interface systems. In brain computer interface systems, the neural activity (electric signals) of the brain is detected using sensors (electrodes) on the surface of the brain or the scalp. This signal is contaminated …

Effects Of High Voltage Nanosecond Electric Pulses On Eukaryotic Cells (In Vitro): A Systematic Review, Tina Batista Napotink, Matej Reberšek, P. Thomas Vernier, Babara Mali, Damijan Miklavčič

Bioelectrics Publications

For this systematic review, 203 published reports on effects of electroporation using nanosecond high-voltage electric pulses (nsEP) on eukaryotic cells (human, animal, plant) in vitro were analyzed. A field synopsis summarizes current published data in the field with respect to publication year, cell types, exposure configuration, and pulse duration. Published data were analyzed for effects observed in eight main target areas (plasma membrane, intracellular, apoptosis, calcium level and distribution, survival, nucleus, mitochondria, stress) and an additional 107 detailed outcomes. We statistically analyzed effects of nsEP with respect to three pulse duration groups: A: 1–10 ns, B: 11–100 ns and C: …