Effect Of Osmolytes On The Interplay Of Water Protein And Dna In Ecori Dna Recognition Using Molecular Dynamics Simulations,
2025
SASTRA Deemed to be University
Effect Of Osmolytes On The Interplay Of Water Protein And Dna In Ecori Dna Recognition Using Molecular Dynamics Simulations, Aathithya D
Theses and Dissertations
EcoRI is a type II restriction endonuclease that has been widely used as a model system to study protein-DNA interaction owing to its high degree of specificity. This enzyme does not recognize even a single basepair change in its recognition sequence, (GAATTC)2, under normal conditions. However, in the presence of osmolytes, such as glycerol and DMSO, the specificity of EcoRI is slightly relaxed and recognizes sequences that differ from its cognate sequence in the first basepair position. This relaxed specificity has been attributed to the dehydration of the EcoRI-DNA which presumably results in tighter complex formation and subsequent catalysis. However, …
Claudin-1-Mediated Signaling And Therapy Resistance In Colorectal Cancer: From Mechanism To Translation,
2025
University of Nebraska Medical Center
Claudin-1-Mediated Signaling And Therapy Resistance In Colorectal Cancer: From Mechanism To Translation, Mark W. Primeaux
Theses & Dissertations
Colorectal cancer (CRC) remains a leading cause of cancer-related mortality, with metastatic cases showing poor response to chemotherapy due to both intrinsic and acquired therapy resistance. Claudin-1 (CLDN1), a tight junction protein, is overexpressed and mislocalized outside of tight junctions in CRC, where it contributes to an aggressive, metastatic phenotype. Although this causal relationship has been well established, the mechanisms by which CLDN1 promotes tumor progression were unclear due to its lack of intrinsic enzymatic activity. This dissertation investigates the molecular mechanisms through which CLDN1 drives oncogenic signaling, its role in therapy resistance, and its translational potential as both a …
Empowering Science With The World's First High Accuracy And High Throughput Functional Assay,
2025
University of Nevada, Las Vegas
Empowering Science With The World's First High Accuracy And High Throughput Functional Assay, Christopher Giacoletto
UNLV Theses, Dissertations, Professional Papers, and Capstones
Understanding the functional consequences of genetic mutations remains a central challenge in modern biology, with far-reaching implications for human health and disease. While early systematic methods like alanine scanning and phage display provided foundational insights into protein structure and function, the emergence of high-throughput approaches—such as Multiplexed Assays of Variant Effect (MAVEs)—and predictive tools powered by artificial intelligence have vastly expanded our ability to profile mutational landscapes. However, these methods are often constrained by trade-offs between accuracy, scalability, and biological relevance.This dissertation presents the development and application of the GigaAssay, the world’s first high-throughput functional assay capable of delivering both …
Development Of Emerin Mrna Lipid Nanoparticles To Rescue Myogenic Differentiation.,
2025
Rowan University
Development Of Emerin Mrna Lipid Nanoparticles To Rescue Myogenic Differentiation., Nicholas Marano, Liza Elif Guner, Rachel S Riley, James M Holaska
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Emery-Dreifuss muscular dystrophy 1 (EDMD1) arises from mutations in EMD. Most EDMD1 patients lack detectable emerin expression. They experience symptoms such as skeletal muscle wasting, joint contractures, and cardiac conduction defects. Currently, physicians rely on treating patient symptoms without addressing the underlying cause-lack of functional emerin protein. Thus, there is a need for therapeutic approaches that restore emerin protein expression to improve patient outcomes. One way would be to deliver emerin mRNA or protein directly to affected tissues to restore tissue homeostasis. Here, we evaluated the utility of lipid nanoparticles (LNPs) to deliver emerin mRNA to diseased cells. LNPs …
Computational Investigation Of The Structural And Electronic Effects Of Phenyl, Alkyl, And Halogen Fully Substituted Acenes,
2025
Loyola Marymount University
Computational Investigation Of The Structural And Electronic Effects Of Phenyl, Alkyl, And Halogen Fully Substituted Acenes, Emily A A Jarvis, Viraj Jain, Georgia Grace Tully, Peter W. Jarvis
Chemistry and Biochemistry Faculty Works
