DOCSLIB.ORG

UNIVERSITY of CALIFORNIA Los Angeles Cloud-Based Analysis And

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
UNIVERSITY of CALIFORNIA Los Angeles Cloud-Based Analysis And UNIVERSITY OF CALIFORNIA Los Angeles Cloud-based Analysis and Integration of Proteomics and Metabolomics Datasets A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics by Jeong Ho (Howard) Choi 2019 © Copyright by Jeong Ho (Howard) Choi 2019 ABSTRACT OF THE DISSERTATION Cloud-based Analysis and Integration of Proteomics and Metabolomics Datasets by Jeong Ho (Howard) Choi Doctor of Philosophy in Bioinformatics University of California, Los Angeles, 2019 Professor Peipei Ping, Chair Our capabilities to define cardiovascular health and disease using highly multivariate “omics” datasets have substantially increased in recent years. Advances in acquisition technologies as well as bioinformatics methods have paved the way for ultimately resolving every biomolecule comprising various human “omes”. Understanding how different “omes” change and interact with one another temporally will ultimately unveil multi-omic molecular signatures that inform pathologic mechanisms, indicate disease phenotypes, and identify new therapeutic targets. Herein we describe a thesis project that creates novel, contemporary data science methods and workflows to extract temporal molecular signatures of disease from multi-omics analyses, and develops integrated omics knowledgebases for the cardiovascular community at-large. Chapter 1 provides an overview of cardiac physiology and pathophysiology involved in cardiac remodeling and heart failure (HF). A description of the systematic characterization of cardiac proteomes and metabolomes is included, including methodologies for multi-omics phenotyping. Finally, an overview of bioinformatics methods for driver molecule discovery is provided, discussing strategies for characterizing temporal patterns and conducting functional enrichment. ii Chapter 2 describes computational approaches to discern the oxidative posttranslational modification (O-PTM) proteome, an important factor in cardiac remodeling. We developed a novel platform involving a customized, quantitative biotin switch pipeline and advanced analytic workflow to profile O-PTMs in an isoproterenol (ISO)-induced cardiac remodeling mouse model. We identified 1,655 proteins containing 3,324 oxidized sites, and unveiled temporal progression of O-PTM in disease. Chapter 3 discusses computational approaches for identifying temporal metabolomics fingerprints in HF treatment. Pathologic remodeling from a healthy to diseased heart involves a series of alterations over time. Mechanical circulatory support devices (MCSD) are a promising strategy for unloading the heart and reversing this process. We sought to identify molecular drivers of pathologic remodeling and reverse remodeling in the plasma metabolome; however, machine learning (ML)-empowered technological platforms required for these analyses are lacking. Thus, we established a Multiple Reaction Monitoring (MRM)-based MS quantitative platform and ML-based computational workflow to discern metabolomics fingerprints. We quantified 610 plasma metabolites and identified those exhibiting high correlation to cardiac phenotype, demonstrating a novel platform for biomarker discovery. Finally, Chapter 4 integrates all aforementioned innovations into one unified, cloud-based computational knowledgebase, MetProt, equipped to analyze, annotate, and integrate metabolomics and proteomics information. This pipeline fully characterizes the plasma metabolome in HF, unveils the interplay of proteomes and metabolomes, and derives new knowledge in cardiovascular medicine. Innovations include engineered features for addressing