In vivo analysis of zebrafish innate immunity

Methods Mol Biol. 2008;415:337-63. doi: 10.1007/978-1-59745-570-1_20.


Among vertebrate model species, the zebrafish embryo combines at an unprecedented level optical accessibility with easy genetic manipulation. As such, it is gaining recognition as a powerful model to study innate immunity. In this chapter, we provide a protocol for the generation of zebrafish embryos deficient in a protein of interest for innate immune signaling using antisense morpholino oligonucleotides, the systemic or local infection of these embryos with bacteria, and the assessment of various aspects of the following immune response with emphasis on microscopic observation. This example can be easily adapted to study the role of other genes, either knocked down or overexpressed, and in response to any other challenge, from purified microbial compounds to pathogenic viruses. This protocol is aimed at people not necessarily familiar with zebrafish biology and handling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacteria / growth & development
  • Bacterial Infections / immunology
  • Bacterial Infections / microbiology
  • Colony Count, Microbial
  • Embryo, Nonmammalian / drug effects
  • Embryo, Nonmammalian / microbiology
  • Immunity, Innate / drug effects
  • Immunity, Innate / immunology*
  • Leukocytes / drug effects
  • Leukocytes / microbiology
  • Molecular Biology / methods*
  • Myeloid Differentiation Factor 88 / deficiency
  • Survival Analysis
  • Tumor Necrosis Factor-alpha / pharmacology
  • Zebrafish / immunology*
  • Zebrafish / microbiology


  • Myeloid Differentiation Factor 88
  • Tumor Necrosis Factor-alpha