Team:NYMU-Taipei/Modeling/ModSensors

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Revision as of 01:47, 28 September 2013

National Yang Ming University

1 Function of the parts
2 The purpose of this modeling:
3 Explanation:
4 Results

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:

To know the lag time between sensing the invasion and the production of the killing protein.
The minimal Oxidative stress that can activate the switch by choosing the proper constitutive promoter for boosting OxyR's concentration
To know the relation between ROS input and the trxC promoter open strength.
To see to which degree will trxC promoter influence the production of LuxI, LuxR, and TetR, 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 OxyR* 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:

[OxyR*]=KOxyR*\times[ROS]\times[OxyR]

KOxyR* = constant rate of ROS+OxyR→OxyR*

The aim of the equation is to know the concentration of OxyR* 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 TetR, LuxI, and LuxR.

Explanation:

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

In this equation, PoPSconstitutive represents the promoter strength of promoter J23102, which is measured by the rate of RNApolymerase binding to the starting site of DNA transcription.

For the section of the equation, PoPSconstitutive\times\frac{N}{V} represents the synthesizing rate of mRNAOxyR ; -KdegmRNA[mRNAOxyR] represents the degrading rate of mRNAOxyR .

\frac{d[OxyR]}{dt}=RBS\times[mRNAOxyR]-KdegOxyR[OxyR]

In this equation, RBS represents ribosome binding site strength, which is the affinity of ribosome to the starting site of mRNA.

For the section of the equation, RBS×[mRNAoxyR] represents the synthesizing rate of OxyR; KdegOxyR[xyR] represents the degrading rate of OxyR .

[OxyR*]=KOxyR*\times[ROS]\times[OxyR]

This equation shows the equilibrium of ROS + OxyR → OxyR* (KOxyR* is the rate constant of ROS + OxyR → OxyR*)

In this equation, PoPSTrxC represents the promoter strength of promoter TrxC, which is measured by the rate of RNApolymerase binding to the starting site of DNA transcription; represents the hill effect of activator OxyR* to TrxC promoter.

The production rate of mRNATetR, mRNALuxI, mRNALuxR can be written as , which is under the influence of activator OxyR* binding to TrxC promoter.

Results

Retrieved from "http://2013.igem.org/Team:NYMU-Taipei/Modeling/ModSensors"

