Biochemistry, Biophysics, and Structural Biology Commons^™

Development Of Antiviral Peptidomimetics, Songyi Xue

USF Tampa Graduate Theses and Dissertations

Protein-protein interactions (PPIs) are essential for biological processes and are associated with a number of diseases, including cancer, infectious diseases, and neurodegenerative diseases. As a result, modulation of PPIs has been recognized as one of the most promising strategies to develop the novel drugs. Peptide modulators always exhibit higher specificity and affinities with targets than small compounds or monoclonal antibodies, but their broad medicinal effectiveness is constrained by their poor bioavailability and biostability. Peptidomimetics, which have been developed to mimic the structure as well as function of bioactive peptides and proteins, have shown excellent potential in protein surface mimicry and …

Rapidly Developed, Optimized, And Applied Wastewater Surveillance System For Real-Time Monitoring Of Low-Incidence, High-Impact Mpox Outbreak, Chandler H. Wong, Zhihao Zhang, Walaa Eid, Julio Plaza-Diaz, Pervez Kabir, Shen Wan, Jian Jun Jia, Elisabeth Mercier, Ocean Thakali, Lakshmi Pisharody, Nada Hegazy, Sean E. Stephenson, Wanting Fang, Tram B. Nguyen, Nathan T. Ramsay, R. Michael Mckay, Ryland Corchis-Scott, Alex E. Mackenzie

Great Lakes Institute for Environmental Research Publications

Recent MPOX viral resurgences have mobilized public health agencies around the world. Recognizing the significant risk of MPOX outbreaks, large-scale human testing, and immunization campaigns have been initiated by local, national, and global public health authorities. Recently, traditional clinical surveillance campaigns for MPOX have been complemented with wastewater surveillance (WWS), building on the effectiveness of existing wastewater programs that were built to monitor SARS-CoV-2 and recently expanded to include influenza and respiratory syncytial virus surveillance in wastewaters. In the present study, we demonstrate and further support the finding that MPOX viral fragments agglomerate in the wastewater solids fraction. Furthermore, this …

Selected Fermented Indigenous Vegetables And Fruits From Malaysia As Potential Sources Of Natural Probiotics For Improving Gut Health, Olaide Olawunmi Ajibola, Raymond Thomas, Babatunde Femi Bakare

Biochemistry Publications

In the Peninsular Malaysia and Northern Borneo island of Malaysia, various rich indigenous leafy vegetables and fruits grow and contribute to the nutritional and dietary values of the population. They have high water contents, thus, naturally vulnerable to rapid food spoilage. Food preservation and processing play a vital role in the inhibition of food pathogens in fruits and vegetables that are prevalent in Malaysia. Lactic acid fermentation is generally a local-based bioprocess, among the oldest form and well-known for food-processing techniques among indigenous people there. The long shelf life of fermented vegetables and fruits improves their nutritional values and antioxidant …

Out-Of-Distribution Generalization Of Deep Learning To Illuminate Dark Protein Functional Space, Tian Cai

Dissertations, Theses, and Capstone Projects

Dark protein illumination is a fundamental challenge in drug discovery where majority human proteins are understudied, i.e. with only known protein sequence but no known small molecule binder. It's a major road block to enable drug discovery paradigm shift from single-targeted which looks to identify a single target and design drug to regulate the single target to multi-targeted in a Systems Pharmacology perspective. Diseases such as Alzheimer's and Opioid-Use-Disorder plaguing millions of patients call for effective multi-targeted approach involving dark proteins. Using limited protein data to predict dark protein property requires deep learning systems with OOD generalization capacity. Out-of-Distribution (OOD) …

Optimization And Application Of Graph Neural Networks, Shuo Zhang

Dissertations, Theses, and Capstone Projects

Graph Neural Networks (GNNs) are widely recognized for their potential in learning from graph-structured data and solving complex problems. However, optimal performance and applicability of GNNs have been an open-ended challenge. This dissertation presents a series of substantial advances addressing this problem. First, we investigate attention-based GNNs, revealing a critical shortcoming: their ignorance of cardinality information that impacts their discriminative power. To rectify this, we propose Cardinality Preserved Attention (CPA) models that can be applied to any attention-based GNNs, which exhibit a marked improvement in performance. Next, we introduce the Directional Node Pair (DNP) descriptor and the Robust Molecular Graph …

Construction And Performance Optimization Of Bioconjugated Nanosensors For Early Detection Of Breast Cancer And Pro-Inflammatory Diseases, Pooja Gaikwad

