Biophysics Commons^™

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, …

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 …

Source Data For "Flowering Of Developable 2d Crystal Shapes In Closed, Fluid Membranes", Hao Wan, Geunwoong Jeon, Weiyue Xin, Gregory M. Grason, Maria M. Santore

Data and Datasets

Source data for "Flowering of Developable 2D Crystal Shapes in Closed, Fluid Membranes".

Mechanistic Analysis Of Four-Way Dna Junctions And Cytokine-Binding Aptamers For Therapeutic Interventions, Roaa S. Mahmoud

Theses and Dissertations

DNA is inherently dynamic and topologically diverse and can fold into many different structures. Besides the canonical Watson-Crick structure, other higher-order structures such as G-quadruplexes (G4), i-motifs (iM), and four-way DNA junctions are possible. Although these high-order DNA structures are known to form transiently, they are important due to the crucial roles they play in many cellular processes including DNA replication, recombination, and repair. Among these DNA structures, 4-way junctions (also known as Holliday junctions, HJ) which are formed during the repair of double-strand DNA breaks (DSBs) and interact with proteins have garnered significant attention due to their central role …

Quantitative Raman Analysis Of Human Blood Serum Of Glaucoma Patients Supplemented With Macular Pigment Carotenoids., Joy Udensi, Ekaterina Loskutova, James Loughman, Hugh J. Byrne

Datasets

Carotenoids have been widely studied for their high dietary, antioxidant, and vision protection roles in the human body. Blood contains all major dietary carotenoids and hence presents as a suitable and efficient substrate for the estimation of dietary carotenoids in vivo. Following the 18-month supplementation of open angle glaucoma patients with macula pigment carotenoids (Lutein, Zeaxanthin and Meso-Zeaxanthin) in the European Nutrition in Glaucoma Management (ENIGMA) trial, Raman spectroscopic analysis of the pre-supplementation baseline and 18-month supplemented blood serum carotenoids from participants was carried out, to investigate the systemic impact of supplementation in the blood and explore a more direct …

Detecting Interactions Between Mps3 In Linc Complex And Ndj1 In Nuclear Pore Complex In Mechanically Stressed Yeast, Dean Boecher, Rebecca Adams

Belmont University Research Symposium (BURS)

The mechanisms of how mechanical stress is translated into cellular action and structural reorganization within the nuclear envelope are largely unexplored. The Linker of Nucleoskeleton and Cytoskeleton (LINC) complex is a transmembrane protein complex that connects the actin cytoskeleton to the lamin nucleoskeleton, enabling mechanical forces to be translated between the cytoplasm and the nucleus. A better understanding of the translation of physical forces into cell responses can be gained through confirming the existence of interactions between LINC complex proteins and nuclear pore complexes (NPCs), which control the exchange of biochemical signals and macromolecules in and out of the nucleus …

Synthesis And Biophysical Analysis Of Modified Cell-Penetrating Peptides, Joel Mitchell

Theses and Dissertations (Comprehensive)

Cell-penetrating peptides (CPPs) are a family of peptides that have the ability to penetrate biological membranes. They were discovered in the late 1980s and have been the topic of many studies. Much of the interest in CPPs has been due to their ability to translocate biological membranes, and the possibility that they could offer a novel drug delivery method by conjugation to biologically active molecules. Linear CPPs can be modified to form cyclic structures. This change in structure has been observed to enhance the stability and penetrative ability of the CPPs which have been studied. The current thesis focuses on …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Biomolecular Function From Structural Snapshots, Roshanak Etemadpour

Theses and Dissertations

Biological molecules can assume a continuous range of conformations during function. Near equilibrium, the Boltzmann relation connects a particular conformation's free energy to the conformation's occupation probability, thus giving rise to one or more energy landscapes. Biomolecular function proceeds along minimum-energy pathways on such landscapes. Consequently, a comprehensive understanding of biomolecular function often involves the determination of the free-energy landscapes and the identification of functionally relevant minimum-energy conformational paths on these landscapes. Specific techniques are necessary to determine continuous conformational spectra and identify functionally relevant conformational trajectories from a collection of raw single-particle snapshots from, e.g. cryogenic electron microscopy (cryo-EM) …

