Elsevier S & T

The Zebrafish: Genetics, Genomics and Informatics: Genetics, Genomics and Informatics

Detrich, III, H. William

In stock
No reviews
64.750 KD inc. VAT
License
Table of contents
  • Cover
  • CONTENTSv
  • Contributorsxv
  • Prefacexxiii
  • Dedicationxxv
  • PART I: Forward and Reverse Genetics1
  • Chapter 1. Retroviral-Mediated Insertional Mutagenesis in Zebrafish3
  • I. Introduction3
  • II. Mutagenesis5
  • III. Cloning the Mutated Genes8
  • IV. Future Directions14
  • References18
  • Chapter 2. Genetic Screens for Maternal-Effect Mutations21
  • I. Introduction22
  • II. Strategies for Maternal-Effect Screens23
  • III. Selection of Lines for Genetic Screens33
  • IV. Recovery and Maintenance of Maternal-Effect Mutations37
  • V. Mapping Maternal-Effect Mutations41
  • VI. Solutions, Materials, and Protocols44
  • VII. Conclusions48
  • References49
  • Chapter 3. Behavioral Screening Assays in Zebrafish53
  • I. Introduction53
  • II. General Considerations54
  • III. Behavioral Assays56
  • IV. Conclusions66
  • References66
  • Chapter 4. Target-Selected Gene Inactivation in Zebrafish69
  • I. Introduction70
  • II. Gene Targeting Strategies71
  • III. Target-Selected Mutagenesis in Zebrafish75
  • IV. Discussion83
  • V. Materials and Methods85
  • References87
  • Chapter 5. A High-Throughput Method for Identifying N-Ethyl-N-Nitrosourea (ENU)-Induced Point Mutati91
  • I. Introduction92
  • II. Rationale for Reverse Genetics in Zebrafish95
  • III. Rationale for Using the CEL1 Assay to Detect Induced Mutations96
  • IV. Rationale for Generating a Cryopreserved Mutant Library98
  • V. Method of N-Ethyl-N-Nitrosourea (ENU) Mutagenesis and Rearing of F1 Founder Fish98
  • VI. Generating a Cryopreserved Mutant Library99
  • VII. Isolating Genomic DNA102
  • VIII. Choosing Fragments to Screen104
  • IX. CEL1 Endonuclease Assay104
  • X. Recovery of Mutations from Cryopreserved Sperm109
  • XI. Materials Cost Estimate110
  • References111
  • Chapter 6. Production of Zebrafish Germline Chimeras by Using Cultured Embryonic Stem (ES) Cells113
  • I. Introduction113
  • II. Methods114
  • III. Reagents117
  • IV. Future Directions118
  • References118
  • Chapter 7. Nonconventional Antisense in Zebrafish for Functional Genomics Applications121
  • I. Introduction121
  • II. General Use of Nonconventional Antisense Tools in Zebrafish123
  • III. Use of Morpholinos (MOs) as Antisense Tools in Zebrafish125
  • IV. Comparison of MO-Based Screening Success to Mutational Methods133
  • References134
  • Chapter 8. Downregulation of Gene Expression with Negatively Charged Peptide Nucleic Acids (PNAs) in137
  • I. Introduction138
  • II. Materials and Methods143
  • III. Results146
  • IV. Discussion155
  • V. Summary156
  • References156
  • Chapter 9. Photo-Mediated Gene Activation by Using Caged mRNA in Zebrafish Embryos159
  • I. Introduction160
  • II. Synthesis of Bhc-Caged mRNA161
  • III. Microinjection of the Bhc-Caged mRNA165
  • IV. Uncaging by Illumination of UV Light167
  • V. Titration of Caging Efficiency168
  • VI. Injection of Dimethyl Sulfoxide (DMSO) Solution of Caged mRNA170
  • References170
  • Chapter 10. Current Status of Medaka Genetics and Genomics The Medaka Genome Initiative (MGI)173
  • I. Introduction174
  • II. Current Status of Medaka Genetics175
  • III. Current Status of Medaka Genomics186
  • IV. Other Progress193
  • V. Internet Web Sites Relevant to Medaka Resources and Databases193
  • References194
  • Chapter 11. Transgenesis and Gene Trap Methods in Zebrafish by Using the Tol2 Transposable Element201
  • I. Introduction201
  • II. Transgenesis by Using the Tol2 Transposable Element in Zebrafish203
  • III. A Gene Trap Approach that Uses the Tol2 Transposon System in Zebrafish210
  • IV. Summary and Perspectives219
  • References220
  • PART II: The Zebrafish Genome and Mapping Technologies223
  • Chapter 12. The Zebrafish Genome Project: Sequence Analysis and Annotation225
  • I. Introduction225
  • II. Automated Annotation of Whole Genome Shotgun (WGS) Assemblies227
  • III. Clone-by-Clone Analysis and Annotation230
  • IV. The Sanger Zebrafish Web Services234
  • V. Future Releases238
  • References238
  • Chapter 13. Molecular Cytogenetic Methodologies and a Bacterial Artificial Chromosome (BAC) Probe Pa241
  • I. Introduction241
  • II. Methods242
  • III. First-Generation Zebrafish BAC Probe Panel248
