New Technique Turns Brain Transparent, Gives Scientists Direct Look Into Brain

[Source: Stanford]
[Source: Stanford]
The brain remains one of the most impenetrable frontiers of science. Deciphering how its 85 billion neurons and trillion connections between them function together to allow us to observe and react to our world, to generate emotions and thoughts remains stubbornly well beyond our scientific reach. Apart from their (formidable) intellects, scientists are limited by the tools they use to study the brain. A new technique, developed by a scientist who’d already contributed an extraordinary tool to neuroscience, literally allows scientists to peer directly into the brain by making it transparent.

Like other cells throughout the body, the cells of the brain are bordered by membranes made largely of fatty lipids. While they’re vital to brain structure and function, they represent a double barrier to neuroscientists as they are for the most part impenetrable to both chemicals and light. So Karl Deisseroth and his team at Stanford University have come up with a solution – get rid of the lipids. Their technique, called CLARITY, works by replacing those opaque lipids with a hydrogel.

The hydrogel is formed by first infusing a postmortem mouse brain with small, separate hydrogel molecules. When the brain is heated to body temperature the individual hydrogel molecules, or monomers, fuse together into long, multi-molecule chains, or polymers, creating a mesh that holds brain structures in place, but importantly, does not bind lipids. The free lipids are then flushed away through a process called electrophoresis. What’s left is a transparent, lipid-free brain with its 3-D structure preserved.

The removal of lipids also means that chemicals used to label different brain structures and molecules can pass more easily into the brain and then be viewed. Labeling proteins in a CLARITY-prepped – or clarified – brain with fluorescent markers, for instance, would allow scientists to study individual cell function in ways impossible with other methods. Labeling other molecules also could allow scientists to study the ongoing interaction between proteins, nucleic acids, and the neuron’s signaling molecules, neurotransmitters. And tracing the individual circuits of an intact brain could yield an anatomical picture more complete than what’s possible with current methods. Furthermore, the team showed that a clarified brain can be stained, its molecular labels washed away, and stained again, greatly increasing the number of structures that can be studied with a single brain.

CLARITY is the second game-changing technology developed by Stanford's Karl Deisseroth. He previously co-developed optogenetics. [Source: Stanford]
CLARITY is the second game-changing technology developed by Stanford’s Karl Deisseroth. He previously co-developed optogenetics. [Source: Stanford]
The work was recently published in Nature.

In addition to a mouse brain, the team has used CLARITY to open a window to peer into the brain of a zebrafish. It’s hoped that the technique can be used to study the brains of other organisms as well. Most relevant to medical research would likely be rat and nonhuman primate brains. And beyond brains, the lipid-clearing technique could potentially be used to study other organs in the body.

Right now studying brain structure normally involves cutting in to thin slices to view under a microscope. But separating the brain into slices largely prevents the study of its three-dimensional structure. But with CLARITY, scientists could study the brain with its structure still intact. “This feat of chemical engineering promises to transform the way we study the brain’s anatomy and how disease changes it,” Thomas Insel, director of the National Institutes of Mental Health, said in a press release. “No longer will the in-depth study of our most important three-dimensional organ be constrained by two-dimensional methods.”

Deisseroth is a scientist who has a knack for innovation. Together with Ed Boyden, the two created a technique in 2004 by which neurons can be activated by light. Optogenetics entails giving neurons light-activated proteins called channelrhodopsins that are normally found in green algae. In green algae the proteins are used to guide movement in response to light. In neurons, channelrhodopins allow specific neurons to be activated on demand by aiming a fiber optic laser at them. The technique spread quickly to neuroscience labs across the world.

With CLARITY, the researchers hope to gain new insights into brain disorders such as autism, schizophrenia and post-traumatic stress disorder. And while the technique was not developed as part of the BRAIN Initiative recently announced by President Obama, Deisseroth is among the “dream team” of scientists charged with steering the Initiative – and the $110 million in funds designated for 2014 – toward a profoundly deeper understanding of the brain and toward developing new tools to bring that about. While many experts are skeptical about a big science approach to unlocking the mysteries of the brain, their concerns should be allayed if the program leads to more great tools like CLARITY.

[Source: stanfordmedicine via YouTube]

Peter Murray
Peter Murray
Peter Murray was born in Boston in 1973. He earned a PhD in neuroscience at the University of Maryland, Baltimore studying gene expression in the neocortex. Following his dissertation work he spent three years as a post-doctoral fellow at the same university studying brain mechanisms of pain and motor control. He completed a collection of short stories in 2010 and has been writing for Singularity Hub since March 2011.
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