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This volume on genetics, genomics, and informatics, will cover new technologies in forward and reverse genetics, transgenesis, the zebrafish genome and mapping technologies, in… Read more
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Immediately download your ebook while waiting for your print delivery. No promo code needed.
This volume on genetics, genomics, and informatics, will cover new technologies in forward and reverse genetics, transgenesis, the zebrafish genome and mapping technologies, informatics and comparative genomics, and Infrastructure. This volume of Methods in Cell Biology will prove valuable both to seasoned zebrafish investigators as well as to those who are newly adopting the zebrafish model as part of their research armamentarium.
Seasoned zebrafish investigators as well as to those who are newly adopting the zebrafish model as part of their research armamentarium
Contributors
Preface
Chapter 1: Generating Conditional Mutations in Zebrafish Using Gene-trap Mutagenesis
I. Introduction
II. Rationale for Conditional Mutations
III. Rationale for Gene-trap Mutagenesis to Generate Conditional Mutations
IV. Rationale for Vector Design
V. Methods
VI. Discussion
VII. Summary
Chapter 2: Tol2-mediated Transgenesis, Gene Trapping, Enhancer Trapping, and the Gal4-UAS System
I. Introduction
II. Transgenesis by Using the Tol2 Transposable Element
III. Tol2-mediated BAC Transgenesis
IV. Gene Trapping and Enhancer Trapping with the Tol2 Transposon System
V. Gene Trapping and Enhancer Trapping with the Gal4FF-UAS System
Chapter 3: Engineering Zinc Finger Nucleases for Targeted Mutagenesis of Zebrafish
I. Introduction
II. Methods and Resources for Engineering Zinc Finger Nucleases
III. Choice of Method to Engineer Zinc Finger Nucleases
Chapter 4: Retroviral-mediated Insertional Mutagenesis in Zebrafish
I. Introduction
II. Mutagenesis
III. Cloning the Mutated Genes
IV. Retroviral-mediated Insertional Mutagenesis as a Reverse Genetic Tool
V. Future Directions
Chapter 5: Genetic Screens for Mutations Affecting Adult Traits and Parental-effect Genes
I. Introduction
II. Strategies for Adult Trait and Parental-effect Screens
III. Selection of Lines for Genetic Screens
IV. Recovery and Maintenance of Adult and Parental-effect Mutations
V. Mapping Adult and Parental-effect Mutations
VI. Solutions, Materials, and Protocols
VII. Conclusions
Chapter 6: High-Throughput Target-Selected Gene Inactivation in Zebrafish
I. Introduction
II. Mutagenesis and Library Creation
III. PCR and Re-sequencing of Exons
IV. Analysis of Re-sequencing Data and Retrieval of Mutations
Chapter 7: Genetic Suppressor Screens in Haploids
I. Introduction and Rationale
II. Methods – an Example of Suppressor Screen in Moonshine Mutants
III. Conclusions and Prospective
Chapter 8: Transgenic Zebrafish Using Transposable Elements
I. Introduction
II. Requesting and Assembling Tol2 System
III. Microinjection
IV. Quality Control
V. Select Injected Fish to Raise as Founder Generation F0
VI. Production of F1 Generation
VII. Select the Best Substrain(s) Based on Observation of F2 Generation
VIII. Discussion
Chapter 9: Spatiotemporal Control of Embryonic Gene Expression Using Caged Morpholinos
I. Introduction
II. Design and Synthesis of cMOs
III. Synthesis of cFD
IV. Microinjection of Caged Reagents
V. Global Photoactivation of Caged Reagents
VI. Titration of cMO Dose for Optimum Dynamic Range
VII. Localized Photoactivation of Caged Reagents
VIII. Conclusion
Chapter 10: Advanced Zebrafish Transgenesis with Tol2 and Application for Cre/lox Recombination Experiments
I. Introduction
II. Transgene Design, Cloning, and Tol2 Transgenesis
III. Tol2 Transgene Genetics
IV. CreERT2-Controlled lox Recombination Using 4-OHT
V. Discussion
Conflict of interest statement
Chapter 11: Use of Phage PhiC31 Integrase as a Tool for Zebrafish Genome Manipulation
I. Introduction
II. Rationale
III. Materials and Methods
IV. Discussion
V. Summary
Chapter 12: Method for Somatic Cell Nuclear Transfer in Zebrafish
I. Methods
II. Materials
Chapter 13: Single Nucleotide Polymorphism (SNP) Panels for Rapid Positional Cloning in Zebrafish
I. Introduction
II. Extraction of Zebrafish Genomic DNA
III. Affymetrics Molecular Inversion Probe Panel
IV. Suggested Mapping Strategy
V. General Considerations
Chapter 14: Molecular Cytogenetic Methodologies and a BAC Probe Panel Resource for Genomic Analyses in the Zebrafish
I. Introduction
II. Cytogenetic Methods
III. Application of Cytogenetic Methods in Zebrafish Studies
IV. Methods for Array CGH
V. Application of Array CGH in Zebrafish Studies
VI. Summary
Chapter 15: Conserved Synteny and the Zebrafish Genome
I. Introduction
II. Rationale: Gene Duplication and Orthology Assignments
III. Methods
IV. Using the Synteny Database: A Case Study of Nerve Growth Factor Receptors
V. Zebrafish, Conserved Syntenies, and the Teleost Genome Duplication
VI. Summary
Chapter 16: 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. General Flow of Information from the Zebrafish Genome Sequence Assemblies
VIII. Synteny between Human, Zebrafish, Fugu, and Tetraodon Genomes
IX. Proving a Candidate Gene is Responsible for the Mutant Phenotype
X. Morpholinos
XI. Future Technologies
Chapter 17: Data Extraction, Transformation, and Dissemination through ZFIN
I. Introduction
II. Extracting Data and Data Flow
III. Ensuring Accurate and Rapid Data Dissemination
IV. Submitting Data Directly to ZFIN
V. Conclusions
Chapter 18: DNA Methylation Profiling in Zebrafish
I. Introduction
II. Rationale
III. Methods
IV. Discussion
Chapter 19: Chromatin Immunoprecipitation in Adult Zebrafish Red Cells
I. Introduction
II. Adult Zebrafish Exsanguination
III. Chromatin Immunoprecipitation (Lee et al., 2006)
IV. ChIP-seq Sample Preparation (Guenther et al., 2008)
V. ChIP-seq Data Analysis
VI. Summary and Conclusions
VII. Online tools
VIII. Conflicts of Interest
Chapter 20: Discerning Different In vivo Roles of MicroRNAs by Experimental Approaches in Zebrafish
I. Introduction
II. Using Zebrafish to Study the Function of miRNAs
III. Summary
Chapter 21: Sequencing-based Expression Profiling in Zebrafish
I. Introduction
II. Digital Gene Expression
III. Potential Issues in DGE
Chapter 22: Chromatin Modification in Zebrafish Development
I. Chromatin Modifications
II. Chromatin Modifications in Development
III. Functions of Chromatin Modifications in Tissue Regeneration
IV. Outlook
Chapter 23: Advances in Zebrafish Husbandry and Management
I. Introduction
II. Breeding
III. Larviculture
IV. Aquaculture Systems
V. Nutrition
VI. Health Management
VII. Genetic Management
VIII. Regulatory Compliance
IX. Education and Training
X. Summary
Chapter 24: Aquaculture and Husbandry at the Zebrafish International Resource Center
I. Introduction
II. Methods
III. Materials
Index
Volumes in Series
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