The Zebrafish: Genetics, Genomics and Informatics

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

Academic Press

2nd Edition

Published on 30. December 2004

630 pages

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978-0-08-052251-7 (ISBN)

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Front Cover
The Zebrafish: Genetics, Genomics, and Informatics
Copyright Page
CONTENTS
Contributors
Preface
Dedication
PART I: Forward and Reverse Genetics
Chapter 1. Retroviral-Mediated Insertional Mutagenesis in Zebrafish
I. Introduction
II. Mutagenesis
III. Cloning the Mutated Genes
IV. Future Directions
References
Chapter 2. Genetic Screens for Maternal-Effect Mutations
I. Introduction
II. Strategies for Maternal-Effect Screens
III. Selection of Lines for Genetic Screens
IV. Recovery and Maintenance of Maternal-Effect Mutations
V. Mapping Maternal-Effect Mutations
VI. Solutions, Materials, and Protocols
VII. Conclusions
References
Chapter 3. Behavioral Screening Assays in Zebrafish
I. Introduction
II. General Considerations
III. Behavioral Assays
IV. Conclusions
References
Chapter 4. Target-Selected Gene Inactivation in Zebrafish
I. Introduction
II. Gene Targeting Strategies
III. Target-Selected Mutagenesis in Zebrafish
IV. Discussion
V. Materials and Methods
References
Chapter 5. A High-Throughput Method for Identifying N-Ethyl-N-Nitrosourea (ENU)-Induced Point Mutations in Zebrafish
I. Introduction
II. Rationale for Reverse Genetics in Zebrafish
III. Rationale for Using the CEL1 Assay to Detect Induced Mutations
IV. Rationale for Generating a Cryopreserved Mutant Library
V. Method of N-Ethyl-N-Nitrosourea (ENU) Mutagenesis and Rearing of F1 Founder Fish
VI. Generating a Cryopreserved Mutant Library
VII. Isolating Genomic DNA
VIII. Choosing Fragments to Screen
IX. CEL1 Endonuclease Assay
X. Recovery of Mutations from Cryopreserved Sperm
XI. Materials Cost Estimate
References
Chapter 6. Production of Zebrafish Germline Chimeras by Using Cultured Embryonic Stem (ES) Cells
I. Introduction
II. Methods
III. Reagents
IV. Future Directions
References
Chapter 7. Nonconventional Antisense in Zebrafish for Functional Genomics Applications
I. Introduction
II. General Use of Nonconventional Antisense Tools in Zebrafish
III. Use of Morpholinos (MOs) as Antisense Tools in Zebrafish
IV. Comparison of MO-Based Screening Success to Mutational Methods
References
Chapter 8. Downregulation of Gene Expression with Negatively Charged Peptide Nucleic Acids (PNAs) in Zebrafish Embryos
I. Introduction
II. Materials and Methods
III. Results
IV. Discussion
V. Summary
References
Chapter 9. Photo-Mediated Gene Activation by Using Caged mRNA in Zebrafish Embryos
I. Introduction
II. Synthesis of Bhc-Caged mRNA
III. Microinjection of the Bhc-Caged mRNA
IV. Uncaging by Illumination of UV Light
V. Titration of Caging Efficiency
VI. Injection of Dimethyl Sulfoxide (DMSO) Solution of Caged mRNA
References
Chapter 10. Current Status of Medaka Genetics and Genomics The Medaka Genome Initiative (MGI)
I. Introduction
II. Current Status of Medaka Genetics
III. Current Status of Medaka Genomics
IV. Other Progress
V. Internet Web Sites Relevant to Medaka Resources and Databases
References
Chapter 11. Transgenesis and Gene Trap Methods in Zebrafish by Using the Tol2 Transposable Element
I. Introduction
II. Transgenesis by Using the Tol2 Transposable Element in Zebrafish
III. A Gene Trap Approach that Uses the Tol2 Transposon System in Zebrafish
IV. Summary and Perspectives
References
PART II: The Zebrafish Genome and Mapping Technologies
