|
|
| Line 3: |
Line 3: |
| | {{:Team:TU-Delft/Templates/Frog}} | | {{:Team:TU-Delft/Templates/Frog}} |
| | {{:Team:TU-Delft/Templates/Logo}} | | {{:Team:TU-Delft/Templates/Logo}} |
| - |
| |
| | <html> | | <html> |
| | | | |
| | <div style="margin-top:10px;margin-left:30px;margin-right:30px;float:left;display:inline-block;"> | | <div style="margin-top:10px;margin-left:30px;margin-right:30px;float:left;display:inline-block;"> |
| - | <h2 align="center">Timer Plus Sumo</h2> | + | <h2 align="center">Timer-SUMO-KillSwitch</h2> |
| | <br> | | <br> |
| - | <p align="justify">The separate modules: <a href="https://2013.igem.org/Timer_Plus_Sumo">Timer plus SUMO </a> and <a href="https://2013.igem.org/KillSwitch">Kill Switch</a> are combined to form the complete model of the system: Timer - SUMO - Kill Switch. For the final model, the kill switch module is converted in such a way so as the holin and antiholin to be activated by the Pci promoter. | + | <p align="justify">The separate modules: <a href="https://2013.igem.org/Timer_Plus_Sumo">Timer plus SUMO </a> and <a href="https://2013.igem.org/KillSwitch">Kill Switch</a> are combined to form the complete model of the system: Timer - SUMO - Kill Switch. For the final model, the kill switch module is converted in such a way so as the holin and antiholin to be activated by the Pci promoter. |
| | </p> | | </p> |
| - | <br>
| |
| - | <center>
| |
| - | <img src="https://static.igem.org/mediawiki/2013/9/96/Timer%2Bsumo.png" >
| |
| - | <p>Figure 1: Circuit of the timer including sumo cleaving</p></div>
| |
| - | </center>
| |
| - |
| |
| - | <div style="margin-top:40px;margin-left:30px;margin-right:30px;float:left;display:inline-block;">
| |
| - | <h2 align="center">Differential Equations</h2>
| |
| - |
| |
| - | <p align="justify">
| |
| - | The above circuit can be represented by the following differential equations. We assume a binary
| |
| - | behavior of the T7 promoter. In the presence of IPTG, the T7 promoter will be active. So, we make
| |
| - | the assumption that the T7 is binary variable with two possible states: either active 1 or inactive 0.</p>
| |
| - | <br>
| |
| - | <center>
| |
| - | <img src="https://static.igem.org/mediawiki/2013/b/b0/Equations_SumoUpd.png" >
| |
| - | </center>
| |
| | | | |
| | <div style="margin-left:30px;margin-right:30px;float:left;display:inline-block;"> | | <div style="margin-left:30px;margin-right:30px;float:left;display:inline-block;"> |
| - | <h2 align="center">Parameters</h2>
| |
| - | <br>
| |
| - |
| |
| - | </html>
| |
| - | <p>
| |
| - | {| align="center" border="1"
| |
| - | |'''Parameter'''
| |
