Biochemistry, Biophysics, and Structural Biology Commons^™

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 …

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 …

Yizhi Sun: Profile Of The Newest Chbc Faculty Member., Danna Jaimes-Fajardo, Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

Presents the research profile of Yizhi Sun, Assistant Professor, Chemistry and Biochemistry department. It highlights his research interests, education, and impact of his research.

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, 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, 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 …

Elucidating The Mechanisms Underlying A Functional Plant-Arbuscular Mycorrhizal Symbiosis Using Omics Approaches, Jasmine Gill

All Dissertations

Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs forming symbiotic association with plants. The plant-AMF symbiosis has gained much attention due to its ability to improve plant nutrient uptake, especially phosphorus, which is often inadequately available to plants due to its limited mobility and complex formation in many soils. Phosphorus (P) is a crucial nutrient for plants, and most phosphate fertilizers are derived from phosphate rock, a finite natural resource. Thus, optimizing P uptake is vital for sustaining crop yields and addressing the needs of a growing global population. Plant-AMF symbioses are significant in this context, as AMF can acquire P …

Small Angle X-Ray Scattering Studies Of Collagenase H Mutant, Colh-E416q, Madelyn Millsap

Graduate Theses and Dissertations

Collagenase H (ColH) from Hathewaya histolytica plays a central role in collagen degradation through endopeptidase and carboxytripeptidase reactions. To better understand how its domain architecture supports these functions, we examined the solution structure of a catalytically inactive mutant, ColH-E416Q, using small-angle X-ray scattering (SAXS). The E416Q mutant is catalytically inactive because the glutamate residue at position 416, which normally functions as a general acid/base during catalysis, is replaced by glutamine—an amide that cannot donate or accept protons effectively, thus disabling the proton transfer steps essential for peptide bond hydrolysis. SAXS results indicate that the E416Q substitution leaves overall domain architecture …

Analysis Of An Ethanol Sensitive Bmp-Nkx2.3-Fgf Signaling Pathway In Pouch Morphogenesis., Hieu Dai Le Vo

Electronic Theses and Dissertations

Craniofacial malformations lie at the heart of Fetal Alcohol Spectrum Disorders (FASD). While there is growing evidence for a genetic component to FASD, little is known of the cellular mechanisms underlying these ethanol-sensitive loci in facial development. Bone Morphogenetic Protein (Bmp) signaling pathway dependent pouch formation is a key mechanism in facial development. We have previously shown that multiple Bmp mutants are sensitized to ethanol-induced facial defects. However, ethanol does not directly impact Bmp signaling. This suggests that downstream effectors, like nkx2.3 and Fibroblast Growth Factor (Fgf) signaling, may mediate the impact of ethanol on Bmp mutants. Here, I …

Acute Exposure Of American Oyster (Crassostrea Virginica) To Selected Antidepressant Drug: Histological, Biochemical, And Immunohistochemical Assessments, Md. Faisal Amin

Theses and Dissertations

The rapid increase in pharmaceutical use has brought significant health benefits to humans. Studies have shown that many pharmaceuticals, such as antidepressants, are often detected in surface waters, groundwater, and even drinking water. These pharmaceuticals in aquatic environments threaten marine life seriously. Marine bivalves are vital source of seafood for people worldwide. In this study, we examined the effects of short-term exposure to fluoxetine, an antidepressant used to treat depression, at low (0.5 μg/L) and high (5 μg/L) doses over a one-week period on American oysters (Crassostrea virginica) under controlled laboratory conditions. Histological analysis revealed atrophy in the gills and …

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 …

Aptamer Selection And Development Of Electrochemical Aptamer-Based Sensors For Neuropeptide Y, Evelyn Adela Carreto Guevara

Department of Chemistry: Dissertations, Theses, and Student Research

In this thesis, we report the results of four aptamers obtained from an aptamer selection process called the systematic evolution of ligands by exponential enrichment (SELEX) with affinity to Neuropeptide Y (NPY). NPY is a highly abundant peptide transmitter with widespread distribution throughout the body which affects various physiological functions. These functions include energy homeostasis, appetite regulation, stress response, and anxiety regulation. Dynamic monitoring of NPY levels is crucial for better understanding behaviors in individuals with neurological disorders associated with NPY. Aptamers are synthetic oligonucleotides obtained through SELEX which have a binding affinity to a target of interest when in …

Exploring Variability Of The Cg18562578 Methylquant Assay For The Forensic Discrimination Of Monozygotic Twins, Sydney E. Arnold

