%This script is used to perform dynamic FBA with Y. lipolytica. %Author: Martin Kavš?ek; martin.kavscek@uni-graz.at %date: 25.9.2015 model = readCbModel ('D:\Users\martin\Google Drive\Sluzba\perlanje\yl_model\model\Paper\YL_iMK735.xml'); %dFBA calculation %standard conditions with glucose uptake model = changeRxnBounds (model, 'EX_co2(e)', -1000, 'l'); model = changeRxnBounds (model, 'EX_h2o(e)', -1000, 'l'); model = changeRxnBounds (model, 'EX_h(e)', -1000, 'l'); model = changeRxnBounds (model, 'EX_inost(e)', -1000, 'l'); model = changeRxnBounds (model, 'EX_k(e)', -1000, 'l'); model = changeRxnBounds (model, 'EX_na1(e)', -1000, 'l'); model = changeRxnBounds (model, 'EX_nh4(e)', -1000, 'l'); model = changeRxnBounds (model, 'EX_o2(e)', -1000, 'l'); model = changeRxnBounds (model, 'EX_pi(e)', -1000, 'l'); model = changeRxnBounds (model, 'EX_so4(e)', -1000, 'l'); model = changeRxnBounds (model, 'EX_glc(e)', -4.0, 'l'); model = changeRxnBounds (model, 'EX_glc(e)', 1000, 'u'); model = changeRxnBounds (model, 'EX_glyc(e)', 0, 'l'); model = changeRxnBounds (model, 'EX_glyc(e)', 1000, 'u'); uptakeRxns = printUptakeBound(model) model = changeObjective (model, 'biomass_013',1); mantainance = 4 * 5 %mantainannce = 8.78 * 2.28 %config fur function dynamicFBA(model,substrateRxns,initConcentrations,initBiomass,timeStep,nSteps,plotRxns) substrateRxns = 'EX_glc(e)'; initConcentrations = 111; % 20g/L initBiomass = 0.03; timeStep = 0.5; nSteps = 40; plotRxns = {'EX_glc(e)'}; [concentrationMatrix,excRxnNames,timeVec,biomassVec] = dynamicFBA(model,substrateRxns,initConcentrations,initBiomass,timeStep,nSteps,plotRxns); model = changeRxnBounds (model, 'ATPM', mantainance, 'b'); GR = optimizeCbModel(model, 'max', 'one') %Citric acid production %standard conditions with glucose uptake model = changeRxnBounds (model, 'EX_glc(e)', -0.350, 'l'); %calculated only for stationary phase uptakeRxns = printUptakeBound(model); mantainance1 = 0.35*5.3; model = changeRxnBounds (model, 'ATPM', mantainance1, 'b'); model = changeObjective (model, 'LDparticle_SC_e_tp'); %lipid production LIPIDwoCIT = optimizeCbModel(model, 'max', 'one') %lipid production without citrate excretion mantainance2 = 0.35*4.75; model = changeRxnBounds (model, 'ATPM', mantainance2, 'b'); LIPIDwoCIT = optimizeCbModel(model, 'max', 'one') %lipid production without citrate excretion CAexcretion = 3.339; CAmol = 192.194; duration = 29; biomass = 3.0; CAkonc = (CAexcretion / CAmol) * 1000; %conc of CA in mmoles CArate = (CAkonc / biomass) / duration; model = changeRxnBounds (model, 'EX_cit(e)', CArate, 'b'); LIPIDCIT = optimizeCbModel(model, 'max', 'one') %lipid production with citrate excretion diff = LIPIDCIT.f/LIPIDWT.f