Tag Archives: Rodent

Looking through the brain with CLARITY!

Imaging single layers of cells is very easy since the light can penetrate the cells quite easily. Imaging a tissue sample of several layers of cells is more difficult, because the passage of light is gradually blocked. To image a whole organ without slicing it was near-impossible, until now.

CLARITY is a new method, developed by the lab of Karl Deisseroth, a neuroscientists from Stanford university and published in the Nature Online. In essence, they took a whole mouse brain, infused it with a hydrogel, which was cross-linked to all the “important” biomolecules (proteins & nucleic acids). They then removed all the lipids and other “non-important” molecules (which were not cross-linked to the hydrogel), with a detergent, SDS.

The result was a transparent mouse brain, that maintained all of it original cellular (and presumably sub-cellular) structure.

Mouse brain before & after CLARITY. Source: Chung, K. et al Nature (2013)

They could then image into the brain, using pre-expressed fluorescent proteins, immunofluorescence (IF) or FISH. Importantly, they claim that one can perform several rounds of IF (and similarly FISH) and they show images to proved that.

They also show that the signal intensity of the IF signal does not diminish when going deeper into the tissue, or using different z-sections.

Structural and molecular phenotyping of a piece of human brain using CLARITY. Source: Chung, K. et al Nature (2013).

Structural and molecular phenotyping of a piece of human brain using CLARITY. Source: Chung, K. et al Nature (2013).

It is my understanding that people in the Neuroscience field have known about CLARITY for quite some time, just waited for it to get published already. It IS very exciting and amazing.

Watch the Clarity Video:

Once CLARITY becomes widespread, we should get immense amount of data on the cellular & molecular structure of many types of whole (unsliced) tissues.  We could follow development, disease and much more.

Perhaps one day even whole animals will be imaged.

ResearchBlogging.orgChung, K., Wallace, J., Kim, S., Kalyanasundaram, S., Andalman, A., Davidson, T., Mirzabekov, J., Zalocusky, K., Mattis, J., Denisin, A., Pak, S., Bernstein, H., Ramakrishnan, C., Grosenick, L., Gradinaru, V., & Deisseroth, K. (2013). Structural and molecular interrogation of intact biological systems Nature DOI: 10.1038/nature12107