Student Theses

Monozygotic (MZ) twins possess identical DNA sequences, posing a problem for forensic scientists, as they are incapable of distinguishing MZ twins from each other using traditional DNA identification methods. However, the epigenomes of MZ twins will differ and might be used for their forensic discrimination. Here, we explored the variability of an assay previously developed by our laboratory that showed high discrimination potential for MZ twins using buccal swab DNA, cg18562578 MethylQuant. We measured precision at each step: bisulfite conversion, nested PCR, and qPCR, reproducibility, and repeatability. DNA methylation ratios were compared between two analysts carrying each step using the …

Cg18562578 Methylquant Assay For The Discrimination Of Monozygotic Twins, Amber P. Chauca

Student Theses

Monozygotic (MZ) twins have identical DNA, making traditional profiling methods insufficient in their discrimination. However, MZ twins can be differentiated by their levels of DNA methylation. Our research group previously developed a methodology to detect cg18562578 DNA methylation levels in MZ twins based on a two- step PCR approach and a cg18562578 MethylQuant Assay. That study generated data for only 64% of the samples it investigated, and showed a discrimination power of 77% to discriminate between MZ twins. Here, we used the same methodology but a different approach to determine DNA methylation in 73 previously unsuccessful twin pairs. We diluted …

Biological, Histological, And Immunohistochemical Responses To Heat Stress In Common Goldfish, Carassius Auratus, Ngozichukwu Francis Ngozichukwu

Theses and Dissertations

Global climate change has led to rising temperatures, posing significant challenges to aquatic ecosystems and the health of ectothermic species such as goldfish (Carassius auratus) This thesis investigated the effects of heat stress on growth performance, histological alterations, and molecular stress responses in the gill and kidney tissues of goldfish Fish were exposed to control (24°C), medium (28°C), and high (32°C) temperatures for two weeks Growth parameters, including instantaneous growth rate (IGR), absolute growth rate (AGR), body value gain (BVG), and condition factor, were evaluated alongside histological and immunohistochemical markers of stress Results revealed that high temperature significantly reduced AGR …

Analyzing How Taste And Nutrition Impact Learning And Memory In Honey Bees Through Olfactory Associative Conditioning, Alessandra Elizabeth Perry

Theses and Dissertations

Honey bees detect sweet nectar, but not all sweet-tasting sugars provide nutrition. Unlike fruit flies, which can learn to avoid non-nutritious sweet foods, bees may lack this ability. To test if bees form caloric frustration memory (CFM), we conditioned them using odors paired with L-glucose (sweet but non-nutritious) or D-glucose (sweet and nutritious). Bees rewarded with L-glucose showed lower learning and long-term memory compared to D-glucose. Bees cannot differentiate between an odor associated with rewards containing malaise-causing compounds and an odor associated with a reward alone during differential conditioning. Therefore, we used differential conditioning to determine if lower acquisition in …

Transcriptomic Study On The Effect Of Salt Stress In Sorghum Bicolor Seedlings, Joshwa A. Gandy

Theses and Dissertations

The global impact and reliance on cereal crops, and sorghum in particular, is paramount for worldwide food security and for the livelihood of hundreds of millions of people. The detrimental effects of salt stress on crop plants and the huge economic losses it causes by affecting agricultural output worldwide is a devastating issue with huge impacts, which have prompted research to combat salinity in numerous ways. Understanding how cereals respond to the negative effects of salt stress is crucial for enhancing their salt tolerance. In this study of sorghum, we used a 3’-end RNA sequencing approach to elucidate major salt …

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 …

Use Of The Protein Misfolding Cyclic Amplification For Food Safety And Drug Discovery, Maria R. Benavente Garcia-Huidobro

Dissertations and Theses (Open Access)

Prion diseases are fatal neurodegenerative disorders caused by the misfolding of the normal prion protein (PrP^C) into its infectious form (PrP^Sc). While the zoonotic potential of chronic wasting disease (CWD) remains uncertain, the presence of prions in food products raises public health concerns. Additionally, therapeutic strategies for prion diseases remain limited. This thesis presents a methodological exploration of the Protein Misfolding Cyclic Amplification (PMCA) technique to address these challenges in two key areas: (1) detecting CWD prions in processed meats subjected to common cooking procedures, and (2) identifying potential anti-prion compounds through a high-throughput PMCA adaptation. …

Structural Functional Investigation Of Hap40, Amanda M. Solbach

Dissertations and Theses (Open Access)

STRUCTURAL FUNCTIONAL INVESTIGATION OF HAP40

Amanda Marie Solbach

Dissertation Advisor: Sheng Zhang, Ph.D.

