Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis PDF
Preview Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis
METABOLIC PROFILING: ITS ROLE IN BIOMARKER DISCOVERY AND GENE FUNCTION ANALYSIS METABOLIC PROFILING: ITS ROLE IN BIOMARKER DISCOVERY AND GENE FUNCTION ANALYSIS edited by George G. Harrigan Pharmacia Corporation Chesterfield, MO 63198 U.S.A. Royston Goodacre Department of Chemistry, UM/Sr, PO Box 88, Manchester, M60 1Q D, United Kingdom. ~. " SPRINGER SCIENCE+BUSINESS MEDIA, LLC Library of Congress CataIoging-in-Publication Data Metabolie profiling : its role in biomarker discovery and gene function analysis / edited by George G. Harrigan, Royston Goodacre. p.;cm. Includes bibliographical references and index. ISBN 978-1-4613-5025-5 ISBN 978-1-4615-0333-0 (eBook) DOI 10.1007/978-1-4615-0333-0 1. Metabolites 2. Metabolie profile tests 3. Biochemical markers 4. Proteomics 5. Genetic regulation.!. Harrigan, George G. 11. Goodacre, Royston. QP171 .M37752003 612.3'9--dc21 Copyright © 2003 Springer Science+Business Media New York Originally published by Kluwer Academic Publisher in 2003 Softcover reprint of the hardcover 1s t edition 2003 All rights reserved. No part of this work may be reproduced, stored in a retrleval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without the written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Permission for booles published in Europe: [email protected] Permissions for books published in the United States of America: [email protected] Printed on acid-free paper. TOBETH, SEANANDEVANand TOELIZABETH, TAMARA ANDPICKLES Contents Contributors ix Preface Xlll 1. Introduction GeorgeG. Harriganand Royston Goodacre 2. MetabolomeAnd ProteomeProfilingForMicrobial Characterization 9 Seetharaman Vaidyanathan and Royston Goodacre 3. Can 18NMRDerived MetabolicProfilesContributeTo ProteomicAnalyses? 39 Julian L. Griffin and ElizabethSang 4. Application OfMetabonomicsInThePharmaceutical Industry 69 Alan P. Breauand Glenn H. Cantor 5. MetabolicProfilingIn TumorsByIn Vivo And In Vitro NMRSpectroscopy 83 Yeun-LiChung, Marion StubbsandJohnR. Griffiths 6. Raman SpectroscopyForWholeOrganism And Tissue Profiling 95 SarahClarkeand Royston Goodacre VIII Contents 7. MetabolicFingerprintingWithFourierTransform InfraredSpectroscopy 111 DavidI.Ellis,GeorgeG. HarriganandRoyston Goodacre 8. MetabolomicAnalysisWithFourierTransform Ion CyclotronResonance MassSpectrometry 125 DayanGoodenowe 9. StableIsotope-BasedDynamicMetabolicProfilingIn DiseaseAndHealth 141 LaszloG. Boros,MartaCascanteand Wai-NangPaul Lee 10. TheRoleOfMetabolomicsIn SystemsBiology 171 Jan vanderGreef, EugeneDavidov, ElwinVerheij, JackVogels,RobvanderHeijden,Aram S.Adourian, Matej Oresic, EdwardW. MarpleandStephenNaylor 11. UseOfMetabolomicsToDiscoverMetabolicPatterns AssociatedWithHumanDiseases 199 OliverFiehnand Joachim Spranger 12. BioactiveLipidsInReproductiveDiseases 217 JaideepChaudhary, Tim Comptonand JeffA. Parrott 13. EvolutionaryComputationForTheInterpretationOf MetabolomicData 239 Royston Goodacreand DouglasB.Kell 14. DynamicProfilingAnd CanonicalModeling 257 EberhardO.Voitand JonasAlmeida 15. Databases,DataModelingAnd Schemas 277 NigelHardyand HelenFuell 16. DatabasesAnd VisualizationForMetabolomics 293 X. JingLi,OlgaBrazhnik,AejaazKamal,DianjingGuo, ChristineLee, StefanHoopsand PedroMendes 17. TheHumanMetabolome 311 ChrisW.W. Beecher Index 321 Contributors Aram S. Adourian. Beyond Genomics Inc., 40 Bear Hill Road, Waltham, MA02451, USA Jonas Almeida. DepartmentofBiometryand Epidemiologyand Department of Biochemistry and Molecular Biology, Medical University of South Carolina,Charleston, SC 29435,USA Christopher W. W. Beecher. Paradigm Genetics, 108 TW Alexander Dr., ResearchTriangle,NC 27709, USA Laszlo G. Boros. Harbor-UCLA Research and Education Institute, 1124 WestCarsonStreetRBI, Torrance, CA90502,USA Olga Brazhnik. Virginia Bioinforrnatics Institute, Virginia Tech (0477),1880 PrattDr., Blacksburg,VA24061, USA Alan P. Breau. Global Drug Metabolism, Pharrnacia Corporation, 4901 Searle Parkway, Skokie,IL 60077,USA Glenn H. Cantor. Investigative Toxicology, Pharrnacia Corporation, 301 HenriettaSt., Kalamazoo, MI 49007,USA Marta Cascante. Department of Biochemistry and Molecular Biology, University ofBarcelona, Marti/I Franques 1, Barcelona 08028, Catalonia, Spain x Contributors Jaideep Chaudhary. AtairginTechnologies, 101 Theory, Irvine, CA 92612, USA Yeun-Li Chung. Cancer Research UK Biomedical Magnetic Resonance Research Group, Department of Biochemistry and Immunology, St. George'sHospital Medical School, London, SWl7ORE, UK Sarah Clarke. Institute of Biological Sciences, University of Wales, Aberystwyth, SY23 3DD, UK TimCompton.AtairginTechnologies, 101 Theory,Irvine,CA92612,USA Eugene Davidov.Beyond Genomics Inc., 40 BearHill Road, Waltham, MA 02451, USA David I. Ellis. Institute of Biological Sciences, University of Wales, Aberystwyth, SY23 3DD,UK Oliver Fiehn. Max-Planck-Institute of Molecular Plant Physiology, 14424 PotsdamlGolm,Germany Helen Fuell. Department of Computer Sciences, University of Wales, Aberystwyth, SY23 3DB,UK. Royston Goodacre. Department of Chemistry, University of Manchester Institute of Science and Technology, PO Box 88, Sackville St., Manchester, M60 1QD, UK Dayan Goodenowe. Phenomenome Discoveries Inc., 204-407 Downey Road, Saskatoon SK S7N4L8,Canada Julian L. Griffin. Division of Biomedical Sciences, Imperial College of Science,Technologyand Medicine, London, SW72AZ,UK John R. Griffiths. Cancer Research UK Biomedical Magnetic Resonance Research Group, Department of Biochemistry and Immunology, St. George'sHospital Medical School, London, SW17ORE, UK DianjingGuo. VirginiaBioinformaticsInstitute,VirginiaTech(0477), 1880 Pratt Dr., Blacksburg, VA 24061, USA Contributors XI Nigel Hardy. Department of Computer Sciences, University of Wales, Aberystwyth, SY23 3DB,UK George G. Harrigan. Global HTS, Pharmacia Corporation, 700 Chesterfield Parkway,Chesterfield,MO 63198, USA Stefan Hoops. Virginia BioinformaticsInstitute,VirginiaTech(0477), 1880 Pratt Dr., Blacksburg, VA 24061, USA Aejaaz Kamal. Virginia Bioinformatics Institute, Virginia Tech (0477), 1880PrattDr., Blacksburg,VA24061, USA Douglas B. Kell. Department of Chemistry, University of Manchester Institute of Science and Technology, PO Box 88, Sackville St., Manchester, M60 1QD, UK Christine Lee. VirginiaBioinformaticsInstitute,VirginiaTech(0477), 1880 Pratt Dr., Blacksburg,VA 24061,USA Wai-Nang Paul Lee. Harbor-UCLA Researchand Education Institute, 1124 WestCarson StreetRBI, Torrance,CA90502, USA X. Jing Li. Virginia Bioinformatics Institute, Virginia Tech (0477), 1880 PrattDr., Blacksburg, VA 24061,USA Edward W. Marple. Beyond Genomics Inc., 40 Bear Hill Road, Waltham, MA02451, USA Pedro Mendes. Virginia Bioinformatics Institute, Virginia Tech (0477), 1880PrattDr., Blacksburg,VA24061,USA Stephen Naylor. Beyond Genomics Inc., 40 BearHill Road, Waltham, MA 02451, USA Matej Oresic. Beyond Genomics Inc., 40 Bear Hill Road, Waltham, MA, 02451, USA JeffA. Parrott.AtairginTechnologies, 101 Theory, Irvine, CA92612, USA Elizabeth Sang. Department of Biochemistry, Oxford University, Oxford, OXI 3QV, UK xii Contributors Joachim Spranger. Gennan Instiute of Human Nutrition (DitE), 14558 Bergholz-Rehbriicke,Gennany Marion Stubbs. Cancer Research UK Biomedical Magnetic Resonance Research Group, Department of Biochemistry and Immunology, St. George's HospitalMedical School,London,SWI7ORE,UK Seetharaman Vaidyanathan.Instiute ofBiological Sciences, University of Wales, Aberystwyth,SY23 3DD,UK Jan van der Greef. Beyond Genomics Inc., 40 Bear Hill Road, Waltham, MA 02451, USA, TNO Phanna, PO Box 22152031 CE, Zemikedreff9, 2333 CK, Leiden, Netherlands and Leiden University/Amsterdam Center for Drug Research, Division ofAnalytical Sciences,NL-2300 RA Leiden, Netherlands Rob van der Heijden. Leiden University/Amsterdam Center for Drug Research, Division of Analytical Sciences, NL-2300 RA Leiden, Netherlands Elwin Verheij.TNO Phanna, PO Box 22152031 CE, Zemikedreff9, 2333 CK,Leiden,Netherlands Jack Vogels. TNO Phanna, PO Box 2215 2031 CE, Zemikedreff 9, 2333 CK, Leiden,Netherlands Eberhard O. Voit. Department of Biometry and Epidemiology, Medical UniversityofSouthCarolina,Charleston, SC 29435,USA
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