  • References254
  • Chapter 14. Automated Analysis of Conserved Syntenies for the Zebrafish Genome255
  • I. Introduction256
  • II. The Conservation of Zebrafish and Mammalian Genomes256
  • III. Using Genome Conservation in Zebrafish Research258
  • IV. Genomic Connections Between Zebrafish and Tetrapods Facilitate Disease Research260
  • V. Bioinformatic Approaches to Automating Zebrafish Connections and Comparative Maps264
  • VI. A Conserved Syntenic Map for Zebrafish: Preliminary Results266
  • VII. Conclusion267
  • References268
  • Chapter 15. Update of the Expressed Sequence Tag (EST) and Radiation Hybrid Panel Projects Yi Zhou273
  • I. Expressed Sequence Tag (EST) Projects274
  • II. Radiation Hybrid (RH) Panel Project277
  • III. Future Directions291
  • References292
  • Chapter 16. Bacterial Artificial Chromosome (BAC) Clones and the Current Clone Map of the Zebrafish295
  • I. Introduction296
  • II. Physical Map of Fingerprinted Clones296
  • III. Screening Methods and Utilization of the Current Zebrafish Clone Map300
  • IV. Example: Discovery of the Zebrafish dicer1 Gene302
  • References304
  • Chapter 17. The Zon Laboratory Guide to Positional Cloning in Zebrafish305
  • I. Introduction306
  • II. Mapping Strains306
  • III. Families and Genetic Markers307
  • IV. Crosses for Line Maintenance and Mapping307
  • V. Preparation of the DNA309
  • VI. Mapping Genes310
  • VII. Overgo Strategy for Rapidly Doing Chromosomal Walks and Positional Cloning317
  • VIII. Protocol for Overgo Probing of High-Density Filters318
  • IX. General Flow of Information from the Radiation Hybrid Panel Maps, the Sanger Institute Sequencin321
  • X. Synteny Between Human, Zebrafish, and Fugu Genomes325
  • XI. Proving a Candidate Gene Is Responsible for the Mutant Phenotype326
  • XII. Morpholinos327
  • References328
  • PART III: Transgenesis331
  • Chapter 18. Lessons from Transgenic Zebrafish Expressing the Green Fluorescent Protein (GFP) in the333
  • I. Introduction334
  • II. Myeloid Cells in Zebrafish334
  • III. Expression of pu.1 in Myeloid Development335
  • IV. Analysis of the Zebrafish pu.1 Locus336
  • V. Germline Expression of Enhanced Green Fluorescent Protein (EGFP) Under Control of the Zebrafish p338
  • VI. Conclusions345
  • References346
  • Chapter 19. Sleeping Beauty Transposon for Efficient Gene Delivery349
  • I. Introduction349
  • II. Transgenesis Constructs350
  • III. Microinjection of the Zebrafish Embryo351
  • IV. Raising Injected Embryos355
  • V. Identifying Transgenic Founders356
  • VI. Visualizing Fluorescent Reporters357
  • VII. Molecular Characterization of the Transposon Integration Site358
  • References361
  • Chapter 20. Transgene Manipulation in Zebrafish by Using Recombinases363
  • I. Introduction363
  • II. Recombinase-Mediated Transgene Exchange and Mobilization367
  • III. Summary and Conclusion375
  • References376
  • Chapter 21. Highly Efficient Zebrafish Transgenesis Mediated by the Meganuclease I-SceI381
  • I. Introduction381
  • II. Transgenesis by Meganucleases386
  • References398
  • Chapter 22. Cloning Zebrafish by Nuclear Transfer403
  • I. Introduction403
  • II. Recipes for Cell Culture and Nuclear Transfer404
  • III. Cell Culture404
  • IV. Nuclear Transfer405
  • V. Summary of Nuclear Transfer408
  • VI. Potential Applications of Zebrafish Cloning409
  • References410
  • PART IV: Informatics and Comparative Genomics413
  • Chapter 23. Data Mining the Zebrafish Genome415
  • I. Introduction415
  • II. National Center for Biotechnology Information (NCBI) Tools, Resources, and Data Sets416
  • III. Zebrafish Information Network (ZFIN)428
  • IV. Tutorial433
  • References437
  • Chapter 24. The Zebrafish DVD Exchange Project: A Bioinformatics Initiative439
  • I. Introduction440
  • II. Economic Aspects of Visual Bioinformatics440
  • III. Building Infrastructures to Access Images442
  • IV. Prior Experiences with Visual Data Dissemination (Mark Cooper)443
  • V. Goals of the Zebrafish DVD Exchange Project445
  • VI. Production of the Compact Disc (CD) Set: ‘‘Zebrafish: The Living Laboratory’’ (Greg Somm447
  • VII. Visual Bioinformatics and Databases451
  • VIII. Internet2452
  • IX. Hyper Text Markup Language (HTML) and eXtensible Markup Language XML (Bryan Crawford)453
  • X. Virtual Reality and Data Visualization Tools (Carey Phillips)454
  • XI. Summary456
  • References457
  • Chapter 25. Comparative Genomics„An Application for Positional Cloning of the weissherbst Mutant459
  • I. Introduction459
  • II. Resources for Comparative Genomics Studies460
  • III. An Example of Using Comparative Genomic Resources in a Positional Cloning Project461
  • References473
  • Chapter 26. Comparative Genomics in Erythropoietic Gene Discovery: Synergisms Between the Antarctic475
  • I. Introduction476
  • II. Representational Difference Analysis (RDA) Protocol477
  • III. Analysis of Unidentified RDA Contigs485
  • IV. Isolation of Full-Length cDNAs Corresponding to RDA Products493
  • V. Model Hopping: Functional Analysis of the Zebrafish Ortholog of the Novel Antarctic Fish Gene blo498
  • VI. General Considerations500
  • References501
  • Chapter 27. Spatial and Temporal Expression of the Zebrafish Genome by Large-Scale In Situ Hybridiza505
  • I. Introduction and Goals506
  • II. Preparation of Antisense Digoxigenin (DIG)-Labeled RNA Probes506
  • III. Preparation of Embryos508
  • IV. Reagents and Buffers for In Situ Hybridization509
  • V. In Situ Hybridization Protocol510
  • VI. Double In Situ Protocol514
  • VII. Recording Results517
  • VIII. Concluding Remarks517
  • References519
  • Chapter 28. Design, Normalization, and Analysis of Spotted Microarray Data521
  • I. Introduction522
  • II. Design of Microarray Experiments522
  • III. Array Preprocessing530
  • IV. Analysis of Microarray Experiments535
  • V. Discussion540
  • References542
  • Chapter 29. Comparative Genomics, cis-Regulatory Elements, and Gene Duplication545
  • I. Introduction545
  • II. Comparative Genomics and Identification of cis-Regulatory Elements (CREs)546
  • III. Duplicated Genomes, Duplicated Genes552
  • References556
  • PART V: Infrastructure563
  • Chapter 30. Zebrafish Facilities for Small and Large Laboratories565
  • I. Introduction566
  • II. Zebrafish Biology568
  • III. Fish Housing569
  • IV. Quarantining586
  • V. Injections587
  • VI. Mutagenesis Room587
  • VII. Treating Outflow588
  • VIII. Disposing of the Dead588
  • IX. Disease Prevention589
  • X. Cleaning590
  • XI. Human Safety590
  • References591
  • Chapter 31. A Nursery that Improves Zebrafish Fry Survival593
  • I. Introduction593
  • II. General Methods for Raising Embryos and Larvae594
  • III. A Nursery that Improves Fry Survival594
  • References598
  • Chapter 32. Genetic Backgrounds, Standard Lines, and Husbandry of Zebrafish599
  • I. Introduction599
  • II. Nomenclature and Definitions602
  • III. Goals for Line Use603
  • IV. Breeding Strategies604
  • V. Cryopreservation612
  • VI. Monitoring and Response613
  • VII. Distribution614
  • VIII. Summary and Recommendations614
  • References615
  • Chapter 33. Common Diseases of Laboratory Zebrafish617
  • I. Introduction617
  • II. Diagnostic Evaluation618
  • III. Common Diseases of Laboratory Zebrafish618
  • IV. Zoonosis640
  • References641
  • Chapter 34. Zebrafish Sperm Cryopreservation645
  • I. Introduction: Benefits of Zebrafish Sperm Cryopreservation645
  • II. Critical Variables Affecting Sperm Cryopreservation646
  • III. Zebrafish Sperm Cryopreservation with N,N-Dimethylacetamide650
  • IV. Future Directions656
  • References658
  • Index661
  • Volumes in Series679
Book details
  • Vendor Elsevier S & T
  • SKU 9780125641722
  • ISBN-13 9780080522517
  • Author Detrich, III, H. William
  • Edition 2nd
  • Category Science
  • Subject Cell Biology

Do you have questions about this book?

Ask an expert!

Description eBook delivery & access Reviews
This volume of Methods in Cell Biology, the second of two parts on the subject of zebrafish, provides a comprehensive compendia of laboratory protocols and reviews covering all the new methods developed since 1999. This second volume covers advances in forward and reverse genetic techniques, provides an update on the zebrafish genome and gene/mutant mapping technologies, examines the new systems for efficient transgenesis in the zebrafish, provides an in-depth view of informatics and the emerging field of comparative genomics, and considers the extensive infrastructure now available to the zebrafish community.

* Details state-of-the art zebrafish protocols, delineating critical steps in the procedures as well as potential pitfalls
* Illustrates many techiques in full-color
* Summarizes the Zebrafish Genome Project