$ProjectVersion: Release2-2.16 $ Purkinje tutorial ----------------- 1. THE PURKINJE CELL The cerebellar Purkinje cell is the only output neuron of the cerebellar cortex. It is also among the largest and most complex neurons in the mammalian brain. The about 200,000 synaptic inputs received by each Purkinje cell constitute the most massive synaptic convergence found on any neuron in the brain. Purkinje cells are also distinguished by high densities of calcium channels on their dendrite which cause them to easily fire dendritic calcium spikes. The synaptic input to Purkinje cells comes from multiple sources, four of which are explicitly represented in this model: - excitatory input from cerebellar granule cells over their parallel fiber axon. A Purkinje cell receives more than 150,000 such parallel fiber inputs onto the spiny dendrite (thin dendrites). Both 'background' (i.e. continuous random) and synchronous parallel fiber inputs can be given. - excitatory input from the inferior olive by the climbing fiber input. Each Purkinje cell receives only ONE climbing fiber input, which is only rarely activated. The single climbing fiber makes multiple synapses on the smooth dendrite (i.e. the thicker parts of the dendrite). Only synchronous activation is possible. - inhibitory input from the cerebellar stellate cells onto most of the dendrite. Only 'background' stellate cell inputs can be simulated. - inhibitory input from the cerebellar basket cells onto the proximal smooth dendrite and soma. Only synchronous activation is possible. 2. MODELING A PURKINJE CELL A good general introduction of the model can be found at http://www.tnb.ua.ac.be/publications/pub009/TNB_pub9.shtml, and many other of our publications about this model are also available. A general overview of the model scripts can be found at http://www.tnb.ua.ac.be/models/PM9.shtml This is a compartmental model. The detailed dendritic geometry of the cell is based on morphological data provided by Rapp, Yarom and Segev which is replicated by 1600 electrically distinct compartments. These are divided in three functional zones: the soma, the main dendrite and the rest of the dendrite. Ten different types of voltage dependent channels are modelled, 8021 channels in total, using Hodgkin Huxley-like equations based on Purkinje cell specific voltage clamp data or, when necessary, on data from other vertebrate neurons. The soma possesses fast (NaF) and persistent (NaP) sodium channels, low threshold (CaT) calcium channels, and delayed rectifier (Kdr), A-current (KA) and non-inactivating (KM) potassium channels, and an anomalous rectifier (h1 and h2). The dendritic membrane includes P-type (CaP) and T-type (CaT) calcium channels, two different calcium-activated potassium channels (BK and K2) and a non-inactivating potassium channel. The P-type calcium channel is a high-threshold, very slowly inactivating channel, first described in the Purkinje cell and responsible for the dendritic calcium spikes. The changes in calcium concentration caused by voltage-activated calcium influx is computed in a submembrane shell. 3. THE INTERFACE When the simulation is first run, three windows pop up: the first window contains a picture of a typical Purkinje cell with buttons on the right for options on the graphical output. Beneath the window with the Purkinje cell is a control panel to do several types of experiments. The Output Menu, to the right of the Simulation control panel, allows you to select what graphs will be displayed. a. Buttons in the control panel The buttons in the Simulation control panel fall into three categories : 1. Buttons for Simulation control: standard GENESIS simulation control RESET Resets the simulation and clears the graphical output (unless in overlay mode, see below). RUN Initiates the simulation and performs a simulation run for the time as given in the time dialog. STOP Stops the current simulation (if any) QUIT Quits the simulation (and GENESIS). Time (default : 500 msec) Sets the total time in milliseconds to be simulated during one run (after clicking the 'RUN' button). Output rate (default : 10) Sets the output rate for the graphical output relative to the simulation time step (which is 0.020 msec). The default rate of 10 means that only once every 10 steps the Purkinje cell picture is updated. Output mode : Normalized / Absolute Toggle between Normalized (default) or Absolute values. For channel types only. In the Normalized output mode the conductance or current is normalized relative to the surface area of the compartment, this allows you to compare relative activation levels between different compartments (the units are arbitrary). In the Absolute output mode the real values are shown in Amperes (current) or Siemens (conductance); these are typically much larger for large compartments so that changes in smaller ones might not be discernible. 2. Buttons for Simulation mode: Purkinje cell simulation experiments (Depending on the cell that you are simulating, some of the experiments may not be available. The following applies if you are simulating the 1994 Purkinje cell model of Erik De Schutter.) Toggle In vivo - In vitro (default : In vitro) This toggle switches between In vitro mode (where there is no background input from stellate cells or parallel fibers) and In vivo mode. The Settings window let you set the mean firing frequency for stellate (inhibitory) cells and parallel (excitatory) fibers. The Settings are only available for the 'In vivo' mode. Current injection (default : on, constant current of 0.5 nA) This is a toggle which switches between simulated current injection directly into the soma or not. In the Settings window the current level (in nano amperes) can be set and a choice must be made between constant or current pulses. The current pulses are generated with a pulsegen object. Activate parallel fibers Hitting this button activates excitatory synaptic input from a specified number of parallel fibers. In the Settings window you can choose the number of parallel fibers that will be activated and the relative synaptic strength of each. You can also toggle between activating parallel fibers uniformly distributed over the whole dendritic tree (default) or activating parallel fibers locally on one specific branch of the tree. In the latter case the number of synchronous activated parallel fibers synapses is