SM_EmEx2_data

Excitability – a threshold governed transient in trans-membrane voltage – is a fundamental physiological process that controls the function of the heart, endocrine, muscles and neuronal tissues. The 1950's Hodgkin and Huxley explicit formulation provides a mathematical framework for understanding excitability, as the consequence of the properties of voltage-gated sodium and potassium channels. The Hodgkin-Huxley model is more sensitive to parametric variations of protein densities and kinetics than biological systems whose excitability is apparently more robust. Ori et al (bioRxiv 10.1101/766154, 2019), experimentally examined functional relations in the Hodgkin-Huxley parameter space, by assembling excitable membranes using the dynamic clamp and voltage-gated potassium ionic channels (Kv1.3) expressed in Xenopus oocytes. Their analysis is based on a theoretically derived phase diagram (Ori et al, PNAS 201808552, 10.1073/pnas.1808552115, 2018), where the phenomenon of excitability is reduced to two dimensions (S and K) defined as combinations of the Hodgkin-Huxley model parameters.

The Archive.zip set contains HDF5 dynamic clamp data files of Kv1.3 injected Xenopus oocytes, described in Ori et al (2019). In each data file, the n-th trace is stored in "/Trialn/Synchronous Data/Channel Data", containing lists of 4 numbers: {scaled voltage, scaled current, maximal sodium conductance, \alpha-m}. Traces of voltage responses may be extracted from the first column; the S–K phase diagram coordinates are determined by the second two columns (fixed throughout a trace), given the measured maximal Kv1.3 conductance (gKmax, mS/µF) below:

file 170208_K1_random, gKmax =0.65
file 170208_K2_random, gKmax =0.55
file 170208_K3_random, gKmax =0.64
file 170208_K4_random, gKmax =0.52
file 170223_K1_random, gKmax =0.74
file 170608_K1_random, gKmax =0.61
file 180308_K1_random, gKmax =1.54
file 180517_K1_random, gKmax =1.04
file 180530_K3_random, gKmax =1.30

Example Mathematica (Wolfram Research, Inc.) script to extract trace number 220 from file "170208_random_K3.h5", calculate S–K coordinates and plot the voltage response:

filename = "170208_random_K3.h5"
trial = 220
trialNumber =
"/Trial" <> ToString[trial] <> "/Synchronous Data/Channel Data"
spike = Import[filename, trialNumber];
s = spike[[ 1, 3]]/( spike[[ 1, 3]] + gKmax)
k = 2/(3 + spike[[ 1, 4]])
ListLinePlot[spike[[All, 1]]/10]