Zoology 421 Neuron simulations:

Exercise 8: Simulation of a cortical pyramidal neuron

PLEASE PRINT OUT THESE PAGES FIRST AND THEN KEEP THE PRINTED TEXT BESIDE YOU AS A GUIDE WHEN YOU LOAD AND RUN "NEURON". THIS WILL SAVE YOU HAVING TO JUGGLE BETWEEN NEURON AND NETSCAPE WINDOWS ONCE YOU HAVE THE SIMULATION LOADED.

To begin working with this chapter you should have downloaded and installed Neuron, as described in Chapter 1.
 
Preparing for the simulation: This simulation brings together all of the concepts presented in Exercise 1 through 5. Load the simulation.
This simulation of a  "real" nerve cell is offered to demonstrate some features of synaptic integration and impulse generation. For this example we have chosen a cortical pyramidal neuron whose shape was imported into Neuron from a neuroanatomical study. Both the model and some of the language used here to describe it were developed by John Moore and Michael Hines at Duke and Yale universities.

The pyramidal neuron model accepts  two synapses on its many dendrites. A voltage electrode is placed in the cell's soma:

 
 
 

The various graphs and windows that you will see are described below.
 

Hypotheses to be tested and observations to be made:

• When you first run the simulation, you will observe two successive depolarizations produced  by the activation of the two synapses at 1 and 5 ms. Activation of  neither synapse elicits an action potential. Just try moving the synapses around and altering the time interval between their activation  so as to observe the effects on action potential generation of spatial and temporal integration and the effect of distance on synaptic strength and delay. Briefly describe the general rules that seem to govern the effectiveness of the synapses at various positions.
• Try to vary the positions of the two synapses so as to create situations when the neuron:
• (a) only produces an action potential in response to  synapse 1
• (b) only produces an action potential in response to synapse 2
• (c) only produces an action potential when 1 and 2 are activated simultaneously

When you have loaded the simulation you should see Windows arranged as below. Click on the following letters: A  B C D for a description of the function of each Window.
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A and B. These Windows are used to show and alter the position and characteristics of the two synapses.
Click on "Show" to bring down a menu that allows you to switch between viewing the "Shape" of the neuron or the "Parameters" of the synapse:

    In "Shape" (as shown above), clicking on any part of the neuron will move the synapse (blue dot) to that point.

    In "Parameters", the time of onset, amplitude (maximal conductance)  duration (tau) and reversal potential  (e) of the synapse can be modified.

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C.   Graph of  membrane potential (mV) vs time (ms) recorded by a voltage electrode placed in the soma of the neuron

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D.  The Run/Control Box - click on Init & Run to run a simulation.

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