Huntington’s disease (HD) is a devastating neurodegenerative disorder caused by an expanded CAG trinucleotide repeat in the Huntingtin (HTT) gene, resulting in a mutant huntingtin (mHTT) protein with an elongated polyglutamine tract. While the genetic basis of HD is well established, the mechanisms underlying mHTT toxicity and its impact on cellular function remain incompletely understood. Recent discoveries implicate Huntingtin-associated protein 40 (HAP40) as a critical regulator of HTT stability and intracellular function. However, the physiological and pathological significance of this interaction has not been fully explored.

This …

Bifunctional Fusion Protein Pdl1sfv/Micae For Cancer Immunothearpy, Junyi Li

All Dissertations

Cancer immunotherapy has highlighted the importance of immune checkpoint blockade and innate immune cell engagement in battling tumor-mediated immune suppression in the past few decades. However, with cancer development, advanced tumors are often found to develop resistance towards single-target immunotherapy due to the complexity of the immunosuppressive mechanisms within the tumor microenvironment (TME). To address this, we developed a novel bifunctional fusion protein, PDL1sFv/MICAe, which combines the tumor-targeting capability of an anti-PDL1 single-chain variable fragment (sFv) with the NK cells immunostimulatory properties of the MICA extracellular domain.

In vitro functional assays revealed that PDL1sFv/MICAe significantly enhanced cytotoxicity towards natural killer …

Molecular And Clinical Insights Into Role Of Gper In Hepatocellular Carcinoma (Hcc), Hossain Ahmed

Theses and Dissertations

Metabolic dysfunction–associated steatotic liver disease (MASLD), encompassing stages from steatosis (MASLD) to steatohepatitis (MASH), cirrhosis, and hepatocellular carcinoma (HCC), is the most prevalent chronic liver disease worldwide, yet molecular markers of progression remain limited. The G protein–coupled estrogen receptor (GPER), a non-genomic estrogen receptor with metabolic and anti-inflammatory roles, emerges as a candidate regulator in hepatic pathophysiology. In this Dissertation thesis, we have delineated for the first time clinicopathological assessment of liver biopsies across MASLD stages revealing a robust inverse correlation between GPER expression and disease severity. Higher GPER levels in early MASLD associated with favorable metabolic and biochemical profiles, …

Crystal Structures Of Escherichia Coli Glucokinase And Insights Into Phosphate Binding, Joseph Andrews, Joshua Sakon, Chenguang Fan

Chemistry & Biochemistry Faculty Publications and Presentations

Here, we report the crystal structure of Escherichia coli glucokinase (GLK), which has phosphate bound in the cleft between the alpha and beta domains adjacent to the active site. A ternary complex consisting of GLK, glucose and phosphate is also reported in this work. Diffraction data were collected at 2.63 angstrom resolution for the phospate-bound form (R-work/R-free = 0.191/0.230) and at 2.54 angstrom resolution for the ternary complex (R-work/R-free = 0.202/0.258), both at 297 K. A B-factor analysis of the phosphate-bound GLK structure revealed consistently lower values for phosphate-interacting basic residues in the alpha 4, alpha 5 and alpha 9 …

Non-Spectator Behavior Of A Neutral Phosphine Ligand Driven By A Redox-Active Boron Cluster, Jared R. Riffle, Cash L. Jowers, Sarah Luna, Mark D. Smith, Dmitry V. Peryshkov

Faculty Publications

A new concept of ligand ambiphilicity that relies on the redox behavior of the indirectly coordinated boron cluster scaffold instead of the direct involvement of a single center in a ligand is introduced. A copper(I) complex of a carboranyl-based triphosphine, [t^BuP-closo-{C₂B₁₀}-^PhP-closo-{C₂B₁₀}-t^BuP]CuPF₆, in acetonitrile solution coordinates an exogenous X− anion (X− = Cl− or N3−) at the phosphorus center of the ligand and not at the cationic metal site to form [t^BuP(X)-nido-{C₂B …

In Silico Prediction Of Cytotoxic T-Cell Epitopes From Helicobacter Pylori Virulence Factors Using An Immunoinformatics Approach, Demy Valerie Chacon, Kiana Alika Co, Daphne Noreen Enriquez, Aubrey Love Labarda, Reanne Eden Manongsong, Edward Kevin B. Bragais

Biology Faculty Publications

Background: Helicobacter pylori infects approximately half of the global population, leading to gastric and duodenal ulcers. Despite the availability of antibiotics, challenges such as patient reluctance, high treatment costs, and antibiotic resistance limit their effectiveness, making vaccination a promising alternative. This study used immunoinformatics to identify candidate epitopes for a multiepitope vaccine construct against H. pylori.