Chapter 12. The Zebrafish Genome Project: Sequence Analysis and Annotation
I. Introduction
II. Automated Annotation of Whole Genome Shotgun (WGS) Assemblies
III. Clone-by-Clone Analysis and Annotation
IV. The Sanger Zebrafish Web Services
V. Future Releases
References
Chapter 13. Molecular Cytogenetic Methodologies and a Bacterial Artificial Chromosome (BAC) Probe Panel Resource for Genomic Analyses in Zebrafish
I. Introduction
II. Methods
III. First-Generation Zebrafish BAC Probe Panel
References
Chapter 14. Automated Analysis of Conserved Syntenies for the Zebrafish Genome
I. Introduction
II. The Conservation of Zebrafish and Mammalian Genomes
III. Using Genome Conservation in Zebrafish Research
IV. Genomic Connections Between Zebrafish and Tetrapods Facilitate Disease Research
V. Bioinformatic Approaches to Automating Zebrafish Connections and Comparative Maps
VI. A Conserved Syntenic Map for Zebrafish: Preliminary Results
VII. Conclusion
References
Chapter 15. Update of the Expressed Sequence Tag (EST) and Radiation Hybrid Panel Projects Yi Zhou
I. Expressed Sequence Tag (EST) Projects
II. Radiation Hybrid (RH) Panel Project
III. Future Directions
References
Chapter 16. Bacterial Artificial Chromosome (BAC) Clones and the Current Clone Map of the Zebrafish Genome
I. Introduction
II. Physical Map of Fingerprinted Clones
III. Screening Methods and Utilization of the Current Zebrafish Clone Map
IV. Example: Discovery of the Zebrafish dicer1 Gene
References
Chapter 17. The Zon Laboratory Guide to Positional Cloning in Zebrafish
I. Introduction
II. Mapping Strains
III. Families and Genetic Markers
IV. Crosses for Line Maintenance and Mapping
V. Preparation of the DNA
VI. Mapping Genes
VII. Overgo Strategy for Rapidly Doing Chromosomal Walks and Positional Cloning
VIII. Protocol for Overgo Probing of High-Density Filters
IX. General Flow of Information from the Radiation Hybrid Panel Maps, the Sanger Institute Sequencing Project, and Fingerprinting the
X. Synteny Between Human, Zebrafish, and Fugu Genomes
XI. Proving a Candidate Gene Is Responsible for the Mutant Phenotype
XII. Morpholinos
References
PART III: Transgenesis
Chapter 18. Lessons from Transgenic Zebrafish Expressing the Green Fluorescent Protein (GFP) in the Myeloid Lineage
I. Introduction
II. Myeloid Cells in Zebrafish
III. Expression of pu.1 in Myeloid Development
IV. Analysis of the Zebrafish pu.1 Locus
V. Germline Expression of Enhanced Green Fluorescent Protein (EGFP) Under Control of the Zebrafish pu.1 Promoter
VI. Conclusions
References
Chapter 19. Sleeping Beauty Transposon for Efficient Gene Delivery
I. Introduction
II. Transgenesis Constructs
III. Microinjection of the Zebrafish Embryo
IV. Raising Injected Embryos
V. Identifying Transgenic Founders
VI. Visualizing Fluorescent Reporters
VII. Molecular Characterization of the Transposon Integration Site
References
Chapter 20. Transgene Manipulation in Zebrafish by Using Recombinases
I. Introduction
II. Recombinase-Mediated Transgene Exchange and Mobilization
III. Summary and Conclusion
References
Chapter 21. Highly Efficient Zebrafish Transgenesis Mediated by the Meganuclease I-SceI
I. Introduction
II. Transgenesis by Meganucleases
References
Chapter 22. Cloning Zebrafish by Nuclear Transfer
I. Introduction
II. Recipes for Cell Culture and Nuclear Transfer
III. Cell Culture
IV. Nuclear Transfer
V. Summary of Nuclear Transfer
VI. Potential Applications of Zebrafish Cloning
References
PART IV: Informatics and Comparative Genomics
Chapter 23. Data Mining the Zebrafish Genome
I. Introduction
