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	-	0,0011183	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$k_{nor_no}$	NorR NOdissociation rate	min-1	-	0,0363665	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$knorV1$	DNorR NO2binding rate	nM-1min-1	-	0,0014788	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$k_norV1$	DNorR NO2unbinding rate	min-1	-	0,00081	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$knorV2$	DNorR NO2binding rate	nM-1min-1	-	0,00185016	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$k_norV2$	DNorR NO2unbinding rate	min-1	-	7.1	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$knorV3$	DNorR NO2binding rate	nM-1min-1	-	0,986026	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$k_norV3$	DNorR NO2unbinding rate	min-1	-	6.1	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$knorprod$	NorR constitutive production rate	nM min-1	-	0,958777	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$dnor$	NorR degradation rate	min-1	-	89,159	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$d_{nor_no}$	NorR NOdegradation rate	min-1	-	46,678	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$kdnor$	DNorR dimerization constant	nM-1min-1	-	75698,5	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$k_dnor$	DNorR dissociation rate	min-1	-	1,91699	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$kmrna$	mRNA production rate for pnorV promoter	min-1	-	3438,47	MEIGO metaheuristic evaluation from plate reader	Computed from parameter estimation
$dmrna$	mRNA degradation rate	min-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 min-1	-	3,24412	MEIGO metaheuristic evaluation from FACS Datas	Computed from parameter estimation
$desar$	DEsaR degradation rate	min-1	-	0,0152529	MEIGO metaheuristic evaluation from FACS Datas	Computed from parameter estimation
$kl$	promoter leakiness	-	-	0,00242729	MEIGO metaheuristic evaluation from FACS Datas	Computed from parameter estimation
$k5$	DEsaR production rate	nM-1min-1	-	0,01	MEIGO metaheuristic evaluation from FACS Datas	Computed from parameter estimation
$k_5$	DEsaR dissociation rate	min-1	- 0	0,65492	MEIGO metaheuristic evaluation from FACS Datas	Computed from parameter estimation
$k6$	DEsaR AHL production rate	nM-1min-1	-	0,0100102	MEIGO metaheuristic evaluation from FACS Datas	Computed from parameter estimation
$k_6$	DEsaR AHL dissociation rate	min-1	-	0,719465	MEIGO metaheuristic evaluation from FACS Datas	Computed from parameter estimation
$k7$	AHL to Pesar promoter binding rate	nM-1min-1	-	0,4878	MEIGO metaheuristic evaluation from FACS Datas	Computed from parameter estimation
$k_7$	AHL to Pesar promoter unbinding rate	min-1	-	0,0383841	MEIGO metaheuristic evaluation from FACS Datas	Computed from parameter estimation
$kmrna$	mRNA production rate for Pconst+esaboxes promoter	min-1	-	0,0121775	MEIGO metaheuristic evaluation from FACS Datas	Computed from parameter estimation
$dmrna$	mRNA degradation rate	min-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
$k_lac_{pyr}$	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
$K_{lact}$	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 $k_{mNect}=0.1\cdot k_{GFP}$