Dissertations, Theses, and Capstone Projects

In recent years, nanosensors have emerged as a tool with strong potential in medical diagnostics. Single-walled carbon nanotube (SWCNT) based optical nanosensors have notably garnered interest due to the unique characteristics of their near-infrared fluorescence emission, including tissue transparency, photostability, and various chiralities with discrete absorption and fluorescence emission bands. Additionally, the optoelectronic properties of SWCNT are sensitive to the surrounding environment, which makes them suitable for in vitro and in vivo biosensing. Single-stranded (ss) DNA-wrapped SWCNTs have been reported as optical nanosensors for cancers and metabolic diseases. Breast cancer and cardiovascular diseases are the most common causes of death …

Characterization Of The Conformational Binding Of N-Methyl Mesoporphyrin Ix With Dna Model Telomeric G-Quadruplex Forming Sequences, Jessica Desamero

Dissertations, Theses, and Capstone Projects

DNA G-quadruplexes are alternative secondary structures formed from guanine rich DNA sequences. G-quadruplexes are found most abundantly at the ends of chromosomes called telomeres, where they can ultimately prevent further tumor growth and progression. Thus, quadruplex interactive agents, or ligands that can bind to and stabilize DNA G-quadruplex structures, are of high interest for their potential chemotherapeutic abilities. One quadruplex interactive agent is the porphyrin N-methyl mesoporphyrin IX (NMM), which has high binding selectivity for quadruplex structures. While the NMM-quadruplex complex in crystallized form has been greatly studied, this complex in solution form is not as well studied. Through circular …

Characterization Of Pathological Tau Mutants, Charles J. Mcdonald

Dissertations, Theses, and Capstone Projects

Tau is a protein expressed exclusively in glia and neurons in the central nervous system and implicated in several neurogenerative diseases called “tauopathies”. Among all the tauopathies, one third is characterized by the presence of genetic mutations leading to the synthesis of tau proteins with single amino acid substitutions at specific locations and affecting protein function. While most of the initial studies have emphasize the functional role of tau as modulator of the axonal cytoskeleton, it has recently been well accepted that tau is also an intrinsically disordered protein that tends to form membraneless organelles called coacervates, due to a …

Magnetically-Driven Therapeutic Agents Delivery System Using Iron Oxide Nanocages And Enhancement Of Exosome Secretion, A Potential Biological Drug Delivery Carrier, Min A Kang

Dissertations, Theses, and Capstone Projects

Nano-scale particles have attracted research attention due to their differences in properties such as penetration, circulation, and toxicity compared to bulk materials. This thesis mainly focused on using 20 nm iron oxide nanoparticles as siRNA delivery carriers under the alternating magnetic field and the development of a method to amplify the secretion of 150 nm exosomes from the cells, which could potentially use as a biological drug carrier.

Chapter 2 discusses a magnetically driven nanoparticle therapeutic agent delivery system, which efficiently modified the gene expression post-transcriptionally. In this work, we examined whether the caged-shaped 20nm iron oxide nanoparticles (IO-nanocages) can …

A Combined Microscopy And Single-Cell Sequencing Approach Reveals The Ecology, Morphology, And Phylogeny Of Uncultured Lineages Of Zoosporic Fungi, Kensuke Seto, D. Rabern Simmons, C. Alisha Quandt, Thijs Frenken, Alden C. Dirks, Rebecca A. Clemons, Katelyn M. Mckindles, R. Michael L. Mckay, Timothy Y. James

Great Lakes Institute for Environmental Research Publications

Environmental DNA analyses of fungal communities typically reveal a much larger diversity than can be ascribed to known species. Much of this hidden diversity lies within undescribed fungal lineages, especially the early diverging fungi (EDF). Although these EDF often represent new lineages even at the phylum level, they have never been cultured, making their morphology and ecology uncertain. One of the methods to characterize these uncultured fungi is a single-cell DNA sequencing approach. In this study, we established a large data set of single-cell sequences of EDF by manually isolating and photographing parasitic fungi on various hosts such as algae, …

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 …

Nanodiscs: A Novel Approach To The Study Of The Methionine Abc Transporter System, Michael T. Winslow

Master's Theses

Membrane transporter proteins play the vital role of moving compounds in and out of the cell and are essential for all living organisms. ATP Binding Cassette (ABC) family transporters function both as importers and exporters in prokaryotes. MetNI is an E. coli Type I ABC transporter responsible for the uptake of methionine into the cytosol from the cell periplasmic space through the cell membrane to maintain intracellular methionine pools. ABC transporters, like other membrane proteins, are most often mechanistically and structurally studied in vitro, solubilized by detergents. However, detergent micelles may affect the conformational changes of membrane proteins relative to …

Relationship Between Plasma Fluoride Levels, Glutathione Peroxidase Activity, Hemoglobin, And Abortion In Rural And Urban Pregnant Women From Settat (Morocco), Lalla Asmaa Katir Masnaoui, Abdellatif Rahim, Habiba Bouchab, Bouchra El Amiri, Boubker Nasser, Essamadi Abdel Khalid

Makara Journal of Health Research

Background: This study aimed to investigate the relationship between plasma fluoride and hemoglobin levels, glutathione peroxidase (GPx) activity, and abortion among rural and urban pregnant women from Settat province (Morocco).

