Comparative Toxicogenomics PDF
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COMPARATIVE TOXICOGENOMICS Edited by Christer Hogstrand King’s College London Nutritional Sciences Division Franklin-Wilkins Building 150 Stamford Street London SE1 9NH, UK and Peter Kille Cardiff School of Biosciences Biomedical Sciences Building Cardiff University Cardiff CF10 3US, UK Amsterdam – Boston– Heidelberg – London– NewYork –Oxford Paris – SanDiego – SanFrancisco– Singapore – Sydney– Tokyo Elsevier Radarweg29,POBox211,1000AEAmsterdam,TheNetherlands LinacreHouse,JordanHill,OxfordOX28DP,UK Firstedition2008 Copyrightr2008ElsevierB.V.Allrightsreserved Nopartofthispublicationmaybereproduced,storedinaretrievalsystem ortransmittedinanyformorbyanymeanselectronic,mechanical,photocopying, recordingorotherwisewithoutthepriorwrittenpermissionofthepublisher PermissionsmaybesoughtdirectlyfromElsevier’sScience&TechnologyRights DepartmentinOxford,UK:phone(+44)(0)1865843830;fax(+44)(0)1865853333; email:permissions@elsevier.com.Alternativelyyoucansubmityourrequestonlineby visitingtheElsevierwebsiteathttp://www.elsevier.com/locate/permissions,andselecting ObtainingpermissiontouseElseviermaterial Notice Noresponsibilityisassumedbythepublisherforanyinjuryand/ordamagetopersons orpropertyasamatterofproductsliability,negligenceorotherwise,orfromanyuse oroperationofanymethods,products,instructionsorideascontainedinthematerial herein.Becauseofrapidadvancesinthemedicalsciences,inparticular,independent verificationofdiagnosesanddrugdosagesshouldbemade LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress BritishLibraryCataloguinginPublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary ISBN:978-0-444-53274-9 ISSN:1872-2423 ForinformationonallElsevierpublications visitourwebsiteatbooks.elsevier.com PrintedandboundinHungary 08 09 10 11 12 10 9 8 7 6 5 4 3 2 1 v Information about the Society for Experimental Biology (SEB) The Society for Experimental Biology (SEB) is Europe’s leading, not- for-profit organisation embracing all disciplines of experimental biology. ThroughitslargemembershipandpassionforsciencetheSocietysupports and promotes experimental biology, from molecular to ecological, to benefit both the scientific community and the general public. The Society was foundedin 1923atBirkbeck College and is now well establishedwith a current worldwide membership of over 1,900 biological researchers, teachers and students. The SEB is somewhat unusual in catering for both plant and animal biologists. The Animal Section of the SEB launched this serial ‘‘Advances in Experimental Biology’’ (AEB) in 2006, with the first volume published in 2007. The aim of this new serial is to provide state-of-the-art review volumes on timely issues that have international topicality within the field of Comparative and Integrative Biology. The series as a whole will therefore cover a rather broad range of topics from the role of individual molecules (e.g. nitric oxide) to system-level approaches applied to a particular research discipline (e.g. toxicogenomics). Each volume will contain approximately ten chapters each providing a detailed review of current understanding within a sub-topic of the volume title.Insomevolumesthechapterswillbeorganisedaccordingtothelevel at which the research is focused (e.g. molecular, biochemical, physiologi- cal, behavioural,ecological);in others thechaptersmaybeorganisedona more taxonomic basis. Each chapter is written by leading authorities in science that have been invited, based on their international reputation, to provide their perspective on the current status and recent developments withinthefield.Allchaptersarepeer-reviewedbyatleasttwoindependent referees prior to acceptance for publication. The series thus aims to provide an excellent, up-to-date resource for a global research audience within each of the volume topics. vii ADVANCES IN EXPERIMENTAL BIOLOGY EDITORIAL BOARD Series Editors Mike Thorndyke Royal Swedish Academy of Sciences, Kristineberg Marine Research Station, SE-450 34 Fiskebackskil, Sweden Rod Wilson School of Biological Sciences, University of Exeter, Hatherly Laboratories, Prince of Wales Road, Exeter EX4 4PS, United Kingdom Members of the Editorial Advisory Board Mike Burrell Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom Julian Dow Molecular Genetics, IBLS, University of Glasgow, Pontecorvo Building, Glasgow G11 6NU, United Kingdom Maurice Elphick School of Biological Sciences, Queen Mary & Westfield College, Mile End Road, London E1 4NS, United Kingdom Richard Handy Department of Biological Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, United Kingdom Pat Walsh Division of Marine Biology and Fisheries, RSMAS, The University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA Tobias Wang Department ofZoophysiology,University ofAarhus,Aarhus 8000C,Denmark ix Information about the Series Editors Professor