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Articles 1 - 21 of 21
Full-Text Articles in Life Sciences
Applied Molecular Dynamics: From Targeting Viral Helicases, To Understanding The Interactions Of Cucurbituril Complexes In Ionic Solutions, Bryan Raubenolt
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 …
Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso
Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso
University of New Orleans Theses and Dissertations
One of the most important gene families to play a role in adaptive immunity is the major histocompatibility complex (MHC). MHC class II loci are considered to be the most variable loci in the vertebrate genome, and studies have shown that this variability can be maintained through complex co-evolutionary dynamics between host and parasite. Despite the rich body of research into the MHC, there is comparatively little understanding of its genomic architecture in reptiles. Similarly, loci associated with innate immunity have received little attention in reptiles compared to other vertebrates. In the first chapter, we investigated the structure and organization …
Effective Statistical Energy Function Based Protein Un/Structure Prediction, Avdesh Mishra
Effective Statistical Energy Function Based Protein Un/Structure Prediction, Avdesh Mishra
University of New Orleans Theses and Dissertations
Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D structure, have dynamic characteristics and therefore, exist in multiple states. Based on …
Characterization Of Genes Involved In The Biosynthesis Of Phycoerythrin I And Ii In Cyanobacteria, Adam Nguyen
Characterization Of Genes Involved In The Biosynthesis Of Phycoerythrin I And Ii In Cyanobacteria, Adam Nguyen
University of New Orleans Theses and Dissertations
Cyanobacteria are photosynthetic prokaryotes that able to produce oxygen. They have light harvesting complexes called phycobilisomes (PBS). PBS are generally composed of an allophycocyanin core with phycocyanin and phycoerythrin rods connected to the core. PBS are able to efficiently harvest light energy from different wavelengths of visible light due to the evolution of PBP. Phycoerythrin has five chromophores that are attached to six cysteine residues and is essential for efficient green light capture and transfer of energy for use in photosynthesis. The attachment of these chromophores to PBP is facilitated by enzymes known as bilin lyases.
In this study, we …
Machine Learning Based Protein Sequence To (Un)Structure Mapping And Interaction Prediction, Sumaiya Iqbal
Machine Learning Based Protein Sequence To (Un)Structure Mapping And Interaction Prediction, Sumaiya Iqbal
University of New Orleans Theses and Dissertations
Proteins are the fundamental macromolecules within a cell that carry out most of the biological functions. The computational study of protein structure and its functions, using machine learning and data analytics, is elemental in advancing the life-science research due to the fast-growing biological data and the extensive complexities involved in their analyses towards discovering meaningful insights. Mapping of protein’s primary sequence is not only limited to its structure, we extend that to its disordered component known as Intrinsically Disordered Proteins or Regions in proteins (IDPs/IDRs), and hence the involved dynamics, which help us explain complex interaction within a cell that …
Negative Regulation Of Haa1 By Casein Kinase I Protein Hrr25 In Saccharomyces Cerevisiae, Morgan Collins
Negative Regulation Of Haa1 By Casein Kinase I Protein Hrr25 In Saccharomyces Cerevisiae, Morgan Collins
University of New Orleans Theses and Dissertations
Haa1 is a transcription factor that adapts Saccharomyces cerevisiae cells to weak organic acid stresses by activating the expression of various genes. How Haa1 is activated by weak acids is not clear. This study proposes that Hrr25 is an important regulator of cellular adaptation to weak acid stress by inhibiting Haa1 through phosphorylation. YRO2, one of the targets of Haa1, shows increase in expression during stationary phase. This increase is due to basal activity of Haa1 and another, unknown, transcription factor. This study proposes that Gsm1 is another transcription factor that regulates YRO2 expression in the stationary phase. Finally, …
Characterization Of Genes Involved In Phycobiliprotein Biosynthesis In Fremyella Diplosiphon And Thermosynechococcus Elongatus, Christina M. Kronfel
Characterization Of Genes Involved In Phycobiliprotein Biosynthesis In Fremyella Diplosiphon And Thermosynechococcus Elongatus, Christina M. Kronfel
University of New Orleans Theses and Dissertations
Cyanobacteria are photosynthetic organisms that efficiently capture light by utilizing the light-harvesting complexes called phycobilisomes. In many cyanobacteria, phycobilisomes are composed of an allophycocyanin core with phycocyanin and phycoerythrin (PE) rods radiating from the core. These phycobiliproteins have multiple bilin chromophores, such as phycoerythrobilin (PEB), covalently attached to specific cysteine (Cys) residues for efficient photosynthetic light capture. Chromophore ligation on phycobiliprotein subunits occurs through bilin lyase catalyzed reactions.
