Team:NYMU-Taipei/Modeling/MainParts

From 2013.igem.org

(Difference between revisions)

Revision as of 13:25, 27 October 2013

National Yang Ming University

1 main part

main part

Function of the parts:

circuit regulators:

• LacI regulated promoter(pLac) : when LacI exists, it will bind to LacI regulated promoter(pLac) and represses the promoter.

• pLux/cI hybrid promoter(plux/cI) : when luxR/AHL exists, it will open pLux/cI hybrid promoter(plux/cI), while cI will repress the promoter. What’s more, plux/cI is cI-dominant, which means when cI exists, the hybrid promoter will be repressed whether luxR/AHL exists or not.

Circuit regulation:

• Circuit condition without Nosema:

Without Nosema Ceranae, the first circuit will not open, and thus, no LacI will be produced. Since there is no LacI binding to pLac, pLac will not be repressed, which means cI will be produced. After that, cI will bind to pLux/cI hybrid promoter, leading the third circuit to be off.

• Circuit condition with Nosema:

When Nosema Ceranae infects the bee, bee’s immune system will be activated, leading to the concentration of ROS (reactive oxygen species) to be high. In response, Bee. coli will enhance the production of oxyR, which forms a complex with ROS and binds to transcription binding site ahead of trxC (an oxyR-activated promoter; namely, the sensor), leading to the first circuit to be on.

Since the first circuit is on, the downstream LacI gene will be produced and bind to pLac, leading to the second circuit to be off.

After the second circuit is closed, no cI is produced, leading to the third circuit to be on (no repressor at all). And then, kill protein will be produced and kill Nosema Ceranae.

•Positive feedback:

Besides the LuxI and LuxR(which then form a complex called luxR/AHL) produced by first circuit, the third circuit will also produce LuxI and LuxR, which acts as a positive feedback and strongly enhances the production of killer protein.

•Circuit condition when Nosema is killed:

After Nosema is killed, the sensor will be off and no lacI will be produced.

Without LacI, the pLac will not be repressed, and the second circuit will be on, leading to the production of cI. After cI binds to pLux/cI hybrid promoter, the third circuit to be off. After that, the overall circuit will switch to the beginning stage when there is no Nosema.

Aims

1. To know how much time it needs from sensing to killing the Nosema after infection

2. To know whether the pathway is effective or not

3. To know the range of kill protein concentration (from the minimal concentration which Is effective to kill Nosema to the maximal concentration which will not do harm to the bees)

It is assumed that AHL is abundant and thus the formation of AHL2LuxR complex is determined only by the concentration of LuxR; CI’s mechanism of binding to the promoter is assumed to act as hill effect form; kill protein will sustain a period of time before it is degraded naturally without any other types of decomposition.

Equations

Equation1:

\frac{d[mRNACI]}{dt}= \frac{1-[LacI]^nLacI}{ KdLacI^nLacI+ [LacI]^nLacI} \times PoPSconstitutive\times\frac{N}{V} -KdegmRNA\times [mRNACI]

KdLacI = dissociation constant of CI

nLacI = Hill coefficient of LacI

PoPSpLac = promoter strength of pLac

kdegmRNA = degrading constant of sensor promoter mRNA

N = number of plasmid in a single cell

V = volume of a cell

The aim of the equation is to knowmRNACI production rate and when it can reach the level to translate the desired concentration.

Equation2:

\frac{d[mRNALacI]}{dt}= \frac{1-[ROSoxyR]^nROSoxyR }{ KdROSoxyR ^nROSoxyR + [ROSoxyR]^nROSoxyR} PoPStrxC\times\frac{N}{V}-KdegmRNA[mRNALacI]

KdROSoxyR = dissociation constant ofROSoxyR

nROSoxyR = Hill coefficient of ROSoxyR

PoPStrxC = promoter strength of trxC

kdegmRNA = degrading constant of sensor promoter mRNA

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.