large-scale clinical datasets as well as algorithms to connect various types of molecules (e.g., proteins and metabolites). Chapter 4 is subdivided into 3 projects: Project 1 describes a computational pipeline to characterize the plasma metabolome using datasets from the ISO mouse model of HF and human HF; Project 2 develops bioinformatics strategies to integrate proteome and metabolome datasets from six genetically distinct mouse strains; and Project 3 establishes the cloud-based MetProt to disseminate the above computational pipelines for the iii cardiovascular community at-large. Taken together, these innovations offer new approaches and workflows for integrated omics investigations that enable novel discovery and ultimately advance precision cardiovascular science and medicine. iv The dissertation of Jeong Ho (Howard) Choi is approved Alex Bui Mario C. Deng Wei Wang Peipei Ping, Committee Chair University of California, Los Angeles 2019 v To my family. vi TABLE OF CONTENTS Abstract of the Dissertation ………………………………………………………………………… ii Table of Contents …………………………………………………………………………………… vii List of Figures ……………………………………………………………………………………….. viii List of Tables ………………………………………………………………………………………… ix Recurring Notations and Abbreviations …………………………………………………………... x Acknowledgements …………………………………………………………………………………. xi Biographical Sketch …………………………………………………………………………………. xii CHAPTER 1: INTRODUCTION AND OVERVIEW. 1.I. The Landscape of the Human Heart and Disease ………………………………………….. 2 1.II. Systematic Characterization of the Cardiac Proteome and Metabolome ……………….. 5 1.III. Overview of Bioinformatic Methods for Driver Molecule Identification and Integration .. 6 1.IV. Overview and Rationale ……………………………………………………………………… 12 CHAPTER 2: COMPUTATIONAL APPROACHES TO DISSECT THE CYSTEINE O-PTM PROTEOME DURING CARDIAC HYPERTROPHY. 2.I. Abstract ………………………………………………………………………………………….. 15 2.II. Introduction ……………………………………………………………………………………… 15 2.III.Methods and Materials ……………………………………………………………………….... 17 2.IV.Results ………………………………………………………………………..…………………. 26 2.V. Discussion ………………………………………………………………………………………. 56 2.VI.Conclusions …………………………………………………………………………………...... 58 CHAPTER 3: COMPUTATIONAL APPROACHES TO IDENTIFY METABOLOME FINGERPRINTS OF PATHOLOGICAL STAGES FOLLOWING HEART FAILURE TREATMENT. 3.I. Abstract ………………………………………………………………………………………….. 60 3.II. Introduction ……………………………………………………………………………………… 61 3.III. Methods and Materials ………………………………………………………………………... 64 3.IV.Results ………………………………………………………………………..…………………. 68 3.V. Discussion ………………………………………………………………………………………. 83 CHAPTER 4: CLOUD-BASED COMPUTATIONAL KNOWLEDGEBASE TO ANALYZE, ANNOTATE, AND INTEGRATE METABOLOMICS AND PROTEOMICS DATASETS 4.I. Abstract ………………………………………………………………………………………….. 93 4.II. Introduction ……………………………………………………………………………………… 94 4.III.Results ………………………………………………………………………..…………………. 99 4.IV.Discussion ………………………………………………………………………………………. 108 4.V. Conclusions …………………………………………………………………………………...... 115 REFERENCES ..…………………………………………………………………………………...... 116 vii LIST OF FIGURES FIGURE 1.1 Hierachical Structure of Hypothesis Tests ………………………………………… 8 FIGURE 2.1 Quantitative cysteine O-PTM proteomics workflow ………………………………. 25 FIGURE 2.2 Impact of ISO-induced cardiac hypertrophy on the reversible cysteine O-PTM profile ………………………………………………………………………… 37 FIGURE 2.3 Temporal profiling of reversible cysteine O-PTM proteomes using cubic spline-based clustering. ………………………………………………………. 43 FIGURE 2.4 Temporal profiling combining reversible cysteine O-PTM and total cysteine proteomes using cubic spline-based co-clustering …………………….. 45 FIGURE 2.5 Phenotypic alteration and corresponding cysteine site fingerprints during ISO-induced cardiac hypertrophy ………………………………………….. 