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GEN News Highlights : Apr 11, 2013

Studying the Brain: Hold the Fat

Scientists report that they can now study the brain’s finer workings while preserving its 3D structure and integrity of its circuitry and other biological machinery. A new method called CLARITY, developed by NIH-funded researchers, opens the intact postmortem brain to chemical, genetic, and optical analyses that previously could only be performed using thin slices of tissue. By replacing fat that normally holds the brain’s working components in place with a clear gel, they made its normally opaque and impenetrable tissue see-through and permeable. This made it possible to image an intact mouse brain in high resolution down to the level of cells and molecules. The technique was even used successfully to study a human brain.

Until now, to gain access to deeply buried structures and achieve high enough resolution to study cells, molecules, and genes, researchers had to cut brain tissue into extremely thin sections, deforming it. Loss of an intact brain also makes it difficult to relate such microlevel findings to more macro-level information about wiring and circuitry, which cuts across slices.


The team, led by Karl Deisseroth, M.D., Ph.D., of Stanford University, infused into the brain a high-tech cocktail, including a plastic-like material and formaldehyde. When heated, it formed a transparent, porous gel that biochemically integrated with, and physically supported, the brain’s working tissue, while excluding the lipids, which were safely removed via an electrochemical process. The result was a brain transformed for optimal accessibility.

They called the new method Clear Lipid-exchanged Anatomically Rigid Imaging/immunostaining-compatible Tissue Hydrogel—or CLARITY, for short.


In a series of experiments using CLARITY in the mouse brain, the researchers demonstrated that, for the first time, standard immune- and genetics-based tests can be performed repeatedly in the same intact brain. Tracer molecules, such as antibodies, can be readily delivered for staining tissue, or removed, leaving brain tissue undisturbed.

The researchers found that CLARITY outperformed conventional methods across a range of previously problematic technical challenges. When they used CLARITY to analyze a postmortem human brain of a person who had autism, even though it had been hardening in formaldehyde for six years, they were able to trace individual nerve fibers, neuronal cell bodies, and their extensions.

“CLARITY will help support integrative understanding of large-scale, intact biological systems,” says Dr. Deisseroth. “It provides access to subcellular proteins and molecules, while preserving the continuity of intact neuronal structures such as long-range circuit projections, local circuit wiring, and cellular spatial relationships.”

The paper was published yesterday in Nature, titled “Structural and molecular interrogation of intact biological systems”.