Team:ETH Zurich/Parameters

PARAMETERS

ESTIMATION METHODS

We used two different approaches for parameter estimation from experimental data:

MEIGO

MEIGO is an open source global optimization toolbox that provides several solvers for different applications. In our project we used the Cooperative enhanced Scatter Solver (CeSS) from the MATLAB version of the toolbox. Parameters were estimated by fitting ODE simulations to the experimental data using a least-square error function.

INSIGHT

INSIGHT is a parameter estimation method based on stochastic simulations and Approximate Bayesian computation (ABC). Parameters are estimated by minimizing the Kolmogorov distance between simulated and measured (through flow cytometry) distributions. This distance is defined as the tolerance of the fit, and is progressively reduced using Sequential Monte Carlo (SMC). The result is a posterior distribution of parameters that fit the data within a specific tolerance. As final value of the parameters we select the Maximum A Posteriori (MAP) estimates.

The estimations have been performed using the INSIGHTv3 implementation developed by Jan Mikelson. The tool is freely available online, but we highly encourage to check the website of our department, as a new improved version is expected to be published in the months after the Jamboree.

Parameter constant for the NO module

Name Description Unit range values value Estimation method of Evaluation Source
knor_no NorR NOproduction rate nM-1min-1 0.001 - 10 0,0011183 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
k_nor_no NorR NOdissociation rate nM-1min-1 0.01 - 10 0,0363665 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
knorV1 DNorR NO2binding rate nM-1min-1 0.01 - 1 0,0014788 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
k_norV1 DNorR NO2unbinding rate nM-1min-1 0.01 - 1 0,00081 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
knorV2 DNorR NO2binding rate nM-1min-1 0.01 - 10 0,00185016 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
k_norV2 DNorR NO2unbinding rate nM-1min-1 0.01 - 1 7.1 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
knorV3 DNorR NO2binding rate nM-1min-1 0.01 - 10 0,986026 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
k_norV3 DNorR NO2unbinding rate nM-1min-1 0.01 - 10 6.1 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
knorprod NorR constitutive production rate nM-1min-1 0.01 - 10 0,958777 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
dnor NorR degradation rate nM-1min-1 0.01 - 1 89,159 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
dnor_no NorR NOdegradation rate nM-1min-1 0.01 - 1 46,678 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
kdnor DNorR dimerization constant nM-1min-1 0.01 - 1 75698,5 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
k_dnor DNorR dissociation rate nM-1min-1 0.01 - 1 1,91699 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
kmrna mRNA production rate for pnorV promoter nM-1min-1 0.01 - 1 3438,47 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation
dmrna mRNA degradation rate min-1 0.01 - 1 0,0199458 MEIGO metaheuristic evaluation from plate reader Computed from parameter estimation

Parameter constant for the AHL module

Name Description Unit range values value Estimation method of Evaluation Source
kesarProd EsaR constitutive production rate nM-1min-1 0.01 - 10 3,24412 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation
desar DEsaR degradation rate min-1 0.01 - 1 0,0152529 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation
kl promoter leakiness nM-1min-1 0.01 - 10 0,00242729 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation
k5 DEsaR production rate nM-1min-1 0.01 - 1 0,01 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation
k_5 DEsaR dissociation rate nM-1min-1 0.01 - 10 0,65492 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation
k6 DEsaR AHL production rate nM-1min-1 0.01 - 10 0,0100102 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation
k_6 DEsaR AHL dissociation rate nM-1min-1 0.01 - 10 0,719465 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation
k7 AHL to Pesar promoter binding rate nM-1min-1 0.01 - 1 0,4878 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation
k_7 AHL to Pesar promoter unbinding rate nM-1min-1 0.01 - 1 0,0383841 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation
kmrna mRNA production rate for Pconst+esaboxes promoter nM-1min-1 0.01 - 1 0,0121775 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation
dmrna mRNA degradation rate min-1 0.01 - 1 0,0142082 MEIGO metaheuristic evaluation from FACS Datas Computed from parameter estimation

Parameter constant for the AHL module

Name Description Unit range values value Estimation method of Evaluation Source
klac_pyr NorR NOproduction rate nM-1min-1 0.01 - 10 0.1 Litterature Source
k_lac_pyr NorR NOdissociation rate nM-1min-1 0.01 - 10 1.5 Litterature Source
kdlldr DNorR NO2binding rate nM-1min-1 0.01 - 1 0.1 Litterature Source
k_dlldr DNorR NO2unbinding rate nM-1min-1 0.01 - 1 8.1 Litterature Source
kgoff DNorR NO2binding rate nM-1min-1 0.01 - 10 0.1 Litterature Source
k_goff DNorR NO2unbinding rate nM-1min-1 0.01 - 1 7.1 Litterature Source
kdlldr_lac DNorR NO2binding rate nM-1min-1 0.01 - 10 0.1 Litterature Source
k_dlldr_lac DNorR NO2unbinding rate nM-1min-1 0.01 - 10 6.1 Litterature Source
kgoff_lac NorR constitutive production rate nM-1min-1 0.01 - 10 3 Litterature Source
k_goff_lac NorR degradation rate nM-1min-1 0.01 - 1 0.1 Litterature Source
dlld NorR NOdegradation rate nM-1min-1 0.01 - 1 1 Litterature Source
kllddProd DNorR dimerization constant nM-1min-1 0.01 - 1 1 Litterature Source
klldrProd DNorR dissociation rate nM-1min-1 0.01 - 1 10 Litterature Source
kl DEsaR production rate nM-1min-1 0.01 - 10 1.5 Litterature Source
nlact DNorR NO2binding rate nM-1min-1 0.01 - 1 0.1 Litterature Source
Klact DEsaR degradation rate nM-1min-1 0.01 - 1 8.1 Litterature Source

REPORTER MODULE PARAMETERS

Name Description Unit Prior range Value Source
$l_{pTet}$ Tet promoter leakiness $-$ 0.0 - 0.5 0.057 Estimated with INSIGHT
$n$ Sensitivity of the tet promoter $-$ 0.8 - 2.8 1.57 Estimated with INSIGHT
$K_m$ aTc concentration for half occupation $nM$ 10 - 15000 9853.6 Estimated with INSIGHT
$k_{mRNAgfp}$ sfGFP mRNA transcription rate $min^{-1}$ 10 - 15000 0.382 Estimated with INSIGHT
$k_{mRNAgfp}$ sfGFP mRNA transcription rate $min^{-1}$ 0.001 - 10 0.382 Estimated with INSIGHT
$d_{mRNAgfp}$ sfGFP mRNA degradation rate $min^{-1}$ 0.05 - 20 8.93 Estimated with INSIGHT
$k_{GFP}$ sfGFP translation rate $min^{-1}$ 0.00005 - 0.5 0.012 Estimated with INSIGHT
$d_{GFP}$ sfGFP degradation rate $min^{-1}$ 0.0001 - 0.1 0.018 Estimated with INSIGHT


Parameters for mNectarine ($k_{mRNAmnect}$, $d_{mRNAmnect}$, $d_{mNect}$) are assumed to be on the same order of magnitude as the parameters for sfGFP. Since sfGFP is engineered for faster folding, we assume $k_{mNect}=0.1\cdot k_{GFP}$

Thanks to the sponsors that supported our project: