Table Of ContentMethods in Cell
Biology
The Zebrafish: Cellular and
Developmental Biology,
Part A Cellular Biology
Volume 133
Series Editors
Leslie Wilson
DepartmentofMolecular,CellularandDevelopmentalBiology
UniversityofCalifornia
SantaBarbara,California
Phong Tran
University of Pennsylvania
Philadelphia, USA &
Institut Curie, Paris, France
Methods in Cell
Biology
The Zebrafish: Cellular and
Developmental Biology,
Part A Cellular Biology
Volume 133
Edited by
H. William Detrich, III
Northeastern University Marine Science Center,
Nahant,MA,United States
Monte Westerfield
University of Oregon, Eugene,OR,United States
Leonard I. Zon
Harvard University, Boston,MA,United States
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experiencebroadenourunderstanding,changesinresearchmethods,professional
practices,ormedicaltreatmentmaybecomenecessary.
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Len,Monte,andIdedicatethe4thEditionofMethodsinCellBiology:
The Zebrafish to the postdoctoral fellows and graduate students
who conducted the genetic screens that established the zebrafish as a
preeminent vertebrate model system for analysis of development.
Contributors
J.L. Anderson
Carnegie Institution for Science,Baltimore, MD, UnitedStates
J.D. Carten
Carnegie Institution for Science,Baltimore, MD, UnitedStates
D. Castranova
NationalInstituteofChild Health and Human Development, Bethesda, MD,
United States
C.A. Ciarlo
Harvard Medical School and Children’sHospital, Boston, MA, United States
K.W. Eliceiri
University ofWisconsineMadison, Madison, WI,United States; Morgridge
Institute for Research,Madison, WI, United States
S.A. Farber
Carnegie Institution for Science,Baltimore, MD, UnitedStates
A.V.Gore
NationalInstituteofChild Health and Human Development, Bethesda, MD,
United States
K. Hazime
The University ofSheffield,Sheffield,United Kingdom
X.J. He
NationalInstituteon Deafnessand Other Communication Disorders,NIH,
Bethesda, MD, United States
A. Huttenlocher
University ofWisconsineMadison, Madison, WI,United States
S. Isogai
IwateMedical University,Morioka,Japan
H.M. Jung
NationalInstituteofChild Health and Human Development, Bethesda, MD,
United States
M. Kamei
SouthAustralian Health and Medical Research Institute,Adelaide, SA,
Australia
xi
xii Contributors
K.S. Kindt
NationalInstitute onDeafness and Other Communication Disorders,NIH,
Bethesda,MD, United States
D.Kromm
Centre for Organismal Studies, HeidelbergUniversity,Heidelberg, Germany
D.C. LeBert
University ofWisconsineMadison, Madison, WI, United States
E.Leventea
The University of Sheffield, Sheffield, United Kingdom
J. Malicki
The University of Sheffield, Sheffield, United Kingdom
W. Marcotti
University ofSheffield, Sheffield, UnitedKingdom
M.A. Mohr
Eidgeno¨ssischeTechnischeHochschuleZurich(ETHZurich),Basel,Switzerland
Q.Nie
University ofCalifornia, Irvine, CA, United States
J. Olt
University ofSheffield, Sheffield, UnitedKingdom
A.J.Ordoobadi
Amherst College, Amherst, MA, United States
P.Pantazis
Eidgeno¨ssische TechnischeHochschuleZurich(ETHZurich), Basel,
Switzerland
T.F.Schilling
University ofCalifornia, Irvine, CA, United States
J. Sosnik
University ofCalifornia, Irvine, CA, United States
J.M. Squirrell
University ofWisconsineMadison, Madison, WI, United States
D.L. Stachura
California State University,Chico, Chico, CA, United States
T.Thumberger
Centre for Organismal Studies, HeidelbergUniversity,Heidelberg, Germany
Contributors xiii
J.G. Trapani
Amherst College, Amherst,MA, UnitedStates
D. Traver
University ofCalifornia,San Diego, San Diego, CA, United States
B.M. Weinstein
NationalInstituteofChild Health and Human Development, Bethesda, MD,
United States
J. Wittbrodt
Centre for OrganismalStudies, Heidelberg University, Heidelberg, Germany
H.C. Wong
NationalInstituteon Deafnessand Other Communication Disorders,NIH,
Bethesda, MD, United States
Q.X. Zhang
NationalInstituteon Deafnessand Other Communication Disorders,NIH,
Bethesda, MD, United States
C. Zhao
The University ofSheffield,Sheffield,United Kingdom;Ocean University of
China, Qingdao, China
L.I. Zon
Children’s Hospitaland Dana Farber Cancer Institute,Boston, MA, United
States; Harvard University,Cambridge, MA, UnitedStates
Preface
Len, Monte, and I are pleased to introduce the fourth edition of Methods in Cell
Biology:TheZebrafish.Theadvantagesofthezebrafish,Daniorerio,arenumerous,
includingitsshortgenerationtimeandhighfecundity,externalfertilization,andthe
opticaltransparencyoftheembryo.Theeaseofconductingforwardgeneticscreens
inthezebrafish,basedonthepioneeringworkofGeorgeStreisinger,culminatedin
screensfromthelaboratoriesofWolfgangDriever,MarkC.Fishman,andChristiane
Nu¨sslein-Volhard, published in a seminal volume of Development (Volume 123,
December 1, 1996) that described a “candy store” of mutants whose phenotypes
spannedthegamutofdevelopmentalprocessesandmechanisms.Lifeforgeneticists
who study vertebratedevelopmentbecame really fine.