This study mainly focuses on characterizing the roles of enzymes that are involved in the biosynthetic pathway of the phycobiliproteins within two cyanobacteria Thermosynechococcus elongatus and Fremyella diplosiphon. A combination of molecular …
Purification And Characterization Of Antibodies Against Killifish Hif-1Α, Janet Gonzalez-Rosario
Purification And Characterization Of Antibodies Against Killifish Hif-1Α, Janet Gonzalez-Rosario
University of New Orleans Theses and Dissertations
Many fish face low oxygen concentrations (hypoxia) in their natural environments, and they respond to hypoxia through a variety of behavioral, physiological, and cellular mechanisms. Some of these responses involve changes in gene expression. In mammals, the hypoxia inducible factor (HIF) family of transcription factors are the “master regulators” of gene expression during hypoxia, but the study of HIF in fish has been hampered by the lack of reagents to detect this protein in non-mammalian vertebrates. The goals of this thesis are to affinity purify antibodies against HIF from the killifish Fundulus heteroclitus and use them to recover and quantify …
A Novel Transcription Factor In Arabidopsis Thaliana Abiotic Stress Response, Achira S. Weerathunga Arachchilage
A Novel Transcription Factor In Arabidopsis Thaliana Abiotic Stress Response, Achira S. Weerathunga Arachchilage
University of New Orleans Theses and Dissertations
Plants respond to environmental stress by altering their gene expression. Under stress conditions some genes are activated and some genes are repressed. Even though a lot of work has been done to understand mechanisms of gene activation under abiotic stress very little information is available on how stress responsive genes are kept repressed under normal growth conditions. Recent work has revealed that plants use transcriptional repression as common mechanism of gene repression. Transcriptional repression is achieved by recruitment co-repressor complexes to the target genes. Recent studies have revealed that the co-repressor LUH complexes with SLK1 and SLK2 to silence Arabidopsis …
Role Of Ime4 Protein In Pho Regulon Of S.Cerevisiae., Jenisha Ghimire
Role Of Ime4 Protein In Pho Regulon Of S.Cerevisiae., Jenisha Ghimire
University of New Orleans Theses and Dissertations
In the yeast Saccharomyces cerevisiae, the IME4 methyltransferase, interacts genetically with methyl binding protein, Pho92, to affect the expression of PHO regulon target genes. Cells mutant in IME4 or PHO92 show increases in the RNA abundance of PHO regulon target genes. The increase in the RNA abundance of the PHO regulon target genes is not additive in the cells double mutant in IME4 and PHO92. Hence, Ime4 and Pho92 interact in a single pathway in PHO regulon. Surprisingly, cells overexpressing IME4 and MUM2 shows increase in some PHO regulon target genes, indicating that IME4 affects the PHO regulon target …
Magnetic Nanoparticles Containing Labeling Reagents For Cell Surface Mapping, Ujwal S. Patil
Magnetic Nanoparticles Containing Labeling Reagents For Cell Surface Mapping, Ujwal S. Patil
University of New Orleans Theses and Dissertations
Cell surface proteins play an important role in understanding cell-cell communication, cell signaling pathways, cell division and molecular pathogenesis in various diseases. Commonly used biotinylation regents for cell surface mapping have shown some potential drawbacks such as crossing the cell membrane, difficult recovery of biotinylated proteins from streptavidin/avidin beads, interference from endogenous biotin and nonspecific nature of streptavidin. With aim to solve these problems, we introduced sulfo-N-hydroxysuccinimidyl (NHS) ester functionalized magnetic nanoparticles containing cleavable groups to label solvent exposed primary amine groups of proteins. Silica coated iron oxide magnetic nanoparticles (Fe3O4@SiO2 MNPs) were …
Three-Dimensional Ideal Gas Reference State Based Energy Function, Avdesh Mishra
Three-Dimensional Ideal Gas Reference State Based Energy Function, Avdesh Mishra
University of New Orleans Theses and Dissertations
Energy functions are found to be a key of protein structure prediction. In this work, we propose a novel 3-dimensional energy function based on hydrophobic-hydrophilic properties of amino acid where we consider at least three different possible interaction of amino acid in a 3-dimensional sphere categorized as hydrophilic versus hydrophilic, hydrophobic versus hydrophobic and hydrophobic versus hydrophilic. Each of these interactions are governed by a 3-dimensional parameter alpha used to model the interaction and 3-dimensional parameter beta used to model weight of contribution. We use Genetic Algorithm (GA) to optimize the value of alpha, beta and Z-score. We obtain three …
Identification Of The Transcriptional Co-Repressor Complex And Its Functions In Arabidopsis Thaliana, Barsha Shrestha
Identification Of The Transcriptional Co-Repressor Complex And Its Functions In Arabidopsis Thaliana, Barsha Shrestha
University of New Orleans Theses and Dissertations
No abstract provided.