@@ Line 3: / Line 3: @@
 ==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.
+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.
+	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.
@@ Line 11: / Line 11: @@
 #To know the lag time between sensing the invasion and the production of the killing protein.
-#The minimal oxidative stress that can activate the switch by choosing the proper constitutive promoter for boosting OxyR's concentration
+#The minimal Oxidative stress that can activate the switch by choosing the proper constitutive promoter for boosting OxyR's concentration
 #To know the relation between ROS input and the trxC promoter open strength.
-#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.
+#To see to which degree will trxC promoter influence the production of LuxI, LuxR, and TetR, 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.
+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 OxyR* and reach equilibrium.
 '''Equation1:'''
@@ Line 21: / Line 21: @@
 <html>
 <div lang="latex" class="equation">
-\frac{d[mRNAoxyR]}{dt}=PoPSconstitutive\times\frac{N}{V}-KdegmRNA[mRNAoxyR]
+\frac{d[mRNAOxyR]}{dt}=PoPSconstitutive\times\frac{N}{V}-KdegmRNA[mRNAOxyR]
 </div>
 </html>
@@ Line 31: / Line 31: @@
 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.'''
+'''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:'''
 <html>
 <div lang="latex" class="equation">
-\frac{d[oxyR]}{dt}=RBS\times[mRNAoxyR]-KdegoxyR[oxyR]
+\frac{d[oxyR]}{dt}=RBS\times[mRNAOxyR]-KdegOxyR[OxyR]
 </div>
 </html>
@@ Line 42: / Line 42: @@
 RBS = binding site strength
-KdegoxyR = degrading constant of oxyR
+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.'''
+'''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:'''
@@ Line 50: / Line 50: @@
 <html>
 <div lang="latex" class="equation">
-[ROSoxyR]=KROSoxyR\times[ROS]\times[oxyR]
+[OxyR*]=KOxyR*\times[ROS]\times[OxyR]
 </div>
 </html>
-KROSoxyR = constant rate of ROS+oxyR&rarr;ROS/oxyR(complex)
+KOxyR* = constant rate of ROS+OxyR&rarr;OxyR*
-'''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.'''
+'''The aim of the equation is to know the concentration of OxyR* given the concentration of ROS and OxyR, which will know the relation between ROS input and the TrxC promoter open time.'''
@@ Line 73: / Line 73: @@
 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.
+The aim of the equation is to know how trxC promoter strength (in PoPS) influences the production of TetR, LuxI, and LuxR.
 ==Explanation:==
 <html>
 <div lang="latex" class="equation">
-\frac{d[mRNAoxyR]}{dt}=PoPSconstitutive\times\frac{N}{V}-KdegmRNA[mRNAoxyR]
+\frac{d[mRNAOxyR]}{dt}=PoPSconstitutive\times\frac{N}{V}-KdegmRNA[mRNAOxyR]
 </div>
 </html>
@@ Line 84: / Line 84: @@
 In this equation, '''PoPSconstitutive''' represents the promoter strength of promoter J23102, which is measured by the rate of RNApolymerase binding to the starting site of DNA transcription.
-For the section of the equation, '''<span lang="latex">PoPSconstitutive\times\frac{N}{V}</span>''' represents the synthesizing rate of '''mRNAoxyR''' ; '''-KdegmRNA[mRNAoxyR]''' represents the degrading rate of '''mRNAoxyR''' .
+For the section of the equation, '''<span lang="latex">PoPSconstitutive\times\frac{N}{V}</span>''' represents the synthesizing rate of '''mRNAOxyR''' ; '''-KdegmRNA[mRNAOxyR]''' represents the degrading rate of '''mRNAOxyR''' .
 <html>
 <div lang="latex" class="equation">
-\frac{d[oxyR]}{dt}=RBS\times[mRNAoxyR]-KdegoxyR[oxyR]
+\frac{d[OxyR]}{dt}=RBS\times[mRNAOxyR]-KdegOxyR[OxyR]
 </div>
 </html>
@@ Line 94: / Line 94: @@
 In this equation, '''RBS'''  represents ribosome binding site strength, which is the affinity of ribosome to the starting site of mRNA.
-For the section of the equation, '''RBS&times;[mRNAoxyR]''' represents the synthesizing rate of '''oxyR''';  '''KdegoxyR[oxyR]''' represents the degrading rate of '''oxyR''' .
+For the section of the equation, '''RBS&times;[mRNAoxyR]''' represents the synthesizing rate of '''OxyR''';  '''KdegOxyR[xyR]''' represents the degrading rate of '''OxyR''' .
 <html>
 <div lang="latex" class="equation">
-[ROSoxyR]=KROSoxyR\times[ROS]\times[oxyR]
+[OxyR*]=KOxyR*\times[ROS]\times[OxyR]
 </div>
 </html>
-This equation shows the equilibrium of ROS + oxyR &rarr; ROSoxyR complex ('''KROSoxyR''' is the rate constant of ROS + oxyR &rarr; ROSoxyR complex)
+This equation shows the equilibrium of ROS + OxyR &rarr; OxyR* ('''KOxyR*''' is the rate constant of ROS + OxyR &rarr; OxyR*)
 <html>
@@ Line 110: / Line 110: @@
 </html>
-In this equation, '''PoPStrxC''' represents the promoter strength of promotertrxC, which is measured by the rate of RNApolymerase binding to the starting site of DNA transcription; <span>https://static.igem.org/mediawiki/2013/8/81/NYMU-Taipei_Mod_Image029.png</span> represents the hill effect of activator ROSoxyR to trxCpromoter.
+In this equation, '''PoPSTrxC''' represents the promoter strength of promoter TrxC, which is measured by the rate of RNApolymerase binding to the starting site of DNA transcription; <span>https://static.igem.org/mediawiki/2013/8/81/NYMU-Taipei_Mod_Image029.png</span> represents the hill effect of activator OxyR* to TrxC promoter.
-The production rate of ''mRNALacI, mRNALuxI, mRNALuxR'' can be written as <span>https://static.igem.org/mediawiki/2013/8/81/NYMU-Taipei_Mod_Image029.png</span>, which is under the influence of activator ''ROSoxyR'' binding to trxC promoter.
+The production rate of ''mRNATetR, mRNALuxI, mRNALuxR'' can be written as <span>https://static.igem.org/mediawiki/2013/8/81/NYMU-Taipei_Mod_Image029.png</span>, which is under the influence of activator ''OxyR*'' binding to TrxC promoter.
 ==Results==
 {{:Team:NYMU-Taipei/Footer}}