Tracing Beta Strands Using Strandtwister From Cryo-Em Density Maps At Medium Resolutions, 2014 Old Dominion University
Tracing Beta Strands Using Strandtwister From Cryo-Em Density Maps At Medium Resolutions, Dong Si, Jing He
Computer Science Faculty Publications
Major secondary structure elements such as α helices and β sheets can be computationally detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5–10 A˚ . However, a critical piece of information for modeling atomic structures is missing, because there are no tools to detect β strands from cryo-EM maps at medium resolutions. We propose a method, StrandTwister, to detect the traces of β strands through the analysis of twist, an intrinsic nature of a β sheet. StrandTwister has been tested using 100 β sheets simulated at 10 A˚ resolution and 39 β sheets computationally detected from cryo-EM …
Sumoylation Affects Ns1'S Ability To Neutralize The Interferon Response, 2014 University of Texas at El Paso
Sumoylation Affects Ns1'S Ability To Neutralize The Interferon Response, Jeanette Cecilia Gonzalez
Open Access Theses & Dissertations
It is of huge concern the possibility that at some point in the future we may face a new pandemic involving a highly pathogenic virus due to our current preventive and treatment options to fight this viral disease. The main reason for such limitations is the ability of the virus to go over constant antigenic shifts and drifts on its viral surface proteins HA and NA. The constant mutations that affect this virus cause the need of developing new vaccines for each influenza season. Periodically, the World Health Organization (WHO) reports that around 10% of the world population gets infected …
Global Sphingolipid Profile Of Giardia Lamblia During Stage Differentiation: The Influence Of Sphingomyelin Abundance On Viable Cyst Production, 2014 University of Texas at El Paso
Global Sphingolipid Profile Of Giardia Lamblia During Stage Differentiation: The Influence Of Sphingomyelin Abundance On Viable Cyst Production, Trevor Thomas Duarte
Open Access Theses & Dissertations
Giardia lamblia is a protozoan parasite and a major cause of the waterborne-illness, giardiasis, worldwide. Giardiasis is endemic in developing countries and is a leading cause of non-viral- and non-bacterial-associated intestinal disorders. Acute symptoms of giardiasis include diarrhea, cramps, and malabsorption. The disease is often self-limiting, although the infection can result in long-term disorders such as chronic fatigue, stunted cognitive skills, and failure to thrive even after the parasite has been cleared.
This parasite exists in two morphologic forms--infective trophozoites and transmissible, water-resistant cyst, which is passed by the fecal-oral route and is likely to be spread by contaminated drinking …
A Comparative Approach To Assessing The Functional And Structural Characteristics Of Human Fkbp52 In The Regulation Of Steroid Hormone Receptor Signaling Pathway, 2014 University of Texas at El Paso
A Comparative Approach To Assessing The Functional And Structural Characteristics Of Human Fkbp52 In The Regulation Of Steroid Hormone Receptor Signaling Pathway, Diondra Crystal Harris
Open Access Theses & Dissertations
The 52 kDa FK506 binding protein (h52) is a key positive regulator of Androgen Receptor (AR) in cellular and animal models and is an attractive target for the treatment of prostate cancer. Human FKBP52 is a known regulatory protein and co-chaperone that has been shown to play an important role in the regulation of the AR signaling pathway, and in the development of the male sexual phenotype. Cellular studies in mammalian and yeast cells reveal that FKBP52 is a positive regulator of AR, glucocorticoid receptor (GR), and progesterone receptor (PR), potentiating receptor-mediated gene expression up to 60-fold in some systems. …
Il-2rβ T450 Phosphorylation Is A Positive Regulator For Receptor Complex Stability And Activation Of Signaling Molecules, 2014 University of Texas at El Paso
Il-2rβ T450 Phosphorylation Is A Positive Regulator For Receptor Complex Stability And Activation Of Signaling Molecules, Blanca Estela Ruiz-Medina
Open Access Theses & Dissertations
Homeostasis of the immune system is required for proper defense against pathogenic insult. Cells of the innate and adaptive compartments provide a strictly regulated response to clear infections while allowing for self-tolerance. Dysregulation of the components of the immune system can lead to immunodeficiency, autoimmunity, and cancer. Key players of the immune response are T, B, and NK cells, which become strongly activated by IL2 through its receptor. The β subunit of the receptor becomes tyrosine, serine, and threonine phosphorylated upon induction with IL2. Phosphorylation of tyrosine residues has been extensively studied, however, the putative regulatory role of serine and …
Characterization Of Ns1 Sumoylation And Its Effect On Influenza A Viral Infection, 2014 University of Texas at El Paso
Characterization Of Ns1 Sumoylation And Its Effect On Influenza A Viral Infection, Katherine Anne Meraz
Open Access Theses & Dissertations
Influenza virus is a contagious respiratory virus responsible for seasonal epidemics and several catastrophic pandemics in the last century. Its genome is comprised of negative sense, single-stranded RNA and, after entering the cell, it is capable of hijacking the host cellular machinery for reproducing its own genetic material. The activation of cellular defenses against influenza viral infection are triggered upon viral entry and help regulate the course of viral infection. This study focused on the interplay between the influenza A virus and the cellular SUMOylation system during viral infection. The first part of this Dissertation deals with the relevance of …
Dna Interaction And Cytotoxic Activities Of Square Planar Platinum(Ii) Complexes With N, S-Donor Ligands, 2014 Sheridan College
Dna Interaction And Cytotoxic Activities Of Square Planar Platinum(Ii) Complexes With N, S-Donor Ligands, Mohan N. Patel, Chintan R. Patel, Hardik Joshi, Khyati P. Thakor
Publications and Scholarship
The platinum(II) complexes with N, S-donor ligands have been synthesized and characterized by physicochemical methods viz. elemental, electronic, FT-IR, 1H NMR and LC–MS spectra. The binding mode and potency of the complexes with HS DNA (Herring Sperm) have been examined by absorption titration and viscosity measurement studies. The results revealed that complexes bind to HS DNA via covalent mode with the intrinsic binding constant (Kb) in the range 1.37–7.76 × 105 M−1. Decrease in the relative viscosity of HS DNA also supports the covalent mode of binding. The DNA cleavage activity of synthesized complexes has been carried out …
Functions Of Mitoneet: What The Protein-Protein Interactions Reveal, 2014 Eastern Illinois University
Functions Of Mitoneet: What The Protein-Protein Interactions Reveal, Fran Hirschfelder
Masters Theses
MitoNEET is a [2Fe-2S] cluster protein found on the outer mitochondrial membrane. First discovered as a binding site for pioglitazone, an anti-diabetic drug, it was the first protein described containing a CDGSH iron-sulfur domain (CISD). However, the function(s) of mitoNEET in both normal cellular physiology and the physiology in type-2 diabetes remains unclear. The proposed functions of mitoNEET, include cluster transfer, electron transport and oxidative respiration. This thesis describes the use of proteomic pull-down techniques to identify possible protein binding partners of mitoNEET from both mouse and human liver cell lysates. In order to accomplish this, the expression and purification …
A Structure-Function Analysis Of The Arabidopsis Chloroplast Import Protein Attic20, 2014 Wilfrid Laurier University
A Structure-Function Analysis Of The Arabidopsis Chloroplast Import Protein Attic20, James H. Campbell
Theses and Dissertations (Comprehensive)
Arabidopsis thaliana protein Tic20 (atTic20) is a member of the translocon at the inner envelope membrane of chloroplasts. Evidence to date suggests it is part of the main preprotein conducting aperture in the complex, but its exact role is still debated. To help characterize its role, a protocol optimizing yield and purity of recombinantly expressed atTic20 was developed, and a series of experiments was performed to examine its secondary structure and its ability to interact with chloroplast transit peptides. The attempt to increase protein yield was successful, with growth at 20oC in the auto-inducing media ZYP-5052 showing the …
Characterizing Dsrna Production In Virus-Infected Fish Cells, 2014 Wilfrid Laurier University
Characterizing Dsrna Production In Virus-Infected Fish Cells, Amal Brek Aloufi
Theses and Dissertations (Comprehensive)
Viral dsRNA is produced by almost all viruses sometime during their replicative cycle. These viral nucleic acids are potent inducers of both innate and adaptive immune responses, and are therefore considered important immuno-modulators. Previous studies have shown that viruses produce dsRNA when replicating in mammalian cells; however, to date no one has demonstrated viral dsRNA production in virus infected fish cells. Therefore, the goal of this study is to investigate dsRNA production by fish viruses in fish cells, verifying production and performing initial characterization of the dsRNA molecules being produced. Three different rainbow trout cell lines were used in this …
Nuclear Import And Interactions Of Potato Yellow Dwarf Virus Nucleocapsid, Matrix, And Phosphoprotein, 2014 University of Kentucky
Nuclear Import And Interactions Of Potato Yellow Dwarf Virus Nucleocapsid, Matrix, And Phosphoprotein, Gavin Lloyd Franklin Anderson
Theses and Dissertations--Plant Pathology
Potato yellow dwarf virus (PYDV) is the type species of the genus Nucleorhabdovirus and, like all members of this genus, replication and morphogenesis occurs inside the nuclei of infected cells. Protein localization prediction algorithms failed to identify a nuclear localization signal (NLS) in PYDV nucleocapsid (N) protein, although PYDV-N has been shown to localize exclusively to the nucleus when expressed as a green fluorescent protein (GFP):N fusion in plant cells. Deletion analysis and alanine-scanning mutagenesis identified two amino acid motifs, 419QKR421 and 432KR433, that were shown to be essential for nuclear import and interaction with …
Ether Bridge Formation And Chemical Diversification In Loline Alkaloid Biosynthesis, 2014 University of Kentucky
Ether Bridge Formation And Chemical Diversification In Loline Alkaloid Biosynthesis, Juan Pan
Theses and Dissertations--Plant Pathology
Loline alkaloids, found in many grass-Epichloë symbiota, are toxic or feeding deterrent to invertebrates. The loline alkaloids all share a saturated pyrrolizidine ring with a 1-amine group and an ether bridge linking C2 and C7. The steps in biosynthesis of loline alkaloids are catalyzed by enzymes encoded by a gene cluster, designated LOL, in the Epichloë genome. This dissertation addresses the enzymatic, genetic and evolutionary basis for diversification of these alkaloids, focusing on ether bridge formation and the subsequent modifications of the 1-amine to form different loline alkaloids.
Through gene complementation of a natural lolO mutant and comparison …
Purification Of An Inducible Dnase From A Thermophilic Fungus, 2013 University of Massachusetts Amherst
Purification Of An Inducible Dnase From A Thermophilic Fungus, Kyle Landry, Andrea Vu, Robert Levin
Kyle S Landry
Requirements Of Rab5 Activity In Highly Invasive Breast Cancer Cell Lines, 2013 Nova Southeastern University
Requirements Of Rab5 Activity In Highly Invasive Breast Cancer Cell Lines, Nicole Porther, M Alejandro Barbieri
Nicole Porther
Introduction To Genome Browsers, 2013 Yale University
Introduction To Genome Browsers, Rolando Garcia-Milian
Rolando Garcia-Milian
In this workshop we will learn how to navigate the genome browsers from NCBI's Genome Workbench, UCSC Genome Browser, and Ensembl. These browsers are valuable tools when identifying, localizing genes, and looking at their information in the genomic context. By using concrete examples, it will be shown how to locate a human gene, download a gene sequence and its upstream sequence, locate Single Nucleotide Polymorphisms (SNPs) and conserved regions, and use the browsers to download results in a batch.
Jmu 4-Va Grant: Characterizing Epigenetic Regulation Of Gene Experession During Development Of The Vertebrate Retina, 2013 enkera@jmu.edu
Jmu 4-Va Grant: Characterizing Epigenetic Regulation Of Gene Experession During Development Of The Vertebrate Retina, Raymond A. Enke
Ray Enke Ph.D.
The Global Translation Profile In A Ribosomal Protein Mutant Resembles That Of An Eif3 Mutant, 2013 University of Tennessee - Knoxville
The Global Translation Profile In A Ribosomal Protein Mutant Resembles That Of An Eif3 Mutant, Bayu Sisay Tiruneh, Byung-Hoon Kim, Daniel R. Gallie, Bijoyita Roy, Albrecht G. Von Arnim
Faculty Publications and Other Works -- Biochemistry, Cellular and Molecular Biology
Background
Genome-wide assays performed in Arabidopsis and other organisms have revealed that the translation status of mRNAs responds dramatically to different environmental stresses and genetic lesions in the translation apparatus. To identify additional features of the global landscape of translational control, we used microarray analysis of polysomal as well as non-polysomal mRNAs to examine the defects in translation in a poly(A) binding protein mutant, pab2 pab8, as well as in a mutant of a large ribosomal subunit protein, rpl24b/shortvalve1.
Results
The mutation of RPL24B stimulated the ribosome occupancy of mRNAs for nuclear encoded ribosomal proteins. Detailed analysis …
The Function Of Carmil1 In Migrating Cells, 2013 Washington University in St. Louis
The Function Of Carmil1 In Migrating Cells, Marc Edwards
All Theses and Dissertations (ETDs)
This dissertation describes the physiological role of the Capping Protein- CARMIL interaction in migrating cells. I establish the CARMIL-CP complex as a key regulator of lamellipodial actin assembly and of lamellipodial dynamics. Membrane ruffling at the leading edge of motile cells and macropinocytosis were also found to be dependent on the CARMIL1-CP interaction. This is consistent with macropinocytosis and ruffling being dependent on a functional and dynamic lamellipodium.: Kerr and Teasdale, 2009).
In chapter two I demonstrate that the CBR of CARMIL1 is competent to inhibit CP in cells. I show that overexpression of the CBR in cells leads to …
The Effects Of Salinity, Ph, Temperature, And Dissolved Oxygen On Sensitivity Of Pcr Identification Of T4 Bacteriophage, 2013 Coastal Carolina University
The Effects Of Salinity, Ph, Temperature, And Dissolved Oxygen On Sensitivity Of Pcr Identification Of T4 Bacteriophage, Joesph F. Cannon, Nicholas A. Thurn, Paul E. Richardson
Journal of the South Carolina Academy of Science
Bacteriophages are used as indicators of pathogenic bacteria in drinking, and wastewaters. They also show potential in limiting aquatic bacterial populations through their lytic properties. The effect of different water characteristics (salinity, pH, dissolved oxygen, and temperature) on the sensitivity of the PCR identification of virus particles were analyzed to determine at what levels bacteriophage can be detected in environmental samples. Results from this preliminary study indicate that a PCR bacteriophage detection technique has potential as a relatively efficient and economical indicator of coliform contamination in multiple aquatic environments. While further evaluation is needed, the protocol appears to function in …
Valproic Acid Causes Proteasomal Degradation Of Dicer And Influences Mirna Expression, 2013 University of Kentucky
Valproic Acid Causes Proteasomal Degradation Of Dicer And Influences Mirna Expression, Zhaiyi Zhang, Paolo Convertini, Manli Shen, Xiu Xu, Frédéric Lemoine, Pierre De La Grange, Douglas A. Andres, Stefan Stamm
Molecular and Cellular Biochemistry Faculty Publications
Valproic acid (VPA) is a commonly used drug to treat epilepsy and bipolar disorders. Known properties of VPA are inhibitions of histone deacetylases and activation of extracellular signal regulated kinases (ERK), which cannot fully explain VPA's clinical features. We found that VPA induces the proteasomal degradation of DICER, a key protein in the generation of micro RNAs. Unexpectedly, the concentration of several micro RNAs increases after VPA treatment, which is caused by the upregulation of their hosting genes prior to DICER degradation. The data suggest that a loss of DICER protein and changes in micro RNA concentration contributes to the …