Effects of isoproterenol

Contents

Effects of isoproterenol#

using ModelingToolkit
using OrdinaryDiffEq, SteadyStateDiffEq, DiffEqCallbacks
using Plots
using CSV
using DataFrames
using Dates
using CaMKIIModel
using CaMKIIModel: second, μM
Plots.default(lw=1.5)

Setup model#

sys = build_neonatal_ecc_sys(simplify=true, reduce_iso=true, reduce_camk=true)
tend = 205second
prob = ODEProblem(sys, [], tend)
stimstart = 30second
stimend = 120second
alg = KenCarp47()

KenCarp47(; linsolve = nothing, nlsolve = OrdinaryDiffEqNonlinearSolve.NLNewton{Rational{Int64}, Rational{Int64}, Rational{Int64}, Rational{Int64}}(1//100, 10, 1//5, 1//5, false, true, 0//1), precs = DEFAULT_PRECS, smooth_est = true, extrapolant = linear, controller = PI, autodiff = ADTypes.AutoForwardDiff(),)

Without isoproterenol#

@unpack Istim = sys
callback = build_stim_callbacks(Istim, stimend; period=1second, starttime=stimstart)
@time sol = solve(prob, alg; callback)

  1.041096 seconds (65.98 k allocations: 212.864 MiB, 3.59% gc time)

retcode: Success
Interpolation: 3rd order Hermite
t: 4071-element Vector{Float64}:
      0.0
      0.019333123284849308
      0.09098129546757994
      0.20735582943983855
      0.45611910276862533
      1.0472562928406122
      2.0342667657223696
      3.451776641148454
      6.733792423912806
     12.450117081023194
      ⋮
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 158165.8598019807
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 169611.6642461836
 176342.19489586214
 183684.1140466068
 191258.90946281631
 199427.37350661293
 205000.0
u: 4071-element Vector{Vector{Float64}}:
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 ⋮
 [0.0020427822499612955, 784.5705928361841, 784.9343641366844, 0.006285742961033888, 0.9997476285219717, 0.9996108819600831, 0.0015108660008011888, 0.0024264390093091466, 0.0015675234985916397, 0.0011157701814057516  …  0.13694598688419785, 0.13694596415399624, 0.13694593696562474, 0.13694590539945886, 0.13694586953267518, 0.13694582943940806, 0.13694578519089703, -70.43082440918127, 13607.749833006837, 151185.30233112013]
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 [0.001996646756046244, 784.362779202432, 784.7160349787207, 0.006335401714923246, 0.9997412411483091, 0.999734172546418, 0.0015363302060718079, 0.0024473974939953746, 0.0015810714524005405, 0.0011360309269089165  …  0.13623415561768498, 0.13623388970007247, 0.13623362344661866, 0.13623335680902646, 0.13623308974091072, 0.13623282219770474, 0.1362325541365715, -70.31510224724333, 13545.998515545509, 151247.1533714861]
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i = (sys.t / 1000, sys.vm)
plot(sol, idxs=i, tspan=(100second, 101second), title="Action potential", xlabel="Time (s)")

_images/b190ca3a982f55a403368609cdf6fe61a4533dca62ac65b6a50d883eda173a26.png

plot(sol, idxs=(sys.t / 1000, [sys.Cai_sub_SR, sys.Cai_sub_SL, sys.Cai_mean]), tspan=(100second, 101second), title="Calcium transient", xlabel="Time (s)", ylabel="Conc. (μM)", label=["Ca (SR)" "Ca (SL)" "Ca (avg)"])

_images/f2ae0291809546749ce7b6b2d2d27fb2c92bb674ae2856816276820116c7f0de.png

plot(sol, idxs=(sys.t / 1000, sys.CaMKAct * 100), title="Active CaMKII", label=false, ylabel="Active fraction (%)", xlabel="Time (s)")

