Team:NTU-Singapore/Modelling/Parameter

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<div id="maincontent" style="margin-top:200px;">
<div id="maincontent" style="margin-top:200px;">
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=Variables=
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=Parameters=
 +
[[Image:800px-VanDusen_Botanical_Garden_maze.jpg|500px|center|thumb|What Parameters Should We USE??]]
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 +
 
==Lactose controlled production of E7 + Imm==
==Lactose controlled production of E7 + Imm==
#LacI = A
#LacI = A
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=Parameter Estimation=
=Parameter Estimation=
-
Estimation of different parameters
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'''Estimation of different parameters'''
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# Transcription         : 70nt/s
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{|border="0"
-
# Translation : 40aa/s
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|# Transcription :
-
# Number of Essential Genes : 297
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|70nt/s
-
# Number of mRNA per cell : 4000
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|-
-
# Average mRNA half life : 5min
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|# Translation:
-
# Average mRNA length         : 1100
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|40aa/s
 +
|-
 +
|# Number of Essential Genes:
 +
|297
 +
|-
 +
|# Number of mRNA per cell:
 +
|4000
 +
|-
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|# Average mRNA half life:
 +
|5min
 +
|-
 +
|# Average mRNA length:
 +
|1100
 +
|-
 +
|}
-
Assumptions  
+
'''Assumptions'''
#Rate of transcription is dependent on length of gene
#Rate of transcription is dependent on length of gene
#Number of amino acids is 1/3 of the number of nucleotides in a gene
#Number of amino acids is 1/3 of the number of nucleotides in a gene
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==E7 production system==
==E7 production system==
  {| align="center" border="1"
  {| align="center" border="1"
-
|Type
+
|'''Type'''
-
|Parameter
+
|'''Parameter'''
-
|Values
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|'''Values'''
-
|Comments
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|'''Comments'''
|-
|-
|Transcription Rate of Lac I gene
|Transcription Rate of Lac I gene
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|k3AB
|k3AB
|1
|1
-
|Estimate
+
|Estimate. This is based on the assumption <br> that the complex formation is only <br> dependent on the concentrations of <br> Lac I repressor and Lactose
|}
|}
-
==Lysis production system==
+
==Detection & Lysis system==
 +
Some of the parameter values were obtained via trial and error as the values could not be found in literature. The values are chosen to produce the desired behaviour of the graph. More work has to be done to actually find out how much lysis protein quantity is really required for lysis of the cell as this is still an unknown. Readers may find some of the parameters unrealistic but the purpose of this exercise is to observe how changing certain parameters may affect the system overall output. We advise the reader to look more into the behaviour of the system rather than be focused upon the numerical values.
 +
 