Methods: Blood samples were collected from rural pregnant women who had not undergone abortion (N = 224), rural pregnant women who had an abortion (N = 38), urban pregnant women who had not undergone abortion (N = 163), and urban pregnant women who had an abortion (N = 14).

Results: The highest (p < 0.01) plasma fluoride levels and the lowest (p < 0.01) GPx activity were observed in rural pregnant women. In all participants, plasma fluoride levels were significantly higher (p < 0.001), and the GPx activity was significantly (p < 0.001) lower in pregnant women who had an abortion compared with those who did not undergo such process. No significant difference was observed between the hemoglobin levels of all participants. Furthermore, abortion was positively correlated with plasma fluoride levels (p < 0.001) and negatively correlated with GPx activity (p < 0.001) in rural participants.

Conclusions: Rural pregnant women had higher plasma …

Utilizing Low-Cost Sensors To Monitor Indoor Air Quality In Mongolian Gers, Callum Flowerday, Jaron C. Hansen, Phil Lundrigan, Christopher Kitras

Faculty Publications

Air quality has important climate and health effects. There is a need, therefore, to monitor air quality both indoors and outdoors. Methods of measuring air quality should be cost-effective if they are to be used widely, and one such method is low-cost sensors (LCS). This study reports on the use of LCSs in Ulaanbataar, Mongolia to measure PM_2.5 concentrations inside yurts or “gers”. Some of these gers were part of a non-government agency (NGO) initiative to improve insulating properties of these housing structures. The goal of the NGO was to decrease particulate emissions inside the gers; a secondary result …

State-Of-The-Art Approaches For Sequencing, Assembling And Annotating Naphthenic Acid Degrading Bacterial Metagenomes, Henry H. Say

Electronic Thesis and Dissertation Repository

Naphthenic acids (NAs) are the main toxic component of oil refinery wastewater and require special processes to be removed. Harnessing bacterial biodegradation for NA removal has the potential to be effective, yet NA-degrading bacteria and pathways are poorly understood and uncharacterized. To improve our understanding of NA degradation, I characterize the metagenomes of novel NA-degrading bacterial communities seeded in NA-enriched granulated activated carbon (GAC) filters. I demonstrate methods that maximize the throughput of extraction, sequencing, and annotation of novel metagenomes - producing 72 MAGs and other 5432 circular contigs - 226 of which were putative phages. I also include state-of-the-art …

Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas) Coupled With An Interferometer For On-Band And Off-Band Detection Of Glyoxal, Callum Flowerday, Jaron Hansen, Ryan Thalman

ScholarsArchive Data

These data are the raw data from the BBCEAS. The "data_" files are the PMT data and the "DualDetection_08_02_2023" files are the spectrograph data. The PMT data are found in column 7 of the sheet. Column 1 is the time stamp.

Identification Of A Small Regulatory Rna Usps Associated With The Universal Stress Protein In Lactobacillus Species, Zarah M. Fowler, Sasha S. Bronovitskiy, Finn K. Rose, Brian M. Lee

Journal of the South Carolina Academy of Science

The gut microbiome is a complex habitat with many bacterial species, each playing crucial roles in regulating various physiological processes in the body. As the use of probiotics to combat human disease continues to increase, it is important to understand the mechanisms by which probiotic bacteria regulate their interactions with other bacteria and their host. Our exploration of the physiological functions of probiotic bacteria hopes to elucidate the role of small regulatory RNA (sRNA) in regulating gene expression within the microbiome. The goal of this project was to characterize the structure and function of the sRNA, UspS, which is found …

Morphometric Analysis And Biochemical Estimation Of Wild Shrimps (Family: Penaeidae) Found In Coastal Waters Of Pakistan, Noor Us Saher, Syeda Hadiqa Noor

Journal of Bioresource Management

The world recognition of Seafood nutritional value for human consumption remain consistent throughout the time. Different informations and aspects have been studied and considered and generated various data sets but limited informations found about the biochemical concentration of various fishery species caught in the Pakistan. Therefore, the recent study design to evaluate the proximate levels of components in the edible component (flesh) of commercial shrimp species were studied. Four shrimp species; Fenneropenaeus indicus, Metapenaeopsis stridulans, Metapenaeus stebbingi, and Parapenaeopsis stylifera were selected for the assessment of proximate composition. The selected shrimp species were collected from the fishery catch of Korangi …

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 …