Copyright © 2020 Alijevic, Bignucolo, Hichri, Peng, Kucera and Kellenberger.
Creative Commons Attribution License CC BY.
The use, distribution or reproduction must be made in compliance with the terms of the CC BY license while citing the following article:
Alijevic O, Bignucolo O, Hichri E, Peng Z, Kucera JP and Kellenberger S (2020)
Slowing of the Time Course of Acidification Decreases the Acid-Sensing Ion Channel 1a Current Amplitude and Modulates Action Potential Firing in Neurons.
Front. Cell. Neurosci. 14:41.
doi: 10.3389/fncel.2020.00041
The MATLAB code in this folder assumes MATLAB version R2018b or higher, but the code also works with earlier versions (tested up to 2015b).
The published simulations were run on a MacBook Pro 2018 using the 10.12.6 OS and Matlab R2018b.
Minor numerical differences may result when using another configuration (e.g., processor, operating system, MATLAB version).
This MATLAB code reproduces Fig. 5A of the article.
Fig. 5A displays the neuronal response to a pH ramp of 1 s duration.
The parameter controlling ramp duration is SimRamp. (default 1153 for 1 s).
The previous version of this code, used in the article and deposited on Zenodo, contained an alkaline shift of 0.15 pH units of the steady-state desensitisation curve. We have recently found out that this shift was not correct, and that it needs to be removed from the code. In the corrected version of the code provided here, this shift is therefore set to 0.To examine model behaviour with vs. without the shift, the value of the shift can be set explicitly to 0.15 or 0 in line 13 of the function "f_HH_ASIC.m .
Calculations of the model predictions shown in the article by Alijevic et al. in Figs. 4C-G, 4J-K, and Fig. 9A-B were recalculated with the shift set to 0, and the values obtained with the two conditions are provided in the excel file Model_pred_shift.xlsx. For the heat maps of Figs. 4J-K and 9A-B, two pH conditions (end pH 6.6 or 6.0) were calculated for all durations of fall time of these figures, corresponding therefore to two vertical columns in each of these figures. This analysis showed that the influence of the shift on the model predictions is rather small. We recommend however to use the corrected version of the code provided here.
To run the program, simply open the file "HHNeuronModelWithASIC.m" in MATLAB and run.
Make sure that both HHNeuronModelWithASIC.m and f_HH_ASIC.m files are located in the same folder.
File Summary:
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File Name Description
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README.txt This file
HHNeuronModelWithASIC.m Script computing the neuronal response upon application of a pH ramp
f_HH_ASIC.m Function returning ASIC gating parameters as a function of pH
Model_pred_shift.xlsx Results of calculations with the model, carried out with shift =0 or =0.15.