Life Sciences Commons^™

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 …

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 …

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: …

Investigation Of Shot1-Binding Atpases In Arabidopsis Thaliana, Sam Zelman

Masters Theses

Mitochondria play critical roles not only in primary metabolism as a central organelle for ATP generation, but also in responding to abiotic stresses. We identified a mutation in the MTERF18 (Mitochondrial Transcription Termination factor)/SHOT1 (Suppressor of hot1-4 1) gene in Arabidopsis thaliana that enables plants to better tolerate heat and oxidative stresses, presumably due to reduced oxidative damage, but the exact molecular mechanism of the heat tolerance is unknown. In order to reveal the stress tolerance mechanisms of mterf18/shot1 mutations, it is critical to understand the molecular defects of the mutant and to identify …

Assessing Stress Tolerance Of Organelle Small Heat Shock Protein Mutants In Arabidopsis Thaliana, Parth Patel

Masters Theses

Molecular chaperones are proteins found in virtually every organism and are essential to cell survival. When plants are heat stressed, they upregulate and downregulate multiple genes, many of which are associated with the heat shock response. Small heat shock proteins (sHSPs) are one class of molecular chaperones that are upregulated during heat shock. They are proposed to act as the first line of defense by binding to heat sensitive proteins and preventing their irreversible aggregation. However, many details of sHSP function remain to be discovered and exactly what proteins they protect is unresolved. In addition to cytosolic sHSPs found in …

A Rational Design Approach To Developing Second Generation Fabry Disease Treatments, Matthew Metcalf

Doctoral Dissertations

Fabry disease is an X-linked lysosomal storage disorder that affects approximately 1 in 40,000 males in its classical form and as many as 1:4,600 in its late-onset form [1]. The disease is caused by mutations in the gene encoding α- galactosidase (α-GAL), which results in deficient levels of α-GAL activity in the lysosomes of patients [2, 3]. This lack of enzymatic activity causes macromolecular substrates to accumulate in tissues, and can result in a wide range of symptoms such as impaired renal and cardiac function [4]. The severity of disease is linked to the amount of residual …

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 …

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

University of 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 …

Investigating The Accumulation, Sub-Organ Distribution, And Biochemical Effects Of Nanomaterials Using Mass Spectrometry, Kristen Nicole Sikora

Doctoral Dissertations

Gold nanoparticles (AuNPs) are attractive materials for use in various biomedical applications, such as therapeutic delivery, due to their unique chemical properties and modular tunability. Mass spectrometry methods, including laser desorption/ionization mass spectrometry (LDI-MS) and inductively coupled plasma mass spectrometry (ICP-MS) have been successfully used to evaluate the distribution of AuNPs in complex biological systems. As new AuNP-based materials are developed for applications in therapeutic delivery, it is essential to simultaneously develop analytical techniques that can comprehensively assess their behavior in vivo. In this dissertation, novel mass spectrometric methods have been developed and utilized to evaluate the uptake, distribution, …

Mechanisms By Which Mnte-2-Pyp Suppresses Prostate Cancer Cell Growth, Yuxiang Zhu

Theses & Dissertations

Prostate cancer patients are often treated with radiotherapy. MnTE-2-PyP, is a superoxide dismutase (SOD) mimic and a known radioprotector of normal tissues. Our recent work demonstrates that MnTE-2-PyP also inhibits prostate cancer progression with radiotherapy; however, the mechanisms remain unclear. In this thesis, we identified that MnTE-2-PyP-induced intracellular H2O2 levels are critical in inhibiting growth of prostate cancer cells. We found that MnTE-2-PyP induced protein oxidations in PC3 cells and one major group of oxidized protein targets were involved in energy metabolism. The oxidative phosphorylation rates were significantly enhanced in both PC3 and LNCaP cells with MnTE-2-PyP treatment, but mitochondrial …

Examining The Function Of Protein Acyltransferase Via The Dhhc Domain Of The Paz5 Protein In The Organism Dictyostelium Discoideum, George M. Stuart-Ranchev

Electronic Theses and Dissertations

Protein S-palmitoylation plays a crucial role in many biological systems. S-palmitoylation involves the post-translational attachment of palmitate to a cysteine residue through a reversible thioester linkage. S-Palmitoylation is used to modify both integral and membrane proteins, many of which are involved in intracellular trafficking, membrane localization, and signal transduction pathways. Intracellular palmitoylation is mediated by a family of protein acyltransferases (PATs). PAT mutations are associated with neurological diseases and cancer progression. Proteins in the PAT family are defined by the presence of a 51-amino acid cysteine-rich domain (CRD), which contains a highly conserved aspartate-histidine-histidine-cysteine (DHHC) motif. The …

