After providing all the funding for The Brain from Top to Bottom for over 10 years, the CIHR Institute of Neurosciences, Mental Health and Addiction informed us that because of budget cuts, they were going to be forced to stop sponsoring us as of March 31st, 2013.

We have approached a number of organizations, all of which have recognized the value of our work. But we have not managed to find the funding we need. We must therefore ask our readers for donations so that we can continue updating and adding new content to The Brain from Top to Bottom web site and blog.

Please, rest assured that we are doing our utmost to continue our mission of providing the general public with the best possible information about the brain and neuroscience in the original spirit of the Internet: the desire to share information free of charge and with no adverstising.

Whether your support is moral, financial, or both, thank you from the bottom of our hearts!

Bruno Dubuc, Patrick Robert, Denis Paquet, and Al Daigen




Monday, 16 June 2014
Making the Brain Transparent To Explore It More Easily

A relatively new technique can now perform the amazing feat of making a mouse’s brain completely transparent (This same technique has been tried on human brains as well, but so far has succeeded in making only parts of them transparent.)

But enabling scientists to see through the brain would be merely an interesting curiosity if this technique—dubbed “Clarity” by the team that developed it—did not also preserve the brain’s entire underlying cellular and molecular structure, so that existing methods of staining and tracing nerve bundles can be applied to the brain once it has been rendered transparent. The neural pathways throughout the mouse brain thus become visible in the finest detail, while the transparency of the tissues enables researchers to obtain a far more comprehensive overview of the axonal pathways than was ever possible before.

The Clarity technique, first reported on in the journal Nature in May 2013, was developed by a multidisciplinary team directed by Dr. Karl Deisseroth of Stanford University. Dr. Deisseroth and his colleagues at Stanford were already well known for another technique that they had developed a few years earlier: optogenetics, which involves the use of optical fibres, photopigments, and modified genes. The Clarity technique uses none of these. Instead, it uses a chemical substance called hydrogel, composed mainly of water molecules held together by larger molecules, which is the key to the method.

Hydrogel, when applied to brain tissue, forms a kind of mesh that permeates it and connects most of the brain’s molecules, except for the lipids. The brain is then placed in a soapy solution in which it is exposed to an electrical current that drives the lipids out of the brain, precisely because they are not attached to the hydrogel. It is at this time that the brain becomes transparent and ready to be treated with dyes that are specific to certain molecules, because their integrity and locations have been preserved.

Efforts are continuing to refine this technique, in particular to successfully remove all of the lipids from a human brain, which is far larger than a mouse’s. But the data collected in the studies with mice have already shown the tremendous potential of this technique.

i_lien Brains as Clear as Jell-O for Scientists to Explore
i_lien Clarity Brain Imaging from Stanford’s Deisseroth Lab
a_exp Structural and molecular interrogation of intact biological systems

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