| - | |'''Value'''
| |
| - | |'''Description'''
| |
| - | |'''Units'''
| |
| - | |'''Reference'''
| |
| - | |-
| |
| - | | c<sub>a</sub>
| |
| - | |1020
| |
| - | |Translation rate per amino acid
| |
| - | |min<sup>-1</sup>#<sub>a</sub><sup>-1</sup>
| |
| - | | [[Team:TUDelft/Modeling_References|[7]]]
| |
| - | |-
| |
| - | | c<sub>T7</sub>
| |
| - | |4.16
| |
| - | |Maximum transcription rate of T7
| |
| - | |#m/min
| |
| - | | [[Team:TUDelft/Modeling_References|[2]]]
| |
| - | |-
| |
| - | | c<sub>ptet</sub>
| |
| - | |2.79
| |
| - | |Maximum transcription rate of Ptet
| |
| - | |#m/min
| |
| - | | [[Team:TUDelft/Modeling_References|[4]]]
| |
| - | |-
| |
| - | | c<sub>ci</sub>
| |
| - | |1.79
| |
| - | |Maximum transcription rate of Pci
| |
| - | |#m/min
| |
| - | | [[Team:TUDelft/Modeling_References|[3]]]
| |
| - | |-
| |
| - | | d<sub>mRNA</sub>
| |
| - | |0.231
| |
| - | |Degradation rate of mRNA
| |
| - | |min<sup>-1</sup>
| |
| - | | [[Team:TUDelft/Modeling_References|[8]]]
| |
| - | |-
| |
| - | | d<sub>TET</sub>
| |
| - | |0.1386
| |
| - | |Degradation rate of TET
| |
| - | |min<sup>-1</sup>
| |
| - | | [[Team:TUDelft/Modeling_References|[9]]]
| |
| - | |-
| |
| - | | d<sub>CI</sub>
| |
| - | |0.042
| |
| - | |Degradation rate of CI
| |
| - | |min<sup>-1</sup>
| |
| - | | [[Team:TUDelft/Modeling_References|[9]]]
| |
| - | |-
| |
| - | | d<sub>PEP</sub>
| |
| - | |6.3*10<sup>-3</sup>
| |
| - | |Degradation rate of the peptide
| |
| - | |min<sup>-1</sup>
| |
| - | |Assumed the same as GFP
| |
| - | |-
| |
| - | | d<sub>PSU</sub>
| |
| - | |6.3*10<sup>-3</sup>
| |
| - | |Degradation rate of the peptide plus SUMO
| |
| - | |min<sup>-1</sup>
| |
| - | |Assumed the same as GFP
| |
| - | |-
| |
| - | | d<sub>Ulp</sub>
| |
| - | |1.263*10<sup>-2</sup>
| |
| - | |Degradation rate of Ulp
| |
| - | |min<sup>-1</sup>
| |
| - | |Assumed the same as GFP
| |
| - | |-
| |
| - | |l<sub>t7</sub>
| |
| - | |0.002
| |
| - | |Leakage factor of T7
| |
| - | | -
| |
| - | |Assumption
| |
| - | |-
| |
| - | |l<sub>ptet</sub>
| |
| - | |0.002
| |
| - | |Leakage factor of Ptet
| |
| - | | -
| |
| - | |Assumption
| |
| - | |-
| |
| - | |l<sub>ci</sub>
| |
| - | |0.002
| |
| - | |Leakage factor of Pci
| |
| - | | -
| |
| - | |Assumption
| |
| - | |-
| |
| - | |k<sub>tet</sub>
| |
| - | |6
| |
| - | |Dissociation constant of Ptet
| |
| - | |#m
| |
| - | |[[Team:TUDelft/Modeling_References|[10]]]
| |
| - | |-
| |
| - | |k<sub>ci</sub>
| |
| - | |20
| |
| - | |Dissociation constant of Pci
| |
| - | |#m
| |
| - | |[[Team:TUDelft/Modeling_References|[10]]]
| |
| - | |-
| |
| - | |k<sub>cUlp</sub>
| |
| - | |3
| |
