Adenine Aminohydrolase: Occurrence and Possible Significance in Trypanosomid Flagellates (Crithidia/Leishmania/ Coformycin/Deoxycoformycin) G
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Structural Insights Into Histone Modifying Enzymes
Wayne State University Wayne State University Theses January 2019 Structural Insights Into Histone Modifying Enzymes Shruti Amle Wayne State University, [email protected] Follow this and additional works at: https://digitalcommons.wayne.edu/oa_theses Part of the Biochemistry Commons, and the Molecular Biology Commons Recommended Citation Amle, Shruti, "Structural Insights Into Histone Modifying Enzymes" (2019). Wayne State University Theses. 693. https://digitalcommons.wayne.edu/oa_theses/693 This Open Access Embargo is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Theses by an authorized administrator of DigitalCommons@WayneState. STRUCTURAL INSIGHTS INTO HISTONE MODIFYING ENZYMES by SHRUTI AMLE THESIS Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE 2019 MAJOR: BIOCHEMISTRY AND MOLECULAR BIOLOGY Approved By: _________________________________________ Advisor Date _________________________________________ _________________________________________ _________________________________________ i ACKNOWLEDGEMENTS Writing this thesis has been extremely captivating and gratifying. I take this opportunity to express my deep and sincere acknowledgements to the number of people for extending their generous support and unstinted help during my entire study. Firstly, I would like to express my respectful regards and deep sense of gratitude to my advisor, Dr. Zhe Yang. I am extremely honored to study and work under his guidance. His vision, ideals, timely motivation and immense knowledge had a deep influence on my entire journey of this career. Without his understanding and support, it would not have been possible to complete this research successfully. I also owe my special thanks to my committee members: Dr. -
Gentaur Products List
Chapter 2 : Gentaur Products List • Rabbit Anti LAMR1 Polyclonal Antibody Cy5 Conjugated Conjugated • Rabbit Anti Podoplanin gp36 Polyclonal Antibody Cy5 • Rabbit Anti LAMR1 CT Polyclonal Antibody Cy5 • Rabbit Anti phospho NFKB p65 Ser536 Polyclonal Conjugated Conjugated Antibody Cy5 Conjugated • Rabbit Anti CHRNA7 Polyclonal Antibody Cy5 Conjugated • Rat Anti IAA Monoclonal Antibody Cy5 Conjugated • Rabbit Anti EV71 VP1 CT Polyclonal Antibody Cy5 • Rabbit Anti Connexin 40 Polyclonal Antibody Cy5 • Rabbit Anti IAA Indole 3 Acetic Acid Polyclonal Antibody Conjugated Conjugated Cy5 Conjugated • Rabbit Anti LHR CGR Polyclonal Antibody Cy5 Conjugated • Rabbit Anti Integrin beta 7 Polyclonal Antibody Cy5 • Rabbit Anti Natrexone Polyclonal Antibody Cy5 Conjugated • Rabbit Anti MMP 20 Polyclonal Antibody Cy5 Conjugated Conjugated • Rabbit Anti Melamine Polyclonal Antibody Cy5 Conjugated • Rabbit Anti BCHE NT Polyclonal Antibody Cy5 Conjugated • Rabbit Anti NAP1 NAP1L1 Polyclonal Antibody Cy5 • Rabbit Anti Acetyl p53 K382 Polyclonal Antibody Cy5 • Rabbit Anti BCHE CT Polyclonal Antibody Cy5 Conjugated Conjugated Conjugated • Rabbit Anti HPV16 E6 Polyclonal Antibody Cy5 Conjugated • Rabbit Anti CCP Polyclonal Antibody Cy5 Conjugated • Rabbit Anti JAK2 Polyclonal Antibody Cy5 Conjugated • Rabbit Anti HPV18 E6 Polyclonal Antibody Cy5 Conjugated • Rabbit Anti HDC Polyclonal Antibody Cy5 Conjugated • Rabbit Anti Microsporidia protien Polyclonal Antibody Cy5 • Rabbit Anti HPV16 E7 Polyclonal Antibody Cy5 Conjugated • Rabbit Anti Neurocan Polyclonal -
Structural Properties of the Nickel Ions in Urease: Novel Insights Into the Catalytic and Inhibition Mechanisms
