Cell Types Lesson Background

Background

Targeting different cell types

How did the Allen Institute actually distinguish between different cell types? To do so, they capitalized on the fact that different cells in the brain often express different genes. With genetic engineering, we can express glowing proteins (such as green fluorescent protein) in cells that express a specific gene. This approach takes advantage of an enzyme called Cre recombinase, which is found in bacteriophages, but not mammals. When we artificially express Cre recombinase in a specific cell type and include LoxP sites around our glowing protein, the Cre recombinase comes and flips those LoxP sites around, leading to protein expression and a gorgeous glowing neuron. This system is called the Cre-LoxP system and is one of the main tools that neuroscientists use to identify and target specific cells in the brain. You can learn more about the Cre-LoxP system here.

Whole-cell patch clamp

In order to listen to neurons, the Allen researchers guided glass electrodes towards their glowing neurons under a microscope. Instead of poking into the cell to listen to it, they lowered the electrode very close the cell, and created a tiny bit of suction to break the cell membrane. As a result, the internal cell space becomes continuous with the electrode and enables really clean recordings of the cell's activity. This technique is called whole-cell patch clamp. It's a tough technique, but one that has proven irreplaceable in our understanding of how cells communicate. You can watch a virtual tour of the Allen Institute's patch clamping here.

Characterizing the electrophysiology of cells

You'll find many different metrics which describe what happened when the Allen researchers stimulated and recorded from different cells. Let's breakdown what a few of these properties are actually measuring:

• vrest: resting membrane potential

• upstroke-downstroke: ratio of action potential upstroke to downstroke

• adaptation: the rate at which firing speeds up or slows down during a stimulus

• avg_isi (average ISI): the mean value of all interspike intervals in a sweep

• trough_v_short_square: minimum value of the membrane potential during the after-hyperpolarization in response to a short square input

If you're curious about the other metrics you see, there is a full glossary here. You can also check the detailed Allen Institute for Brain Science Documentation.

Cell Types Lesson Roadmap