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Originally published April 10, 2013 at 9:18 PM | Page modified April 10, 2013 at 10:59 PM

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See-through brains offer scientists a clearer view of disease

The Clarity technique ushers in a new era of brain imaging, offering hope for improving the study of such neurological disorders as autism, schizophrenia, Alzheimer’s disease and Parkinson’s disease.

The New York Times

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The field of science is not perfect. But they proceed in a rational, fact based manner... MORE

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The visible brain has arrived: the consistency of Jell-O, as transparent and colorful as a child’s model, but vastly more useful.

Scientists at Stanford University reported Wednesday that they had made a whole mouse brain, and part of a human brain, transparent, so that networks of neurons that receive and send information can be highlighted in stunning color and viewed in all their three-dimensional complexity without slicing up the organ.

The recipe for transforming cadaver brains into see-through research tools stands to accelerate investigations of Alzheimer’s disease, schizophrenia, post-traumatic stress disorder and a variety of other brain maladies, and has led to a significant insight into the peculiar characteristics of neurons associated with Down syndrome and autism.

Even more important, experts say, is that unlike earlier methods for making the tissue of brains and other organs transparent, the new process, called Clarity by its inventors, preserves the biochemistry of the brain so well that researchers can test it over and over again with chemicals that highlight specific structures within a brain and provide clues to its past activity.

The work, reported Wednesday in the journal Nature, is not part of the Obama administration’s recently announced initiative to probe the secrets of the brain, although the senior author on the paper, Dr. Karl Deisseroth at Stanford, was one of those involved in creating the initiative and is involved in planning its future.

Dr. Thomas Insel, director of the National Institute of Mental Health, which helped pay for the research, described the new work as helping to build an anatomical “foundation” for the Obama initiative, which is meant to look at activity in the brain.

Insel added that the technique works in a human brain that has been in formalin, a preservative, for years, which means that long-saved human brains might be studied.

“Frankly,” he said, “that is spectacular.”

Kwanghun Chung, the primary author on the paper, and Deisseroth worked with a team at Stanford for years to get the technique right. Deisseroth, known for developing another powerful technique, optogenetics, that allows the use of light to switch specific brain activity on and off, said Clarity could have a broader impact than optogenetics.

“It’s really one of the most exciting things we’ve done,” he said, with potential applications in neuroscience and beyond.

“I think it’s great,” said Dr. Clay Reid, a senior investigator at the Allen Institute for Brain Science in Seattle, who was not involved in the work. “One of the very difficult challenges has been making the brain, which is opaque, clear enough so that you can see deep into it.”

This technique, he said, makes brains “extremely clear” and preserves most of the brain chemistry. “It has it all,” he said.

In the mid-2000s, Reid was part of a team led by Dr. Jeff Lichtman at Harvard University that developed a process called Brainbow to breed mice that are genetically altered to make their brain neurons fluoresce in different colors. The new technique would allow whole brains of those mice with their rainbow neurons to be preserved and studied.

“I’m quite excited to try this,” Lichtman said.

The hydrogel factor

There are several ways to make tissue transparent. The key to the new technique is a substance called a hydrogel, a material that is mostly water held together by larger molecules to give it some solidity.

Chung said the hydrogel formed a kind of mesh that permeates the brain and connects to most of the molecules, but not to the lipids, which include fats and some other substances. The brain is then put into a soapy solution and an electric current is applied, which drives the solution through the brain, washing out the lipids. Once they are out, the brain is transparent, and its biochemistry is intact, so it may be infused with chemicals, such as antibody molecules that also have a dye attached, that show fine details of its structure and previous activity.

Techniques like this, said Insel, “should give us a much more precise picture of what is happening in the brains of people who have schizophrenia, autism, post-traumatic stress disorder, bipolar disorder and depression.”

The tricky part was getting the right combination of temperature, electricity and solution, and it was very tricky indeed, Chung said. Over the course of years spent trying to make it work, he said, “I burned and melted more than a hundred brains.”

With the paper’s publication, the recipe is available to anyone who wants to use it, and, he said, “I think it will be relatively easy.”

The technique has its limits. Chung said more work needed to be done before it could be applied to a whole human brain, because a human’s brain is so much larger than a mouse’s and has more lipids.

Their success is apparent in a pair of photographs taken by the researchers. In one of them, an untreated mouse brain sitting in a petri dish atop a printed page partially obscures a block of text. After it was subjected to the new technique, the words of Santiago Ramón y Cajal, the father of neuroscience, become visible: “The brain is a world consisting of a number of unexplored continents and great stretches of unknown territory.”

The team experimented first with mouse brains, then tested its method on a portion of a brain from a human cadaver.

The result was a research tool that stands to be much more versatile than the traditional methods used to study brain tissue.

Test-drive discovery

Deisseroth and his colleagues were eager to take their invention for a test-drive. They tried it out on a human brain that had belonged to someone who had autism and that had been preserved for six years.

What they found surprised them: a deeply buried neuron that “looped back on itself,” Deisseroth said. That strange bridging is not typical of a normal brain, and it resembles abnormalities associated with autism and Down syndrome.

Much more work would need to be done to explore the implications of that find, which also has been seen in animals, but “it’s not out of the question” that the structure is key to autism, said Deisseroth, a bioengineer who also trained in psychiatry.

Chung said he planned to start his own lab soon and to work on refining the technology. But he pointed out that it was already known that it works on all tissue, not just brains, and can be used to look for structures other than nerve cells.

On his laboratory bench, he said, “I have a transparent liver, lungs and heart.”

Reid agreed Clarity had applications in many fields.

“It could permeate biology,” he said.

Material from the Los Angeles Times is included in this report.

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