Coordination Chemistry Reviews 190–192 (1999) 331–355 www.elsevier.com/locate/ccr Structural properties of the nickel ions in urease: novel insights into the catalytic and inhibition mechanisms Stefano Ciurli a,*, Stefano Benini b, Wojciech R. Rypniewski b, Keith S. Wilson c, Silvia Miletti a, Stefano Mangani d a Institute of Agricultural Chemistry, Uni6ersity of Bologna, Viale Berti Pichat 10, I-40127 Bologna, Italy b European Molecular Biology Laboratory, c/o DESY, Notkestraße 85, D-22603 Hamburg, Germany c Department of Chemistry, Uni6ersity of York, Heslington, York YO15DD, UK d Department of Chemistry, Uni6ersity of Siena, Pian dei Mantellini 44, I-53100 Siena, Italy Accepted 13 March 1999 Contents Abstract.................................................... 331 1. Biological background ......................................... 332 2. Spectroscopic investigations of the urease active site structure .................. 333 3. Crystallographic studies of the native enzyme ............................ 334 4. Crystallographic studies of urease mutants.............................. 341 5. Crystallographic studies of urease–inhibitor complexes ...................... 345 6. Crystallographic study of a transition state analogue bound to urease.............. 348 7. A novel proposal for the urease mechanism ............................. 350 References .................................................. 353 Abstract This work provides a comprehensive critical summary of urease spectroscopy, crystallogra- phy, inhibitor binding, and site-directed -
Phylogenetic Analysis, Subcellular Localization, and Expression
BMC Plant Biology BioMed Central Research article Open Access Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants Malona V Alinsug, Chun-Wei Yu and Keqiang Wu* Address: Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan Email: Malona V Alinsug - [email protected]; Chun-Wei Yu - [email protected]; Keqiang Wu* - [email protected] * Corresponding author Published: 28 March 2009 Received: 26 November 2008 Accepted: 28 March 2009 BMC Plant Biology 2009, 9:37 doi:10.1186/1471-2229-9-37 This article is available from: http://www.biomedcentral.com/1471-2229/9/37 © 2009 Alinsug et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Although histone deacetylases from model organisms have been previously identified, there is no clear basis for the classification of histone deacetylases under the RPD3/ HDA1 superfamily, particularly on plants. Thus, this study aims to reconstruct a phylogenetic tree to determine evolutionary relationships between RPD3/HDA1 histone deacetylases from six different plants representing dicots with Arabidopsis thaliana, Populus trichocarpa, and Pinus taeda, monocots with Oryza sativa and Zea mays, and the lower plants with Physcomitrella patens. Results: Sixty two histone deacetylases of RPD3/HDA1 family from the six plant species were phylogenetically analyzed to determine corresponding orthologues. Three clusters were formed separating Class I, Class II, and Class IV. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
Lysine Acetylation: Elucidating the Components of an Emerging Global Signaling Pathway in Trypanosomes
Hindawi Publishing Corporation Journal of Biomedicine and Biotechnology Volume 2012, Article ID 452934, 16 pages doi:10.1155/2012/452934 Review Article Lysine Acetylation: Elucidating the Components of an Emerging Global Signaling Pathway in Trypanosomes Victoria Lucia Alonso1, 2 and Esteban Carlos Serra1, 2 1 Departamento de Microbiolog´ıa, Facultad de Ciencias Bioqu´ımicas y Farmac´euticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina 2 Instituto de Biolog´ıa Molecular y Celular de Rosario, CONICET-UNR, Suipacha 590, Rosario 2000, Argentina Correspondence should be addressed to Esteban Carlos Serra, [email protected] Received 17 April 2012; Revised 20 July 2012; Accepted 30 July 2012 Academic Editor: Andrea Silvana Ropolo´ Copyright © 2012 V. L. Alonso and E. C. Serra. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In the past ten years the number of acetylated proteins reported in literature grew exponentially. Several authors have proposed that acetylation might be a key component in most eukaryotic signaling pathways, as important as phosphorylation. The enzymes involved in this process are starting to emerge; acetyltransferases and deacetylases are found inside and outside the nuclear compartment and have different regulatory functions. In trypanosomatids several of these enzymes have been described and are postulated to be novel antiparasitic targets for the rational design of drugs. In this paper we overview the most important known acetylated proteins and the advances made in the identification of new acetylated proteins using high-resolution mass spectrometry. -
Data-Driven Insights Into Ligands, Proteins, and Genetic Mutations
Data-Driven Insights into Ligands, Proteins, and Genetic Mutations by Jing Lu A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Bioinformatics) in the University of Michigan 2016 Doctoral Committee: Professor Heather A. Carlson, Chair Professor Charles L. Brooks III Assistant Professor Barry Grant Professor David S. Sept Professor Kerby A. Shedden © Jing Lu, 2016 Acknowledgements I would like to thank my advisor, Dr. Heather Carlson, for years of patient guidance, teaching, and support through the course of my PhD. I have learnt how to think critically and be rigorous in every step of research. I also want to express gratitude to my committee: Professor Charles L. Brooks III, Assistant Professor Barry Grant, Professor David S. Sept, Professor Kerby A. Shedden. Their advising is insightful and deepens my understanding of my research projects. I would like to thank Dr. Richard Smith for timely support for both my writing and research. For many Saturdays and Sundays, he promptly responds my requests for proofreading. Much of my work is built on his code in protein and ligand analysis. I would like to thank other members in Dr. Carlson’s lab for helping me with my work. Through the discussion with Dr. Jim Dunbar, I have learnt many critical ideas in Cheminformatics. Also, thank you to Sarah Graham and Jordan Clark for their tremendous friendship and willing to help with my writing. I would also thank previous members in Dr. Carlson’s lab. I would thank Dr. Phani Ghanakota for many late-night discussions and Dr. -
Supplementary Information
Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle. -
PURINE SALVAGE in HELICOBACTER PYLORI by ERICA FRANCESCA MILLER (Under the Direction of Robert J. Maier) ABSTRACT Purines Are Es
PURINE SALVAGE IN HELICOBACTER PYLORI by ERICA FRANCESCA MILLER (Under the Direction of Robert J. Maier) ABSTRACT Purines are essential for all living cells. This fact is reflected in the high degree of pathway conservation for purine metabolism across all domains of life. The availability of purines within a mammalian host is thought to be a limiting factor for infection, as demonstrated by the importance of purine synthesis and salvage genes among many bacterial pathogens. Helicobacter pylori, a primary causative agent of peptic ulcers and gastric cancers, colonizes a niche that is otherwise uninhabited by bacteria: the surface of the human gastric epithelium. Despite many studies over the past 30 years that have addressed virulence mechanisms such as acid resistance, little knowledge exists regarding this organism’s purine metabolism. To fill this gap in knowledge, we asked whether H. pylori can carry out de novo purine biosynthesis, and whether its purine salvage network is complete. Based on genomic data from the fully sequenced H. pylori genomes, we combined mutant analysis with physiological studies to determine that H. pylori, by necessity, must acquire purines from its human host. Furthermore, we found the purine salvage network to be complete, allowing this organism to use any single purine nucleobase or nucleoside for growth. In the process of elucidating these pathways, we discovered a nucleoside transporter in H. pylori that, in contrast to the biochemically- characterized homolog NupC, aids in uptake of purine rather than pyrimidine nucleosides into the cell. Lastly, we investigated an apparent pathway gap in the genome annotation—that of adenine degradation—and in doing so uncovered a new family of adenosine deaminase that lacks sequence homology with all other adenosine deaminases studied to date. -
Optimización De La Producción De Riboflavina En Ashbya Gossypii Basada En El Análisis Funcional De Las Rutas De Recuperación De Nucleobases De Purina