The Effects Of Chronic Simvastatin Treatment On The Expression Of Behavioral Symptoms In A Transgenic Mouse Model Of Huntington’S Disease, Ashley Whitmarsh
The Effects Of Chronic Simvastatin Treatment On The Expression Of Behavioral Symptoms In A Transgenic Mouse Model Of Huntington’S Disease, Ashley Whitmarsh
University of New Orleans Theses and Dissertations
Huntington’s disease (HD) is a heritable, neurodegenerative disorder characterized by motor, cognitive, and psychiatric disturbances. An unstable CAG expansion within the gene normally encoding for the Huntingtin protein is responsible. The expanded mutant form of Huntingtin and the putative protein co-factor Rhes interact and cause cell death within the striatum. We hypothesized chronic treatment with simvastatin, a cholesterol lowering drug, would disrupt the biosynthetical pathway which gives both Rhes and its target cells binding sites and render Rhes inactive. Healthy and HD mice were treated with simvastatin or a vehicle. Animals’ motor behavior was assessed with three separate tests over …
Anion-Peptide Adduct Formation And Decomposition As Studied By Fourier Transform Ion Cyclotron Resonance (Ft-Icr) Mass Spectrometry, Xiaohua Liu
University of New Orleans Theses and Dissertations
A new “best match” match model has been developed to account for adduct formation on multiply charged peptides observed in negative ion electrospray mass spectrometry. To obtain a stable adduct, the model necessitates an approximate matching of apparent gas-phase basicity (GBapp) of a given proton bearing site on the peptide with the gas-phase basicity (GB) of the anion attaching at that site. Evidence supporting the model is derived from the fact that singly charged adducts were only observed for lower GB anions: HSO4-, I-, CF3COO-. Ions that have medium GBs (NO …
A Study On The Regulation Of Amino Acids And Glucose Sensing Pathways In Saccharomyces Cerevisiae, Mengying Chiang
A Study On The Regulation Of Amino Acids And Glucose Sensing Pathways In Saccharomyces Cerevisiae, Mengying Chiang
University of New Orleans Theses and Dissertations
Nutrient availability regulates eukaryotic cell growth. This study focuses on two signaling pathways, involved in sensing amino acids and carbon sources, which allow cells to respond appropriately to their presence. The first part of this study shows that Ssy1, a plasma membrane localized sensor in the Ssy1-Ptr3-Ssy5 (SPS) amino acid sensing pathway, can detect 19 common L-amino acids with different potencies and affinities based on the physiochemical structure of amino acids. Substituents around alpha carbon are critical for amino acid sensing by Ssy1. Furthermore, a high concentration of cysteine is toxic to cells. Inactivation of SPS signaling confers resistance to …
Characterization Of Cpey And Cpez Mutants In Fremyella Diplosiphon Strain Utex 481, Christina M. Kronfel
Characterization Of Cpey And Cpez Mutants In Fremyella Diplosiphon Strain Utex 481, Christina M. Kronfel
University of New Orleans Theses and Dissertations
Phycoerythrin (PE) present on the outer phycobilisome (PBS) rods in Fremyella diplosiphon contains covalently attached phycoerythrobilin (PEB) chromophores for efficient photosynthetic light capture. Chromophore ligation on phycobiliprotein subunits occurs through bilin lyase catalyzed reactions. The cpeY and cpeZ genes in F. diplosiphon were shown to attach PEB on alph-82 of PE. To better understand the individual functions of cpeY and cpeZ in native cyanobacteria, we characterized PBS and PE purified from cpeY and cpeZ deletion mutants and compared them with wild type (WT). Both cpeY and cpeZ mutants generated much less PE than WT as well as assembling much less …
Validation Of Antibodies Used To Study Hypoxia Inducible Factors In Two Species Of Fundulus, Jenna D. Hill
Validation Of Antibodies Used To Study Hypoxia Inducible Factors In Two Species Of Fundulus, Jenna D. Hill
University of New Orleans Theses and Dissertations
Hypoxia inducible factors (HIFs) are transcription factors and the master regulators of oxygen-dependent gene expression in animals. The focus of this thesis is the distribution of HIF protein in tissues of the fish Fundulus heteroclitus and F. grandis, two widespread species that occur in naturally hypoxic waters. Polyclonal antibodies against HIF-1α, HIF-2α, and HIF-3α were tested on proteins made in vitro and on extracts made from several tissues of normoxic and hypoxic fish. Antibodies against HIF-1α and 3α bound specifically to full length protein made in vitro, and produced bands on western blots of nuclear extracts of near …
Regulation Of The Target Of Rapamycin Signaling Pathway In Saccharomyces Cerevisiae, Tammy Pracheil
Regulation Of The Target Of Rapamycin Signaling Pathway In Saccharomyces Cerevisiae, Tammy Pracheil
University of New Orleans Theses and Dissertations
An integrative, biochemical, genetic, and molecular biology approach utilizing gene manipulation, gene knock outs, plasmid based protein expression, and in vivo protein localization of fluorescence tagged proteins was employed to determine the function of an essential protein, Lst8, in TORC1 and TORC2 signaling and a previously uncharacterized complex, the Far3-7-8-9-10-11 complex (Far complex) in the budding yeast, Saccharomyces cerevisiae. Mutations in SAC7 and FAR11 suppressed lethality of both lst8 and tor2-21 mutations but not TORC1 inactivation, suggesting that the essential function of Lst8 is linked only to TORC2.
Far11, a component of a six-member complex, was found to interact …
Cloning, Expression, And Characterization Of Ara H 3, A Major Peanut Allergen, Cathryn E. Garvey
Cloning, Expression, And Characterization Of Ara H 3, A Major Peanut Allergen, Cathryn E. Garvey
University of New Orleans Theses and Dissertations
Abstract There are eight foods that contribute to food allergies in the western world and peanut is the most common. Currently, there are no medical treatments that can cure an individual of food allergy, so avoidance of the allergic food is the only option. In the United States, there are three immunodominant allergic proteins accountable for patient sensitization to peanut, Arachis hypogea 1, 2, and 3 (Ara h 1, Ara h 2, Ara h 3). Therefore, research into why peanuts are more allergic than other foods that have homologous proteins is critical and may be obtained by studying the structural …
Identification And Characterization Of Enzymes Involved In The Biosynthesis Of Different Phycobiliproteins In Cyanobacteria, Avijit Biswas
Identification And Characterization Of Enzymes Involved In The Biosynthesis Of Different Phycobiliproteins In Cyanobacteria, Avijit Biswas
University of New Orleans Theses and Dissertations
A multi-plasmid, co-expression system was used to recreate the biosynthetic pathway for phycobiliproteins from the cyanobacterium Synechococcus sp. PCC 7002 in E. coli. This system efficiently produced chromophorylated allophycocyanin (ApcA/ApcB), -phycocyanin, and -phycocyanin. This system was used to demonstrate that CpcS-I and CpcU proteins are both required attaching PCB to allophycocyanin subunits ApcD (AP-B) and ApcF (18). The N-terminal, AP-like domain of ApcE (LCM99) was produced in soluble form and shown to have intrinsic bilin lyase activity. In addition, this system was used to chromophorylated CpcA from Synechococystis sp. PCC 6803 with a non-cognate bilin; PEB with the aid …