Mike Thorndyke Professor Mike Thorndyke is the Director and Chair of Experimental Marine Biology at the Royal Swedish Academy of Sciences, Kristineberg Marine Research Station, Sweden. His laboratory specialises in under- standing the diversity of cellular, genetic processes in marine organisms, and their importance in terms of evolution, adaptation and ecology, with particular reference to development and adult regeneration. Professor Thorndyke has over 25 years experience working with marine inverte- brates.Hislaboratoryhasbeenthefocusforthecharacterisationofneural complexityininvertebratedeuterostomesincludingechinoderms,tunicates and the Xenoturbellids, recently confirmed as a new Deuterostome phylum. Most recently, Professor Thorndyke has been one of the leaders of the neural group in the sea urchin genome annotation consortium. Dr Rod Wilson Dr Rod Wilson began his academic career reading Biological Sciences at the University of Birmingham, where he subsequently completed a Ph.D. in Fish Physiology and Ecotoxicology. After completing postdoctoral trainingattheUniversityofBirmingham,McMasterUniversityinCanada and the University of Manchester, Dr Wilson moved to the University of ExeterwhereheiscurrentlyaSeniorLecturer.Hisareaofexpertisecovers comparative and integrative physiology, ranging from studies on water absorption in the mammalian kidney to the behaviour and physiology of fishinthewild.DrWilson’sworkcurrentlyfocusesuponfish(marineand freshwater) and he believes it is important to approach research from a multidisciplinary angle in order to guarantee a holistic understanding of homeostasis in animals. He is particularly interested in how multiple physiological systems (e.g., respiratory/cardiovascular, osmoregulation, acid–base balance, nitrogenous waste excretion) respond in an integrated manner to maintain whole animal homeostasis in the face of environ- mentalchanges(bothnaturalandanthropogenic).Hisworkutilisesstudies atthe molecular,cellular, tissueandwhole animal levels. Furthermore, he isincreasinglyintegratingthisapproachwithbehaviouralstudiesthathelp link physiological mechanisms with social behaviour in fish, both in the laboratory and in the wild. xi Information about the Volume Editors Professor Christer Hogstrand Professor Christer Hogstrand’s expertise lies in the biology and toxicology of minerals, with a particular focus on how zinc controls biological processes. Professor Hogstrand completed his Ph.D. at the University of Go¨ teborg before undertaking a postdoctoral research position with Professor Chris Wood at McMaster University, Canada. During this time, he pioneered research on silver toxicity to fish and discovereduptakepathwaysfor zinc acrossthegill. ProfessorHogstrand movedtoKing’sCollegeLondonin2001afterdevelopinghisresearchas Assistant and Associate Professor at the University of Kentucky and the UniversityofMiami.HewaspromotedtoProfessorin2006whereheisa leadingfigureonusingpost-genomicandproteomictechnologiesastools for class prediction and mechanistically relating negative effects to affected networks. Dr Peter Kille Dr Peter Kille’s areas of expertise include the biochemistry of heavy metals, molecular biology, molecular ecotoxicology, environmental biomonitoring and metal binding proteins. Specifically, his research harnesses genomic, proteomic and metabolomic techniques in order to study the mechanisms by which biological systems handle heavy metals and other xenobiotics. Dr Kille began and developed his research career at the University of Wales College of Cardiff. He is currently a Senior Lecturer at the School of Biosciences, University of Wales College of Cardiff, a position he has held since 2001. xiii List of Contributors Ronny van Aerle, Environmental and Molecular Fish Biology, School of Biosciences, The Hatherly Laboratories, University of Exeter, Prince of Wales Road, Exeter, Devon, UK. Jonathan Ball, Environmental and Molecular Fish Biology, School of Biosciences, The Hatherly Laboratories, University of Exeter, Prince of Wales Road, Exeter, Devon, UK. Angela Brown, School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, UK. Amanda Callaghan, School of Biological Sciences, University of Reading, Reading, UK. John K. Colbourne, The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA. Isabelle Colson, Zoologisches Institut, Universita¨t Basel, Biozentrum/Pharma- zentrum, Klingelbergstrasse 50, 4056 Basel, Switzerland. Brian D. Eads, Department of Biology, Indiana University, Bloomington, Indiana, USA. Amy L. Filby, Environmental and Molecular Fish Biology, School of Biosciences, The Hatherly Laboratories, University of Exeter, Prince of Wales Road, Exeter, Devon, UK. Donald Gilbert, Department of Biology, Indiana University, Bloomington, Indiana, USA. Eugene P. Halligan, Molecular Diagnostics, Pathology SDU, St. Thomas’ Hospital, Lambeth Palace Road, London, UK. xiv