Determination And Dissection Of Dna-Binding Specificity For The Thermus Thermophilus Hb8 Transcriptional Regulator Tthb099, Kristi Moncja

Master of Science in Chemical Sciences Theses

Transcription factors (TFs) have been extensively researched in certain well-studied organisms but far less so in others. Following the whole-genome sequencing of a new organism, TFs are typically identified through their homology with related proteins in other organisms. However, recent findings demonstrate that structurally similar TFs from distantly related bacteria are not usually evolutionary orthologs. Here we explore TTHB099, a cAMP receptor protein (CRP)-family TF from the extremophile Thermus thermophilus HB8. Using the in vitro iterative selection method Restriction Endonuclease Protection, Selection and Amplification (REPSA), we identified the preferred DNA-binding motif for TTHB099, 5'-TGT(A/g)n(t/c)c(t/c)(a/g)g(a/g)n(T/c)ACA-3', and mapped potential binding sites, and …

Micro-Physiological Models To Mimic Mucosal Barrier Complexity Of The Human Intestine In Vitro, Abhinav Sharma

Doctoral Dissertations

The mucosal barrier in the intestine is vital to maintain selective absorption of nutrients while protecting internal tissues and maintaining symbiotic relationship with luminal microbiota. This bio-barrier consists of a cellular epithelial barrier and an acellular mucus barrier. Secreted mucus regulates barrier function via in situ biochemical and biophysical interaction with luminal content that continually evolves during digestion and absorption. Increasing evidence suggests that a mucus barrier is indispensable to maintain homeostasis in the gastrointestinal tract. However, the importance of mucus barrier is largely underrated for in vitro mucosal tissue modeling. The major gap is the lack of experimental material …

Elucidating The Role Of Ecdysoneless In Mrna Processing, Irfana Saleem

Theses & Dissertations

The mammalian orthologue of the evolutionarily conserved Ecdysoneless (ECD) protein is required for embryogenesis, cell cycle progression and mitigation of ER stress. However, the molecular mechanisms of ECD function in mammalian cells remain unclear. Here, using mass spectrometry analysis of the mammalian ECD interactome, we identified several components of the mRNA export complexes as binding partners of ECD and then characterized the functional interaction of ECD with key mRNA export-related DEAD BOX protein helicase DDX39A and its associated partners. FISH analysis of Poly-A-tailed mRNAs revealed that ECD depletion/deletion blocks the mRNA export from the nucleus to the cytoplasm. We have …

Deciphering The Catalytic Mechanism Of Human Manganese Superoxide Dismutase, Jahaun Azadmanesh

Theses & Dissertations

The livelihood of human cells is heavily dependent on the ability to modulate the presence of highly reactive oxygen-based molecules termed reactive oxygen species (ROS). In excess, ROS facilitate oxidative damage to the macromolecules of cellular life. SODs are the major family of antioxidant proteins that prevent the buildup of overwhelming amounts of ROS within cells. Sometimes dubbed the “first line of defense” against oxidative damage, SODs defend against the harmful accumulation of ROS by eliminating superoxide. Superoxide is a ROS itself that is also a precursor to much more harmful ROS molecules. MnSOD is the manganese containing form of …

Single-Fluorophore Sensors For Mechanical Force In Living Cells, Sarah Kricheff

Honors Scholar Theses

Mechanotransduction is the process by which a mechanical stimulus is converted to a cellular signal. This process is heavily influential of cell morphology, differentiation, and behavior. However, altered levels of mechanical stimuli are also found in many pathological contexts. For example, cancerous cells have stiffer surrounding tissue than healthy cells, and research suggests that this alters cell behavior and promotes metastasis. Despite these findings, the cellular processes behind these signaling alterations remain widely unknown. Understanding these cascades is critical, as involved proteins can give us a deeper understanding of the role of mechanotransduction, and certain proteins can potentially be targeted …

Pathway‐Extended Gene Expression Signatures Integrate Novel Biomarkers That Improve Predictions Of Patient Responses To Kinase Inhibitors, Ashis Bagchee‐Clark, Eliseos J. Mucaki, Tyson Whitehead, Peter Rogan

Biochemistry Publications

Cancer chemotherapy responses have been related to multiple pharmacogenetic biomarkers, often for the same drug. This study utilizes machine learning to derive multi‐gene expression signatures that predict individual patient responses to specific tyrosine kinase inhibitors, including erlotinib, gefitinib, sorafenib, sunitinib, lapatinib and imatinib. Support vector machine (SVM) learning was used to train mathematical models that distinguished sensitivity from resistance to these drugs using a novel systems biology‐based approach. This began with expression of genes previously implicated in specific drug responses, then expanded to evaluate genes whose products were related through biochemical pathways and interactions. Optimal pathway‐extended SVMs predicted responses in …

