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El. knyga: Essential Zebrafish Methods: Genetics and Genomics

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Edited by Monte Westerfield (Professor, Department of Biology, Institute of Neuroscience, University of Oregon, Euge), Edited by Leonard I. Zon (Howard Hughes Medical Institute, Children's Hospital, Boston, MA, USA), Edited by H. William Detrich III (Professor of Biochemistry and Marine Biology at Northeastern University)

Formatas: EPUB+DRM
Serija: Reliable Lab Solutions
Išleidimo metai: 05-Sep-2009
Leidėjas: Academic Press Inc
Kalba: eng
ISBN-13: 9780123751614

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Formatas: EPUB+DRM
Serija: Reliable Lab Solutions
Išleidimo metai: 05-Sep-2009
Leidėjas: Academic Press Inc
Kalba: eng
ISBN-13: 9780123751614

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Due to its prolific reproduction and the external development of the transparent embryo, the zebrafish is the prime model for genetic and developmental studies, as well as research in genomics. While genetically distant from humans, nonetheless the vertebrate zebrafish has comparable organs and tissues that make it the model organism for study of vertebrate development. This book, one of two new volumes in the Reliable Lab Solutions series dealing with zebrafish, brings together a robust and up-to-date collection of time-tested methods presented by the world’s leading scientists. Culled from previously published chapters in Methods in Cell Biology and updated by the original authors where relevant, it provides a comprehensive collection of protocols describing the most widely used techniques relevant to the study of zebrafish genetics and genomics. The methods in this volume were hand-selected by the editors, whose goal was to a provide a handy and cost-effective collection of fail-safe methods, tips, and "tricks of the trade" to both experienced researchers and more junior members in the lab.

* Provides busy researchers a quick reference for time-tested methods and protocols that really work, updated where possible by the original authors * Gives pragmatic wisdom to the non-specialist from experts in the field with years of experience with trial and error

Contributors

xiii

Preface

xvii

Haploid Screens and Gamma-Ray Mutagenesis

Charline Walker

Update

(1)

Introduction

(1)

Production of Haploid Embryos

(3)

Development of Haploid Embryos

(2)

Genetic Background

(2)

The Haploid Screen

(4)

Limitations of Haploids

(2)

Mosaicism in F1 Screens

(1)

Haploid Screens and Gamma-Ray Mutagenesis

(4)

Nature of Gamma-Ray-Induced Mutations

(3)

Conclusion

(6)

References

(5)

Positional Cloning of Mutated Zebrafish Genes

William S. Talbot

Alexander F. Schier

Update

(1)

Introduction

(2)

Initiating a Positional Cloning Project

(4)

Defining the Critical Region

(3)

Gene Discovery

(2)

Protocol 1

(1)

Protocol 2

(1)

Protocol 3

(5)

References

(3)

The Zebrafish Genome

John Postlethwait

Angel Amores

Allan Force

Yi-Lin Yan

Introduction

(1)

Mapping the Zebrafish Genome

(2)

The Zebrafish Gene Map

(4)

Two Genes in Zebrafish for One in Mammals

(2)

Gene Nomenclature in Zebrafish

(1)

Conclusions

(5)

References

(3)

Retroviral-Mediated Insertional Mutagenesis in Zebrafish

Adam Amsterdam

Nancy Hopkins

Update

(1)

Introduction

(2)

Mutagenesis

(3)

Cloning the Mutated Genes

(7)

Future Directions

(9)

References

(5)

Genetic Screens for Maternal-Effect Mutations

Francisco Pelegri

Mary C. Mullins

Update

(1)

Introduction

(1)

Strategies for Maternal-Effect Screens

(11)

Selection of Lines for Genetic Screens

(3)

Recovery and Maintenance of Maternal-Effect Mutations

(3)

Mapping Maternal-Effect Mutations

101

(4)

Solutions, Materials, and Protocols

105

(4)

Conclusions

109

(4)

References

110

(3)

Behavioral Screening Assays in Zebrafish

Michael B. Orger

Ethan Gahtan

Akira Muto

Patrick Page-McCaw

Matthew C. Smear

Herwig Baier

Introduction

113

(2)

General Considerations

115

(1)

Behavioral Assays

116

(10)

Conclusions

126

(6)

References

126

(6)

Tilling the Zebrafish Genome: A Reverse Genetics Approach

Bruce W. Draper

Claire M. McCallum

Jennifer L. Stout

Cecilia B. Moens

Introduction

132

(3)

Rationale for Reverse Genetics in Zebrafish

135

(1)

Rationale for Using the CEL1 Assay to Detect ENU-Induced Mutations

136

(2)

Rationale for Generating a Cryopreserved Mutant Library

138

(1)

Method of N-Ethyl-N-Nitrosourea (ENU) Mutagenesis and Rearing of F1 Founder Fish

138

(1)

Generating a Cryopreserved Mutant Library

139

(3)

Isolating Genomic DNA

142

(2)

Choosing Fragments to Screen

144

(1)

CEL1 Endonuclease Assay

144

(5)

Recovery of Mutations from Cryopreserved Sperm

149

(1)

Materials Cost Estimate

150

(3)

References

151

(2)

The Transgenesis and Gene and Enhancer Trap Methods in Zebrafish by Using the Toι2 Transposable Element

Koichi Kawakami

Introduction

153

(2)

Transgenesis by Using the Toι2 Transposable Element in Zebrafish

155

(6)

Gene Trap and Enhancer Trap Approaches That Use the Toι2 Transposon System in Zebrafish

161

(8)

Summary and Perspectives

169

(7)

References

171

(4)

Molecular Cytogenetic Methodologies and a Second-Generation BAC Probe Panel Resource for Zebrafish Genomic Analyses

