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African Turquoise Killifish (Nothobranchius furzeri): A Laboratory Manual


Subject Area(s):  Developmental BiologyZoologyLaboratory Techniques

Edited by Anne Brunet

Download a Free Excerpt from African Turquoise Killifish (Nothobranchius furzeri): A Laboratory Manual:

Preface
The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes
Index


Due December 2023 • 286 pages, illustrated (48 color & 1 B&W), index
Paperback • $95
ISBN  978-1-621824-60-2

  •     Description    
  •     Contents    

Description

The African turquoise killifish Nothobranchius furzeri is a short-lived fish species that has been established as a novel vertebrate model to study aging and represents a promising system to examine various other processes. The killifish is relatively easy and inexpensive to maintain. In addition, it has a short life cycle and abundant progeny, facilitating its use. Investigation using this model organism is growing and has provided new insights into aging, age-related diseases, ecology, evolution, and embryonic diapause—a state of “suspended animation.”

This laboratory manual provides a comprehensive collection of protocols covering experimental techniques currently used to study the African turquoise killifish. Husbandry protocols describe how to set up and maintain a killifish colony and how to generate and preserve genetically engineered killifish lines. This collection also includes both general and specific methods to characterize different organs during aging, with a particular focus on the brain. Several genomics methods and analyses for unbiased characterization are also described. Finally, this manual encompasses protocols in other interesting areas of research, including injury repair, development, and embryonic diapause.

This collection should enable studies in the African turquoise killifish and other species of killifish such as the South American killifish, and includes protocols that will be useful both to groups considering the use of these systems for the first time and to those with experience in the field. We also hope that this protocol book will foster a large killifish community and will promote new studies in many different research areas.