Material and methods: The protein variability server was utilized for conservation analysis. The epitopes were screened for antigenicity, allergenicity, toxicity, cross-reactivity, and population coverage. Selected epitopes were docked with their corresponding human leukocyte antigen (HLA) alleles, and thermodynamic quantities were determined. Five virulence …

Fabrication, Calibration, And Deployment Of A Home-Made Radiometer, Callum Flowerday, Ryan Thalman, Jaron Hansen

ScholarsArchive Data

Subfolders and Contents:

Chamber Characterization: Contains emission spectrum measured from inside the chamber with converted spectra to power and photon flux.

LED Calibration: (Each calibration file contains folders of data from each LED used in calibration)

• Cone
• Cone 2
• Dome 2
• Flat Top
• Quartz Rod
• Uniform Dome

Outside:

• Cone 2 front porch
• Cone 2 roof
• Flat top

The Influence Of Myocardin Effector Genes On The Tgf-Beta Smad3 Signaling Pathway In Human Pleural Mesothelial Cells, Hema Chandra Hrushi Dusharla

Biotechnology Theses

Pleural Fibrosis (PF) involves excessive extracellular matrix (ECM) deposition, mainly by myofibroblasts, leading to pleural thickening and impaired lung function. Pleural mesothelial cells (PMCs) contribute via mesothelial and mesenchymal transition (MesoMT), triggered by cytokines like TGF-β. Our lab identified Myocardin (MyoCD), a transcriptional co-activator of cardiac and smooth muscle, is a master regulator of pleural fibrosis through interactions with serum response factor (SRF) and Smad2/3 transcription factors which initiate fibrosis signaling. RNA sequencing and qPCR analysis revealed that silencing MyoCD decreased the expression of CTNNB1, MDFI, and Tspan2. MDFI emerged as a potent candidate, as this gene affecting the expression …

Using The Safety Scissors: Dna Resection Regulation At Dna Double-Strand Breaks And Telomeres, Michael M, Soniat, Logan R. Myler

Department of Biochemistry and Molecular Biology Faculty Papers

DNA resection is a universal process in genome maintenance by which one strand of DNA is degraded, leaving the other strand intact. This sometimes highly processive process is critical for many forms of DNA damage repair, replication-coupled repair, meiotic recombination, and telomere maintenance. Therefore, resection must be tightly regulated to prevent genome instability and promote faithful and accurate repair. Here, we review what is known about how resection functions and how it is controlled, using DNA double-strand break repair and telomere maintenance as examples. We address how resection is regulated in three independent steps: resection initiation, long-range processing, and termination. …

A Cancer Education Needs Assessment: Informing Middle-Aged Female Patients About The Relationships Between Obesity And Women’S Health Concerns In The Reproductive System, Breast, And Endometrial Health, Batul Mirza

MUSC Theses and Dissertations

Obesity significantly impacts women’s health, particularly among middle-aged women, by increasing the risk of hormone-sensitive cancers such as breast, endometrial, and reproductive system cancers. This study examines the educational needs of this demographic group regarding obesity-related cancer risks and explores effective intervention strategies. Obesity-induced mechanisms – hormonal imbalances, chronic inflammation, and insulin resistance – drive cancer susceptibility, emphasizing the need for targeted health education. The study employs a qualitative design, which includes interviews with subject matter experts (SMEs) and surveys of middle-aged women. The goal is to assess awareness, perceived barriers, and preferred learning methods. Findings suggest that with many …

Identification Of Serum Exosome Proteins In Systemic Sclerosis With Interstitial Lung Disease By Aptamer Proteomics, Sonsoles Piera-Velazquez, Simon T. Dillon, Xuesong Gu, Towia A. Libermann, Sergio A. Jimenez

Jefferson Institute of Molecular Medicine Papers and Presentations

OBJECTIVE: A major unmet need for Systemic Sclerosis (SSc) clinical management is the absence of well validated biomarkers for early diagnosis of SSc-associated interstitial lung disease (SSc-ILD). The objective of this study was to identify proteins contained within serum exosomes that may serve as potential biomarkers to differentiate patients with Diffuse SSc without SSc-ILD from patients with Diffuse SSc with SSc-ILD employing aptamer-based proteomics.

METHODS: Serum exosomes were isolated from two cohorts of patients. The first cohort included 15 patients with Diffuse SSc without SSc-ILD and 14 patients with Diffuse SSc with SSc-ILD and the second cohort included 12 patients …