The Zebrafish: Genetics, Genomics and Informatics

The Zebrafish: Genetics, Genomics and Informatics

3rd Edition - September 7, 2011

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  • Editor: H. Detrich, III
  • Hardcover ISBN: 9780123748140
  • eBook ISBN: 9780080888576

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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, 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

Table of Contents

  • Contributors


    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


    Volumes in Series

Product details

  • No. of pages: 528
  • Language: English
  • Copyright: © Academic Press 2011
  • Published: September 7, 2011
  • Imprint: Academic Press
  • Hardcover ISBN: 9780123748140
  • eBook ISBN: 9780080888576

About the Serial Volume Editor

H. Detrich, III

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.

Affiliations and Expertise

Northeastern University, Boston, MA, USA

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