So far you have learned that the brain can be segmented into its parts at the coarsest level based on obvious anatomical markers and structures. At the histological level we can look a differences in cellular organization to differentiate finer structures within brain regions. Histological stains, such as Nissl stains are useful for looking at some of the microarchitecture of the brain as shown in this coronal section through the hippocampus and cortex of a rat. Towards the bottom you can see that cells cluster into specific hippocampal regions, and in the upper part of the image you can make out (barely) the various layers of the cortex.

Source: Brainmaps.org

Within a brain region we can also use neuronal structure to classify cells by shape, like we did in the previous exercise. For example, look at this drawing by Cajal of the various cell classes he found in the hippocampus. Notice that you immediately perceive a much greater richness in the diversity of cell classes than one would appreciate with a Nissl stain.

Cajal's view of the hippocampus

However, the diversity of cell types is even greater than that. For a group of cells in one brain region, even if they look similar and are classified as one cell types, there may be several layer of hidden diversity within them. For example, some cells may receive inputs from specific brain regions, or send their axons to different targets. In order to appreciate this level of diversity, we need to look at the level of gene expression.

Even though all the cells in your body contain the exact same DNA, they only express a specific subset of those genes based on their function. So liver cells will express genes required for glucose metabolism, neurons will express genes for ion channels and white blood cells will express genes for making cytokines. And even within the nervous system gene expression is unique among different classes of neurons, even neurons that look the same and inhabit the same brain region. The genes that a cell expresses will specify what the cell does, for example what neurotransmitters it makes, what receptors it has, or what the shape of its dendrites will look like. Thus, if we are able to look at the different genes a cell expresses, we can further classify this cell based on even finer criteria. One of the most remarkable examples of this is a technique called Brainbow. Jeff Lichtman and Joshua Sanes, researchers at the Harvard Center for Brain Science, have created genetically modified mice that express the genetic machinery to randomly mix green, cyan and yellow fluorescent proteins in individual neurons thereby creating a palette of ninety distinctive hues and colors. The specific hue a cell will express will depend on the specific genes that a cell normally expresses, giving you an incredible view of the diversity of gene expression within a brain region. Compare this Brainbow view of the hippocampus with the previous two.

brainbow2.1.jpg

Brainbow view of the dentate gyrus of the hippocampus.

Click source for more pictures: http://cbs.fas.harvard.edu/science/connectome-project/brainbow

In the case of Brainbow, expression of a specific combination of colors is random, and not very informative about a specific class of cell. Another approach is to use a technique called in situ hybridization to label cells in brain slices that express a specific gene. This is the approach that was taken by the Allen Brain Institute, to generate the Allen Gene Expression Atlas. Basically, they took a bunch of fixed mouse brains and made thin slices through the entire thing. Then, they went through the entire mouse genome and looked for which cells expressed each gene in the mouse brain. They then photographed and uploaded all of these slides and put them in a free online browser! Using a similar approach, they've done this with human brains and developing mouse and human brains too. In this exercise you will learn to use the Allen Brain Atlas to investigate the cells and brain regions that express a gene of interest. You will then identify one of these brain regions and learn to figure out which other brain regions it connects to. Go to the next page to begin the exercise!