Equation3:

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

PoPSconstitutive= promoter strength of constitutive promoter (J23102)

N = number of plasmid in a single cell

V = volume of a cell

kdegmRNA = degrading constant of sensor promoter mRNA

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

Equation4:

\frac{d[mRNALuxI]}{dt}= \frac{1-[ROSoxyR]^n ROSoxyR }{ Kd ROSoxyR ^n ROSoxyR + [ROSoxyR]^n ROSoxyR I} PoPStrxC\times\frac{N}{V}+\frac{1-[ LuxRAHL]^nLuxRAHL}{ KdLuxRAHL ^nLuxRAHL + [LuxRAHL]^nLuxRAHL}\times\frac{1-{1-[CI leak]^nCI}}{ KdCI^nCI+[CI]^nCI}\times PoPSLuxCI\times\frac{N}{V}-KdegmRNA[mRNALuxI]

KdROSoxyR = dissociation constant ofROSoxyR

nROSoxyR = Hill coefficient of ROSoxyR

PoPStrxC = promoter strength of trxC

KdLuxRAHL = dissociation constant ofLuxRAHL

nLuxRAHL = Hill coefficient of LuxRAHL

KdcI = dissociation constant of CI

ncI = Hill coefficient of CI

PoPSLuxcI = promoter strength of LuxcI hybrid promoter

kdegmRNA = degrading constant of sensor promoter Mrna

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 LuxI.

Equation5:

\frac{d[mRNALuxR]}{dt}= \frac{1-[ROSoxyR]^n ROSoxyR }{ Kd ROSoxyR ^n ROSoxyR + [ROSoxyR]^n ROSoxyR I} \times PoPStrxC\times\frac{N}{V}+\frac{1-[ LuxRAHL]^nLuxRAHL}{ KdLuxRAHL ^nLuxRAHL + [LuxRAHL]^nLuxRAHL}\times\frac{1-{1-[CI leak]^nCI}}{ KdCI^nCI+[CI]^nCI}\times PoPSLuxCI\times\frac{N}{V}-KdegmRNA[mRNALuxR]

KdROSoxyR = dissociation constant ofROSoxyR

nROSoxyR = Hill coefficient of ROSoxyR

PoPStrxC = promoter strength of trxC

KdLuxRAHL = dissociation constant ofLuxRAHL

nLuxRAHL = Hill coefficient of LuxRAHL

KdcI = dissociation constant of CI

ncI = Hill coefficient of CI

PoPSLuxcI = promoter strength of LuxcI hybrid promoter

kdegmRNA = degrading constant of sensor promoter Mrna

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 LuxR.

Equation6:

\frac{d[mRNAkill]}{dt}= \frac{1-[ LuxRAHL]^nLuxRAHL}{ KdLuxRAHL ^nLuxRAHL + [LuxRAHL]^nLuxRAHL}\times\frac{1-{1-[CI leak]^nCI}}{ KdCI^nCI+[CI]^nCI}\times PoPSLuxCI\times\frac{N}{V}-KdegmRNA[mRNAkill]

KdLuxRAHL = dissociation constant ofLuxRAHL

nLuxRAHL = Hill coefficient of LuxRAHL

KdcI = dissociation constant of CI

ncI = Hill coefficient of CI

PoPSLuxcI = promoter strength of LuxcI hybrid promoter

kdegmRNA = degrading constant of sensor promoter Mrna

N = number of plasmid in a single cell

V = volume of a cell

The aim of the equation is to knowmRNA of kill protein production rate and when it can reach the level ofthe desired concentration.

Equation7:

\frac{d[Mrnat7]}{dt}= \frac{1-[ROSoxyR]^n ROSoxyR }{ Kd ROSoxyR ^n ROSoxyR + [ROSoxyR]^nROSoxyR }\timesPoPStrxC\times\frac{N}{V}\times {a}+ \frac{1-[T7]^nT7}{ Kd T7^nT7 + [T7]^nT7}\times{PoPST7}\times\ frac{N}{V}-KdegmRNA\times [mRNAT7]

KdROSoxyR = dissociation constant ofROSoxyR

nROSoxyR = Hill coefficient of ROSoxyR

PoPStrxC = promoter strength of trxC

KdT7 = dissociation constant of T7

NT7 = Hill coefficient of T7

PoPST7 = promoter strength of T7 promoter

kdegmRNA = degrading constant of sensor promoter Mrna

N = number of plasmid in a single cell

V = volume of a cell

The aim of the equation is to knowmRNA of T7 polymerase production rate and when it can reach the level to translate enough T7 polymerase.

Equation8:

\frac{d[mRNAPDC]}{dt}=\frac{ [T7]^{nT7} }{ KdT7^{nT7}+[T7]^{nY7} }\times{PoPST7}\times\frac{N}{V}-KdegmRNA\times[mRNAPDC]

KdT7 = dissociation constant of T7

NT7 = Hill coefficient of T7

PoPST7 = promoter strength of T7 promoter

KdegmRNA = degrading constant of sensor promoter mRNA

N = number of plasmid in a single cell

V = volume of a cell

The aim of the equation is to knowmRNA of enzyme PDC production rate and when it can reach the level to translate enough PDC.

