Characterization Of Cytochrome P450 3a4 Structure And Ligand Binding Mechanism In Anionic Nanodiscs, David T. Sweeney

Theses and Dissertations

The Cytochromes P450 superfamily are ubiquitous throughout life and are present in some viruses. Humans encode for 57 of these enzymes that are involved in the metabolism of ~90% of all chemicals. These membrane-bound monooxygenase enzymes utilize a heme protoporphyrin at their active site to activate molecular oxygen and oxidize their substrates through an intermediate deemed nature's most powerful oxidizer. They are a powerful system at our disposal yet understanding of their structure and ligand binding mechanisms in the presence of a lipid bilayer remains poorly understood. The focus of this work is on Cytochrome P450 3A4 (CYP3A4). We set …

Development Of Unnatural Amino Acid Mutagenesis Technologies To Control Enzyme Activity And Synthesis Of Chemically Reactive Ubiquitin Probes, Jenny Cheung

Theses and Dissertations

Most of the work vital for the survival of the cell are performed by proteins. The primary sequence of proteins is composed of 20 canonical amino acids. However, these 20 amino acids do not offer the full range of functionalities needed for proteins to do their job. Often times, post-translational modifications (PTM’s) occur to add the required functional group. This interaction between all the different proteins in the proteome in addition to PTM’s create a complex system that scientists are still trying to unravel to this day. Many different tools had been developed for this purpose, and one such tool …

Detrimental Role Of Irf1 In Myeloid Cells During Influenza Infection, Bianca L. Baum

Theses and Dissertations

The influenza virus is constantly evolving new ways to overcome both innate and vaccine-induced host defenses, making the innate immune response a critical therapeutic target for minimizing morbidity and mortality caused by infection. Here we examined the role that interferon regulatory factor 1 (IRF1) plays in regulating host innate immune responses in myeloid cells. We found that knocking out IRF1 from myeloid cells in mice (IRF1^DMy) led to a partial protection during IAV infection. Interestingly, recruitment of bone marrow derived myeloid cells as well as NLRP3 inflammasome expression were decreased in the lungs of IRF1^DMy mice, whereas …

Virtual Reality Tool For Visualizing The Oral Microbiome, Alexus M. Harris

Theses and Dissertations

There are limited teaching tools for helping both students and patients understand the oral microbiome. It is important to understand the oral microbiome as it heavily influences the health of your oral cavity and the dysbiosis of disease. The oral microbiome influences other aspects of health and serves as an indicator for health. With a greater understanding of the oral microbiome, patients can make healthier lifestyle changes and dentists can better educate their patients. For that reason, the goal of this project was to create a virtual reality tool for visualizing the oral microbiome. The assets for the VR tool …

A Bioinformatic Analysis Of The Biosynthesis Of Carotenoids In The Copepod Tigriopus Californicus, Anchalya Balasubramaniam

Theses and Dissertations (Comprehensive)

Abstract

Biological pigments, also called biochromes, are coloured compounds which are displayed by a variety of life forms, including animals, due to selective colour absorption. The combination of light absorption and reflection enables each pigment to portray a distinct colour which results in the broad spectrum of colours we observe in our surroundings. Carotenoids are a large group of yellow, orange, and red biological pigments found in living organisms. Our current biomolecular knowledge of carotenoids is heavily derived from studying the pathway in photosynthetic prokaryotes, bacteria, fungi, and plants. Carotenoid pigments are exceptionally multifunctional as they act as photo-protectors against …

Photoreceptor Phosphodiesterase (Pde6): Structure, Regulatory Mechanisms, And Implications For Treatment Of Retinal Diseases, Rick H. Cote, Richa Gupta, Michael J. Irwin, Xin Wang

Faculty Publications

The photoreceptor phosphodiesterase (PDE6) is a member of large family of Class I phosphodiesterases responsible for hydrolyzing the second messengers cAMP and cGMP. PDE6 consists of two catalytic subunits and two inhibitory subunits that form a tetrameric protein. PDE6 is a peripheral membrane protein that is localized to the signaling-transducing compartment of rod and cone photoreceptors. As the central effector enzyme of the G-protein coupled visual transduction pathway, activation of PDE6 catalysis causes in a rapid decrease in cGMP levels that results in closure of cGMP-gated ion channels in the photoreceptor plasma membrane. Because of its importance in the phototransduction …

Understanding The Relationship Between Local Environmental Changes And The Function Of The Ph Low Insertion Peptide, Violetta Burns Casamayor

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cancer is the second leading cause of death in the US with over 1.7 million new cases each year. Current cancer treatments tend to also target healthy tissues due to similarities with cancerous ones, resulting in acute side effects. Early detection is the best approach towards defeating cancer, however, modern imaging techniques require sizeable samples, often implying a late stage in the disease. One common attribute of tumors is their acidic microenvironment, which can be taken advantage of.

The pH Low Insertion Peptide (pHLIP) is a membrane-active peptide that can take advantage of the acidic microenvironment surrounding cancer cells. pHLIP …

Applications Of Machine Learning In Microbial Forensics, Ryan B. Ghannam

Dissertations, Master's Theses and Master's Reports

Microbial ecosystems are complex, with hundreds of members interacting with each other and the environment. The intricate and hidden behaviors underlying these interactions make research questions challenging – but can be better understood through machine learning. However, most machine learning that is used in microbiome work is a black box form of investigation, where accurate predictions can be made, but the inner logic behind what is driving prediction is hidden behind nontransparent layers of complexity.

Accordingly, the goal of this dissertation is to provide an interpretable and in-depth machine learning approach to investigate microbial biogeography and to use micro-organisms as …

Spatial And Temporal Comparison Of Persistent Organic Pollutants In The Boardman River, Collin Diedrich

Dissertations, Master's Theses and Master's Reports

Dam removal is a critical part of river and stream remediation projects around the world. Frequently dams are associated with impoundment ponds containing sediments that can act as a sink of various persistent organic pollutants (POPs) that can pose risks for human and aquatic wildlife. In this study, we deployed semi-permeable membrane devices (SPMDs) at multiple locations along a 25-mile stretch of the Boardman River in Traverse City Michigan to passively sample POP concentrations in this area that has recently undergone dam and impoundment pond sediment removal. Concentrations of polychlorinated biphenyl (PCB), di-chloro-diphenyl-trichloroethane (DDT) and cyclodiene compounds were in the …

On The Structure And Function Of Mitochondrial Uncoupling Proteins: The Case Of Ucp2, Afshan Ardalan

Theses and Dissertations (Comprehensive)

Uncoupling proteins (UCPs) are regulated proton transporters of the mitochondrial inner membrane. UCP-mediated proton leak negatively impacts the rate of ATP synthesis. Despite the importance of their physiological role(s) in certain tissues, molecular aspects of UCPs’ structure-function relationships are not fully understood. The current study explores the tertiary and quaternary structure of UCP2, as well as its proton transport mechanism in lipid membranes. The proteins were expressed in the E. coli inner membrane, purified and reconstituted into liposomes. Proteins were characterized by semi-native SDS-PAGE. Circular dichroism spectroscopy (CD) and fluorescence quenching assays were utilized to study the conformation of proteins …

Examining The Effects Of Netropsin On The Mobility Of Dna A-Tracts Using Capillary Electrophoresis, Jillian Miller

Honors Program Theses

A-tracts are sequences of repeated adenine bases that cause a natural curvature of DNA. The biological function of A-tracts is not fully understood. Research into how A-tract sequences affect mobility in an electric field contributes more knowledge in this area. For this research project, the electrophoretic mobility of multiple double-stranded DNA (dsDNA) fragments of the same length, with varying shapes due to the amount and orientation of A-tracts along the helix axis, was studied using capillary electrophoresis under varying conditions with the small molecule netropsin. Previous semesters of research showed a change in mobility due to shape of three fragments …

Optimizing Dna Extraction From Microorganisms Living In Wind Cave, Allison Warming

Honors Program Theses

Wind Cave National Park in South Dakota is home to many creatures, from the giant buffalo to microscopic single-celled organism. This study focused on the single-celled organisms living in Wind Cave. A total of 81 samples were collected and grown on culture media. The goal of this project was to determine which commercially available kit would yield the highest amount of purified DNA from the samples cultured from the cave. Following the protocols provided by the manufacturer, a control sample as well as samples from three plates had their DNA isolated and purified using seven commercially available DNA purification kits. …

Identification Of Fungi And Their Secondary Metabolites From Wind Cave, Kyle Biscoglia

Honors Program Theses

Eighteen fungal samples were isolated from samples of water collected in Wind Cave, South Dakota. Ten of the samples underwent chemical extraction, a growth inhibition test, and were analyzed using proton nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectroscopy. Structural analysis and identification of one secondary metabolite that demonstrated antimicrobial growth inhibition was performed. All eighteen of the fungal samples were able to be identified to the genus level using the ITS region of their DNA, however confident identification of the species level was more difficult to attain just looking at one portion of the sequence.

Physiological Impacts Of Lampricides On Invasive Sea Lamprey (Petromyzon Marinus) And Non-Target Fishes, Razvan, Adrian Ionescu

Theses and Dissertations (Comprehensive)

Parasitic sea lamprey (Petromyzon marinus) ingest large quantities of blood from fishes using their oral disc and rasping tongue, most often killing the host. In the early 1900s, sea lamprey invaded the Laurentian Great Lakes, decimating sport, commercial and culturally significant fisheries. Since the early 1960s, chemical control using the lampricides 3- trifluoromethyl-4-nitrophenol (TFM) and niclosamide have helped to reduce sea lamprey populations by 90%. Lampricides are applied to larval lamprey nursery streams targeting many generations of lamprey at once. However, there is concern about the potential adverse effects of lampricides on other fishes, particularly vulnerable lake sturgeon (Acipenser fulvescens) …

Molecular Mechanism Of Cyanobacteria Circadian Clock Oscillator And Effect Of Co Factors On Its Oscillation, Manpreet Kaur

