Ordinarily, when scientists want to see specific cells within a piece of biological tissue, they first have to remove that tissue from the body, slice it very thin, then examine those two-dimensional slices using a microscope. Imagine, though, if the tissue could be made transparent – seeing tagged cells within it would be sort of like looking at three-dimensional bubbles inside an ice cube. Well, that's just what a team at Caltech have done using a technique known as PARS, or perfusion-assisted agent release in situ.

PARS is an extension of the Caltech-designed CLARITY technique, which has previously been used to render the brains of lab mice transparent. It does so via a process in which the brains are infused with detergents that dissolve lipids – lipids are molecules within cells that provide them with structural support, but which also block the passage of light through those cells. A clear polymer hydrogel is additionally introduced, to replace the now-lacking structural support.

This is also the principle behind PARS, although in its case, the detergents and hydrogel are quickly diffused throughout a dead mouse's entire body via its circulatory system. After the liquids are injected into its bloodstream, most of the animal's major organs become completely clarified within two to three days, with the brain and the rest of the body taking two weeks.

Molecules such as DNA are left intact, and cells of interest can either be pre-tagged with genetically introduced fluorescent proteins, or marked with dyes after the "tissue-clearing" process has been performed. In cases where it isn't necessary to clarify the whole body, a variation on PARS known as PACT (passive clarity technique) can be used on individual organs within it. In either case, the cells can be imaged within the transparent tissue using standard microscopy techniques.

A 3D visualization of fluorescently-labeled kidney cells within intact kidney tissue (Image: Cell, Bin Yang, Viviana Gradinaru)

Along with its potential for use on animal models, the technology has already been utilized to view the distribution of individual tumor cells within a human skin tumor.

"I think these new techniques are very practical for many fields in biology," said assistant professor of biology Viviana Gradinaru, who led the research. "When you can just look through an organism for the exact cells or fine axons you want to see – without slicing and realigning individual sections – it frees up the time of the researcher. That means there is more time to the answer big questions, rather than spending time on menial jobs."

A paper on the research was recently published in the journal Cell.

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