Equation9:

\frac{d[mRNAADH]}{dt}=\frac{ [T7]^{nT7} }{ KdT7^{nT7}+[T7]^{nY7} }\times{PoPST7}\times\frac{N}{V}-KdegmRNA\times[mRNAADH]

KdT7 = dissociation constant of T7

NT7 = Hill coefficient of T7

PoPST7 = promoter strength of T7 promoter

kdegmRNA = degrading constant of sensor promoter mRNA

N = number of plasmid in a single cell

V = volume of a cell

The aim of the equation is to knowmRNA of enzyme ADH production rate and when it can reach the level to translate enough ADH.

Equation10:

\frac{d[CI]}{dt}={RBS}\times{[mRNACI]} -KdegCI\times{[CI]}

RBS = binding site strength

KdegCI = degrading constant of CI

The aim of the equation is to know the production rate of CI and when it can reach the concentration to repress LuxCI hybrid promoter.

Equation11:

\frac{d[LacI]}{dt}={RBS}\times{[mRNA LacI]} - {Kdeg LacI} \times{[LacI]}

RBS = binding site strength

KdegLacI = degrading constant of LacI

The aim of the equation is to knowLacI production rate and when it can reach the concentration to repress promoter LacI.

Media:read more

'Equation12:

\frac{d[LuxI]}{dt}={RBS}\times{[mRNA LuxI]} -KAHL\times{[LuxI]} -Kdeg {[LuxI]} \times{[LuxI]}

RBS = binding site strength

KAHL = LuxI to AHL rate constant

KdegLuxI = degrading constant of LuxI

The aim of the equation is to know the production rate of LuxI concerning the LuxIAHL reaction and LuxI degrading.

'Equation13:

\frac{d[LuxR]}{dt}={RBS}\times{[mRNA LuxR]} – {KmAHL}\times{[AHL]} - {Kdeg LuxR} \times{[LuxR]} \times {KmAHL}\{times[AHL]^{2}} \times{[LuxR]}- KdegAHL\times{[AHL]}

RBS = binding site strength

KmAHL =AHL to LuxI rate constant

KdegLuxR= degrading constant of LuxR

KonAHL = 2AHL + LuxR to (AHL)2/LuxR complex rate constant

KdegAHL = degrading constant of AHL

The aim of the equation is to know the production rate of LuxR concerning the 2AHL + LuxR to (AHL)2/LuxR reaction , AHL to LuxI reaction, and LuxR, AHL degrading.

'Equation14:

\frac{d[AHL]}{dt}={KAHL}\times{[LuxI]}+2\times KoffAHL \times [AHLLuxR] - 2\times KonAHL \times {[AHL]}^{2}\times {[LuxR]} - KdegAHL\times{[AHL]}

KAHL = LuxI to AHL rate constant

KonAHL = 2AHL + LuxR to (AHL)^2/LuxR complex rate constant

KoffAHL = (AHL)2/LuxR complex to 2AHL + LuxR rate constant

KdegAHL = degrading constant of AHL

The aim of the equation is to know the production rate of AHL concerning the LuxIAHL reaction, 2AHL + LuxR to (AHL)2/LuxR reaction, (AHL)2/LuxR complex to 2AHL + LuxR reaction and AHL degrading.

'Equation15:

\frac{d[T7]}{dt}={RBS}\times{[mRNAT7]} –KdegT7\times{[T7]}

RBS = binding site strength

KdegT7 = degrading constant of T7

The aim of the equation is to know the threshold concentration of oxyR to conquer the terminal and when T7 polymerase can reach the required concentration to activate T7 promoter.

'Equation16:

\frac{d[PDC]}{dt}=RBS\times{PoPST7effect}\times\frac{N}{V}-{kdegPDC}\times{[PDC]}

RBS = binding site strength

PoPST7 = promoter strength of T7 promoter

N = number of plasmid in a single cell

V = volume of a cell

KdegPDC = degrading constant of PDC (pyruvate decarboxylase)

The aim of the equation is to know PDC production rate and when it can reach the concentration of ethanol pathway equilibrium.

'Equation17:

\frac{d[ADH]}{dt}=RBS\times{PoPST7effect}\times\frac{N}{V}-{KdegADH}\times{[ADH]}

RBS = binding site strength

PoPST7 = promoter strength of T7 promoter

N = number of plasmid in a single cell

V = volume of a cell

KdegADH = degrading constant of ADH (Acetaldehyde)

The aim of the equation is to know ADH production rate and when it can reach the concentration of ethanol pathway equilibrium.