50 FIGURE 2.6 Signature pathways and proteins that contribute to cardiac hypertrophy …….. 52 FIGURE 3.1 Schematic Overview of Experimental Protocol for Global Plasma Metabolomics Profiling in ISO-stimulated Mice, Healthy Humans, and HF Patients. …………………………………………………………………….. 69 FIGURE 3.2 Metabolomics Dynamics in Mouse Plasma During ISO-induced Cardiac Remodeling.. ……………………………………………………………….. 71 FIGURE 3.3 Phenotypic Alteration and Corresponding Metabolic Fingerprints During ISO-induced Cardiac Remodeling in Mice .…………………….…………. 74 FIGURE 3.4 Healthy Human Subjects Plasma Metabolomics Stability and Their Distinction from HF Patients ……………………..…………………………... 77 FIGURE 3.5 Metabolomics Dynamics in Plasma from HF Patients Before and After MCSD Implantation.……………………………………………………………. 78 FIGURE 3.6 Temporal Changes of Clinical Manifestation and Corresponding Metabolomic Dynamics in HF Patients Following MCSD Implantation.………… 81 FIGURE 4.1 MetProt Integrated workflws .……………...…..…………..……………………… 100 FIGURE 4.2 Intersections where metabolome meets proteome .………………..…………... 103 FIGURE 4.3 MetProt Distributed System Archiecture ……..…..…………..………..…………. 106 FIGURE 4.4 MetProt User Interface ……..…..…………..………..………………………………107 viii LIST OF TABLES TABLE 2.1 Summary information of raw file contents and statistics for all experimental groups ……………………………………………………………... 23&24 TABLE 2.2 List of cysteine sites with alterations in modification abundance during cardiac hypertrophy ………………………………………………………. 28-32 TABLE 2.3 Enriched biological pathways of proteins bearing cysteine sites with significantly increased/decreased modification abundance ………….…. 33-35 TABLE 2.4 List of cysteine sites significantly correlated with the hypertrophy phenotype ………………………………………………………………………..... 46-48 TABLE 2.5 Enriched biological pathways of proteins associated with cysteine sites significantly correlated with the hypertrophy phenotype …………………… 51 TABLE 3.1 Biological Calsses of 610 Targeted Metabolites in Mouse and Human Plasma …………………………………………........................................ .63 TABLE 3.2 Demographics of the Human Cohorts …………………………………………. 65-66 ix RECURRING NOTATIONS AND ABBREVIATIONS
Load more

Recommended publications
  • Metatranscriptomic Analysis of Community Structure And
    School of Environmental Sciences Metatranscriptomic analysis of community structure and metabolism of the rhizosphere microbiome by Thomas Richard Turner Submitted in partial fulfilment of the requirement for the degree of Doctor of Philosophy, September 2013 This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derived there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. i Declaration I declare that this is an account of my own research and has not been submitted for a degree at any other university. The use of material from other sources has been properly and fully acknowledged, where appropriate. Thomas Richard Turner ii Acknowledgements I would like to thank my supervisors, Phil Poole and Alastair Grant, for their continued support and guidance over the past four years. I’m grateful to all members of my lab, both past and present, for advice and friendship. Graham Hood, I don’t know how we put up with each other, but I don’t think I could have done this without you. Cheers Salt! KK, thank you for all your help in the lab, and for Uma’s biryanis! Andrzej Tkatcz, thanks for the useful discussions about our projects. Alison East, thank you for all your support, particularly ensuring Graham and I did not kill each other. I’m grateful to Allan Downie and Colin Murrell for advice. For sequencing support, I’d like to thank TGAC, particularly Darren Heavens, Sophie Janacek, Kirsten McKlay and Melanie Febrer, as well as John Walshaw, Mark Alston and David Swarbreck for bioinformatic support.
