Characterize model network components with CellClamp

Here, we walk through how to characterize basic components of the model using the Cell Clamp tool. This tool can characterize ion channel dynamics, single cell intrinsic properties, and synaptic connections in common experimental terms. This tutorial shows each of these characterizations using the CA1 network.

  1. From the SimTracker Tools menu, choose ’Cell Clamp’. The Cell Clamp tool will open.
  2. Within Cell Clamp, first, scroll through the table of ion channels to find the entry for Nav, or the voltage-gated sodium channel. Fill out the entries for this row in the table, entering a Gmax (maximum conductance density) value of 0.001 (micro Siemens per square centimeter) and an ENa (reversal potential) value of +55 (mV). The variable used to store the reversal potential for this channel, ena, has already been populated in the table.
  3. Next, click the checkboxes to the right of the ion channel table, for ’IV Curve’ and ’Act./Inact.’. Then, click the ’Conductance’ radio button below them so that the results will display in terms of ion channel conductance rather than current.
  4. Then, click the ’Get Results’ button below. A dialog box will appear, asking the user to add comments for this particular characterization run. Enter ’Characterize Nav channel in conductance terms’ and then click ’OK’. It will take a little while for the characterization simulations to complete before the result figures appear. Because the Nav row in the table was filled out, the CellClamp will run an activation/inactivation curve and a current/voltage relation for the Nav channel and display the resulting graphs in terms of channel conductance.
  5. Next, prepare CellClamp to run a simulation at the single cell level rather than the macroscopic ion channel level. Uncheck the ’IV Curve’ and ’Act./Inact.’ checkboxes so that these protocols will not run again, and instead check the ‘Current Clamp’ checkbox to the right of the list of cells (in the middle of the tool).
  6. Check the popup menu above the list of cells and set it to the ‘cellnumbers_100’ dataset. All the cell types included in that dataset will populate the list of cells below.
  7. From the list of cells, click to select the ’pyramidalcell’ cell type.
  8. Set the current clamp protocol to be applied to the selected cells. The top row of numbers gives the time before the pulse is applied, then the length of the pulse, followed by the time after the pulse has finished that the cell behavior continues to be recorded. The row below gives all the current injection (or voltage clamp) levels that will be used. Note that MATLAB’s vector syntax can be used to specify which currents to apply. For example, rather than listing -0.300, -0.250, -0.200, -0.150 ... all the way up to +0.500, users can specify that every current injection level between -.300 nA and +.500 nA should be tested, increasing in steps of 0.050 nA, with the following syntax: [-0.300:0.050:0.500]. Users can also add additional values to use before or after that syntax within the brackets: [-0.500 -0.300:0.050:0.500 0.510 0.540 0.580 0.600]. For this tutorial, leave the row of times alone but change the current list to say: [-0.3:0.05:0.5].
  9. Now click ’Get Results’ and enter into the comments dialog that appears ’Single cell characterization’. After a few moments, several figures will appear, characterizing the cell’s behavior. Note: For even more in-depth characterization, the results of this CellClamp protocol can be loaded into the CellData tool to compare the model cell’s properties directly with those of experimental cells.
  10. Next, prepare the CellClamp tool to run a paired recording rather than a single cell recording by unchecking the ’Current Clamp’ checkbox in the single cell section.
  11. In the lower left area of CellClamp, set the popup menu to ‘syndata_120’ to populate the synapse list below with all synapses listed in that dataset.
  12. From the synapse list, select the pvbasketcell -> pyramidalcell entry to characterize connections from PV+ basket cells to pyramidal cells.
  13. Click the current clamp checkbox to apply a current clamp to the postsynaptic cell in the pair (the pyramidal cell), and to the right of the checkbox, enter ’0’ (nA) into the current injection box so that the cell’s response to the incoming synaptic activity will be recorded relative to its baseline resting potential.
  14. Above the current injection amount, the row of boxes indicated relevant times for the paired recording protocol: 15 ms after the recording starts, the presynaptic cell will spike, triggering the synaptic activity in the postsynaptic cell after a short delay due to axonal conduction. The next entry, 100 ms, shows the length of time to record the postsynaptic cell’s response after the presynaptic spike. For most current clamp of synapse types, 100 ms is adequate; only for slow synapses such as those with GABAB would the recording window need to be longer in a current clamp paired recording.
  15. Finally, click the ’Get Results’ button and for the comment dialog, enter ’Synaptic recording’ and then click ’OK’. The CellClamp will now perform 10 paired recordings of the synaptic connection using the protocol specified, and then will average the results. It will then display a graph of the individual recordings and the averaged recording, along with the time constants and amplitude of the synaptic connection computed from the averaged trace.

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