Understanding The Kinetics Of Laser-Induced Nanowelding Of Nanoparticles And The Motility Of Bacteria When Faced With Obstacles, Ariel Rogers

Graduate Theses and Dissertations

This dissertation has two focus areas: nanoparticle nanowelding and bacteria motility in the presence of micrometer sized structures. There are two main projects for the nanoparticle nanowelding studies: “Real-time imaging of laser-induced nanowelding in solution” and “Two-color laser-induced nanostructure shape modulation.” For the real-time imaging project, I used a fluorescence microscope, a 405 nm laser, and various python packages to quantify the average size of nanowelded nanostructures as a function of time and found that the average nanostructure growth over time fit the parameters of A¯(t) ∝ c0(1−e−t/τ), where c0 represents the initial concentration of nanoparticles in the solution and …

Caulobacter Clpxp Adaptor Popa’S Domain Interactions In The Adaptor Hierarchy Of Ctra Degradation, Thomas P. Scudder

Masters Theses

The degradation and recycling of protein is a process essential for the maintenance and regulation of cellular function. More specifically, in Caulobacter crescentus, the ClpXP protease is responsible for driving progression through the cell cycle and protein quality control. This protease utilizes three known adaptors to selectively degrade proteins that initiate different stages of development. This thesis will elaborate on the specific binding interface on one of these adaptors, PopA, with another, RcdA, and focus in on specific residues on PopA and investigate their roles in adaptor binding and delivery of CtrA, the master regulator of Caulobacter. Finally, I …

Combining Simulation And The Mspa Nanopore To Study P53 Dynamics And Interactions, Samantha A. Schultz

Masters Theses

p53 is a transcription factor and an important tumor suppressor protein that becomes activated due to DNA damage. Because of its role as a tumor suppressor, mutations in the gene that encodes it are found in over 50% of human cancers. The N-terminal transactivation domain (NTAD) of p53 is intrinsically disordered and modulates the function and interactions of p53 in the cell. Its disordered structure allows it to be controlled closely by post-translation modifications that regulate p53’s ability to bind DNA and interact with regulatory binding partners. p53 is an attractive target for developing cancer therapeutics, but its intrinsically disordered …

Atomistic Simulations Of Intrinsically Disordered Protein Folding And Dynamics, Xiping Gong

Doctoral Dissertations

Intrinsically disordered proteins (IDPs) are crucial in biology and human diseases, necessitating a comprehensive understanding of their structure, dynamics, and interactions. Atomistic simulations have emerged as a key tool for unraveling the molecular intricacies and establishing mechanistic insights into how these proteins facilitate diverse biological functions. However, achieving accurate simulations requires both an appropriate protein force field capable of describing the energy landscape of functionally relevant IDP conformations and sufficient conformational sampling to capture the free energy landscape of IDP dynamics. These factors are fundamental in comprehending potential IDP structures, dynamics, and interactions. I first conducted explicit solvent simulations to …

Evaluating The Response Of Glycine Soja Accessions To Fungal Pathogen Macrophomina Phaseolina During Seedling Growth, Shirley Jacquet, Layla Rashad, Sonia Viera, Francisco Reta, Juan Reta

Biological Science Student Working Papers

Charcoal rot caused by the fungal pathogen Macrophomina phaseolina (Tassi) Goid is one of various devastating soybean (Glycine max (L.) Merr.) diseases, which can severely reduce crop yield. The investigation into the genetic potential for charcoal rot resistance of wild soybean (Glycine soja) accessions will enrich our understanding of the impact of soybean domestication on disease resistance; moreover, the identified charcoal rot-resistant lines can be used to improve soybean resistance to charcoal rot. The objective of this study was to evaluate the resistance of wild soybean accessions to M. phaseolina at the seedling stage and thereby select the disease-resistant lines. …

Langevin Dynamic Models For Smfret Dynamic Shift, David Frost, Keisha Cook Dr, Hugo Sanabria Dr

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Substrate Specificity In Abc Transporters Using The E. Coli Methionine Import System, John H. Guardado