II. National Center for Biotechnology Information (NCBI) Tools, Resources, and Data Sets
III. Zebrafish Information Network (ZFIN)
IV. Tutorial
References
Chapter 24. The Zebrafish DVD Exchange Project: A Bioinformatics Initiative
I. Introduction
II. Economic Aspects of Visual Bioinformatics
III. Building Infrastructures to Access Images
IV. Prior Experiences with Visual Data Dissemination (Mark Cooper)
V. Goals of the Zebrafish DVD Exchange Project
VI. Production of the Compact Disc (CD) Set: ''Zebrafish: The Living Laboratory'' (Greg Sommers-Herivel)
VII. Visual Bioinformatics and Databases
VIII. Internet2
IX. Hyper Text Markup Language (HTML) and eXtensible Markup Language XML (Bryan Crawford)
X. Virtual Reality and Data Visualization Tools (Carey Phillips)
XI. Summary
References
Chapter 25. Comparative Genomics-An Application for Positional Cloning of the weissherbst Mutant
I. Introduction
II. Resources for Comparative Genomics Studies
III. An Example of Using Comparative Genomic Resources in a Positional Cloning Project
References
Chapter 26. Comparative Genomics in Erythropoietic Gene Discovery: Synergisms Between the Antarctic Icefishes and the Zebrafish
I. Introduction
II. Representational Difference Analysis (RDA) Protocol
III. Analysis of Unidentified RDA Contigs
IV. Isolation of Full-Length cDNAs Corresponding to RDA Products
V. Model Hopping: Functional Analysis of the Zebrafish Ortholog of the Novel Antarctic Fish Gene bloodthirsty
VI. General Considerations
References
Chapter 27. Spatial and Temporal Expression of the Zebrafish Genome by Large-Scale In Situ Hybridization Screening
I. Introduction and Goals
II. Preparation of Antisense Digoxigenin (DIG)-Labeled RNA Probes
III. Preparation of Embryos
IV. Reagents and Buffers for In Situ Hybridization
V. In Situ Hybridization Protocol
VI. Double In Situ Protocol
VII. Recording Results
VIII. Concluding Remarks
References
Chapter 28. Design, Normalization, and Analysis of Spotted Microarray Data
I. Introduction
II. Design of Microarray Experiments
III. Array Preprocessing
IV. Analysis of Microarray Experiments
V. Discussion
References
Chapter 29. Comparative Genomics, cis-Regulatory Elements, and Gene Duplication
I. Introduction
II. Comparative Genomics and Identification of cis-Regulatory Elements (CREs)
III. Duplicated Genomes, Duplicated Genes
References
PART V: Infrastructure
Chapter 30. Zebrafish Facilities for Small and Large Laboratories
I. Introduction
II. Zebrafish Biology
III. Fish Housing
IV. Quarantining
V. Injections
VI. Mutagenesis Room
VII. Treating Outflow
VIII. Disposing of the Dead
IX. Disease Prevention
X. Cleaning
XI. Human Safety
References
Chapter 31. A Nursery that Improves Zebrafish Fry Survival
I. Introduction
II. General Methods for Raising Embryos and Larvae
III. A Nursery that Improves Fry Survival
References
Chapter 32. Genetic Backgrounds, Standard Lines, and Husbandry of Zebrafish
I. Introduction
II. Nomenclature and Definitions
III. Goals for Line Use
IV. Breeding Strategies
V. Cryopreservation
VI. Monitoring and Response
VII. Distribution
VIII. Summary and Recommendations
References
Chapter 33. Common Diseases of Laboratory Zebrafish
I. Introduction
II. Diagnostic Evaluation
III. Common Diseases of Laboratory Zebrafish
IV. Zoonosis
References
Chapter 34. Zebrafish Sperm Cryopreservation
I. Introduction: Benefits of Zebrafish Sperm Cryopreservation
II. Critical Variables Affecting Sperm Cryopreservation
III. Zebrafish Sperm Cryopreservation with N,N-Dimethylacetamide
IV. Future Directions
References
Index
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