Contents

Preface
Anne Brunet
OVERVIEW
The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes
Felix Boos, Jingxun Chen, and Anne Brunet
PROTOCOLS
Husbandry, Reproduction, and Preservation Protocols
1. Husbandry of the African Turquoise Killifish Nothobranchius furzeri
Ravi D. Nath, Claire N. Bedbrook, Rahul Nagvekar, and Anne Brunet
2. Breeding and Reproduction of the African Turquoise Killifish Nothobranchius furzeri
Jingxun Chen, Rishad C. Khondker, and Anne Brunet
3. Sperm Cryopreservation of the African Turquoise Killifish Nothobranchius furzeri
Luca Dolfi, Tsz Kin Suen, Danel Medelbekova, Roberto Ripa, Orsolya Symmons, and Adam Antebi
4. In Vitro Fertilization of the African Turquoise Killifish Nothobranchius furzeri
Luca Dolfi, Tsz Kin Suen, Danel Medelbekova, Roberto Ripa, Orsolya Symmons, and Adam Antebi
5. Noninvasive Ejaculate Collection from the African Turquoise Killifish Nothobranchius furzeri
Silvia Cattelan and Dario Riccardo Valenzano
Genetic Manipulation and Analysis
6. CRISPR–Cas9 Genome Editing in Nothobranchius furzeri for Gene Knockout and Knock-In
Itai Rozenberg, Eitan Moses, and Itamar Harel
7. Efficient Transgenesis in African Turquoise Killifish Using a Gibson Assembly–Based Tol2 Transposon System
Yufei Lou, Weifeng Lin, and Wei Wang
8. Rapid Genotyping of Nothobranchius furzeri Embryos, Larvae, and Adult Fish via High-Resolution Melt Analysis (HRMA)
Johannes Krug, Annekatrin Richter, and Christoph Englert
9. Molecular Sexing of Nothobranchius furzeri Embryos and Larvae
Annekatrin Richter, Johannes Krug, and Christoph Englert
Genomics
10. Chromatin Accessibility Profiling and Data Analysis Using ATAC-seq in Nothobranchius furzeri
G. Adam Reeves, Param Priya Singh, and Anne Brunet
11. Differential Expression Analysis of Nothobranchius furzeri Transposable Elements from RNA-seq Data
Bryan Teefy, Matthew Malone, and Bérénice A. Benayoun
12. Taxonomic Profiling of Fecal and Intestinal Microbiota in the African Turquoise Killifish Nothobranchius furzeri
Jens Seidel, Miriam Popkes, and Dario Riccardo Valenzano
13. Sequencing the Immunoglobulin Heavy-Chain Locus (IgH) in Turquoise Killifish (Nothobranchius furzeri)
Jens Seidel, William John Bradshaw, and Dario Riccardo Valenzano
Aging and Life Span Analysis
14. Life Span Assessment in the African Turquoise Killifish Nothobranchius furzeri
Claire N. Bedbrook, Ravi D. Nath, Rogelio Barajas, and Anne Brunet
15. Molecular and Biochemical Analyses of Aging Hallmarks in the Central Nervous System of the Fast-Aging African Turquoise Killifish
Steven Bergmans, Sophie Vanhunsel, Caroline Zandecki, Eve Seuntjens, Lies De Groef, and Lieve Moons
16. Morphological Analysis of Aging Hallmarks in the Central Nervous System of the Fast-Aging African Turquoise Killifish
Steven Bergmans, Sophie Vanhunsel, Jolien Van houcke, Valerie Mariën, Lut Arckens, and Lieve Moons
Tissue Analysis
General
17. Good Practices for Histological Analysis of the Annual Killifish Nothobranchius furzeri (Nothobranchiidae)
Jakub Žák, Iva Dyková, Radim Blažek, and Martin Reichard
Blood
18. Nonlethal Blood Sampling from the Killifish Nothobranchius furzeri
Luca Dolfi, Roberto Ripa, Danel Medelbekova, Eugen Ballhysa, Orsolya Symmons, and Adam Antebi
Fat
19. Micro-CT Analysis of Fat in the Killifish Nothobranchius furzeri
Roberto Ripa, Andrea Mesaros, Orsolya Symmons, Eugen Ballhysa, Luca Dolfi, and Adam Antebi
Brain
20. Long-Term Brain Organotypic Cultures of the Turquoise Killifish Nothobranchius furzeri
Sara Bagnoli, Letizia Brogi, Baldassare Fronte, Carlo Bibbiani, Eva Terzibasi Tozzini, and Alessandro Cellerino
21. EdU and Immunofluorescence Staining of Nothobranchius furzeri Organotypic Cultures
Sara Bagnoli, Eva Terzibasi Tozzini, and Alessandro Cellerino
22. Immunofluorescence and Aggresome Staining of Nothobranchius furzeri Cryosections
Sara Bagnoli, Eva Terzibasi Tozzini, and Alessandro Cellerino
23. Whole-Brain Clearing and Immunofluorescence in Nothobranchius furzeri
Sara Bagnoli, Eva Terzibasi Tozzini, and Alessandro Cellerino
24. Preparation of High-Viability Single-Cell Suspensions from African Turquoise Killifish Brain Tissue
Valerie Mariën, Lutgarde Arckens, and Jolien Van houcke
Nervous System Injury Methods
25. A Robust and Reproducible Method to Study Neurorepair after Stab Injury in the African Turquoise Killifish Telencephalon
Valerie Mariën, Lutgarde Arckens, and Jolien Van houcke
26. The Optic Nerve Crush Injury Paradigm in African Turquoise Killifish to Study Axonal Regeneration in an Aged Environment
Sophie Vanhunsel, Steven Bergmans, and Lieve Moons
27. Visually Driven Behavior Assays to Study Functionality and Recovery after Damage of the Aged African Turquoise Killifish Visual System
Steven Bergmans, Sophie Vanhunsel, and Lieve Moons
Embryo Development and Diapause
28. Handling Diapause Embryos of the African Turquoise Killifish Nothobranchius furzeri
Chi-Kuo Hu
29. Fluorescent In Situ Hybridization in Embryos of the African Turquoise Killifish Nothobranchius furzeri
Philip B. Abitua
Appendix: General Safety and Hazardous Material Information
Index