Universidad de Salamanca Departamento de Microbiología y Genética Optimización de la producción de riboflavina en Ashbya gossypii basada en el análisis funcional de las rutas de recuperación de nucleobases de purina. José Antonio Uña Álvarez Tesis Doctoral 2013 Dr. Luís Román Fernández Lago, Director del Departamento de Microbiología y Genética de la Universidad de Salamanca. CERTIFICA: Que la memoria titulada “Optimización de la producción de riboflavina en Ashbya gossypii basada en el análisis funcional de las rutas de recuperación de nucleobases de purina”, presentada por D. José Antonio Uña Álvarez para optar al grado de Doctor en Biología, ha sido realizada bajo la dirección de la Dra. Mª Ángeles Santos García y del Dr. José Luis Revuelta Doval, en el Departamento de Microbiología y Genética de la Universidad de Salamanca. Y para que así conste expide el presenta certificado en: Salamanca a de de 2013 Fdo. Dr. Luís Román Fernández Lago Dra. Mª Ángeles Santos García, Profesora Titular del Departamento de Microbiología y Genética de la Universidad de Salamanca y Dr. José Luis Revuelta Doval, Catedrático de Genética del Departamento de Microbiología y Genética de la Universidad de Salamanca. CERTIFICAN: Que el doctorando José Antonio Uña Álvarez ha realizado en el Departamento de Microbiología y Genética de la Universidad de Salamanca, bajo su dirección, el trabajo titulado “Optimización de la producción de riboflavina en Ashbya gossypii basada en el análisis funcional de las rutas de recuperación de nucleobases de purina”, para optar al grado de Doctor en Biología. Y para que así conste, y como directores del trabajo, expiden el presente certificado en: Salamanca a de de 2013 Fdo: Dra. -
Purine and Pyrimidine Metabolism in Human Epidermis* Jean De Bersaques, Md
THE JOURNAL OP INVESTIGATIVE DERMATOLOGY Vol. 4s, No. Z Copyright 1957 by The Williams & Wilkins Co. Fri nte,1 in U.S.A. PURINE AND PYRIMIDINE METABOLISM IN HUMAN EPIDERMIS* JEAN DE BERSAQUES, MD. The continuous cellular renewal occurring inthine, which contained 5% impurity, and for uric the epidermis requires a very active synthesisacid, which consisted of 3 main components. The reaction was stopped after 1—2 hours in- and breakdown of nuclear and cytoplasmiecubation at 37° and the products were spotted on nucleic acids. Data on the enzyme systemsWhatman 1 filter paper sheets. According to the participating in these metabolic processes arereaction products expected, a choice was made of rather fragmentary (1—9) and some are, inat least 2 among the following solvents, all used terms of biochemical time, in need of up- in ascending direction: 1. isoamyl alcohol—5% Na2HPO4 (1:1), dating. In some other publications (10—18), 2. water-saturated n-butanol, the presence and concentration of various in- 3. distilled water, termediate products is given. 4. 80% formic acid—n-hutanol——n-propanol— In this paper, we tried to collect and supple- acetone—30% trichloro-aeetic acid (5:8:4: ment these data by investigating the presence 5:3), 5. n-butanol——4% boric acid (43:7), or absence in epidermis of enzyme systems 6. isobutyrie acid—water—ammonia 0.880—ver- that have been described in other tissues. sene 0.1M(500:279:21:8), This first investigation was a qualitative one, 7. upper phase of ethyl acetate—water—formic and some limitations were set by practical acid (12:7:1), 8. -
From Helicobacter Pylori
Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori Han-Pil Choi1, Silvia Juarez2, Sergio Ciordia2, Marisol Fernandez2, Rafael Bargiela3, Juan P. Albar2, Varun Mazumdar4, Brian P. Anton5, Simon Kasif1,4, Manuel Ferrer3*, Martin Steffen1,6* 1 Dept of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America, 2 Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, Darwin 3, Madrid, Spain, 3 Spanish National Research Council (CSIC), Institute of Catalysis, Madrid, Spain, 4 Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America, 5 New England Biolabs, Ipswich, Massachusetts, United States of America, 6 Dept of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America Abstract The functional characterization of Open Reading Frames (ORFs) from sequenced genomes remains a bottleneck in our effort to understand microbial biology. In particular, the functional characterization of proteins with only remote sequence homology to known proteins can be challenging, as there may be few clues to guide initial experiments. Affinity enrichment of proteins from cell lysates, and a global perspective of protein function as provided by COMBREX, affords an approach to this problem. We present here the biochemical analysis of six proteins from Helicobacter pylori ATCC 26695, a focus organism in COMBREX. Initial hypotheses were based upon affinity capture of proteins from total cellular lysate