preset to 20, for distributed activation the number of activated synapses is cut to a multiple of 25 with a maximum of 475. You can choose the branch that will receive local activation by clicking the button 'Change area from xcell'. Then click anywhere on the spiny dendrite of the Purkinje cell, the name of the selected branch will be updated. Activate basket axon Hitting this button activates inhibitory input from the basket axons that are wrapped around the main dendrite (the thicker dendrite directly attached to the soma) and the soma. The Settings window let you set the relative synaptic strength of all contacts. Activate climbing fiber Hitting this button activates excitatory synaptic input from the climbing fiber that makes strong synapses on the main and thick dendrites. The Settings window let you set the relative synaptic strength and the delay between consequent climbing fiber synapses (so it defines the actual speed of signal transmission within the climbing fiber axon). 3. Buttons for Simulation information HELP Shows you this information CREDITS Shows authors and contributors b. Output windows There are many output windows: the windows with the picture of a Purkinje cell (the cell viewer), and multiple graph windows that are not visible when the simulation is first started. The cell and graph windows can be displayed or hidden by clicking the appropriate toggle buttons in the output menu. The use of the graph windows is explained in further detail below. 1. The cell output window (Depending on the cell that you are simulating, some of the output modes may not be available. The following applies if you are simulating the 1994 Purkinje cell model of Erik De Schutter.) The cell output window displays the value of a calculated variable by changing the (rainbow) color of the compartment the variable belongs to. Red means a high value, blue means a low value. The default is to display the compartmental voltage. It is possible to display the calcium concentration or the conductance or current for all the types of channels implemented in this Purkinje cell model. If a channel or value is not present in a compartment, a default of zero is used. You select the output type by clicking one of the buttons to the upper right of the cell output window. The simulation will stop (simulation time is reset to zero) and GENESIS will take some time to change all the display messages. The name of the selected variable will appear above the cell and the range of values displayed is shown below the cell (Color maximum or minimum). The tutorial automatically selects an appropriate range for each variable, but you can change this if desired. For the channels (the synaptic Exc. chan. or Inh. chan, or the voltage-gated CaP, CaT, K2 and so on), an additional choice can be made between channel conductance (Gk button, the default), channel current (Ik button) and for the CaP or CaT channels the reversal potential (Ek button; for the other channels this is constant). Channel conductance and current can be shown as Normalized values (default) or Absolute values. For the other possible outputs (compartmental voltage, concentration) there are no further options. Buttons : Comp. Vm Output compartmental voltage (in volts). Comp. Ca Output compartmental calcium concentration (in milli molar). Exc. chan. Output excitatory synaptic channels. Inh. chan. Output inhibitory synaptic channels. CaP, CaT, ... h1, h2 Output different channel types. h1 and h2 are two components of the same anomalous rectifier current. Ik, Gk, Ek Output current (in Amperes or aribitrary units), conductance (in Siemens or arbitrary units) or reversal potential (in volts) of a channel. These buttons are only available if the main output for the cell is a channel type. Electrodes / No Electrodes Toggle between hide (default) / show the recording electrodes in the cell window. Compartment Namer The compartment namer allows to figure out the name of compartments by clicking on the dendritic tree of the cell. Color maximum and Color minimum Set the color scales for the cell display. Updated automatically when a different output is selected. 2. The graph output windows The graph output windows are used to plot membrane potential (Vm) and Calcium concentration (Ca) of selected compartments, and channel current (Ik), conductance (Gk), or reversal potential (Em) for a specified current in the compartment. The current is selected with the buttons under "Possible outputs" in the cell window, as described above in the section on the cell output window. After a click on a compartment in the cell view, each graph will do a best effort attempt to add a new plot for the selected compartment. If the selected current does not exist in the compartment, or none was selected, the graph windows for Ik, Gk, and Em will indicate that this output does not exist. Buttons : Clear graph Clear the graph and remove all recording sites for this graph. This should be done after changing to a different output in the cell window. Then, it is necessary to re-select the compartments to be plotted. Overlay off / on When a reset is performed, normally all plots are cleared. When overlay is on, they are saved so that you can compare plots from different runs. Set scales Allows to set the range of the axes of the graph. The graph is automatically scaled for the type of the first recording site selected. Reset axes Resets the axes to their default values. The default values are taken from the current active variable in the cell view. If this is not appropriate, push the 'a' key, when the mouse cursor is over the graph to rescale the graph such that all plots fit in the graph. Next rescale the axes of the graph, using the zoom functions of Xodus : click below the X axis or next to the Y axis to select the region of interest. Note that an appropriate scale is needed to show low amplitude oscillations. 3. Ascii plots The output menu allows to save a variable to a file. First put the cell view in the appropriate mode, next click on the cell's dendrite to save the variable for the clicked compartment to an ascii file. The directory where the ascii file is saved is 'simulation_sequences/Purkinje/' and the name of the file is chosen to match the variable name and the compartment name (note : this implies that if you choose the same variable twice, the second file will overwrite the first file).