Dynamic characterization of synthetic genetic circuits in living cells

A non-transitory computer-readable storage medium comprising code which upon execution performs a method for determining an intrinsic property of a DNA component, from a plurality of measurements obtained over a time period from a cell culture, with each cell comprising the DNA component,

• the DNA component being involved in transcription of a target signal,
• the plurality of measurements comprising measurements relating to a density of the cell culture over the time period and measurements relating to an amount of the target signal in the cell culture over the time period,
• the method comprising:
• (a) estimating parameter values, for a first mathematical model that describes cell culture density over time, from a minimized measure of a difference between an output of the first mathematical model and the measurements relating to the density of the cell culture over the time period;
• and
• (b) identifying a parameter quantifying the intrinsic property of the DNA component, from a minimized measure of a difference between an output of a further mathematical model, which has the identified parameter embedded therein and describes a production of the target signal over time, and the measurements relating to the amount of the target signal, wherein the further mathematical model additionally uses the parameter values estimated in (a).

A computer-implemented method for determining an intrinsic property of a DNA component, from a plurality of measurements obtained over a time period from a cell culture, with each cell comprising the DNA component and wherein each cell further comprises a reference promoter that initiates transcription of a reference signal, wherein the intrinsic property is an ability to recruit a polymerase enzyme or an ability to bind transcription factors,

• the DNA component being involved in transcription of a target signal,
• the plurality of measurements comprising measurements relating to a density of the cell culture over the time period, measurements relating to an amount of the reference signal in the cell culture over the time period, and measurements relating to an amount of the target signal in the cell culture over the time period,
• the method comprising:
• (a) estimating parameter values, for a first mathematical model that describes cell culture density over time, from a minimized measure of a difference between an output of the first mathematical model and the measurements relating to the density of the cell culture over the time period;
• (b) estimating parameter values for a second mathematical model that describes a capacity of the cell culture to produce the reference signal over time, from a minimized measure of a difference between an output of the second mathematical model and the measurements relating to the amount of the reference signal in the cell culture over the time period, wherein the second mathematical model additionally uses the parameter values estimated in (a);
• and
• (c) estimating a parameter quantifying the intrinsic property of the DNA component, from a third mathematical model that describes a production of the target signal over time, and from a minimized measure of a difference between an output of the third mathematical model and the measurements relating to the amount of the target signal, wherein the third mathematical model additionally uses the parameter values estimated in (a) or parameter values based thereon,
• wherein said additional use of the parameter values comprises using the parameter values estimated based on (a) by the second mathematical model, taking the second mathematical model to provide an estimate of the capacity of the cell culture to produce the target signal over time,
• wherein parameters for the first mathematical model are selected from per capita culture growth rate, carrying capacity, and initial cell density,
• wherein the first mathematical model is a logistic growth model,
• wherein the second mathematical model models the capacity of the cell culture to produce the reference signal over the time period as a chemical reaction network.