Sestrins: Emerging Dynamic Stress-Sensors In Metabolic And Environmental Health, Seung Hyun Ro, Julianne Fay, Cesar I. Cyuzuzo, Yura Jang, Naeun Lee, Hyun Seob Song, Edward N. Harris

Department of Biochemistry: Faculty Publications

Proper timely management of various external and internal stresses is critical for metabolic and redox homeostasis in mammals. In particular, dysregulation of mechanistic target of rapamycin complex (mTORC) triggered from metabolic stress and accumulation of reactive oxygen species (ROS) generated from environmental and genotoxic stress are well-known culprits leading to chronic metabolic disease conditions in humans. Sestrins are one of the metabolic and environmental stress-responsive groups of proteins, which solely have the ability to regulate both mTORC activity and ROS levels in cells, tissues and organs. While Sestrins are originally reported as one of several p53 target genes, recent studies …

Computer Simulations Of Biological Systems: From Protein Dynamics To Drug Discovery, Rupesh Agarwal

Doctoral Dissertations

Computational biophysics methods such as molecular dynamics (MD) simulations are often used in combination with experimental techniques like neutron scattering, NMR, and FTIR to explore protein conformational landscapes. With the improvements in experimental techniques, there is also a need to continually optimize the MD forcefield parameters to make precise predictions that match experimental results. To complement many of these experiments, an accurate model of deuteration is frequently required, but has been elusive. In our work, we developed a novel method to capture isotope effects in classical MD simulations by re-parameterization of the bonded terms of the CHARMM forcefield using quantum …

Finding The Balance​ The Effects Of Α-Cyclodextrin, 2-Hydroxypropyl-Β-Cyclodextrin, And Cholesterol Bacteroides Vulgatus And Clostridium Bolteae​, Bethany Weaver

Pence-Boyce STEM Student Scholarship

Atherosclerosis is a cardiovascular disease that is characterized by the hardening of arteries through the formation of cholesterol plaques. Cyclodextrins could potentially treat atherosclerosis by shrinking plaques. These cyclic oligosaccharides can make complexes with cholesterol but have also shown toxic side effects. This study looked for potential negative effects of cyclodextrins and cholesterol on gut bacteria. It was hypothesized that Bacteroides vulgatus will have decreased growth when grown in broth with cholesterol. In contrast, Clostridium bolteae will have decreased growth when grown in broth with cyclodextrins. Due to the fact that these bacteria are anaerobic, Clostridium bolteae and Bacteroides vulgatus …

Structural Characterization Of Two Large Icosahedral Dna Viruses And Their Capsid Assembly Mechanisms, Yuejiao Xian

Open Access Theses & Dissertations

In the last three decades, many large DNA viruses were discovered and grouped into a loosely defined clade of Nucleocytoplasmic Large DNA Viruses (NCLDVs). NCLDVs infect a wide range of hosts from single cellular protists to large animals. Recently, these viruses were classified as a new phylum of Nucleocytoviricota under the kingdom of Bamfordvirae. The genomes of these Nucleocytoviricota viruses (NCVs) are remarkedly large and complicated, containing many cellular genes from all three domains of life, which raised intensive debates on their evolutionary origins. Despite being classified in the same phylum, their physical structures vary and can be roughly classified …

Unconventional Constituents And Shared Molecular Architecture Of The Melanized Cell Wall Of C. Neoformans And Spore Wall Of S. Cerevisiae, Christine Chrissian, Coney Pei-Chin Lin, Emma Camacho, Arturo Casadevall, Aaron M. Neiman, Ruth E. Stark

Publications and Research

The fungal cell wall serves as the interface between the cell and the environment. Fungal cell walls are composed largely of polysaccharides, primarily glucans and chitin, though in many fungi stress-resistant cell types elaborate additional cell wall structures. Here, we use solid-state nuclear magnetic resonance spectroscopy to compare the architecture of cell wall fractions isolated from Saccharomyces cerevisiae spores and Cryptococcus neoformans melanized cells. The specialized cell walls of these two divergent fungi are highly similar in composition. Both use chitosan, the deacetylated derivative of chitin, as a scaffold on which a polyaromatic polymer, dityrosine and melanin, respectively, is assembled. …

The Circadian Clock—A Molecular Tool For Survival In Cyanobacteria, Pyonghwa Kim, Manpreet Kaur, Hye-In Jang, Yongick Kim

Chemistry Faculty Research

Cyanobacteria are photosynthetic organisms that are known to be responsible for oxygenating Earth’s early atmosphere. Having evolved to ensure optimal survival in the periodic light/dark cycle on this planet, their genetic codes are packed with various tools, including a sophisticated biological timekeeping system. Among the cyanobacteria is Synechococcus elongatus PCC 7942, the simplest clock-harboring organism with a powerful genetic tool that enabled the identification of its intricate timekeeping mechanism. The three central oscillator proteins—KaiA, KaiB, and KaiC—drive the 24 h cyclic gene expression rhythm of cyanobacteria, and the “ticking” of the oscillator can be reconstituted inside a test tube just …