Featured Student Work

ATP-binding cassette (ABC) transporters use the energy of ATP to move substrates across membranes against a concentration gradient. The role of ABC transporters is crucial in several essential cellular functions and mutations in ABC transporters in humans have been linked to several conditions, including cystic fibrosis, liver disease, and diabetes. Despite their central roles in homeostasis, the mechanism of ABC transporters remains poorly understood. Our research is focused on studying an ABC importer in E. coli, as a model system, to examine the mechanism of substrate specificity and transport. The bacterial methionine import system consists of a membrane-embedded transporter, MetNI, …

Using Hyperosmotic Shock To Study The Cell Wall Of Myxococcus Xanthus, Ian Sabol

Harrisburg University Research Symposium: Highlighting Research, Innovation, & Creativity

No abstract provided.

Effects Of Growth Rate On Peptidoglycan Crosslink Density Of E. Coli Using Fluorescent Labeling, Morgan Olszewski

Harrisburg University Research Symposium: Highlighting Research, Innovation, & Creativity

Peptidoglycan (PG) is a polymer composed of polysaccharides and crosslinked peptide chains found in bacterial cell walls. It helps to protect the cell from environmental stress and maintain cell morphology throughout its life cycle and further generations. The PG is made up of two sugars, N-acetyl muramic acid (NAM) and N-acetyl glucosamine (NAG). NAM and NAG are connected by glycosidic linkages to form repeated chains. The chains are formed in layers, which are interconnected via a polypeptide stem linked by a peptide bridge. During cell growth, continuous turnover of existing PG occurs by severing existing crosslinks, inserting new PG into …

Biomechanical Adaptations While Performing Bilateral Drop Landings With A Unilateral Ankle Tape Application, Eric Daniel Jenkins

Rehabilitation Sciences Theses & Dissertations

Ankle sprains are the most common injury in sport and exercise performance, which makes the utilization of ankle taping a common procedure to both prevent potential sprain, as well as protect against reinjury. However, unilateral ankle taping may have unintended consequences on the mechanics of the ankle and other joints of both legs. The aim of this dissertation was to determine the effects of ankle taping on lower body kinetics and kinematics, stiffness, and coordination during a bilateral landing task.

Twelve female participants completed a total of 90 drop landings across two visits, randomized from landing platforms of 30, 45, …

Modeling Nonsegmented Negative-Strand Rna Virus (Nnsv) Transcription With Ejective Polymerase Collisions And Biased Diffusion, Felipe-Andres Piedra

Research Symposium

Background: The textbook model of NNSV transcription predicts a gene expression gradient. However, multiple studies show non-gradient gene expression patterns or data inconsistent with a simple gradient. Regarding the latter, several studies show a dramatic decrease in gene expression over the last two genes of the respiratory syncytial virus (RSV) genome (a highly studied NNSV). The textbook model cannot explain these phenomena.

Methods: Computational models of RSV and vesicular stomatitis virus (VSV – another highly studied NNSV) transcription were written in the Python programming language using the Scientific Python Development Environment. The model code is freely available on GitHub: …

Rna World And The Development Of Rna Protocells, Benjamin C. Mayfield

PANDION: The Osprey Journal of Research and Ideas

Origins of life research, also known as pre-biotic chemistry or astrobiology, aims to unravel the mystery of the first cell’s origin on Earth. This interdisciplinary field encompasses biology, chemistry, and physics, with the primary goal of understanding the conditions necessary for life to emerge from abiotic environments. The RNA world hypothesis suggests that early life initially used RNA instead of DNA to store genomic information and for enzymatic functions. Protocells, membrane-bound entities with metabolic processes and self-replication capabilities, likely preceded the emergence of true cells. The challenges associated with RNA world is currently an active field of research. Advancements in …

Molecular Mechanisms Of Amyloid-Like Fibril Formation, Sharareh Jalali

Dissertations

Proteins play a critical role in living systems by performing most of the functions inside cells. The latter is determined by the protein's three-dimensional structure when it is folded in its native state. However, under pathological conditions, proteins can misfold and aggregate, accounting for the formation of highly ordered insoluble assemblies known as amyloid fibrils. These assemblies are associated with diseases like Parkinson's and Alzheimer's. Strong evidence suggests that three mechanisms are critical for forming amyloid fibrils. These mechanisms are the nucleation of amyloid fibrils in solution (primary nucleation) as well as on the surface of existing fibrils (secondary nucleation) …