  {| align="center" border="1"
  {| align="center" border="1"
-
|Type
+
|'''Type'''
-
|Parameter
+
|'''Parameter'''
-
|Values
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|'''Values'''
-
|Comments
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|'''Comments'''
|-
|-
|Phosphorylation Rate of Ai-2
|Phosphorylation Rate of Ai-2
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|nD
|nD
|50
|50
-
|[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/LysisnD Trial And Error]
+
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/LysisnD Trial And Error]</span>
|-
|-
|Hill coefficeint for t7 pTag
|Hill coefficeint for t7 pTag
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|KE
|KE
|1
|1
-
|Estimate
+
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/LysisKE Trial And Error]</span>
|-
|-
|Dissociation Constant for Lysis
|Dissociation Constant for Lysis
|KF
|KF
-
|0.8
+
|1
-
|Estimate
+
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/LysisKF Trial And Error]</span>
|-
|-
|Constitutive Portion for SupD
|Constitutive Portion for SupD
|aD
|aD
|0.01
|0.01
-
|[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/LysisaD Trial and Error]
+
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/LysisaD Trial and Error]</span>
|-
|-
|Constitutive Portion for t7 pTag
|Constitutive Portion for t7 pTag
|aE
|aE
|0.01
|0.01
-
|Estimate
+
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/LysisaE Trial And Error]</span>
|-
|-
|Constitutive Portion for Lysis
|Constitutive Portion for Lysis
|aF
|aF
|0.0001
|0.0001
-
|[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/LysisaF Trial and Error]
+
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/LysisaF Trial and Error]</span>
|-
|-
|Complex Formation Rate Between <br> LsrR Repressor and Ai-2-Phosphorylated
|Complex Formation Rate Between <br> LsrR Repressor and Ai-2-Phosphorylated
|k3BC
|k3BC
|0.01
|0.01
-
|[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/Lysisk3BC Trial and Error]
+
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/Lysisk3BC Trial and Error]</span>
|-
|-
|Complex Formation Rate Between <br> SupD tRNA and t7 pTag mRNA
|Complex Formation Rate Between <br> SupD tRNA and t7 pTag mRNA
|k3DE
|k3DE
|0.000000001
|0.000000001
-
|[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/Lysisk3DE Trial and Error]
+
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/Lysisk3DE Trial and Error]</span>
|-
|-
|Amount of Protein Kinase
|Amount of Protein Kinase
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|-
|-
|}
|}
 +
 +
==GFP production system with logistic growth==
 +
{| align="center" border="1"
 +
|'''Type'''
 +
|'''Parameter'''
 +
|'''Values'''
 +
|'''Comments'''
 +
|-
 +
|Forward Reaction rate of Complex
 +
|kf
 +
|1.2
 +
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/kF Trial And Error]</span>
 +
|-
 +
|Reverse Reaction rate of Complex
 +
|kr
 +
|0.5
 +
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/kr Trial And Error]</span>
 +
|-
 +
|Rate of Logistic Growth
 +
|r
 +
|0.01
 +
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/r_logistic Trial And Error]</span>
 +
|-
 +
|Varying Capacity
 +
|A & B
 +
|1 & 0.9
 +
|<span style="font-size:16px;">[https://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter/A_B Trial And Error]</span>
 +
|-
 +
|}
 +
==References==
==References==
-
1. [http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters]<br>
+
1. [https://2007.igem.org/title=ETHZ/Parameters https://2007.igem.org/title=ETHZ/Parameters]<br>
2. Grass G, Otto M, Fricke B, et al., FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress, ARCHIVES OF MICROBIOLOGY,  Volume: 183  Issue: 1  Pages: 9-18  Published: JAN 2005
2. Grass G, Otto M, Fricke B, et al., FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress, ARCHIVES OF MICROBIOLOGY,  Volume: 183  Issue: 1  Pages: 9-18  Published: JAN 2005
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<br><br>
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Latest revision as of 15:14, 28 October 2008

Contents

Parameters

What Parameters Should We USE??


Lactose controlled production of E7 + Imm

  1. LacI = A
  2. Lactose =B
  3. E7 = C

Iron and Ai2 controlled production of Lysis

  1. Ai-2 : A
  2. ai-2-phos : B
  3. LsrR : C
  4. SupD derivatives : D
  5. T7ptag : E
  6. Lysis : F

Parameter Estimation

Estimation of different parameters

# Transcription : 70nt/s
# Translation: 40aa/s
# Number of Essential Genes: 297
# Number of mRNA per cell: 4000
# Average mRNA half life: 5min
# Average mRNA length: 1100

Assumptions

  1. Rate of transcription is dependent on length of gene
  2. Number of amino acids is 1/3 of the number of nucleotides in a gene
  3. Rate of Translation is dependent on number of nucleotides
  4. For each gene mRNA = 10 at steady state
  5. Rate of degradation of average mRNA = 1100/ 5 min
  6. Rate of degradation of protein is equivalent to time for cell division i.e. 40 min