_images/87094db655d7faa2b8cc50192c9697906db4e325dd22053b852ae79b24a361ea.png

0.1uM isoproterenol#

prob2 = remake(prob, p=[sys.ISO => 0.1μM])
sol2 = solve(prob2, alg; callback)

retcode: Success
Interpolation: 3rd order Hermite
t: 4138-element Vector{Float64}:
      0.0
      0.019332211071584192
      0.09097534627605569
      0.20734339686524408
      0.4561200538541287
      1.0549952720719427
      2.0687580593126613
      3.5324261824253345
      6.954473747659736
     12.881140201769806
      ⋮
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 157174.07587050938
 162194.01343084572
 168138.29627423352
 174916.26987407374
 181898.84288967986
 189304.81198883272
 197588.1225791665
 205000.0
u: 4138-element Vector{Vector{Float64}}:
 [0.0026, 830.0, 830.0, 0.00702, 0.966, 0.22156, 0.09243, 0.00188, 0.00977, 0.26081  …  0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, -68.79268, 13838.37602, 150952.75035000002]
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 [0.00246109996477572, 829.9585434198331, 830.1479502978362, 0.0068472036120339344, 0.9661946906443825, 0.22198703092009986, 0.09218048699222062, 0.0018222096890642774, 0.009762833375314839, 0.26045565430474177  …  0.12118006281992985, 0.12119663497761278, 0.12121718646328616, 0.12124217405786958, 0.12127196546348169, 0.12130680044052823, 0.12134675555621606, -69.27157622080777, 13838.346581408403, 150952.75679928518]
 [0.002382758683301369, 829.9422438990155, 830.2409658671871, 0.0066990037339929405, 0.9663315006590419, 0.22228882452599166, 0.09200417115231563, 0.0017811002406865244, 0.009763716676849107, 0.26032881924894974  …  0.12123448815456439, 0.12125657408666768, 0.1212817846915382, 0.12131020885887851, 0.12134186045923348, 0.12137666702212292, 0.12141446087873138, -69.58534388478576, 13838.326681500257, 150952.76194966168]
 [0.002249831541002491, 829.9364424528658, 830.4298664467993, 0.0063983355059790605, 0.9666490840575152, 0.22299376432344578, 0.09159274697262061, 0.0016985405358012685, 0.009783000857592001, 0.2603166532077402  …  0.12132652897086686, 0.12134992079665141, 0.12137464276885106, 0.12140056903109953, 0.12142753330789122, 0.12145532836849124, 0.12148370617698084, -70.2425024040955, 13838.282994292276, 150952.77573103318]
 [0.0021239182944550387, 829.9982399691283, 830.6928613527689, 0.0060038545810325245, 0.9671939916127574, 0.22421393887512645, 0.09088324181611296, 0.0015916044910949695, 0.009862701804147046, 0.2607890677215021  …  0.12137592664517363, 0.12139282572293232, 0.1214091612631606, 0.12142480441004644, 0.12143960641561434, 0.1214533998189489, 0.12146599978828718, -71.1550700755306, 13838.215505646505, 150952.80458617522]
 ⋮
 [0.0073146875004273795, 921.3111350424876, 922.8372442673206, 0.00621632953768987, 0.9997563697872119, 0.9995674489205083, 0.0014756873624894675, 0.0023971671168631684, 0.0015486035494228147, 0.001087827177827683  …  0.12690731956341642, 0.1269071553885708, 0.12690698535411543, 0.12690680954319294, 0.1269066280356576, 0.12690644090823658, 0.1269062482346817, -70.59411328190205, 13855.447607237578, 150927.44243962405]
 [0.00722290818564516, 921.4901697334809, 922.9973924318351, 0.0062433363972850256, 0.9997529999609079, 0.9997032071128521, 0.0014892812418353196, 0.0024085528978078563, 0.0015559585586829552, 0.001098556090082494  …  0.12644089018468604, 0.12644072850764165, 0.12644056118440006, 0.1264403882943622, 0.1264402099137888, 0.1264400261159544, 0.12643983697129246, -70.53036749029351, 13820.442136600705, 150962.49883417104]
 [0.007132108627847399, 921.6620339611582, 923.150557185851, 0.006270727254031783, 0.9997495493507649, 0.9997381113366643, 0.0015031331537414113, 0.002420104889598678, 0.00156342418330898, 0.0011095708614125453  …  0.12597799318211722, 0.12597783414482552, 0.12597766966765508, 0.1259774998264211, 0.12597732469394182, 0.12597714434018578, 0.12597695883240992, -70.46599490741474, 13785.406967581663, 150997.58514476087]
 [0.007028583082949953, 921.8514954087509, 923.3186796523768, 0.006302819980298003, 0.9997454633663905, 0.9997449540510915, 0.0015194458293461555, 0.002433645223031485, 0.00157217239732809, 0.0011225355991132883  …  0.12544833103095102, 0.1254481749666311, 0.12544801370186628, 0.1254478473083215, 0.125447675854829, 0.12544749940752703, 0.12544731802999107, -70.39092616937515, 13744.94321311874, 151038.10815449725]
 [0.006915552382464886, 922.0500067523041, 923.4938704460396, 0.006338953528049358, 0.9997408078707524, 0.9997426766644008, 0.0015379203360093734, 0.00244889711467549, 0.0015820251283820395, 0.0011372511426259075  …  0.1248678046342907, 0.12486765205464238, 0.12486749452901216, 0.12486733212471628, 0.12486716490641103, 0.12486699293622192, 0.12486681627386738, -70.30685771446443, 13700.121315694741, 151082.99594042663]
 [0.006804459843946287, 922.2361636601723, 923.6570847387662, 0.006375667093771092, 0.9997360201470834, 0.9997382835800523, 0.0015568059542802523, 0.0024644027648597347, 0.001592046998596164, 0.0011523065215193354  …  0.12429479326782757, 0.12429464424155347, 0.12429449052612665, 0.12429433218447485, 0.12429416927703935, 0.12429400186189714, 0.1242938299948755, -70.22192860931602, 13655.37030331296, 151127.81298682958]
 [0.0066922417332850185, 922.4148307507354, 923.8125540268298, 0.00641403017111655, 0.9997309526599988, 0.9997332832912299, 0.0015766664531288673, 0.002480613061087455, 0.0016025195303765618, 0.0011680748522190849  …  0.12371356472390317, 0.12371341943311376, 0.1237132697054624, 0.12371311559962239, 0.12371295717194818, 0.12371279447658921, 0.1237126275655968, -70.13370023408227, 13609.434641207708, 151173.81666220704]
 [0.006573203256253084, 922.5934983659067, 923.9665888758834, 0.0064562278992018616, 0.9997253010148252, 0.9997276295977502, 0.001598658841927146, 0.0024984529975030883, 0.001614047794745646, 0.0011856577970248887  …  0.12309422660091429, 0.12309408550324269, 0.12309394023740704, 0.12309379085759026, 0.12309363741583354, 0.12309347996214129, 0.12309331854458028, -70.03725612195532, 13559.858385460602, 151223.46657862776]
 [0.0064721693428980796, 922.7358937568729, 924.088057654229, 0.006493344733516329, 0.9997202628390558, 0.9997225836604192, 0.001618131395065923, 0.0025141532138503696, 0.0016241926698836691, 0.0012012301821853206  …  0.1225663038391262, 0.12256616646164024, 0.12256602513991986, 0.12256587992446184, 0.12256573086376693, 0.1225655780044376, 0.12256542139127033, -69.95294083205617, 13517.05790484642, 151266.3308482879]

plot(sol2, idxs=(sys.t / 1000, sys.vm), tspan=(100second, 101second), title="Action potential", xlabel="Time (s)")

_images/82abf60cd4110d279b8c0bea881452ff9428320206a2edecd1ed933f435d6b66.png

plot(sol2, idxs=(sys.t / 1000, [sys.Cai_sub_SR, sys.Cai_sub_SL, sys.Cai_mean]), tspan=(100second, 101second), title="Calcium transcient", xlabel="Time (s)", ylabel="Conc. (μM)", label=["Ca (SR)" "Ca (SL)" "Ca (avg)"])

_images/8396ed7435d858b7c06d74d688d3d40555e92d49bc1951be46750f3b184ffc34.png

plot(sol2, idxs=(sys.t / 1000, sys.CaMKAct * 100), title="Active CaMKII", label=false, ylabel="Active fraction (%)", xlabel="Time (s)")

_images/c0592c7164c01edbb39075d389ad1b9dcc7cd0912071d1c3ecf4d3a1c344c52f.png

Comparison#

i = (sys.t / 1000, sys.Cai_mean)
tspan = (100second, 101second)
plot(sol, idxs=i, title="Calcium transcient", lab="ISO (-)"; tspan)
plot!(sol2, idxs=i, lab="ISO (0.1uM)", xlabel="Time (s)", ylabel="Concentration (μM)"; tspan)

_images/f8881b20b73c069d36d29de5badc77a116d6f333379ba08b50ec45bf33dd92fc.png

Compare the numbers

ca_ctl = sol(tspan[1]:1:tspan[2], idxs=sys.Cai_mean)
println(extrema(ca_ctl))

(0.23505056446792008, 0.5781214777886791)

ca_iso = sol2(tspan[1]:1:tspan[2], idxs=sys.Cai_mean)
println(extrema(ca_iso))

(0.19033626526983588, 0.711093945093875)

savefig("iso-caT.pdf")
savefig("iso-caT.png")

"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/.cache/docs/iso-caT.png"

i = (sys.t / 1000, sys.CaMKAct * 100)
plot(sol, idxs=i, title="Active CaMKII", lab="ISO (-)")
plot!(sol2, idxs=i, lab="ISO (0.1uM)", ylabel="Active fraction (%)", xlabel="Time (s)")

_images/4ab3bc3617e3a5bce825e65dabbea725d7cd155fffb3e30f9e506bab71e46295.png

savefig("iso-camkact.pdf")
savefig("iso-camkact.png")

"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/.cache/docs/iso-camkact.png"

i = (sys.t / 1000, sys.vm)
tspan = (100second, 101second)
plot(sol, idxs=i, title="Action potential", lab="ISO (-)"; tspan)
plot!(sol2, idxs=i, lab="ISO (0.1uM)", xlabel="Time (ms)", ylabel="Voltage (mV)"; tspan)

_images/7e23b9b339879ceacc079ccb7b1e589f057c05dac0c9a39fde163fa9fade18ea.png

Experimental data#

chemicaldf = CSV.read(joinpath(@__DIR__, "data/CaMKAR-chemical.csv"), DataFrame)
ts = Dates.value.(chemicaldf[!, "Time"]) ./ 10^9
ctl = chemicaldf[!, "Ctrl Mean"]
ctl_error = chemicaldf[!, "Ctrl SD"] ./ sqrt.(chemicaldf[!, "Ctrl N"])

iso = chemicaldf[!, "isoproterenol 100nM Mean"]
iso_error = chemicaldf[!, "isoproterenol 100nM SD"] ./ sqrt.(chemicaldf[!, "isoproterenol 100nM N"])

plot(ts, ctl, yerr=ctl_error, lab="Control", color=:blue, markerstrokecolor=:blue)
plot!(ts, iso, yerr=iso_error, lab="ISO 100nM", color=:red, markerstrokecolor=:red)
plot!(xlabel="Time (sec.)", ylabel="CaMKII activity (A.U.)")

_images/e151e9cc176acf7e0374a623a6bdf51ee537fba88b436053999e3ebc4d9d0996.png

savefig("iso-exp.pdf")

"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/.cache/docs/iso-exp.pdf"

This notebook was generated using Literate.jl.