This is the second volume of a two-volume, comprehensive treatment of the methodologies used in researching the zebrafish, an emerging vertebrate model system. The text includes discussions on development, genetic methodologies, and model applications.
Contributors xiii(4) Preface xvii 1 A Gynogenesis-Based Screen for Maternal-Effect Genes in the Zebrafish, Danio Rerio 1(21) Francisco Pelegri Stefan Schulte-Marker I. Introduction 1(3) II. Optimization of the Gynogenetic Method 4(6) III. A Pilot Screen for Maternal-Effect Mutations 10(1) IV. Recovery of Mutations 11(1) V. Solutions, Materials, and Protocols for Gynogenetic Method 12(4) VI. Conclusions 16(1) References 17(5)
2. Developmental Mutant Screens in the Zebrafish 22(22) Fredericus J.M. van Eeden Michael Granata Jog Odenthal Pascal Haffter I. Introduction 22(1) II. Mutagenesis 22(4) III. Breeding Scheme 26(1) IV. Screening Procedure 27(4) V. Allele Screens 31(3) VI. Dominant Screens 34(1) VII. Managing the Outcome of Screens 35(2) VIII. Potential of Future Screens 37(1) Appendix--Recipes and Media 38(1) References 38(6)
3. Haploid Screens and Gamma-Ray Mutagenesis 44(27) Charline Walkar
1. Introduction 44(1) II. Production of Haploid Embryos 44(4) III. Development of Haploid Embryos 48(3) IV. Genetic Background 51(2) V. The Haploid Screen 53(4) VI. Limitations of Haploids 57(2) VII. Mosaicism in F(1) Screens 59(1) VIII. Haploid Screens and Gamma-Ray Mutagenesis 60(4) IX. Nature of Gamma-Ray Induced Mutations 64(3) X. Conclusion 67(1) References 68(3)
4. Early Pressure Screens 71(16) Christine E. Beattie David W. Raible Paul D. Henion Judith S. Eisen I. Introduction 71(1) II. Rational for Use of Early Pressure to Produce Diploid Embryos for Genetic Screens 72(4) III. Rationale for Use of Screens Focused on Specific Phenotypes 76(1) IV. Design of Our Screen and Mutant Phenotypes Isolated 76(6) V. Closing Remarks 82(1) References 83(4)
5. Retrovirus-Mediated Insertional Mutagenesis in Zebrafish 87(12) Adam Amsterdam Nancy Hopkins I. Introduction 87(2) II. Insertional Mutagenesis: A Pilot Screen 89(6) III. Considerations for a Large-Scale Screen 95(2) References 97(2)
6. Genetic Applications of Transposons and Other Repetitive Elements in Zebrafish 99(34) Zoltan Lvics Zsuzsanna Izsvak Perry B. Hackett I. Introduction 99(2) II. Classification of Repetitive Elements 101(12) III. Genetic Applications of Repetitive Elements 113(11) IV. Summary and Perspectives 124(2) References 126(7)
7. Transgenesis 133(16) Anming Meng Jason R. Jessen Shuo Lin I. Introduction 133(1) II. Materials 134(2) III. Methods 136(10) IV. Discussion 146(1) References 147(2)
8. The Zebrafish Genome 149(16) John Postlethwait Angle Amores Allan Force Yi-Lin Yan I. Introduction 149(1) II. Mapping the Zebrafish Genome 150(2) III. The Zebrafish Gene Map 152(5) IV. Two Genes in Zebrafish for One in Mammals 157(2) V. Gene Nomenclature in Zebrafish 159(1) Conclusions 160(1) References 161(4)
9. Using Random Amplified Polymorphic DNAs in Zebrafish Genomic Analysis 165(17) John H. Postlethwait Yi-Lin Yan Michael A. Gates I. Introduction 165(1) II. What are RAPDs? 166(4) III. Advantages and Disadvantages of RAPDs as Polymorphic Markers 170(1) IV. Methods for Developing RAPD Markers 171(1) V. Using RAPDs to Identify Markers Closely Linked to a Mutation 172(4) VI. Conversion of RAPD Markers to Sequence Tagged Sites 176(1) VII. Conclusions 177(1) References 177(5) 10 Simple Sequence-Length Polymorphism Analysis 182(3) Eric C. Liao Leonard I. Zon I. Analysis in DNA Sequencing Gels 182(1) II. Alternative Analysis of SSLP-Containing PCR Product in High-Resolution Agarose Gels 182(1) III. Troubleshooting and Other Considerations 183(1) References 183(2)
11. Gene Mapping in Zebrafish Using Single-Strand Conformation Polymorphism Analysis 185(10) Dorothee Foernzler David R. Beier I. Introduction 185(2) II. SSCP Methodology 187(2) III. Gene Mapping 189(1) IV. Methods 190(2) References 192(3)
12. Mapping Zebrafish Mutations by AFLP 195(18) David G. Ransom Leonard I. Zon I. Introduction 195(3) II. Extraction of Zebrafish Genomic DNA 198(1) III. AFLP Methods 199(10) IV. General Considerations 209(1) References 210(3)
13. Zebrafish Expressed Sequence Tags and Their Applications 213(23) Zhiyuan Gong I. Introduction 213(1) II. Procedure of cDNA Clone Tagging 214(6) III. Management of Tagged cDNA Clones 220(3) IV. Applications of Tagged cDNA Clones 223(9) References 232(4)
14. Zebrafish YAC, BAC, and PAC Genomic Libraries 236(24) Chris T. Amemiya Tao P. Zhong Gary A. Silverman Mark C. Fishman Leonard I. Zon I. Introduction 236(1) II. Cloning Systems 236(3) III. Available Zebrafish Genomic Libraries and the Need for Multiple Libraries 239(2) IV. Screening Methods 241(2) V. Positional Cloning Using YAC, BAC, and PAC Libraries 243(7) VI. Further Applications of YAC, BAC, and PAC Resource to Zebrafish Genetics 250(1) VII. Summary 251(1) Internet Web Sites Relevant to YAC, BAC, and PAC Cloning 252(1) Reference 252(8)
15. Positional Cloning of Mutated Zebrafish Genes 260(28) William S. Talbot Alexander F. Schier I. Introduction 260(2) II. Initiating a Positional Cloning Project 262(10) III. Isolating Genomic Clones and Defining the Critical Region 272(7) IV. Gene Discovery 279(5) References 284(4)
16. Construction and Characterization of Zebrafish Whole Genome Radiation Hybrids 288(16) Cheni Kwak Ricky Critcher Karin Schmitt I. Introduction 288(1) II. Basic Protocol: Construction of Radiation Hybrids 288(4) III. Characterization of Radiation Hybrids by PCR 292(2) IV. Characterization of Radiation Hybrids Using FISH Analysis 294(4) V. Commentary 298(1) VI. Critical Parameters and Troubleshooting 299(3) References 302(2)
17. Zebrafish/Mouse Somatic Cell Hybrids for the Characterization of the Zebrafish Genome 304(19) Marc Ekker Fengchun Ye Lucille Joly Patricia Tellis Mario Chevrette I. Introduction 304(1) II. Production of Zebrafish/Mouse Somatic Cell Hybrids 304(4) III. Analysis of Zebrafish Chromosomes in Hybrid Cells by Fluorescence in Situ Hybridization 308(5) IV. Identification of Chromosomes in Hybrids Using PCR 313(4) V. Inter-DANA/Mermaid PCR on Hybrids 317(1) VI. Stability of Zebrafish/Mouse Hybrids 318(1) VII. Perspectives 319(1) References 320(3)
18. Banded Chromosomes and the Zebrafish Karyotype 323(16) Angel Amores John H. Postlethwait I. Introduction 323(1) II. Methods 324(8) III. Results and Discussion 332(4) References 336(3)
19. Zebrafish Informatics and the ZFIN Database 339(18) Monte Westerfield Eckchard Doerry Arthur E. Kirkpatrick Sarah A. Douglas I. Introduction 339(1) II. Database Design Process 340(2) III. The Data Model and the Contents of the Database 342(9) IV. Using the ZFIN Database 351(3) References 354(3) Appendix
1. Genetic Backgrounds and Some Standard Stocks and Strains Used in Zebrafish Developmental Biology and Genetics 357(6) Stephen L. Johnson Leonard I. Zon Summary of Genetic Backgrounds 357(2) References 359(4) Appendix
2. Centromeric Markers in the Zebrafish 363(2) Don Kane Leonard I. Zon H. William Detrich III References 363(2) Appendix
3. Collection, Storage, and use of Zebrafish Sperm 365(8) David G. Ransom Leonard I. Zon I. Introduction 365(1) II. Materials 366(2) III. Collection of Zebrafish Sperm 368(1) IV. Cryopreservation of Zebrafish Sperm 369(1) V. In Vitro Fertilization 370(1) VI. General Considerations 371(1) References 372(1) Appendix
4. Zebrafish Web Site Listings 373(14) Pat Edwards Zebrafish Web Servers 373(1) Lab URLs 374(13) Index 387
University of California, Santa Barbara, USA 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