Results

E7 production system

Type Parameter Values Comments
Transcription Rate of Lac I gene k1A 21 Made using Earlier assumptions
Transcription Rate of E7 + Imm gene k1C 2.470588 Made using Earlier assumptions
Degradation Rate of Lac I mRNA d1A 0.76246 Made using Earlier assumptions
Transcription Rate of E7 + Imm mRNA d1C 0.0897 Made using Earlier assumptions
Translation Rate of Lac I mRNA k2A 36 Made using Earlier assumptions
Translation Rate of E7 + Imm mRNA k2C 4.23539 Made using Earlier assumptions
Protein Degradation Rate d2A,d2C 0.03465 Made using Earlier assumptions
Hill coefficeint for E7 + Imm nC 1 This is obtained on the assumption that one Repressor
Protein binds to one Lactose molecule complex
Dissociation Constant for E7 + Imm KC 0.8 [1]
Constitutive Portion for E7 + Imm aC 0.5 Estimate since a is between 0 and 1
Implication that Lactose may not be
a very strongly Regulated Promoter
Complex Formation Rate Between
Lac I Repressor and Lactose 		k3AB 1 Estimate. This is based on the assumption
that the complex formation is only
dependent on the concentrations of
Lac I repressor and Lactose

Detection & Lysis system

Some of the parameter values were obtained via trial and error as the values could not be found in literature. The values are chosen to produce the desired behaviour of the graph. More work has to be done to actually find out how much lysis protein quantity is really required for lysis of the cell as this is still an unknown. Readers may find some of the parameters unrealistic but the purpose of this exercise is to observe how changing certain parameters may affect the system overall output. We advise the reader to look more into the behaviour of the system rather than be focused upon the numerical values.

Type Parameter Values Comments
Phosphorylation Rate of Ai-2 kPF 1 Estimate
Dephosphorylation Rate of Ai-2 kPB 1 Estimate
Transcription Rate of LsrR gene k1C 4.402517 Made using Earlier assumptions
Transcription Rate of SupD gene k1D 46.667 Made using Earlier assumptions
Transcription Rate of t7pTag gene k1E 1.5556 Made using Earlier assumptions
Transcription Rate of Lysis gene k1F 28 Made using Earlier assumptions
Degradation Rate of LsrR mRNA d1C 0.159845 Made using Earlier assumptions
Degradation Rate of SupD mRNA d1D 1.694359 Made using Earlier assumptions
Degradation Rate of t7pTag mRNA d1E 0.056478 Made using Earlier assumptions
Degradation Rate of Lysis mRNA d1F 1.0166 Made using Earlier assumptions
Translation Rate of LsrR Protein k2C 7.54716 Made using Earlier assumptions
Translation Rate of t7 pTag Protein k2E 2.6667 Made using Earlier assumptions
Translation Rate of Lysis Protein k2F 48 Made using Earlier assumptions
Protein Degradation Rate d2C,d2E,d2F 0.03465 Made using Earlier assumptions
Hill coefficeint for SupD nD 50 Trial And Error
Hill coefficeint for t7 pTag nE 1 Estimate. It is assuming that
one molecule of iron ion is required
to activate the production of one t7mRNA
Hill coefficeint for Lysis nF 1 Estimate. It is assumed that
one molecule of t7 is required
for activation of one Lysis mRNA
Dissociation Constant for SupD KD 15 [2]
Dissociation Constant for t7 pTag KE 1 Trial And Error
Dissociation Constant for Lysis KF 1 Trial And Error
Constitutive Portion for SupD aD 0.01 Trial and Error
Constitutive Portion for t7 pTag aE 0.01 Trial And Error
Constitutive Portion for Lysis aF 0.0001 Trial and Error
Complex Formation Rate Between
LsrR Repressor and Ai-2-Phosphorylated 		k3BC 0.01 Trial and Error
Complex Formation Rate Between
SupD tRNA and t7 pTag mRNA 		k3DE 0.000000001 Trial and Error
Amount of Protein Kinase S 28.747 From Earlier Assumptions

GFP production system with logistic growth

Type Parameter Values Comments
Forward Reaction rate of Complex kf 1.2 Trial And Error
Reverse Reaction rate of Complex kr 0.5 Trial And Error
Rate of Logistic Growth r 0.01 Trial And Error
Varying Capacity A & B 1 & 0.9 Trial And Error

References

1. https://2007.igem.org/title=ETHZ/Parameters
2. Grass G, Otto M, Fricke B, et al., FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress, ARCHIVES OF MICROBIOLOGY, Volume: 183 Issue: 1 Pages: 9-18 Published: JAN 2005

Retrieved from "http://2008.igem.org/Team:NTU-Singapore/Modelling/Parameter"