    [Show full text]
  • Advances in Enzyme Biotechnology Advances in Enzyme Biotechnology
    Pratyoosh Shukla Brett I. Pletschke Editors Advances in Enzyme Biotechnology Advances in Enzyme Biotechnology Pratyoosh Shukla • Brett I. Pletschke Editors Advances in Enzyme Biotechnology Editors Pratyoosh Shukla Brett I. Pletschke Department of Microbiology Department of Biochemistry, Maharshi Dayanand University Microbiology and Biotechnology Rohtak, Haryana , India Rhodes University Grahamstown, South Africa ISBN 978-81-322-1093-1 ISBN 978-81-322-1094-8 (eBook) DOI 10.1007/978-81-322-1094-8 Springer New Delhi Heidelberg New York Dordrecht London Library of Congress Control Number: 2013945175 © Springer India 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifi cally for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 9,689,046 B2 Mayall Et Al
    USOO9689046B2 (12) United States Patent (10) Patent No.: US 9,689,046 B2 Mayall et al. (45) Date of Patent: Jun. 27, 2017 (54) SYSTEM AND METHODS FOR THE FOREIGN PATENT DOCUMENTS DETECTION OF MULTIPLE CHEMICAL WO O125472 A1 4/2001 COMPOUNDS WO O169245 A2 9, 2001 (71) Applicants: Robert Matthew Mayall, Calgary (CA); Emily Candice Hicks, Calgary OTHER PUBLICATIONS (CA); Margaret Mary-Flora Bebeselea, A. et al., “Electrochemical Degradation and Determina Renaud-Young, Calgary (CA); David tion of 4-Nitrophenol Using Multiple Pulsed Amperometry at Christopher Lloyd, Calgary (CA); Lisa Graphite Based Electrodes', Chem. Bull. “Politehnica” Univ. Kara Oberding, Calgary (CA); Iain (Timisoara), vol. 53(67), 1-2, 2008. Fraser Scotney George, Calgary (CA) Ben-Yoav. H. et al., “A whole cell electrochemical biosensor for water genotoxicity bio-detection”. Electrochimica Acta, 2009, 54(25), 6113-6118. (72) Inventors: Robert Matthew Mayall, Calgary Biran, I. et al., “On-line monitoring of gene expression'. Microbi (CA); Emily Candice Hicks, Calgary ology (Reading, England), 1999, 145 (Pt 8), 2129-2133. (CA); Margaret Mary-Flora Da Silva, P.S. et al., “Electrochemical Behavior of Hydroquinone Renaud-Young, Calgary (CA); David and Catechol at a Silsesquioxane-Modified Carbon Paste Elec trode'. J. Braz. Chem. Soc., vol. 24, No. 4, 695-699, 2013. Christopher Lloyd, Calgary (CA); Lisa Enache, T. A. & Oliveira-Brett, A. M., "Phenol and Para-Substituted Kara Oberding, Calgary (CA); Iain Phenols Electrochemical Oxidation Pathways”, Journal of Fraser Scotney George, Calgary (CA) Electroanalytical Chemistry, 2011, 1-35. Etesami, M. et al., “Electrooxidation of hydroquinone on simply prepared Au-Pt bimetallic nanoparticles'. Science China, Chem (73) Assignee: FREDSENSE TECHNOLOGIES istry, vol.
    [Show full text]
  • Biochemical Studies on Redox Regulation in Different Dormancy Models of Mycobacteria
    Biochemical Studies on Redox Regulation in Different Dormancy Models of Mycobacteria Thesis Submitted to Savitribai Phule Pune University For The Degree Of DOCTOR OF PHILOSOPHY IN BIOTECHNOLOGY By Ketaki Dilip Shurpali Research Supervisor Dr. Dhiman Sarkar Combichem Bioresource Center Organic Chemistry Division CSIR-National Chemical Laboratory Pune-411008 India October 2014 Certificate This is to certify that the work incorporated in the thesis entitled “ Biochemical Studies on Redox Regulation in Different Dormancy Models of Mycobacteria ” submitted by Ketaki Dilip Shurpali was carried out under my supervision at Combichem Bioresource Center, Organic Chemistry Division, National Chemical Laboratory, Pune-411008, Maharashtra, India. Materials obtained from other sources have been duly acknowledged in the thesis. Dr. Dhiman Sarkar (Research Guide) I Declaration by Research Scholar I hereby declare that the thesis entitled " Biochemical Studies on Redox Regulation in Different Dormancy Models of Mycobacteria ", submitted for the Degree of Doctor of Philosophy to the Savitribai Phule Pune University, has been carried out by me at Combichem Bioresource Center, Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune-411008, Maharashtra, India, under the supervision of Dr. Dhiman Sarkar (Research supervisor). The work is original and has not been submitted in part or full by me for any other degree or diploma to any other University. Ketaki Dilip Shurpali (Research Scholar) II Dedications This thesis is dedicated to all those people who were always besides me in my good and bad times. First dedication goes to my father Mr. Dilip Shurpali and mother Mrs. Devyani Shurpali who instilled in me the desire to learn new things and confidence to achieve my dreams.
