Comparative Toxicogenomics

337 Pages·2008·3.838 MB·1-328\337

by  Christer Hogstrand and Peter Kille (Eds.)

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
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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