Acenes are a class of polycyclic aromatic hydrocarbons that may hold promise as organic semiconductors (OSCs) in solar cells and electronic devices. Their instability and poor solubility present challenges that may be improved by replacing the hydrogens with phenyl, halogen or alkyl substituents to sterically induce a helical twist to these otherwise planar molecules. This twisted structure also impacts the optical properties of these molecules. We employ time-dependent density functional theory (TD DFT) to investigate acenes spanning from naphthalene to heptacene. We focus on the structural and electronic effects of fully substituting these molecular backbones to create seven distinct substituent …
Growth Of Cylindrical Micelles And Their Use To Prepare Porous Materials With Tailored Dimensions And Alignment,
2025
University of South Carolina
Growth Of Cylindrical Micelles And Their Use To Prepare Porous Materials With Tailored Dimensions And Alignment, Mengxue Zhang, Xiaomeng Li, Chuanbing Tang, Morgan Stefik
Faculty Publications
Materials with cylindrical pores are optimal for electrochemical devices and filtration due to their straight paths with minimal tortuosity when aligned. Polymer templates have led to many individual cylindrical architectures however the independent tailoring of pore and wall dimensions has remained elusive. Here short cylindrical micelle templates (PEO-b-PS) with glassy cores enabled the fabrication of sample series with constant cylindrical pore diameter (∼63 nm) and tailored wall thickness (TiO2, ∼45–100 nm). This ShortCyl series (aspect ratio 4.25) had modest alignment that was attributed to the low free-energy cost for misalignment. Though the plasticized micelles (DCM present) …
Long Intergenic Non-Coding Rna 00511 (Linc00511) Genetic Variations And Haplotype Implication For Colorectal Cancer Susceptibility And Prognosis,
2025
Ain Shams University
Long Intergenic Non-Coding Rna 00511 (Linc00511) Genetic Variations And Haplotype Implication For Colorectal Cancer Susceptibility And Prognosis, Eman Fouad Sanad, Ahmad Abd El Hady, Mohamed Ali, Shorouk Eldash, Nermeen H. Elmorshedy, Farah Ayman, Hams M. Khattab, Amr Maher, Hadeel Ashree, Mahitab Abdelhady, Mazen Mohamed, Ahmed Adel, Sajed Khalil, Omar Alyan, Ahmed Samir, Alhassan A. Bakr, Nadia Hamdy
Pharmacy
Long intergenic non-coding RNA 00,511 (LINC00511) is considered an oncogene for various cancers. However, the association between LINC00511 single nucleotide polymorphisms (SNPs) and colorectal cancer (CRC) remains unclear. Our study aims to study whether LINC00511 SNPs could predict CRC susceptibility or prognosis, an important step-toward precision-health, based on an Egyptian CRC patient cohort. A total of 200 CRC patients and 200 cancer-free controls were genotyped for three LINC00511 SNPs − rs9906859, rs1558535, and rs17780195 using qRT-PCR. Studied SNPs were in strong linkage disequilibrium and moderately correlated in all groups. Genotype association concerning tumor stage, revealed rs1558535 AT and rs17780195 AG …
An Rna Modification Prevents Extended Codon-Anticodon Interactions From Facilitating +1 Frameshifting,
2025
Thomas Jefferson University
An Rna Modification Prevents Extended Codon-Anticodon Interactions From Facilitating +1 Frameshifting, Evelyn M. Kimbrough, Ha An Nguyen, Haixing Li, Jacob M. Mattingly, Nevette A. Bailey, Wei Ning, Howard Gamper, Ya-Ming Hou, Ruben L. Gonzalez, Christine M. Dunham
Department of Biochemistry and Molecular Biology Faculty Papers
RNA post-transcriptional modifications act by stabilizing the functional conformations of RNA. While their role in messenger RNA (mRNA) decoding is well established, it is less clear how transfer RNA (tRNA) modifications outside the anticodon contribute to tRNA stability and accurate protein synthesis. Absence of such modifications causes translation errors, including mRNA frameshifting. By integrating single-molecule fluorescence resonance energy transfer and cryogenic electron microscopy, we demonstrate that the N1-methylguanosine (m1G) modification at position 37 of Escherichia coli tRNAProL is necessary and sufficient for modulating the conformational energy of this tRNA on the ribosome so as to suppress +1 frameshifting otherwise induced …
Development Of A Cure In Principles Of Cell And Molecular Biology,
2025
Johnson County Community College
Development Of A Cure In Principles Of Cell And Molecular Biology, Heather Seitz
Sabbatical Projects
This project presentation highlights the work done during sabbatical to develop an authentic research experience into BIOL135 Principles of Cell and Molecular Biology. The sabbatical allowed for development time but further work was done to measure impact and outcomes for future implementation.