'Equation18:

\frac{d[AHL]}{dt}=\times KonAHL \times [AHL]^{2}\times{[LuxR]}- {KoffAHL} \times {[AHLLuxR]} - KdegAHL\times{[AHL]}

KAHL = LuxI to AHL rate constant

KonAHL = 2AHL + LuxR to (AHL)2/LuxR complex rate constant

KoffAHL = (AHL)2/LuxR complex to 2AHL + LuxR rate constant

KdegAHL = degrading constant of AHL

'Equation19:

\frac{d[kill]}{dt}={RBS}\times{[mRNAkill]} –Kdegkill\times{[kill]}

RBS = binding site strength

Kdegkill = degrading constant of kill

The aim of the equation is to knowkiller protein production rate and when it can reach the effective concentration to killNosema.

'Equation20:

\frac{d[ethanol]}{dt}=Kpyruvateacetaldehyde\times{Kacetaldehydeethanol}\times\frac{[PDC]^{nPDC} }{ KdPDC^{nPDC}+[PDC]^{nPDC}}\times\frac{[ADH]^{nADH} }{ KdADH^{nADH}+[ADH]^{nADH}}-Km\times\frac{[ADH]^{nADH}}{ KdADH^{nADH}+[ADH]^{nADH}}\times{[ethonal]}

Kpyruvateacetaldehyde = pyruvate→acetaldehyde reaction rate constant

Kacetaldehydeethanol = acetaldehyde→ethanol reaction rate constant

Km = ethanol→acetaldehyde reaction rate constant

KdADH = dissociation constant of ADH

'The aim of the equation is to know ethanol production rate and when it can reach the concentration to kill the spores of Nosema Ceranae.

Model	Parameter	Description	Value	Unit	Reference
Sensor	KdegOxyR	OxyR degrading rate	10⁷	M^-1 x min^-1	Regulation of the OxyR transcription factor by hydrogen peroxide and the cellular thiol—disulfide status
	KdOxyR*	Dissociation constant of OxyR*	10^-7.33	M
	KOxyR	OxyR producing rate constant	5.012 x 10¹⁴	X
	nOxyR*	Hill coefficient of OxyR*	Ranging from 0.75~3.5,depends on what kind of ROS it react with	X	OxyR: A Molecular Code for Redox-Related Signaling
	N	Copy number	887(cells containing 25％ plasmid bearing cells)	Single piece	Escherichia coli Plasmid Copy Number Assay Improved determination of plasmid copy number using quantitative real-time PCR for monitoring fermentation processes
Ethanol	pyruvate	Initial concentration of pyruvate in MG1655	1.18 x 2	g/L	Expression of pyruvate carboxylase enhances succinate production in Escherichia coli without affecting glucose uptake
	nPDC	Hill coefficient of PDC	2.1	-	Purification, characterization and cDNA sequencing of pyruvate decarboxylase Zygosaccharomyces biporus
	nADH	Hill coefficient of ADH	at high pH values, 30◦C, n=1; at low temperature, n=3	-	Evidence for co-operativity in coenzyme binding to tetrameric Sulfolobus solfataricus alcohol dehydrogenase and its structural basis: ﬂuorescence, kinetic and structural studies of the wild-type enzyme and non-co-operative N249Y mutant
SEIR(exponential)	b	Infection rate constant of Nosema ceranae to the suspected	24/75	Period(days)-1
	r1	Infection rate constant of K12 to the suspected	3/20	Period(days)-1	1. Environment protection administration executive yuan of R.O.C Medical bacteriology of J.A.T
	r2	Infection rate constant of K12 to the latent	3/20	Period(days)-1	2. Environment protection administration executive yuan of R.O.C. 3. Medical bacteriology of J.A.T
	e	rate of the latent turns infectious	1/4	Period(days)-1
	u	Death rate of the infected	1/8	Period(days)-1
	k	Rate of intaking capsule	24/11	Period(days)-1
SEIR(exponential&linear)	S	x(1)	Amount of total population
	E	x(2)	Amount of suspected individuals
	I	x(3)	Amount of individuals in the latent period
	R	x(4)	Amount of infected individuals