    [Show full text]
  • Nitrogen Metabolism in Mycobacterium Smegmatis
    Nitrogen metabolism in Mycobacterium smegmatis Michael Petridis Dipl. Biol. (Goethe University Frankfurt) University of Otago June 30th 2015 This dissertation is submitted in publication format for the degree of Doctor of Philosophy. Declaration This dissertation is the result of my own work and contains nothing, which is the outcome of work done in collaboration with others, except where clearly stated. No part of this dissertation has been submitted for any other degree or qualification. This research project was undertaken in the laboratory of Prof. Gregory M. Cook at the Department of Microbiology and Immunology, University of Otago in Dunedin, New Zealand between July 2012 and June 2015. A portion of this research was also performed in the laboratory of Prof. Stewart T. Cole at the École Polytechnique Fédérale de Lausanne in Lausanne, Switzerland in December 2013. i Thesis by Publication Format This dissertation has been submitted by publication format. The Otago School of Medical Sciences and the Department of Microbiology & Immunology provided consultation on how to submit by this format. This thesis is presented in accordance with their guidelines. Each of the three results chapters are primary research papers that have been submitted, or prepared for publication. The extended introduction and summary sections were written specifically for this thesis. They serve to place this work in a wider context and bring together the findings as a whole. In accordance with requirements, each chapter has been reformatted for consistency. I took the leading role in the work presented here. For each study, I planned experiments, performed research and interpreted data. I wrote the majority of each manuscript.
    [Show full text]
  • Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes
    bioRxiv preprint doi: https://doi.org/10.1101/2020.04.29.067207; this version posted April 30, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophic Afipia and Thiobacillus strains within complex microbiomes Robert J. Huddy1,2, Rohan Sachdeva3, Fadzai Kadzinga1,2, Rose Kantor4, Susan T.L. Harrison1,2 and Jillian F. Banfield3,4,5,6* 1The Center for Bioprocess Engineering Research, University of Cape Town, South Africa 2The Future Water Institute, University of Cape Town, South Africa 3The Innovative Genomics Institute at the University of California, Berkeley, California, USA 4The Department of Earth and Planetary Science, University of California, Berkeley, California, USA 5The Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA 6The University of Melbourne, Victoria, Australia *Corresponding Author: [email protected] Abstract Thiocyanate (SCN-) contamination threatens aquatic ecosystems and pollutes vital fresh water supplies. SCN- degrading microbial consortia are commercially deployed for remediation, but the impact of organic amendments on selection within SCN- degrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCN- could be reproducibly selected for based on SCN- loading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCN- contaminated water were exposed to systematically increased input SCN concentrations in molasses-amended and -unamended reactors and in reactors switched to unamended conditions after establishing the active SCN- degrading consortium.
    [Show full text]
  • Rhodococcus Erythropolis and Gordonia Alkanivorans: Interesting Desulfurizing
    IN SILICO MODELING AND ANALYSIS FOR IMPROVING DESULFURIZING BACTERIAL STRAINS SHILPI AGGARWAL (M.Tech., Indian Institute of Technology, Roorkee, India) A THESIS SUBMITTED FOR THE DEGREE OF PHD OF ENGINEERING DEPARTMENT OF CHEMICAL AND BIOMOLECULAR ENGINEERING NATIONAL UNIVERSITY OF SINGAPORE 2012 Declaration DECLARATION I hereby declare that the thesis is my original work and it has been written by me in its entirety. I have duly acknowledged all the sources of information which have been used in the thesis. This thesis has also not been submitted for any degree in any university previously. Shilpi Aggarwal 10 April 2013 i Acknowledgments ACKNOWLEDGMENTS I take this chance to express my sincere gratitude and love for my parents (Mr Subash and Mrs Renu) for their undying faith, encouragement, and unconditional love throughout my life. This PhD thesis is dedicated to them as I could have never come so far without their support. It is with immense pleasure and respect I take this opportunity to express my thankfulness to all those who have helped me in shaping my research career and making my stay in Singapore a truly memorable one. With the term ‘PhD’, the first person who comes to my mind is my supervisor, Prof I. A. Karimi. I take this chance to thank him for giving me an opportunity to pursue my research career under his able guidance. As a mentor he has made me acquire skills for critical and logical thinking. His directions and guidance has helped me get deeper insights into the subject and made my learning a great experience.
    [Show full text]
  • Investigation of Bioprocesses to Enhance Metal Extraction from Ores and Wastes in Mining Operations
    Investigation of Bioprocesses to Enhance Metal Extraction from Ores and Wastes in Mining Operations By Laís Mazullo Mascarenhas Pereira A thesis submitted in conformity with the requirements for the degree of Master of Applied Science Chemical Engineering and Applied Chemistry University of Toronto © Copyright by Laís Mazullo Mascarenhas Pereira 2019 Investigation of Bioprocesses to Enhance Metal Extraction from Ores and Wastes in Mining Operations Laís Mazullo Mascarenhas Pereira Master of Applied Science Chemical Engineering and Applied Chemistry University of Toronto 2019 Abstract Mine sites are a large source of genetic information that can be studied to explore ways of processing minerals using bacteria. This study investigates the bioleaching potential to extract nickel from ores and wastes at circumneutral pH and denitrifying conditions, and the cyanide biodegradation phenomenon at a gold heap leaching operation by examining naturally growing bacteria at two mine sites. Neutral pH bioleaching of nickel was achieved using nitrate as electron acceptor and oxidant. A mass balance revealed that about 20-30% of the original concentrate was leached over a period of more than 500 days. Faster rates could possibly be achieved by increasing biomass concentration. Thiobacillus was the dominant microbe identified in these microcosms. In gold heap leaching with cyanide, the microbial community was found to be almost entirely composed of a Hydrogenophaga with 16S sequence most similar to other alkaliphilic strains. This strain is presumably growing on the cyanide. ii Acknowledgments I would like to first express my deepest appreciation to my thesis supervisor Dr. Elizabeth Edwards for her continuous guidance of my Master research, patience, encouragement and immense knowledge.
    [Show full text]
  • Trinuclear Copper Biocatalytic Center Forms an Active Site of Thiocyanate Dehydrogenase
    Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase Tamara V. Tikhonovaa,1, Dimitry Y. Sorokina,b,1, Wilfred R. Hagenb, Maria G. Khrenovaa,c, Gerard Muyzerd, Tatiana V. Rakitinae,f, Ivan G. Shabaling, Anton A. Trofimovh, Stanislav I. Tsallagova, and Vladimir O. Popova,f,2 aResearch Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; bDepartment of Biotechnology, Delft University of Technology, Delft, 2629 HZ The Netherlands; cDepartment of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; dDepartment of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, 1098 XH The Netherlands; eShemyakin- Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; fKurchatov Complex NBICS-Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; gDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903; and hEngelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia Edited by Edward I. Solomon, Stanford University, Stanford, CA, and approved January 27, 2020 (received for review December 29, 2019) Biocatalytic copper centers are generally involved in the activation via initial formation of (NCS)2Cu, comprises multiple stages, and and reduction of dioxygen, with only few exceptions known. gives sulfate as the final sulfur reaction product. Some sulfur- Here we report the discovery and characterization of a pre- oxidizing bacteria (SOB) known to play an important role in viously undescribed copper center that forms the active site of global geochemical cycles can utilize thiocyanate as the sole a copper-containing enzyme thiocyanate dehydrogenase (sug- source of energy and nitrogen.
    [Show full text]
  • 12) United States Patent (10
    US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S.
    [Show full text]
  • Isotopic Fractionation of Sulfur in Carbonyl Sulfide by Carbonyl Sulfide Hydrolase of Thiobacillus Thioparus THI115
    Microbes Environ. Vol. 32, No. 4, 367-375, 2017 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME17130 Isotopic Fractionation of Sulfur in Carbonyl Sulfide by Carbonyl Sulfide Hydrolase of Thiobacillus thioparus THI115 TAKAHIRO OGAWA1, SHOHEI HATTORI2, KAZUKI KAMEZAKI2, HIROMI KATO3, NAOHIRO YOSHIDA2,4, and YOKO KATAYAMA1* 1Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3–5–8 Saiwai-cho, Fuchu, Tokyo 183–8509, Japan; 2Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226–8502, Japan; 3Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-Ku, Sendai, Miyagi 980–8577, Japan; and 4Earth-Life Science Institute, Tokyo Institute of Technology, 2–12–1–IE–1 Ookayama, Meguro-ku, Tokyo 152–8550, Japan (Received August 15, 2017—Accepted September 24, 2017—Published online December 2, 2017) Carbonyl sulfide (COS) is one of the major sources of stratospheric sulfate aerosols, which affect the global radiation balance and ozone depletion. COS-degrading microorganisms are ubiquitous in soil and important for the global flux of COS. We examined the sulfur isotopic fractionation during the enzymatic degradation of COS by carbonyl sulfide hydrolase (COSase) fromThiobacillus thioparus THI115. The isotopic fractionation constant (34ε value) was –2.2±0.2‰. Under experimental conditions performed at parts per million by volume level of COS, the 34ε value for intact cells of T. thioparus THI115 was –3.6±0.7‰, suggesting that, based on Rees’ model, the 34ε value mainly depended on COS transport into the cytoplasm.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur Et Al
    US 2012026.6329A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur et al. (43) Pub. Date: Oct. 18, 2012 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/10 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/24 (2006.01) CI2N 9/02 (2006.01) (75) Inventors: Eric J. Mathur, Carlsbad, CA CI2N 9/06 (2006.01) (US); Cathy Chang, San Marcos, CI2P 2L/02 (2006.01) CA (US) CI2O I/04 (2006.01) CI2N 9/96 (2006.01) (73) Assignee: BP Corporation North America CI2N 5/82 (2006.01) Inc., Houston, TX (US) CI2N 15/53 (2006.01) CI2N IS/54 (2006.01) CI2N 15/57 2006.O1 (22) Filed: Feb. 20, 2012 CI2N IS/60 308: Related U.S. Application Data EN f :08: (62) Division of application No. 1 1/817,403, filed on May AOIH 5/00 (2006.01) 7, 2008, now Pat. No. 8,119,385, filed as application AOIH 5/10 (2006.01) No. PCT/US2006/007642 on Mar. 3, 2006. C07K I4/00 (2006.01) CI2N IS/II (2006.01) (60) Provisional application No. 60/658,984, filed on Mar. AOIH I/06 (2006.01) 4, 2005. CI2N 15/63 (2006.01) Publication Classification (52) U.S. Cl. ................... 800/293; 435/320.1; 435/252.3: 435/325; 435/254.11: 435/254.2:435/348; (51) Int. Cl. 435/419; 435/195; 435/196; 435/198: 435/233; CI2N 15/52 (2006.01) 435/201:435/232; 435/208; 435/227; 435/193; CI2N 15/85 (2006.01) 435/200; 435/189: 435/191: 435/69.1; 435/34; CI2N 5/86 (2006.01) 435/188:536/23.2; 435/468; 800/298; 800/320; CI2N 15/867 (2006.01) 800/317.2: 800/317.4: 800/320.3: 800/306; CI2N 5/864 (2006.01) 800/312 800/320.2: 800/317.3; 800/322; CI2N 5/8 (2006.01) 800/320.1; 530/350, 536/23.1: 800/278; 800/294 CI2N I/2 (2006.01) CI2N 5/10 (2006.01) (57) ABSTRACT CI2N L/15 (2006.01) CI2N I/19 (2006.01) The invention provides polypeptides, including enzymes, CI2N 9/14 (2006.01) structural proteins and binding proteins, polynucleotides CI2N 9/16 (2006.01) encoding these polypeptides, and methods of making and CI2N 9/20 (2006.01) using these polynucleotides and polypeptides.
    [Show full text]