Effect Of Histidine Tag On The Enzymatic Activity Of Pseudolysin And Its Interaction With The Streptomyces Metalloprotease Inhibitor (Smpi) Protein,
2025
Stephen F Austin State University
Effect Of Histidine Tag On The Enzymatic Activity Of Pseudolysin And Its Interaction With The Streptomyces Metalloprotease Inhibitor (Smpi) Protein, Adewale Adeboye Adewole
Electronic Theses and Dissertations
Pseudolysin (PLN) protein is a major virulent factor in Pseudomonas aeruginosa infection. PLN belongs to the family of zinc-dependent metalloproteases. It is naturally inhibited by a smaller protein called streptomyces metalloprotease inhibitor (SMPI), secreted by Streptomyces nigrescens. Previous and current studies demonstrate that the interaction between PLN and SMPI offers unique mechanistic insights for drug development against infections caused by P. aeruginosa. This study investigated the effect of N-terminal Histidine (His) tag on the enzymatic activity of PLN and its interaction with SMPI. His-tagged PLN and SMPI proteins were expressed in bacteria and purified by affinity chromatography …
Unwrapping The Cube Visual Essay,
2025
Rhode Island School of Design
Unwrapping The Cube Visual Essay, Arthur L. Loeb, C. Todd Stewart
Loeb Design Science: Documents
A visual and conceptual essay illustrating the many faces and properties of the cube.
Development Of A Physiologically Based Pharmacokinetic (Pbpk) Model And Evaluation Of Antioxidant Capacity For Polypodium Leucotomos Extract,
2025
Liberty University
Development Of A Physiologically Based Pharmacokinetic (Pbpk) Model And Evaluation Of Antioxidant Capacity For Polypodium Leucotomos Extract, Christopher L. Basel
Doctoral Dissertations and Projects
The purpose of this study was to develop an equation to calculate the approximate concentration of active components in orally administered Polypodium leucotomos fern extract (PLE) and to develop physiologically based pharmacokinetic (PBPK) models for an active component of PLE or its metabolite to address the need for human pharmacokinetics (PK). Model differences based on ethnic groups were also investigated. This was a quantitative study using secondary data. It has been estimated that skin cancers account for approximately 40% of all human cancers and that approximately 13,000 people will die of skin cancer in 2024. People with darker skin experience …
Advancing Single-Molecule Nanopore Sensing: From Protein Conformation And Metal Binding To Dna Transport Via Hybrid Nanostructures,
2025
Southern Methodist University
Advancing Single-Molecule Nanopore Sensing: From Protein Conformation And Metal Binding To Dna Transport Via Hybrid Nanostructures, Matthew J. Odonohue
Multidisciplinary Studies Theses and Dissertations
This dissertation presents the development and application of solid-state and hybrid nanopore platforms for single-molecule analysis of biomolecular interactions. First, a silicon nitride nanopore was employed to characterize the conformational states of the transferrin receptor (TfR), enabling discrimination between its monomeric and dimeric forms, as well as from its ligand, human serum transferrin (hSTf), despite their similar molecular weights. In a separate study, the same nanopore configuration was used to track the real-time binding of titanium ions to transferrin, demonstrating single-molecule sensitivity to metal-induced conformational changes. A hybrid microtubule–solid-state nanopore (MT–SSN) was then engineered, repurposing microtubules as electrostatically anchored conduits …
Novel Nanomaterials For Developing Bone Scaffolds And Tissue Regeneration,
2025
University of Arkansas, Fayetteville
Novel Nanomaterials For Developing Bone Scaffolds And Tissue Regeneration, Nazim Uddin Emon, Lu Zhang, Shelby Dawn Osborne, Mark Allen Lanoue, Yan Huang, Z. Ryan Tian
Cell and Molecular Biology Faculty Publications and Presentations
Nanotechnologies bring a rapid paradigm shift in hard and soft bone tissue regeneration (BTR) through unprecedented control over the nanoscale structures and chemistry of biocompatible materials to regenerate the intricate architecture and functional adaptability of bone. This review focuses on the transformative analyses and prospects of current and next-generation nanomaterials in designing bioactive bone scaffolds, emphasizing hierarchical architecture, mechanical resilience, and regenerative precision. Mainly, this review elucidated the innovative findings, new capabilities, unmet challenges, and possible future opportunities associated with biocompatible inorganic ceramics (e.g., phosphates, metallic oxides) and the United States Food and Drug Administration (USFDA) approved synthetic polymers, including …
Metabolic Regulation Of Cardiac Fibroblast Phenotype And Function.,
2025
University of Louisville
Metabolic Regulation Of Cardiac Fibroblast Phenotype And Function., Collin Kleis Wells
Electronic Theses and Dissertations
Cardiac fibroblasts are central effectors of cardiac repair after myocardial infarction (MI). In response to signaling cues, they differentiate to a range of phenotypes with robust capacities to synthesize and secrete extracellular matrix (ECM) and signaling molecules. Although activated fibroblast phenotypes are associated with pronounced changes in metabolism, it remains unclear how the metabolic network upholds the effector functions of fibroblasts in the post-infarcted heart. Here, we identified that critical enzymes in the phosphoenolpyruvate (PEP) cycle, i.e. pyruvate kinase muscle-2 (PKM2) and phosphoenolpyruvate carboxykinase-2 (PCK2), are elevated in the heart after MI and examined their role in regulating post-MI remodeling …
