Xenopus Protocols: Post-Genomic Approaches

ISBN-13: 9781617799914 / Angielski / Twarda / 2012 / 584 str.

Stefan Hoppler; Peter D. Vize

Opis

During the 20th century Xenopus has flourished as an accessible experimental model system for studying vertebrate biology. The second edition of Xenopus Protocols: Post-Genomic Approaches expands upon the previous edition with novel approaches inspired by Xenopus tropicalis and the sequencing of its genome. Xenopus tropicalis genomics and tractable genetics combined with the unique experimental advantages of Xenopus laevis and their distinctive phylogenetic position make them unique model systems for vertebrate embryonic development in the 21st century. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Xenopus Protocols: Post-Genomic Approaches, Second Edition provides a toolkit that will enable every laboratory to maximize the power of this extraordinary experimental system in the post-genomic age.

Spis treści

Part I: Xenopus Tropicalis

1. Xenopus tropicalis as a Model Organism for Genetics and Genomics: Past, Present and Future

Robert M. Grainger

2. Husbandry of Xenopus tropicalis

Alan Jafkins, Anita Abu-Daya, Anna Noble, Lyle Zimmerman, and Matthew Guille

3. Generating Diploid Embryos from Xenopus tropicalis

Florencia del Viso and Mustafa Khokha

4. Navigating the Xenopus tropicalis Genome

Ira L. Blitz

Part II: Genetics in Xenopus

5. Genetic Analysis of Xenopus tropicalis

Timothy J. Geach, Derek L. Stemple, and Lyle B. Zimmerman

6. Forward Genetic Screens in Xenopus using Transposon-mediated Insertional Mutagenesis

Donald A. Yergeau, Clair M. Kelley, Haiqing Zhu, Emin Kuliyev and Paul E. Mead

7. Targeted Gene Disruption with Engineered Zinc-finger Nucleases (ZFNs)

John J. Young and Richard M. Harland

8. Reverse Genetic Studies using Antisense Morpholino Oligonucleotides

Yanan Zhao, Shoko Ishibashi and Enrique Amaya

9. Chemical Genetics and Drug Discovery in Xenopus

Matthew L. Tomlinson, Adam Hendry, and Grant N. Wheeler

10. Maternal mRNA Knock-down Studies: Antisense Experiments using the Host-transfer Technique in Xenopus laevis and Xenopus tropicalis

David J. Olson, Alissa M. Hulstrand and Douglas W. Houston

Part II: Xenopus Trangenesis

11. Generating Transgenic Frog Embryos by Restriction Enzyme Mediated Integration (REMI)

Shoko Ishibashi, Kristen L. Kroll and Enrique Amaya

 

12. A Simple Method of Transgenesis using I-SceI meganuclease in Xenopus

Shoko Ishibashi, Nick R. Love and Enrique Amaya

13. Using FC31 Integrase to Mediate Insertion of DNA in Xenopus Embryos

You E. Li, Bryan G. Allen and Daniel L. Weeks

14. Xenopus Transgenics: Methods using Transposons

Clair M. Kelley, Donald A. Yergeau, Haiqing Zhu, Emin Kuliyev and Paul E. Mead

15. Comparative Genomics-based Identification and Analysis of Cis-regulatory Elements

Hajime Ogino, Haruki Ochi, Chihiro Uchiyama, Sarah Louie, and Robert M. Grainger

16. Tet-On Binary Systems for Tissue-specific and

Inducible Transgene Expression

Daniel R. Buchholz

Part III: Gene Expression: From Gene to Transcript to Protein

17. Chromatin Immunoprecipitation Analysis of Xenopus Embryos

 Robert C. Akkers, Ulrike G. Jacobi and Gert Jan C. Veenstra

18. Transcriptomics Using Next Generation Sequencing Technologies

Dasfne Lee-Liu, Leonardo I. Almonacid, Fernando Faune, Francisco Melo, Juan Larrain

19. Databases of Gene Expression in Xenopus Development

Michael J. Gilchrist, Nicolas Pollet

20. Investigating Alternative RNA Splicing in Xenopus

Agnès Mereau and Serge Hardy

21. Immunoisolation of Protein Complexes from Xenopus

Frank L. Conlon, Yana Miteva, Erin Kaltenbrun, Lauren Waldron, Todd M. Greco, Ileana M. Cristea

22. Complementary Proteomic Analysis of Protein Complexes

Todd M. Greco, Yana Miteva, Frank L. Conlon, Ileana M. Cristea

Part IV: Imaging Xenopus Development

 

23. Antibody Development and use in Chromogenic and Fluorescent Immunostaining

Eamon Dubaissi, Niki Panagiotaki, Nancy Papalopulu, and Peter D. Vize

24. Multiple fluorescent  in situ mRNA Hybridization (FISH) on Whole Mounts and Sections

Robert Lea, Boyan Bonev, Eamon Dubaissi, Peter D. Vize and Nancy Papalopulu

25. Methods to Analyze microRNA Expression and Function During Xenopus Development

Boyan Bonev and Nancy Papalopulu

26. A Bromodeoxyuridine (BrdU) Based Protocol for Characterizing Proliferating Progenitors in Xenopus Embryos

Helene Auger, Raphael Thuret, Warif El Yakoubi, and Nancy Papalopulu

27. Microscopy Tools for Quantifying Developmental Dynamics in Xenopus Embryos

Sagar D. Joshi, Hye Young Kim, Lance A. Davidson

Part V: Novel Approaches in Xenopus

28. Mathematical Modelling of Gene RegulatoryNetworks in Xenopus Development

Yasushi Saka

29. Stem-cell-like Embryonic Explants to Study Cardiac Development

Boni A. Afouda

30. Studying Regeneration in Xenopus

Caroline W. Beck

31. On-line Resources for Xenopus

Jeff Bowes

Boyan Bonev and Nancy Papalopulu