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

@@ Line 74: / Line 74: @@
 ''' The aim of the equation is to knowmRNACI production rate and when it can reach the level to translate the desired concentration.'''
+[[read more]]
 '''Equation2:'''
@@ Line 95: / Line 97: @@
 ''' The aim of the equation is to know how trxC promoter strength (in PoPS) influences the production of lacI.'''
+[[read more]]
 '''Equation3:'''
@@ Line 113: / Line 117: @@
 ''' The aim of the equation is to know the production rate ofmRNAoxyR, and choose the proper constitutive promoter for boosting OxyR's concentration.'''
+[[read more]]
 '''Equation4:'''
@@ Line 143: / Line 148: @@
 ''' The aim of the equation is to know how trxC promoter strength (in PoPS) influences the production of LuxI. '''
+[[read more]]
 '''Equation5:'''
@@ Line 173: / Line 180: @@
 ''' The aim of the equation is to know how trxC promoter strength (in PoPS) influences the production of LuxR. '''
+[[read more]]
 '''Equation6:'''
@@ Line 197: / Line 206: @@
 '''The aim of the equation is to knowmRNA of kill protein production rate and when it can reach the level ofthe desired concentration. '''
+[[read more]]
 '''Equation7:'''
@@ Line 223: / Line 234: @@
 '''The aim of the equation is to knowmRNA of T7 polymerase production rate and when it can reach the level to translate enough T7 polymerase. '''
+[[read more]]
 '''Equation8:'''
@@ Line 245: / Line 258: @@
 '''The aim of the equation is to knowmRNA of enzyme PDC production rate and when it can reach the level to translate enough PDC. '''
+[[read more]]
 '''Equation9:'''
@@ Line 267: / Line 282: @@
 '''The aim of the equation is to knowmRNA of enzyme ADH production rate and when it can reach the level to translate enough ADH. '''
+[[read more]]
 '''Equation10: '''
@@ Line 281: / Line 298: @@
 '''The aim of the equation is to know the production rate of CI and when it can reach the concentration to repress LuxCI hybrid promoter. '''
+[[read more]]
 '''Equation11:'''
@@ Line 295: / Line 314: @@
 '''The aim of the equation is to knowLacI production rate and when it can reach the concentration to repress promoter LacI.'''
+[[Media:read more]]
 '''Equation12:''
@@ Line 312: / Line 333: @@
 '''The aim of the equation is to know the production rate of LuxI concerning the LuxIAHL reaction and LuxI degrading. '''
+[[read more]]
 '''Equation13:''
@@ Line 333: / Line 356: @@
 '''The aim of the equation is to know the production rate of LuxR concerning the 2AHL + LuxR to (AHL)2/LuxR reaction , AHL to LuxI reaction, and LuxR, AHL degrading. '''
+[[read more]]
 '''Equation14:''
@@ Line 351: / Line 376: @@
 '''The aim of the equation is to know the production rate of AHL concerning the LuxIAHL reaction, 2AHL + LuxR to (AHL)2/LuxR reaction, (AHL)2/LuxR complex to 2AHL + LuxR reaction and AHL degrading. '''
+[[read more]]
 '''Equation15:''
@@ Line 365: / Line 392: @@
 '''The aim of the equation is to know the threshold concentration of oxyR to conquer the terminal and when T7 polymerase can reach the required concentration to activate T7 promoter. '''
+[[read more]]
 '''Equation16:''
@@ Line 385: / Line 414: @@
 '''The aim of the equation is to know PDC production rate and when it can reach the concentration of ethanol pathway equilibrium.'''
+[[read more]]
 '''Equation17:''
@@ Line 406: / Line 437: @@
 '''The aim of the equation is to know ADH production rate and when it can reach the concentration of ethanol pathway equilibrium.'''
+[[read more]]
 '''Equation18:''
@@ Line 424: / Line 457: @@
 '''The aim of the equation is to know the production rate of AHL concerning the LuxIAHL reaction, 2AHL + LuxR to (AHL)2/LuxR reaction, (AHL)2/LuxR complex to 2AHL + LuxR reaction and AHL degrading. '''
+[[read more]]
 '''Equation19:''
@@ Line 438: / Line 473: @@
 '''The aim of the equation is to knowkiller protein production rate and when it can reach the effective concentration to killNosema. '''
+[[read more]]
 '''Equation20:''
@@ Line 458: / Line 495: @@
 '''The aim of the equation is to know ethanol production rate and when it can reach the concentration to kill the spores of Nosema Ceranae.''
+[[read more]]
 ==Parameters:==

Team:NYMU-Taipei/Modeling/MainParts

From 2013.igem.org

Revision as of 13:25, 27 October 2013

Contents

main part

Function of the parts:

Aims

Equations

Parameters: