Biochemistry, Biophysics, and Structural Biology Commons^™

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 …

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 …

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 …

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 …

A Small Molecule Screen On Zebrafish Embryos Identifies Pathways Vital To Hypaxial Muscle Precursor Migration, Teresa Easterbrooks

Electronic Theses and Dissertations

Hypaxial muscles form through long-range migration of muscle precursor cells (MMPs) from the somites. In zebrafish, the MMPs migrate in three compact streams to generate four muscles - the sternohyoideus muscle, homologous to mammalian neck and tongue; the posterior hypaxial muscle; and the two pectoral fin muscles, homologous to mammalian limbs. Several factors, such as Six1/4, are known to promote this migration; however, many aspects of guidance, pathing, and modulation of these streams are still unknown. To fill this gap, we conducted a small-molecule screen. This pharmacological approach allows us to identify molecules that cause pronounced changes in the normal …

Endothelial Interleukin-17 Receptor D (Il17rd) Promotes Western Diet-Induced Aortic Myeloid Cell Infiltration, Shivangi Pande

Electronic Theses and Dissertations

The Interleukin-17 (IL17) family is a group of cytokines implicated in the etiology of several inflammatory diseases. Interleukin-17 receptor D (IL17RD), also known as Sef (similar expression to fibroblast growth factor), belonging to the family of IL17 receptors, has been shown to modulate IL17A-associated inflammatory phenotypes. The objective of this study was to test the hypothesis that IL17RD promotes endothelial cell activation and consequent monocyte adhesion. We utilized primary human aortic endothelial cells and demonstrated that RNAi targeting of IL17RD suppressed transcript levels by 83% compared to non-targeted controls. Further, RNAi knockdown of IL17RD decreased the adhesion of THP-1 cells …

The Effects Of Resistance Exercise Training On Insulin Resistance Development In Female Rodents With Type 1 Diabetes, Mitchell James Sammut

Electronic Thesis and Dissertation Repository

The etiology of insulin resistance (IR) development in type 1 diabetes mellitus (T1DM) remains unclear; however, impaired skeletal muscle metabolism may play a role. While IR development has been established in male T1DM rodents, female rodents have yet to be examined in this context. Resistance exercise training (RT) has been shown to improve IR and is associated with a lower risk of hypoglycemia onset in T1DM compared to aerobic exercise. Additionally, the molecular mechanisms mediating RT-induced improvements in insulin sensitivity remain unclear. Therefore, the purpose of this study was to investigate the effects of RT on IR development in female …

Rural Science Teachers Social Network Analysis Matrices, Rebecca L. Sansom, Tracy Poulsen

ScholarsArchive Data

These are the social network matrices for our study of rural science teachers. Each matrix is located on a separate tab on the spreadsheet.

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 …

Rhythms In Rna And Proliferation In Intestinal Stem Cell Organoids, Kristina Skurvidayte

Electronic Theses and Dissertations

The circadian clock is a transcription-translation feedback loop that controls our body’s daily rhythms. Previous work in our lab has shown that the circadian clock controls regeneration in the small intestinal epithelium and that the Hippo signaling pathway may serve as a link between regeneration and the circadian clock. In order to elucidate if the circadian clock directly controls the Hippo pathway as well as the Wnt pathway, both vital for intestinal homeostasis, intestinal stem cell-derived organoids, a 3D culture system that is able to recapitulate the cell biology of the intestinal epithelium in vitro, were used to examine the …

Dynamics Of Site Search Process And Formation Of Synaptosome Assembly Characterized By Single Molecule Approaches, Sridhar Vemulapalli

Theses & Dissertations

Genome dynamics and integrity are the two crucial features defining the successful functioning of cells and their maintenance and evolution. The genetic processes in the cell require distant communications between the regulatory regions controlled by specific proteins. Mistakes in this interaction process will lead to termination of the genetic process may lead to the cell damage, disease development or the cell death. Similar distant regulatory process is required for numerous genome integration systems such as Variable Diversity Joining (V(D)J) recombination system resulting in the specificity of the immunoresponse, a defining property of the adaptive immune system. A common feature of …

Exploiting Vulnerabilities In The Ras-Rac Signaling Pathway For The Selective Targeting Of Pancreatic Cancer Cells, Neha Chaudhary

Theses & Dissertations

Deregulation of the KRas (Kirsten rat sarcoma virus) GTPase is one of the early hallmarks of Pancreatic Cancer (PC). The most common genetic alteration found in PC are mutations in the KRas protein that block its ability to hydrolyze GTP to GDP and resulting in higher levels of GTP-bound KRas, its active form. Pancreatic tumors driven by oncogenic mutants of KRas tend to be addicted to the oncogene, to the extent that its repression leads to the induction of cell death. This addiction to the KRAS oncogene makes the KRas protein an ideal target for cancer therapy. However, the globular …

Gap Junctional Intercellular Communication: Role Of Cx43 Phosphorylation By Tyrosine Kinases, Ishika Basu

Theses & Dissertations

Phosphorylation of Cx43 is a process that regulates various functionalities of the gap junction including assembly, stability, internalization, turnover, channel permeability and channel gating. Src has been shown to phosphorylate Cx43 at Y247, Y265, Y313 and regulate gap junctions. Intercellular communication in B and T cells is necessary to mediate adaptive immune response. However, there is little-to-no expression of Src in these lymphocytes. An in vitro kinase screen identified Bruton’s tyrosine kinase (BTK) and Interleukin 2-inducible T-cell kinase (ITK) to phosphorylate Cx43. Mass spectrometry identified Tyr residues to be phosphorylated by BTK and ITK, and these residues are similar to …

Profiling And Verifying The Substrates Of E3 Ubiquitin Ligase Rsp5 In Yeast Cells, Shuai Fang, Geng Chen, Yiyang Wang, Rakhee Ganti, Tatiana A Chernova, Li Zhou, Savannah E Jacobs, Duc Duong, Hiroaki Kiyokawa, Yury O Chernoff, Ming Li, Natalia Shcherbik, Bo Zhao, Jun Yin

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

Yeast is an essential model organism for studying protein ubiquitination pathways; however, identifying the direct substrates of E3 in the cell presents a challenge. Here, we present a protocol for using the orthogonal ubiquitin transfer (OUT) cascade to profile the substrate specificity of yeast E3 Rsp5. We describe steps for OUT profiling, proteomics analysis, in vitro and in cell ubiquitination, and stability assay. The protocol can be adapted for identifying and verifying the ubiquitination targets of other E3s in yeast. For complete details on the use and execution of this protocol, please refer to Wang et al.