Exploring Topological Phonons In Different Length Scales: Microtubules And Acoustic Metamaterials, Ssu-Ying Chen

Dissertations

The topological concepts of electronic states have been extended to phononic systems, leading to the prediction of topological phonons in a variety of materials. These phonons play a crucial role in determining material properties such as thermal conductivity, thermoelectricity, superconductivity, and specific heat. The objective of this dissertation is to investigate the role of topological phonons at different length scales.

Firstly, the acoustic resonator properties of tubulin proteins, which form microtubules, will be explored The microtubule has been proposed as an analog of a topological phononic insulator due to its unique properties. One key characteristic of topological materials is the …

A Quantitative Visualization Tool For The Assessment Of Mammographic Risky Dense Tissue Types, Margaret R. Mccarthy

Electronic Theses and Dissertations

Breast cancer is the second most occurring cancer type and is ranked fifth in terms of mortality. X-ray mammography is the most common methodology of breast imaging and can show radiographic signs of cancer, such as masses and calcifcations. From these mammograms, radiologists can also assess breast density, which is a known cancer risk factor. However, since not all dense tissue is cancer-prone, we hypothesize that dense tissue can be segregated into healthy vs. risky subtypes. We propose that risky dense tissue is associated with tissue microenvironment disorganization, which can be quantified via a computational characterization of the whole breast …

Towards Clinical Microscopic Fractional Anisotropy Imaging, Nico Jj Arezza

Electronic Thesis and Dissertation Repository

Microscopic fractional anisotropy (µFA) is a diffusion-weighted magnetic resonance imaging (dMRI) metric that is sensitive to neuron microstructural features without being confounded by the orientation dispersion of axons and dendrites. µFA may potentially act as a surrogate biomarker for neurodegeneration, demyelination, and other pathological changes to neuron microstructure with greater specificity than other dMRI techniques that are sensitive to orientation dispersion, such as diffusion tensor imaging. As with many advanced imaging techniques, µFA is primarily used in research studies and has not seen use in clinical settings.

The primary goal of this Thesis was to assess the clinical viability of …

Elucidating The Biomechanics Of Mertk-Mediated Efferocytosis, Brandon Hayato Dickson

Electronic Thesis and Dissertation Repository

Macrophages are key mediators of efferocytosis – the phagocytic engulfment and removal of apoptotic cells. During engulfment, the coordinated activity of efferocytic receptors induces the remodeling of the actin cytoskeleton, which facilitates the envelopment of the cell by the plasma membrane. Mer receptor tyrosine kinase (MERTK) is a crucial efferocytic receptor, but its role during actin remodeling is not well understood. Previously, our lab showed that MERTK is an activator of β₂ integrins – which are comprised of receptors known to induce the actin polymerization that is required for engulfment. We hypothesized that MERTK is an indirect stimulator of …

Control Of The Electroporation Efficiency Of Nanosecond Pulses By Swinging The Electric Field Vector Direction, Vitalii Kim, Iurii Semenov, Allen S. Kiester, Mark A. Keppler, Bennett L. Ibey, Joel N. Bixler, Ruben M. L. Colunga Biancatelli, Andrei G. Pakhomov

Bioelectrics Publications

Reversing the pulse polarity, i.e., changing the electric field direction by 180°, inhibits electroporation and electrostimulation by nanosecond electric pulses (nsEPs). This feature, known as “bipolar cancellation,” enables selective remote targeting with nsEPs and reduces the neuromuscular side effects of ablation therapies. We analyzed the biophysical mechanisms and measured how cancellation weakens and is replaced by facilitation when nsEPs are applied from different directions at angles from 0 to 180°. Monolayers of endothelial cells were electroporated by a train of five pulses (600 ns) or five paired pulses (600 + 600 ns) applied at 1 Hz or 833 kHz. Reversing …