Charles Lee

Danielle Palmer

Jennifer L. Freeman

Kim H. Brown

Update

175

(1)

Introduction

176

(1)

Methods

177

(7)

Second-Generation Zebrafish BAC Probe Panel

184

(8)

References

188

(4)

The Zon Laboratory Guide to Positional Cloning in Zebrafish

Yi Zhou

Nathan Bahary

Alan Davidson

David Ransom

Jennifer Shepard

Howard Stern

Nikilaus Trede

Bruce Barut

Leonard I. Zon

Introduction

192

(1)

Mapping Strains

192

(1)

Families and Genetic Markers

193

(1)

Crosses for Line Maintenance and Mapping

193

(2)

Preparation of the DNA

195

(1)

Mapping Genes

196

(10)

Overgo Strategy for Rapid Chromosomal Walks and Positional Cloning

206

(1)

Protocol for Overgo Probing of High-Density Filters

207

(2)

General Flow of Information from the Radiation Hybrid Panel Maps, the Sanger Institute Sequencing Project, and Fingerprinting the BACs

209

(4)

Synteny Between Human, Zebrafish, Fugu, and Tetraodon Genomes

213

(2)

Proving a Candidate Gene Is Responsible for the Mutant Phenotype

215

(1)

Morpholinos

216

(4)

References

216

(3)

Sleeping Beauty Transposon for Efficient Gene Delivery

Spencer Hermanson

Ann E. Davidson

Sridhar Sivasubbu

Darius Balciunas

Stephen C. Ekker

Update

219

(1)

Introduction

220

(1)

Transgenesis Constructs

220

(2)

Microinjection of the Zebrafish Embryo

222

(2)

Raising Injected Embryos

224

(3)

Identifying Transgenic Founders

227

(1)

Visualizing Fluorescent Reporters

227

(1)

Molecular Characterization of the Transposon Integration Site

228

(5)

References

232

(1)

Transgene Manipulation in Zebrafish by Using Recombinases

Yang Bai

Jie Dong

Gary W. Stuart

Introduction

233

(5)

Recombinase-Mediated Transgene Exchange and Mobilization

238

(10)

Summary and Conclusion

248

(7)

References

249

(6)

Highly Efficient Zebrafish Transgenesis Mediated by the Meganuclease I-SceI

Clemens Grabher

Jean-Stephane Joly

Joachim Wittbrodt

Introduction

255

(5)

Transgenesis by Meganucleases

260

(17)

References

273

(4)

Cloning Zebrafish by Nuclear Transfer

Haigen Huang

Bensheng Ju

Ki-Young Lee

Shuo Lin

Introduction

277

(1)

Recipes for Cell Culture and Nuclear Transfer

278

(1)

Cell Culture

278

(1)

Nuclear Transfer

279

(3)

Summary of Nuclear Transfer

282

(1)

Potential Applications of Zebrafish Cloning

283

(5)

References

284

(4)

Spatial and Temporal Expression of the Zebrafish Genome by Large-Scale In Situ Hybridization Screening

Bernard Thisse

Vincent Heyer

Aline Lux

Violaine Alunni

Agnes Degrave

Iban Seiliez

Johanne Kirchner

Jean-Paul Parkhill

Christine Thisse

Introduction and Goals

288

(1)

Preparation of Antisense Digoxigenin (DIG)-Labeled RNA Probes

288

(2)

Preparation of Embryos

290

(1)

Reagents and Buffers for In Situ Hybridization

291

(1)

In Situ Hybridization Protocol

292

(4)

Double In Situ Protocol

296

(1)

Recording Results

297

(3)

Concluding Remarks

300

(6)

References

300

(3)

Genetic Backgrounds, Standard Lines, and Their Husbandry

Bill Trevarrow

Barrie Robison

Update

303

(3)

Introduction

306

(1)

Nomenclature and Definitions

307

(1)

Goals for Line Use

307

(1)

Breeding Strategies

308

(8)

Cryopreservation

316

(1)

Monitoring and Response

317

(1)

Distribution

318

(1)

Summary and Recommendations

318

(3)

References

319

(2)

Common Diseases of Laboratory Zebrafish

Jennifer L. Matthews

Introduction

321

(1)

Diagnostic Evaluation

321

(1)

Common Diseases of Laboratory Zebrafish

322

(21)

Zoonosis

343

(5)

References

344

(3)

Zebrafish Sperm Cryopreservation

Stephane Berghmans

John P. Morris IV

John P. Kanki

A. Thomas Look

Update

347

(1)

Introduction: Benefits of Zebrafish Sperm Cryopreservation

348

(1)

Critical Variables Affecting Sperm Cryopreservation

349

(3)

Zebrafish Sperm Cryopreservation with N, N-Dimethylacetamide

352

(8)

Future Directions

360

(5)

References

361

(4)

Index

365

Professor of Biochemistry and Marine Biology at Northeastern University, promoted 1996. Joined Northeastern faculty in 1987. Previously a faculty member in Dept. of Biochemistry at the University of Mississippi Medical Center, 1983-1987.Principal Investigator in the U.S. Antarctic Program since 1984. Twelve field seasons "on the ice" since 1981. Research conducted at Palmer Station, Antarctica, and McMurdo Station, Antarctica.Research areas: Biochemical, cellular, and physiological adaptation to low and high temperatures. Structure and function of cytoplasmic microtubules and microtubule-dependent motors from cold-adapted Antarctic fishes. Regulation of tubulin and globin gene expression in zebrafish and Antarctic fishes. Role of microtubules in morphogenesis of the zebrafish embryo. Developmental hemapoiesis in zebrafish and Antarctic fishes. UV-induced DNA damage and repair in Antarctic marine organisms. Professor, Department of Biology, Institute of Neuroscience, University of Oregon, Eugene, OR, USA

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