Maping The Brain:

Source: http://www.ted.com/talks/allan_jones_a_map_of_the_brain.html

In this presentation, Allan Jones from the Allen Institute for Brain Science, describes an endeavor to map the expression of individual genes in spatial regions. The complex process relies slicing the brain into very thin slices, mapping the gene expression in each slice and then digitally reconstructing each slice into a composite of the whole brain.

The presentation begins by describing the incredible complexity of both our brains and our genome. The presentation includes a visually satisfying animated journey from the surface of the brain all the way down to a look at the individual chromosomes. Next, he describes the process of collecting brain samples. In order to be a viable candidate for the study, the brains must be collected within 24 hours of death, have died a natural death between the ages of 20-60 with no brain damage, no psychiatric issues and no history of drug use. Once the sample are collected, the are frozen and shipped to their labs. They are sliced into 20 micrometer thick slices, stained and placed on to slides. The slides are examined under a microscope and further subdivided by layers of cells. A laser automatically cuts out the regions marked by the technician and separates them into samples. Using a process just like learned in engineering biology, the mRNA is purified from the sample and fluorescently marked. A microarray is then used to determine which genes are being expressed in that region of the brain. 1000 slices of the brain are taken, each slice provides 50,000 data points resulting in 50,000,000 data points per brain. The data from each small slice is digitally recombined and superimposed onto an MRI taken of the brain before it was sliced up. The result is The Allen Brain Atlas, a 3D map of the expression of individual genes in the brain. The 3D model is color coded for particular genes, can be rotated in scaled in 3D and can be subdivided into cross sections. The Brain Atlas is free and open to the public and any researcher. So far only two brains have been fully mapped but more are on their way. Analysis of the similarity of expression between the two brains reveals that they are almost 90% similar. The Atlas brings us one more step closer to understanding how the brain works, the complex interactions between gene expression, how gene expressions is controlled and factors that effect and, and how different regions of the brain are linked. The Brain Atlas also has numerous potential uses in the pharmaceutical and drug industry by providing a tool scientists can use to target drugs to affect particular regions or proteins in the brain. Or, if they have identified a drug that affects a particular region of the brain by acting on a particular protein, the can see which other regions of the brain will also be affected by the drug by identifying where else in the brain the gene that codes for that protein is active. The uses for the Brain Atlas are many and even more are likely to developed in the future.

This picture is an example of color coded regions of the brain being projected onto an MRI. The colors represent different functional regions of the brain identified by Neurologists. The Brain Atlas works in a similar way.