Statistics derived from ZFIN (The Zebrafish Model Organism Database; http://
zfin.org)illustratethedramaticgrowthofresearchinvolvingzebrafish.Thezebrafish
genome has been sequenced, and as of 2014, more than 25,000 genes have been
placed on the assembly. Greater than 15,500 of these genes have been established
asorthologsofhumangenes.Thezebrafishcommunityhasgrownfromw1400re-
searchersin190laboratoriesasof1998tow7000in930laboratoriesin2014.The
annualnumberofpublicationsbasedonthezebrafishhasrisenfrom1,913to21,995
inthe sametimeframe. Clearly, the zebrafish hasarrivedasavertebrate biomedical
modelsystemparexcellence.
Whenwepublishedthefirstedition(Volumes59and60)in1998,ourgoalwasto
encouragebiologiststoadoptthezebrafishasageneticallytractablemodelorganism
for studying biological phenomena from the cellular through the organismal. Our
goal today remains unchanged, but the range of subjects and the suite of methods
have expanded rapidly and significantly in sophistication over the years. With the
second and third editions of MCB: The Zebrafish (Volumes 76 and 77 in 2004;
Volumes 100, 101, 104, and 105 in 2010e11), we documented this extraordinary
growth, again relying on the excellent chapters contributed by our generous
colleagues in the zebrafish researchcommunity.
When Len, Monte, and I began planning the fourth edition, we found that the
zebrafish community had once more developed and refined novel experimental
systems and technologies to tackle challenging biological problems across the
spectrumofthebiosciences.Wepresentthesemethodsfollowingtheorganizational
structureofthethirdedition,withvolumesdevotedtoCellularandDevelopmental
Biology, to Genetics, Genomics, and Transcriptomics, and to Disease Models and
Chemical Screens. Here we introduce the first two volumes, Cellular and
Developmental Biology, Parts A andB.
CDBPartAisdevotedtocellulartechniques.Herethereaderwillfindmethods
for culturing zebrafish cells and advanced light-microscopic strategies for imaging
cells and multicellular structure in living or fixed embryos. Additional chapters
cover the direct measurement of morphogen gradients, the analysis of lipid meta-
bolism, methods to determine the structure and function of cilia, and techniques
xv
xvi Preface
for functional calcium imaging and measuring sensory transduction in lateral line
hair cells.
In CDB Part B, we transition to the study of developmental phenomena. A
chapterongermcellspecificationleadsoff,followedbyseveraldevotedtovarious
aspects of central and peripheral nervous system development and function.
Chapters on the inner ear, lateral line, and retina provide excellent examples of
the relevance of the zebrafish to vertebrate developmental biology. Methods for
studying organogenesis in the zebrafish cover the cardiovascular system, kidney,
pancreas,liver,cartilage,andbone.Thefinalchaptersconsidercancerfromanorgan
perspective,associativelearningandmemory,andmethodsforworkingwithlarval
andjuvenile zebrafish.
Weanticipatethatyou,ourreadership,willapplythesemethodssuccessfullyin
yourownzebrafishresearchprogramsandwilldevelopyourowntechnicaladvances
that may be considered for a future edition of Methods in Cell Biology: The
Zebrafish. The zebrafish is a remarkable experimental systemdthe preeminent
vertebrate model for mechanistic studies of cellular and developmental processes
invivo.
We thank the series editors, Leslie Wilson and Phong Tran, and the staff of
Elsevier/AcademicPress,especiallyZoeKruzeandSarahLay,fortheirenthusiastic
support of our fourth edition. Their help, patience, and encouragement are pro-
foundly appreciated.
H. William Detrich, III
Monte Westerfield
Leonard I. Zon
