Simplified CLARITY for visualizing immunofluorescence labeling in the developing rat brain

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CLARITY is an innovative technological advance in which intact biological tissue is transformed into a “nanoporous hydrogel-hybridized form” (Chung et al. 2013; Chung and Deisseroth 2013) with markedly improved chemical and optical accessibility, permitting fluorescent visualization and extraction of high-resolution structural data from mm-thick blocks of tissue. CLARITY affords an excellent but as yet unexploited opportunity to visualize the growth and maturation of phenotypically identified neurons and axonal processes in the developing brain. This brief report describes a moderately revised, simplified, and less expensive CLARITY protocol that effectively reveals the structure of chemically identified neurons in whole neonatal/juvenile rat brains and tissue slabs. Rats [postnatal day (P)0–24] were transcardially perfused with one of two fixative/hydrogel solutions, followed by hydrogel polymerization to generate brain hybrids. Whole brain hybrids or 2.0-mm-thick coronal slabs were passively cleared of lipid and then processed for dual immunofluorescence labeling, including labeling using tyramide signal amplification. After refractive index matching using 2,20-Thiodiethanol (60 % solution), a Leica confocal microscope equipped with a CLARITY objective was used to view the hypothalamus in whole brain hybrids or slabs. Collected image stacks revealed the distribution and three-dimensional structure of hypothalamic pro-oxyphysin (oxytocin)-, neuropeptide Y-, glucagon-like peptide-1-, and tyrosine hydroxylase-immunopositive neurons and processes within large tissue volumes. Outstanding structural preservation and immunolabeling quality demonstrates the efficacy of this approach for interrogating chemically defined neural circuits as they develop in postnatal rodent brain.

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Correspondence to Linda Rinaman.

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Zheng, H., Rinaman, L. Simplified CLARITY for visualizing immunofluorescence labeling in the developing rat brain. Brain Struct Funct 221, 2375–2383 (2016).

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  • Neonatal
  • Immunofluorescence