Advanced Interactions Of Directed Energy With Retinal Pigment Epithelial Cells And Their Photochemical And Photothermal Responses,
2025
University of the Incarnate Word
Advanced Interactions Of Directed Energy With Retinal Pigment Epithelial Cells And Their Photochemical And Photothermal Responses, Jin B. Ha
Theses & Dissertations
Excess optical radiation can injure the retina through either rapid heat deposition (photothermal damage) or cumulative photo‑oxidative stress (photochemical damage), yet current laser‑safety limits treat these mechanisms as independent. To test that assumption, this dissertation integrated systematic wavelength, duration and temperature‑controlled laser exposures with live/dead fluorescence imaging in a melanin‑loaded hTERT‑RPE1 monolayer model. First, concurrent 447 nm (blue) and 2 µm (infra‑red) beams delivered for 200 s demonstrated a strong thermal–photochemical synergy: each beam alone was sub‑threshold (≤25 % lethality) but together produced 100 % RPE death without exceeding 50 °C, proving that modest heating markedly lowers the photon dose …
Assessing The Impact Of Pll And Ple Concentrations And Aging On Protein Condensates Formation Via Llps,
2025
Montclair State University
Assessing The Impact Of Pll And Ple Concentrations And Aging On Protein Condensates Formation Via Llps, Nabil Harche
Theses, Dissertations and Culminating Projects
Protein droplets, also referred to as condensates, are membrane-less organelles formed through a biophysical process known as liquid-liquid phase separation (LLPS). These structures play an indispensable role in a wide range of cellular functions, including compartmentalizing biochemical reactions, regulating gene expression, and responding to cellular stress. Unlike traditional membrane-bound organelles, these condensates form dynamically and reversibly within the cytoplasm or nucleus, without the need for lipid membranes. The formation of these protein droplets is affected by several physicochemical factors, including pH, temperature, ionic strength, concentration of biomolecules, and specific molecular interactions such as electrostatics and hydrophobic forces. LLPS results in …
Comparative Expression Of Cgmp-Dependent Protein Kinase G (Pkg) From Plasmodium And Toxoplasma,
2025
Montclair State University
Comparative Expression Of Cgmp-Dependent Protein Kinase G (Pkg) From Plasmodium And Toxoplasma, Tsopmo Asaah
Theses, Dissertations and Culminating Projects
Malaria and Toxoplasmosis are life threatening diseases to humans. The search for a cure and control of these diseases is still one of the major challenges of scientists worldwide. In this research we focused on two Malaria species; Plasmodium bergei² (Pb) and Plasmodium falciparum¹ (Pf) and also on Toxoplasma gondii. Part of the life cycle of these organisms is regulated by the enzyme cyclic GMP-dependent protein kinase G (PKG)⁴. This is our drug target in this research. We believe that inhibiting this enzyme will be a great step in fighting these diseases. In this research, we devised a comparative study …
Cultivation Of Botryococcus Braunii For The Production Of Hydrocarbons Suitable For Fuel Use,
2025
Clemson University
Cultivation Of Botryococcus Braunii For The Production Of Hydrocarbons Suitable For Fuel Use, Bryan C. Carroll
All Theses
Energy security, rural poverty, and climate change are pressing issues of our time. Biofuels provide a solution to these issues, with a focus on sustainable aviation fuel, SAF, due to compatibility with aircraft infrastructure and energy density. This research aims to review and produce knowledge about a specific microalga, Botryococcus braunii, for its potential for SAF. First a literature review on the process was conducted followed by an experimental study on the impact of aqueous media and inorganic carbon its growth and hydrocarbon content. The literature review found the process consists of cultivation followed by lipid extraction or hydrothermal …
Functional Genomics Of Phosphatidylcholine Biosynthesis In Saccharomyces Cerevisiae,
2025
University of Nebraska-Lincoln
Functional Genomics Of Phosphatidylcholine Biosynthesis In Saccharomyces Cerevisiae, Amanda Marie Maliva
Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–
Phosphatidylcholine (PtdCho) is a prominent structural building block of cell and organelle membranes in animal, plant, and fungal cells and some bacteria. Due to its abundant nature in the plasma membrane and intracellular organelle membranes in eukaryotes, the biosynthesis of PtdCho must remain regulated to preserve the correct membrane lipid composition. Dysregulations in PtdCho metabolism can lead to mitochondrial dysfunction, cell death, and the development of diseases including cancer, atherosclerosis, and hepatic diseases. Knowledge of PtdCho has remained limited to the genes involved in its three biosynthetic pathways (Kennedy (K), methylation (M), and acyltransferase (A)), despite the growing realization of …
