Team:NYMU-Taipei/Modeling/ModSensors

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\frac{d[mRNAoxyR]}{dt}=PoPSconstitutive\timesN/V-KdegmRNA[mRNAoxyR]
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\frac{d[mRNAoxyR]}{dt}=PoPSconstitutive\times\frac{N}{V}-KdegmRNA[mRNAoxyR]
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Revision as of 18:24, 27 September 2013

National Yang Ming University


Function of the parts

trxC promoter is an oxyR-activated promoter. We use trxC promoter as a sensor/ switch to have the whole circuit opened when Nosema exists, and closed when Nosema is killed.

When Nosema enters the bees, it will trigger bees’ ROS (reactive oxygen species) production, which in turn launches E.coli’s OxyR production. After that ROS and OxyR will form a complex and binds to trxC promoter. To increase the sensitivity of this switch, we add an additional circuit expressing OxyR regulated by a constitutive promoter to enhance the basal OxyR expression in E.coli.

The purpose of this modeling:

  1. To know the lag time between sensing the invasion and the production of the killing protein.
  2. The minimal oxidative stress that can activate the switch by choosing the proper constitutive promoter for boosting OxyR's concentration
  3. To know the relation between ROS input and the trxC promoter open strength.
  4. To see to which degree will trxC promoter influence the production of LuxI, LuxR, and LacI, which will influence the second and the third circuit.

It is assumed that the concentration of ROS in bees is relative to the severity of Nosema infection, and that oxyR is so abundant that once ROS appears, it will soon bind to ROS to form ROSoxyR complex and reach equilibrium.

Equation1:

\frac{d[mRNAoxyR]}{dt}=PoPSconstitutive\times\frac{N}{V}-KdegmRNA[mRNAoxyR]

PoPSconstitutive = promoter strength of constitutive promoter (J23102)

N = number of plasmid in a single cell

V = volume of a cell

The aim of the equation is to know the production rate of mRNAoxyR, and choose the proper constitutive promoter for boosting OxyR's concentration.

Equation2:

\frac{d[oxyR]}{dt}=RBS\times[mRNAoxyR]-KdegoxyR[oxyR]

RBS = binding site strength

KdegoxyR = degrading constant of oxyR

The aim of the equation is to know the production rate of oxyR and when it can reach the concentration activating trxC promoter, which can in turn be deduced to get the lag time between sensing the invasion and the production of the killing protein.

Equation3:

[ROSoxyR]=KROSoxyR\times[ROS]\times[oxyR]

KROSoxyR = constant rate of ROS+oxyR→ROS/oxyR(complex)

The aim of the equation is to know the concentration of ROS/oxyR complex given the concentration of ROS and oxyR, which will know the relation between ROS input and the trxC promoter open time.


Equation4:

PoPSconstitutive = promoter strength of constitutive promoter

N = number of plasmid in a single cell

V = volume of a cell

The aim of the equation is to know how trxC promoter strength (in PoPS) influences the production of lacI, LuxI, and LuxR.

Explanation:

\frac{d[mRNAoxyR]}{dt}=PoPSconstitutive\times\frac{N}{V}-KdegmRNA[mRNAoxyR]
In this equation, <bold>PoPStrxC</bold> represents the promoter strength of promotertrxC, which is measured by the rate of RNApolymerase binding to the starting site of DNA transcription; NYMU-Taipei_Mod_Image029.png represents the hill effect of activator ROSoxyR to trxCpromoter.

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