Richard D. Handy, School of Biological Sciences, University of Plymouth, Drake Circus, Plymouth, UK. Colin R. Harwood, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK. Ian M. Head, School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, UK. Bastiaan Jansen, Laboratory of Aquatic Ecology, Katholieke Universiteit Leuven, Ch. De Beriostraat 32, B-3000, Leuven, Belgium. Peter Kille, Cardiff School of Biosciences, BIOSI 1, University of Cardiff, Cardiff, UK. Rebecca Klaper, Great Lakes WATER Institute, University of Wisconsin- Milwaukee, 600 East Greenfield Ave, Milwaukee, Wisconsin, USA. AnkeLange,EnvironmentalandMolecularFishBiology,SchoolofBiosciences, TheHatherlyLaboratories,UniversityofExeter,PrinceofWalesRoad,Exeter, Devon, UK. Joseph Lunec, Cranfield Health, Cranfield University, Barton Road, Silsoe, Bedfordshire, UK. A.JohnMorgan,CardiffSchoolofBiosciences,BIOSI1,UniversityofCardiff, Cardiff, UK. Michael E. Pfrender, Department of Biology, Utah State University, 5305 Old Main Hill Road, Logan, Utah, USA. Helen C. Poynton, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, USA. Eduarda M. Santos, Environmental and Molecular Fish Biology, School of Biosciences, The Hatherly Laboratories, University of Exeter, Prince of Wales Road, Exeter, Devon, UK. JosephR.Shaw,TheSchoolofPublicandEnvironmentalAffairs,Bloomington, Indiana, USA. xv Richard M. Sibly, School of Biological Sciences, University of Reading, Reading, UK. JasonR.Snape,AstraZeneca, Brixham EnvironmentalLaboratory, Freshwater Quarry Brixham, Devon, UK. David J. Spurgeon, Centre for Ecology and Hydrology, Monks Wood, Abbots Ripton, Huntingdon, Cambridgeshire, UK. Charles R. Tyler, Environmental and Molecular Fish Biology, School of Biosciences, The Hatherly Laboratories, University of Exeter, Prince of Wales Road, Exeter, Devon, UK. ChrisD.Vulpe,BerkeleyInstituteoftheEnvironment,UniversityofCalifornia, Berkeley, California, USA. HenriWintz,DepartmentofNutritionalSciencesandToxicology,Universityof California, Berkeley, California, USA. xvii Preface Functional genomics has come of age. No longer is it an adventure for the avant-garde scientist, but it has become an increasingly standardised main- stream tool accessible to any modern biological laboratory. Toxicogenomics studies are now generating an avalanche of data which, with the aid of established informatic methodology, is being translated into biologically meaningful information. This is enabling us to start harvesting the benefits fromyearsofinvestmentintermsoftechnology,time,and(ofcourse)money.It is therefore timely to bring together leading toxicologists with a wide variety of scientific aims to demonstrate how microarray technology can be successfully applied to different research areas. There are a number of challenges in editing any volume whose remit encompasses the ‘genomics’ arena including jargon busting, demystifying technology or representing the sheer scope of the disciplines embracing this scientific approach. Our aim was to address the latter objective and bringing together a series of papers that represent the breadth of the toxicogenomic landscape. To achieve this we had to consider a myriad of related themes each representing a spectrum of interconnected applications. The major continuum revolves around the applied endpoint of the investigation whether the toxicologicalinvestigationis:directlyappliedtohumanhealth(i.e.,pharmalogical in nature); a surrogate for human response; or a measure of environmental risk (ecotoxicogenomics).Furthermore,intertwinedwiththisisthelevelofgeneticand functionalknowledgethatexistsfortheorganismsexploitedinthestudiesranging from the so-called model organism (such as mouse and zebrafish) to those geneticallyunderrepresentedtaxawherethesmallamountofgenomeinformation is overshadowed by our ignorance of their functional biology. The nature of the application is also reflected by the bio-material exploited with ethical drivers promoting the use of in vitro cell lines whilst tissue specific investigation are employedwherethereisaknownmode-of-action(MOA)towholeorganismsand population based analysiswheredriversincludesize, unknownMOA or a desire to relate molecular responses to population level effects. These aspects are overlaidbythegrowingmaturationofthefieldwhichisseeingatransferfromthe fundamental science forums to the legislative arena. Thus, this book transects biologyfrombacteriatohuman,fromecologicallyrelevantsentinelorganismsto wellcharacterisedmodelspecies,andthetoxicogenomicsarenafromexploratory ‘blue sky’ science to prospects of incorporation into regulatory frameworks. In many ways the implications for toxicology of human genetic variation, as revealed by whole genome sequence analyses, is substantively less controversial than the disclosure of pre-disposure to either conditions that can be mitigated or
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