Dissertations

The circadian rhythms arise as an adaptation to the environmental 24-hour day and night cycle due to Earth's rotation. These rhythms prepare organisms to align their internal biological activities and day to day behavior or events with the environmental change of the 24-hour day and night cycle. Circadian rhythms are found widely in all living kingdoms of life on Earth. Cyanobacteria are photosynthetic prokaryotes which first used to study these circadian rhythms. Among cyanobacterial species, Synechococcus elongatus PCC 7942 (henceforth, S. Elongatus) is the simplest organism with a durable and sturdy circadian clock and is study as a model organism. …

Preliminary Phytochemical Screening, Proximate Analysis, Antioxidant And Antibacterial Activities Of An Algal Species Of Hydrodictyon Reticulatum, Mubashrah Munir, Arshad Mahmood Khan, Rahmatullah Qureshi, Sidra Murtaza, Mehmooda Munazir

Journal of Bioresource Management

The freshwater algae grow in a wide range of aquatic habitats across the globe and are rich in secondary metabolites. The present study was designed to conduct the phytochemical screening, proximate analysis, antioxidant and antibacterial activities of water net (Hydrodictyon reticulatum), an algal weed from Pakistan. The pure and dried algal mass was crushed into a fine powder and four solvent-based extracts were used for phytochemical screening. The results of preliminary qualitative screening indicated the presence of flavonoids, phenols, quinones, steroids, resins, anthraquinones, glycosides, lignin, proteins, saponins, tannins, reducing sugars, alkaloids, terpenoids, fats, and oils, whereas the quantification …

The Supercam Instrument Suite On The Nasa Mars 2020 Rover: Body Unit And Combined System Tests, Roger C. Wiens, Sylvestre Maurice, Scott H. Robinson, Anthony E. Nelson, Philippe Cais, Pernelle Bernardi, Raymond T. Newell, Sam Clegg, Shiv K. Sharma, Steven Storms, Jonathan Deming, Darrel Beckman, Ann M. Ollila, Olivier Gasnault, Ryan B. Anderson, Yves André, Stanley M. Angel, Gorka Arana, Elizabeth Auden, Pierre Beck, Et. Al.

Faculty Publications

The SuperCam instrument suite provides the Mars 2020 rover, Perseverance, with a number of versatile remote-sensing techniques that can be used at long distance as well as within the robotic-arm workspace. These include laser-induced breakdown spectroscopy (LIBS), remote time-resolved Raman and luminescence spectroscopies, and visible and infrared (VISIR; separately referred to as VIS and IR) reflectance spectroscopy. A remote micro-imager (RMI) provides high-resolution color context imaging, and a microphone can be used as a stand-alone tool for environmental studies or to determine physical properties of rocks and soils from shock waves of laser-produced plasmas. SuperCam is built in three parts: …

A Molecular Toolset For The In Vivo Detection Of A Sulfolobus Islandicus Leucyl Trna Synthetase Paralog, Nicholas Michael Bretz

Theses and Dissertations

An ancient and ubiquitous set of enzymes known as the aminoacyl-tRNA synthetases are required for the viability of all organisms. The aminoacyl-tRNA synthetases catalyze the attachment of amino acids onto tRNA molecules. The aminoacylated, or charged, tRNA is then transported and utilized at the ribosome for the synthesis of proteins. The genome of the hyperthermophilic microorganism Sulfolobus islandicus (S. islandicus) harbors a unique leucyl-tRNA synthetase paralog, LeuRS-I, of unknown function. While its duplicate, LeuRS-F, carries out all the classical functions of LeuRS-family enzymes, LeuRS-I fails to charge leucine onto tRNALeu, despite its ability to activate this amino acid and bind …

Applied Molecular Dynamics: From Targeting Viral Helicases, To Understanding The Interactions Of Cucurbituril Complexes In Ionic Solutions, Bryan Raubenolt

LSU New Orleans Theses and Dissertations

Molecular Dynamics simulations are a highly useful tool in helping understand the fundamental interactions present in a variety of chemical systems. The work discussed here illustrates it’s use in determining the conformational dynamics of the Zika and SARS-Cov-2 helicase in a physiological environment, largely in an effort to discover inhibitors capable of rendering the protein inert. Additionally, we show how it can be used to understand paradoxical trends in the anion-induced precipitation of Cucurbituril cavitands.

Viral helicases are motor proteins tasked with unwinding the viral dsRNA, a crucial step in preparing the strand to be translatable by host cells. By …

Rna Structure And Function: Biological Relevance In Neurodegenerative And Infectious Disease Pathogenesis, Joshua Imperatore

Electronic Theses and Dissertations

The studies outlined in this dissertation encompass a broad focus, relating to the pathogenesis of neurological disorders such as Alzheimer’s disease, fragile X syndrome, and amyotrophic lateral sclerosis, as well as a novel infectious disease, COVID-19. However, all four studies detailed within this dissertation contain similar elements, namely, the coordinated role of RNA structure and function in essential molecular mechanisms. The results of these investigations allow us to speculate on various disease- related mechanisms, including dysregulated microRNA processing pathways, nucleocytoplasmic shuttling via distinct RNA-protein interactions, and fine-tuned molecular switches controlling genomic dimerization and viral hijacking of host cellular microRNAs. Taken …