sCRACM: ChR2 circuit mapping

As has become a hallmark of the Svoboda lab, this new paper in Nature (advance online publication) combines several cutting edge technologies (rAAV-delivered ChR2, most prominently, and 2-photon 1-photon laser stimulation) to do some interesting synaptic physiology.

The subcellular organization of neocortical excitatory connections : Article : Nature.

They used ChR2 (with TTX and 4-AP to block action potentials) to find where on the dendritic tree particular inputs synapsed onto L3 and L5 cells and to measure the strength of those inputs. ChR2 depolarizes the input axon locally (60um spot diameter) at points of (potential) axodendritic contact. If you’ve heard the term “potential synapse” before, then think of this technique as a way of checking potential synapses and seeing if there really is an actual synapse there.

The technique allowed them to map on a L3 barrel cortex pyramidal cell where different thalamic inputs (VPm, POm) and cortical inputs (M1, barrel L2/3, barrel L4):


sCRACM stands for subcellular ChR2-assisted circuit mapping.

4 thoughts on “sCRACM: ChR2 circuit mapping

  1. I always wonder how practical using these light activated proteins would be in human subjects. Gene therapy has quite a few hurdles to overcome. So I have my doubts as to whether it will be used much outside of the lab as an actual therapy for brain disorders. Recently researchers have used infrared light to stimulate brain cells, without the need for gene therapy. Also ultrasound pulses can non-invasively stimulate the brain. It should be interesting to see what happens as these new neurotechnologies mature.

    Check out my neurotechnology blog for more information about brain stimulation topics.


  2. This is not a two-photon technique. Action potentials are very difficult to generate using two-photon excitation of ChR2. Plus, with a 60um spot size, the light would be far too diffuse to activate anything. It’s a one-photon technique. We plan to have an in-depth write up on Brain Windows in the coming week.


  3. Andrew, thanks for the correction. I’m not sure how that slipped in there… I have heard from multiple sources here at BCS that 2p ChR2 stimulation is very difficult. Do you think fancy spot scanning techniques might change this? Or is it simply a fundamental problem (need to depolarize simultaneously many channels, with a long-ish minimum dwell time, etc.)?

    I will look out for the Brain Windows post. 🙂


  4. Spot scanning techniques work in culture, barely. They are totally impractical in vivo and I don’t expect that to change. The new bistable ChR2 switches on the other hand might do better. One could even imagine having granular control of tonic spike rates by scanning across a fraction of a neuron expressing bistable ChR2. I’d like to see someone try that experiment, it’s trivial.

    I’m trying to get Petreanu to do a writeup of sCRACM, my time available for blogging has plunged since switching over to Karel’s lab. 😛


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