Sine Oculis Homeobox Homolog 1 (Six1) Plays A Critical Role In The Progression Of Pulmonary Fibrosis., Cory Wilson

Dissertations & Theses (Open Access)

Idiopathic pulmonary fibrosis (IPF) is the most common idiopathic interstitial pneumonia with a median survival time of 2-4 years after diagnosis. The alarming mortality rate is due to the lack of effective treatments. IPF is a chronic disease that is characterized by alveolar destruction due to increasing extracellular matrix deposition that leads to poor lung compliance, impaired gas exchange, and ultimately respiratory failure. Repetitive alveolar epithelial injury is a central process to the underlying pathology with injury to the type II alveolar epithelial cells (AT2) specifically being a key player in the pathogenesis of IPF. Recent studies have shown that …

The Impact Of Microbial Experience On The Murine Innate Immune Response, Cody Thomas Morrison

Masters Theses

The hygiene hypothesis predicts that certain environmental factors shape overall immune system function in animals and humans. While current specific pathogen free (SPF) mouse models are invaluable for studying the immune system, they have limitations for comparison with humans who have microbial exposures throughout their lifetimes. Several studies have shown that the composition of the immune system of SPF mice more closely resembles that of newborns, whereas the immune system from mice exposed to microbial pathogens more closely reflect adult immunity. In this study we have established a model using traditional SPF mice (“clean mice”) and SPF mice that were …

Using Second Harmonic Generation To Study Gram-Positive Bacterial Membranes, Lindsey N. Miller

Doctoral Dissertations

Understanding how small-molecules, such as drugs, interact with bacterial membranes can quickly unravel into much more perplexing questions. No two bacterial species are alike, especially when comparing their membrane compositions which can even be altered by incorporating fatty acids from their surrounding environment into their lipid-membrane composition. To further complicate the comparison, discrete alterations in small-molecule structures can result in vastly different membrane-interaction outcomes, giving rise to the need for more "label-free" studies when analyzing drug mechanisms. The work presented in this dissertation highlights the benefits to using nonlinear spectroscopy and microscopy techniques for probing small-molecule interactions in living bacteria. …

Degree Of Conservation Of Methionines Found To Be Oxidized In The Human Urinary Proteome, Alexis Hall

Graduate Theses and Dissertations

In previous work from this laboratory, methionine containing peptides from the human urinary proteome were examined by mass spectrometry for the degree of methionine oxidation to the sulfoxide form. While this demonstrated that many of the methionines detected were capable of being oxidized, the question of whether these methionines are important in the structure and/or function of the parent proteins came about. In some proteins, methionine oxidation has been linked to conformational changes and alteration of function and thus can serve as a mechanism for reversible regulation of activity. It is hypothesized that methionines which might serve a regulatory purpose …

Ionic Mechanism Of Lysosomal Function And Cell Metabolism, Jian Xiong

Dissertations & Theses (Open Access)

Two Pore Channels (TPCs) are endolysosomal ion channels that are permeable to sodium and calcium. Defects in TPCs have been implicated to impair vesicle trafficking, autophagy and cell metabolism control; however, the detailed mechanism remains largely unknown. In this study, I show that TPCs are critical for appropriate cargo delivery to the lysosomes and deletion of either TPC1 or TPC2 leads to delayed clearance of autophagosomes, resulting in enlarged lysosomes and accumulated contents inside the lysosomes. Cells with both TPC deleted also exhibit 50% reduction in lysosomal amino acids under normal culture conditions, leading to reduced homeostatic mTORC1 activation.

Glutamine …

A Mechanistic Investigation Of Cytochrome C Nitrite Reductase Catalyzed Reduction Of Nitrite To Ammonia: The Search For Catalytic Intermediates, Shahid Shahid

Theses and Dissertations

Cytochrome c Nitrite Reductase (ccNiR) is a periplasmic homodimeric decaheme enzyme that catalyzes the reduction of nitrite to ammonium in a process that involves six electrons and eight protons. Under standard assay conditions, which use a strong reducing agent as an electron source, catalysis takes place rapidly without producing detectable intermediates. However, intermediates do accumulate when weaker reducing agents are employed, allowing the ccNiR mechanism to be studied. Herein, the early stages of Shewanella oneidensis ccNiR-catalyzed nitrite reduction were investigated in isolation by using the weak reducing agents N,N,N’,N’-tetramethyl-p-phenylenediamine (TMPD) and the 2-electron reduced form of indigo trisulfonate. Experiments were …