Craniofacial abnormalities are one of the most frequent birth malformations in humans, affecting around one in every thousand live births. The zebrafish (Danio rerio), a model organism that has seen increased usage in toxicological research in recent years, is ideal for assessing the effects of various chemicals on bone and cartilage structures. Chondrogenesis developed in zebrafish embryos by embryonic day 2, and supporting cartilage components are apparent at hatching (72 h post-fertilization). Individual cartilage may be observed using Alcian Blue staining as early as 2 days post-fertilization (dpf). The preferential binding of Alcian Blue causes the staining of zebrafish cartilage to acidic glycoproteins in an acidic solution (pH 2.2). In 72-120 hpf embryos, the cranial skeleton is easily visible after cartilage staining using Alcian Blue. Various cranial lengths and structures can be determined by measuring specific distances and angles to optimize the quantitative analysis of cranial malformations in zebrafish after exposure to various toxic agents. This chapter explains the Alcian Blue staining procedure to identify craniofacial cartilaginous structures in zebrafish embryos.
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