CLARITY

CLARITY is a method of making brain tissue transparent using acrylamide-based hydrogels built from within, and linked to, the tissue, and as defined in the initial paper, represents "transformation of intact biological tissue into a hybrid form in which specific components are replaced with exogenous elements that provide new accessibility or functionality". When accompanied with antibody or gene-based labeling, CLARITY enables highly detailed pictures of the protein and nucleic acid structure of organs, especially the brain. It was developed by Kwanghun Chung and Karl Deisseroth at the Stanford University School of Medicine.

Subsequent published papers using the CLARITY method of building acrylamide-based tissue-gel hybrids within tissue for improved optical and molecular access, have included studies on Alzheimer's Disease human brains, mouse spinal cords, multiple sclerosis animal models, plants, and microscopy methods including tissue expansion or swelling for use in confocal microscopy (F. Chen et al., Science, Jan. 2015) and CLARITY-optimized light sheet microscopy or COLM.

The process of applying CLARITY imaging begins with a postmortem tissue sample. Next a series of chemical treatments must be applied to achieve transparency, in which the lipid content of the sample is removed, while almost all of the original proteins and nucleic acids are left in place. The purpose of this is to make the tissue transparent and thus amenable to detailed microscopic investigation of its constituent functional parts (which are predominantly proteins and nucleic acids). To accomplish this, the preexisting protein structure has to be placed in a transparent scaffolding which preserves it, while the lipid components are removed. This 'scaffolding' is made up of hydrogel monomers such as acrylamide. The addition of molecules like formaldehyde can facilitate attachment of the scaffolding to the proteins and nucleic acids that are to be preserved, and the addition of heat is necessary to establish the actual linkages between the cellular components and the acrylamide.

Once this step is complete, the protein and nucleic acid components of the target tissue's cells are held firmly in place, while the lipid components remain detached. Lipids are then removed over 1–2 weeks of passive diffusion in detergent, or accelerated by electrophoretic methods. As they pass through, the detergent's lipophilic properties enable it to pick up and excise any lipids encountered along the way. Lipophilic dyes as DiI are removed, however there are CLARITY-compatible lipophilic dyes that can be fixated to neighbouring proteins. The large majority of non-lipid molecules, such as proteins and DNA, remain unaffected by this procedure, thanks to the acrylamide gel and chemical properties of the molecules involved.

...
Wikipedia