| - | |Turnover rate of Ulp
| |
| - | |min<sup>-1</sup>
| |
| - | |[[Team:TUDelft/Modeling_References|[6]]]
| |
| - | |-
| |
| - | |n<sub>ci</sub>
| |
| - | |3
| |
| - | |Hills coefficient
| |
| - | | -
| |
| - | |[[Team:TUDelft/Modeling_References|[11]]]
| |
| - | |-
| |
| - | |n<sub>tet</sub>
| |
| - | |3
| |
| - | |Hills coefficient
| |
| - | | -
| |
| - | |[[Team:TUDelft/Modeling_References|[11]]]
| |
| - | |-
| |
| - | |s
| |
| - | |0 or 1
| |
| - | |Activation/Inactivation of T7 promoter
| |
| - | |Binary
| |
| - | |Assumption
| |
| - | |-
| |
| - | |s<sub>ci</sub>
| |
| - | |228
| |
| - | |Length of CI
| |
| - | |amino acids
| |
| - | |[[Team:TUDelft/Modeling_References|[12]]]
| |
| - | |-
| |
| - | |s<sub>PSU</sub>
| |
| - | |18 + 110
| |
| - | |Length of peptide plus SUMO
| |
| - | |amino acids
| |
| - | |[[Team:TUDelft/Modeling_References|[12]]]
| |
| - | |-
| |
| - | |s<sub>TET</sub>
| |
| - | |206
| |
| - | |Length of TET
| |
| - | |amino acids
| |
| - | |[[Team:TUDelft/Modeling_References|[13]]]
| |
| - | |-
| |
| - | |s<sub>Ulp</sub>
| |
| - | |233
| |
| - | |Length of Ulp1
| |
| - | |amino acids
| |
| - | |[[Team:TUDelft/Modeling_References|[13]]]
| |
| - | |-
| |
| - | |}
| |
| - | </p>
| |
| - |
| |
| - | <br>
| |
| - | <html>
| |
| - |
| |
| - |
| |
| - | <div style="margin-left:30px;margin-right:30px;float:left;display:inline-block;">
| |
| - | <h2 align="center">Results</h2>
| |
| - | <p align="justify">
| |
| - | TET and ULP must be set equal to zero (or a numerical equivalent). For CI the steady state value is
| |
| - | assumed as a starting condition as this is expressed before activation.
| |
| - | </p>
| |
| - | <br>
| |
| - | <center>
| |
| - | <img src="https://static.igem.org/mediawiki/2013/5/5d/Sumo.png">
| |
| - | <p>Figure 2: Simulation Results</p></div>
| |
| - | </center>
| |
| - | <br>
| |
| - |
| |
| - |
| |
| - | </html>
| |
| - | {{:Team:TU-Delft/Templates/Navigation}}
| |
| - | {{:Team:TU-Delft/Templates/Style}}
| |
| - | {{:Team:TU-Delft/Templates/Frog}}
| |
| - | {{:Team:TU-Delft/Templates/Logo}}
| |
| - | <html>
| |
| - |
| |
| - | <div style="margin-top:10px;margin-left:30px;margin-right:30px;float:left;display:inline-block;">
| |
| - | <h2 align="center">Timer Plus Sumo</h2>
| |
| - | <br>
| |
| - | <p align="justify">In this section the system of Figure 1 is modeled. The structure of the timer is very similar version of the timer compared to the construct of iGEM TU Delft team 2009. Here the input is changed to a
| |
| - | T7 promoter and the output to Ulp-1. Furthermore, the Ulp-1 cleaves off the SUMO from the peptide
| |
| - | combined with the SUMO.
