Biophysics Commons^™

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 …

The Mechanobiology Of Cell Plasticity, Yuan Hong

McKelvey School of Engineering Graduate Student Theses & Dissertations

The cell is a sophisticated machine, integrating chemical and physical inputs to decide upon the mechanobiological outputs that the body requires every second, in cardiomyocytes that make heartbeats, in fibroblasts that heal wounds, and in sarcomeres that contract muscles. Malfunction of mechanotransduction or mechanical inputs is implicated in diseases such as fibrosis, cancers, and cardiomyopathies, and a pressing quest is underway to unravel the intricacies of how mechanical force orchestrates the activation of cells. This dissertation explores these fundamental mechanisms of cell activation using integrated mathematical and engineered cell culture models. The work begins with the discovery that the directionality …

Design Of An Fgf-1-Fgf-2 Heterodimer Variant With Enhanced Stability And Cell Proliferation Activity, Nicholas Alan Pohlman

Chemistry & Biochemistry Undergraduate Honors Theses

The FGF-1 subfamily, composed of FGF-1 and FGF-2, assists in broad health-related processes such as cell proliferation and angiogenesis respectively.^1,2 The subfamily shows promising signs as a therapeutic, however, the inherent thermal instability leads to a low half-life in vivo.³ To assist in improving the stability, FGF-1 and FGF-2 were connected via a 12-residue glycine linker ultimately producing a heterodimer. This heterodimer was further examined to discover its novel properties. Inspiration for this project was drawn from previous research which performed five mutations on FGF-1 ultimately improving stability in the protein complex. In addition to these five …

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 …

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.

Shedding Light On Cellular Glycolysis Pathway Kinetics: Combining Kinetic, Mechanistic Modelling Approaches With Label Free Microspectroscopic Imaging. (Cytomechspec), Nitin Patil

Articles

Glycolysis pathway kinetics in cells are known to be modulated for several disorders (cancers, neurodegenerative disorders, diabetes, etc.) and are currently been targeted as a biomarker for disease diagnostics and therapy. Although there are several approaches for monitoring the pathway kinetics, ranging from simple kinetic biochemical assays to sophisticated omics techniques, there remains a significant gap in the field, as there is a noticeable compromise between the extent of insights achievable from approaches which are destructive to the sample, and the real-time, kinetic analysis of a system.

Vibrational spectroscopy is a powerful, label-free, non-invasive tool capable of sub-cellular resolution, the …

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 …

Raman Spectral Cytopathology For Cancer Diagnostic Applications, Fiona Lyng, Damian Traynor, Isha Behl, Declan O'Dea, Hugh Byrne

Books/Book Chapters

Histopathology is currently regarded as the “gold standard” patient sampling technique for cancer diagnostics. It involves extraction of a tissue sample, or biopsy, which is then sectioned and stained for evaluation by a pathologist [1]. Cytopathology, on the other hand, is the field of disease diagnosis at the cellular level [2], necessitating only the microscopic evaluation of samples of cells which can be harvested by less invasive methods such as exfoliative brushing, needle probes or from biofluids. Based on the identification of abnormalities in cellular appearance, cytopathology is currently widely used to aid in the screening of cancer, as well …

Pulsed Electric Field Ablation: Mechanisms Of Differential Cell Sensitivity And Methods To Mitigate Neuromuscular Excitation, Emily Gudvangen

Biomedical Engineering Theses & Dissertations

Ablation therapies aim to destroy tumors while maintaining minimal damage to surrounding healthy tissue. Pulsed electric field (PEF) ablation targets the cell membrane during the destruction of tissues, which consequently spares extracellular structures such as ducts and blood vessels, leaving the framework for tissue regeneration. However, the utility of PEF is limited by neuromuscular excitation, causing pain and involuntary muscle contraction. To identify PEF protocols that efficiently ablate tissue while minimizing neuromuscular stimulation, various PEF protocols differing in pulse duration, shape, and repetition rate were tested. The ratio of cell death and nerve excitation thresholds, which determines the range of …

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 …

Characterization And Modulation Of The Emergent Material Properties Of Biomolecular Condensates, Alfredo Vidal Ceballos

Dissertations, Theses, and Capstone Projects

The discovery of membraneless organelles has revolutionized the field of cell biology and our understanding of cell compartmentalization. These organelles lack a distinct phospholipid bilayer and interact with the cytoplasm mediated by a liquid-liquid interface. The emergent properties and characterization of these organelles are essential for decoding the mechanisms underlying their function and dysfunction. In this thesis, we focus on two reconstituted in-vitro model systems of protein condensates and advance current methodology in order to address these fundamental questions. The first model system examined is the neuronal granule protein Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein, that aids …

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 …

Pharmacological And Pharmacokinetic Studies Of A KCa2.2 Positive Allosteric Modulator, Mohammad Asikur Rahman

Pharmaceutical Sciences (PhD) Dissertations

Small-conductance Ca²⁺-activated potassium channels (K_Ca2.x) family is widely expressed in neurons, the heart, and endothelial cells. K_Ca2.x channels are named small conductance Ca²⁺-activated potassium channels due to their comparatively low single-channel conductance and are activated solely by rises in intracellular Ca²⁺. The family has three subtypes: K_Ca2.1, K_Ca2.2, and K_Ca2.3, encoded by KCNN1, KCNN2, and KCNN3 genes, respectively. K_Ca2.x channels regulate neuronal excitability and responsiveness to synaptic input patterns. Small-conductance Ca²⁺-activated potassium channels subtype 2 (K_Ca2.2, …

Mechanisms Behind The Chaperone Activity Of Nucleic Acids, Theodore J. Litberg

Electronic Theses and Dissertations

Understanding the interplay between nucleic acids and protein aggregation is integral to the understanding of proteostasis, aging, and neurodegenerative disease progression. Nucleic acids are known to modulate the aggregation of PrP, tau, ⍺-synuclein, and other disease relevant proteins. Although the interactions between misfolded protein and nucleic acids can play a role in disease, this interaction may potentially be beneficial as well. Our group and others have shown nucleic acids can be powerful chaperones. Previous work has shown both RNA and DNA can prevent protein aggregation and RNA can pass off protein clients to the heat shock protein (Hsp) system. Here …

Mechanisms Of Fibrillar Aggregation Of The Lens Small Heat Shock Proteins, Αa- And Αb-Crystallin, Russell James Mcfarland

Dissertations and Theses

The protein αB-crystallin represents the archetypical small heat-shock protein (sHSP), and together with αA-crystallin makes up the primary chaperone system in the eye lens, where they play a critical role in maintaining proteostasis. To achieve transparency, the lens undergoes a loss of organelles and both protein turnover halts, requiring that proteins remain functional for long periods of time as they accumulate chemical damage. The α-crystallins are highly abundant in the lens to stabilize proteostasis for multiple decades. Over time though, the small heat-shock proteins become overwhelmed by a high burden of destabilized clients and their own accumulated chemical damage. Mechanistic …

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 …

Effects Of Membrane Components On The Oligomerization Of Amyloid-Β (Aβ) In Alzheimer Disease, Jhinuk Saha

Dissertations

Deposition of extracellular proteinaceous plaques of amyloid-β (Aβ) is one of the major hallmarks of Alzheimer disease (AD). Although, insoluble high molecular fibrils of Aβ are the main constituents of the senile plaques in AD, low molecular weight soluble Aβ oligomers have emerged as the key toxic species involved in memory impairment and neuronal cell death in AD. The process for generation of oligomers can be highly diverse and can involve homotypic interactions of Aβ as well as heterotypic interaction of Aβ with other macromolecules. Previously, the generation of Aβ oligomers with distinct biochemical and biophysical characteristics catalyzed non-esterified fatty …

Exploring The Interaction Of Minor-Groove-Binder Netropsin With Dna Using Optical Tweezers, Irbazhusain Shaikh

Honors Program Theses and Projects

Netropsin is an antibiotic that binds in the minor grooves of DNA, which also exhibits anticancer properties. There have been many previous studies that explored the binding of this drug to DNA using traditional methods where an ensemble averaging is used. In this study we explore the interaction of Netropsin with DNA at a single molecule level using dual beam optical tweezers. We trapped and stretched a single DNA molecule using optical tweezers to measure the force experienced by the DNA as a function of extension in the absence and presence of various concentrations of Netropsin. Our results show the …

Analysis Of The Electrostatic Characteristics Of The Zika Virus Capsid Using Computational Methods, Cassandra Guadalupe Del Rio De Avila

Open Access Theses & Dissertations

Zika virus (ZIKV) is a flavivirus that is usually transmitted through the bite of infected mosquitoes. This virus can cause a variety of neurological disorders, the most common being Guillain-Barré syndrome in adults. Moreover, it is of great concern in pregnant women, since can cause deformities in the brain and other organs of newborns.Studying the structural characteristics of the virus during its mature and infectious phase can provide crucial information on the mechanisms by which it enters and replicates within host cells, as well as its evolution, transmission, and interaction with other living organisms. The symmetric pattern present in the …

Carbon Quantum Dots' Effects On The Structure And Function Of Neurodegenerative And Non-Neurodegenerative Associated Proteins, Shima Masoudi Asil

Open Access Theses & Dissertations

Protein folding is an important physical process in which the sequences of polypeptides fold into a three-dimensional biological active structure. Misfolding is the conversion of a protein molecule into a structure unlike the native form, and therefore misfolded proteins have a strong tendency to aggregate and make fibrils. Amyloid aggregation is constituted by misfolded amyloidogenic proteins. Neurodegenerative diseases, such as Alzheimer’s Disease (AD), stem from the abnormal accumulation of harmful proteins, including Amyloid-ß peptides, tau protein, and the presynaptic protein α-synuclein in the nervous system. Alzheimer's disease is the most common neurodegenerative disorder that causes memory and learning deficits and …

Developing And Applying Computational Methods On Biomolecules, Shengjie Sun

Open Access Theses & Dissertations

Computational biophysics is an interdisciplinary subject that uses numerical algorithms to study the physical principles underlying biological phenomena and processes. Electrostatic interactions play an important role in computational molecular biophysics and their potential impact on disease mechanisms. At distances larger than several Angstroms, electrostatic interactions dominate all other forces, while the alteration of short-range electrostatic pairwise interactions can also have significant effects. The dual nature of electrostatic interactions, being dominant at long-range and specific at short-range, underscores their profound implications for wild-type structure and function. Any disruption of the complex electrostatic network of interactions may abolish wild-type functionality and could …

Microscopic And Spectroscopic Analysis Of Nordihydroguaiaretic Acid Effect On Astrocytes, Lizbeth Vanessa Martinez Lopez

Open Access Theses & Dissertations

Astrocytes, one of the most abundant cell components in the central nervous system (CNS), have been a research target in the last few years. Several studies have found that astrocytes are not only mere supporters of neurons but also of essential processes developed in the CNS. Their malfunction could induce neurodegenerative diseases and brain tumors. Thus, further understanding of astrocytes and their role is of high interest to develop possible new treatments and methods of disease diagnosis, especially in brain cancer. The plant Larrea tridentata (La Gobernadora in Mexico or Creosote bush in the United States) is known to have …

Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel

Honors Scholar Theses

Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …

Microorganisms In Extreme Environmental Conditions, Khanh Mai Nguyen

Graduate Theses and Dissertations

Organisms are known to be able to prosper under normal and extreme environmental conditions, which are classified as mesophile and extremophile, respectively. Extremophiles can thrive under a large array of conditions, from pressures, temperatures, salinity, and pH to a combination of them. For example, to survive on the ocean floor, marine biomass must have its biomolecular machinery adapted to the high pressures and high salinity environment. Moreover, around the hydrothermal vents, aside from pressure and salinity, the microbes that live there also need to adjust to the temperature as well as the pH level. Aside from high temperatures, researchers also …