Newly found CLARITY

Most of us would receive the news of not getting a grant with dread and frustration. Yesterday, finding out I did not get to the second round of the Marsden Fund actually made me feel good. There is a sense of satisfaction about getting funded to do the work I want to do, but at the same time, it does not leave a lot of room to explore new ideas or follow side-tracks that might look interesting.  And it is this serendipity of discovery that I always loved about science. So I am looking at this as an opportunity for a sort of sabbatical during which I plan to go down my “need to explore this further” list “.The first thing I am going to do is try to explore this CLARITY[1] method.

One of the problems with studying the brain is that the neurons are small and have a rather complex architecture. To be able to look at neurons under the microscope, we need to cut the tissue into small slices, thin enough to let the microscope light go through. But neurons don’t seem to care much about the limits of optical physics, and tend to have dendrites and axons that usually don’t fit in each of those single slices. The task then is to try to reconstruct the shape of the neurons and follow their axons by mapping the bits and pieces from serially adjacent slices. I tend to enjoy that work, but it is terribly tedious and time consuming. Another problem with classical histology is that to be able to render the tissue transparent we need to get rid of the fat. Look up almost any paper using classical histology for the light microscope and you will find the typical sentence “the tissue was dehydrated, placed in xylene and covesliped” or something to that effect. The main reason to take the water out of the tissue is to be able to put it in xylene so that we can get rid of the fat. Silverbacks like me call that clearing. This step makes the tissue optically transparent. But even then, there is a limit on how thick the sections can be because to actually “see” the cells they need to be stained with something or other – either a general dye that stains all cells or more specific chemicals that label particular components of the cells (like a  membrane protein or part of the cytoskeleton). These chemicals need to diffuse through the tissue to stain the right structure and that places a limit on the thickness.

Enter the scene Kwanghun Chung and the rest of the CLARITY team [1]. They found a way of removing the fat from the tissue so as to increase the tissue permeability of labeling molecules and also letting light go through thick slabs of tissue. But they needed to remove the fat, which helps hold the tissue together, without letting the tissue fall apart. So the first thing they did is “fix” the non fatty part of the tissue using a hydrogel that holds the non-fatty parts of the cell together. Once the fats are removed from the tissue, light can get through and chemicals can diffuse well. They show results of their technique in a young mouse brain – and the results are remarkable indeed.

CC-BY-SA Heather Katsoulis on Flikr

So my part of my unfunded-mini-sabbatical-time will be spent trying to see if I get CLARITY to work in my lab. This technique is science hacking at its best and I can think of heaps of things I’d like to do with it.

Perhaps not getting funded is a bit of a blessing. We spend a lot of time writing grants, then even more operating the grant, training and supervising staff, writing reports, balancing financial sheets, and doing what we promised to be doing in the grant. A colleague of mine always reminds me that we need to reinvent ourselves as scientists at least every three years . I think he is right – every now and then we need to remove the shackles of what we do and explore other directions. So, I will take this mini-unfunded-sabbatical just to try to do that. Taking John Pickering’s words slightly out of context:

…science at its best is not shackled but free to explore and expand.  Science by its very nature is at a frontier and a journey into lands unknown.  A pathway cannot be chosen for it and any attempt to do so will as often as not go straight past the pot of gold.

Back to the roots. Back to doing some un-shackled  science.


[1] Chung, K., Wallace, J., Kim, S.-Y., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., … Deisseroth, K. (2013). Structural and molecular interrogation of intact biological systems. Nature, advance online publication. DOI 10.1038/nature12107

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