| |
| - | </p>
| |
| - | <br>
| |
| - | <center>
| |
| - | <img src="https://static.igem.org/mediawiki/2013/9/96/Timer%2Bsumo.png" >
| |
| - | <p>Figure 1: Circuit of the timer including sumo cleaving</p></div>
| |
| - | </center>
| |
| - |
| |
| - | <div style="margin-top:40px;margin-left:30px;margin-right:30px;float:left;display:inline-block;">
| |
| | <h2 align="center">Differential Equations</h2> | | <h2 align="center">Differential Equations</h2> |
| - |
| |
| - | <p align="justify">
| |
| - | The above circuit can be represented by the following differential equations. We assume a binary
| |
| - | behavior of the T7 promoter. In the presence of IPTG, the T7 promoter will be active. So, we make
| |
| - | the assumption that the T7 is binary variable with two possible states: either active 1 or inactive 0.</p>
| |
| - | <br>
| |
| | <center> | | <center> |
| - | <img src="https://static.igem.org/mediawiki/2013/b/b0/Equations_SumoUpd.png" > | + | <img src="https://static.igem.org/mediawiki/2013/8/87/Combined_equations.png" > |
| | </center> | | </center> |
| - | | + | <div style="margin-left:30px;margin-right:30px;float:left;display:inline-block;"> |
| - | <div style="margin-left:30px;margin-right:30px;float:left;display:inline-block;"> | + | <p> |
| | <h2 align="center">Parameters</h2> | | <h2 align="center">Parameters</h2> |
| - | <br>
| |
| - |
| |
| - | </html>
| |
| - | <p>
| |
| - | {| align="center" border="1"
| |
| - | |'''Parameter'''
| |
| - | |'''Value'''
| |
| - | |'''Description'''
| |
| - | |'''Units'''
| |
| - | |'''Reference'''
| |
| - | |-
| |
| - | | c<sub>a</sub>
| |
| - | |1020
| |
| - | |Translation rate per amino acid
| |
| - | |min<sup>-1</sup>#<sub>a</sub><sup>-1</sup>
| |
| - | | [[Team:TUDelft/Modeling_References|[7]]]
| |
| - | |-
| |
| - | | c<sub>T7</sub>
| |
| - | |4.16
| |
| - | |Maximum transcription rate of T7
| |
| - | |#m/min
| |
| - | | [[Team:TUDelft/Modeling_References|[2]]]
| |
| - | |-
| |
| - | | c<sub>ptet</sub>
| |
| - | |2.79
| |
| - | |Maximum transcription rate of Ptet
| |
| - | |#m/min
| |
| - | | [[Team:TUDelft/Modeling_References|[4]]]
| |
| - | |-
| |
| - | | c<sub>ci</sub>
| |
| - | |1.79
| |
| - | |Maximum transcription rate of Pci
| |
| - | |#m/min
| |
| - | | [[Team:TUDelft/Modeling_References|[3]]]
| |
| - | |-
| |
| - | | d<sub>mRNA</sub>
| |
| - | |0.231
| |
| - | |Degradation rate of mRNA
| |
| - | |min<sup>-1</sup>
| |
| - | | [[Team:TUDelft/Modeling_References|[8]]]
| |
| - | |-
| |
| - | | d<sub>TET</sub>
| |
| - | |0.1386
| |
| - | |Degradation rate of TET
| |
| - | |min<sup>-1</sup>
| |
| - | | [[Team:TUDelft/Modeling_References|[9]]]
| |
| - | |-
| |
| - | | d<sub>CI</sub>
| |
| - | |0.042
| |
| - | |Degradation rate of CI
| |
| - | |min<sup>-1</sup>
| |
| - | | [[Team:TUDelft/Modeling_References|[9]]]
| |
| - | |-
| |
| - | | d<sub>PEP</sub>
| |
| - | |6.3*10<sup>-3</sup>
| |
| - | |Degradation rate of the peptide
| |
| - | |min<sup>-1</sup>
| |
| - | |Assumed the same as GFP
| |
| - | |-
| |
| - | | d<sub>PSU</sub>
| |
| - | |6.3*10<sup>-3</sup>
| |
| - | |Degradation rate of the peptide plus SUMO
| |
| - | |min<sup>-1</sup>
| |
| - | |Assumed the same as GFP
| |
| - | |-
| |
| - | | d<sub>Ulp</sub>
| |
| - | |1.263*10<sup>-2</sup>
| |
| - | |Degradation rate of Ulp
| |
| - | |min<sup>-1</sup>
| |
| - | |Assumed the same as GFP
| |
| - | |-
| |
| - | |l<sub>t7</sub>
| |
| - | |0.002
| |
| - | |Leakage factor of T7
| |
| - | | -
| |
| - | |Assumption
| |
| - | |-
| |
| - | |l<sub>ptet</sub>
| |
| - | |0.002
| |
| - | |Leakage factor of Ptet
| |
| - | | -
| |
| - | |Assumption
| |
| - | |-
| |
| - | |l<sub>ci</sub>
| |
| - | |0.002
| |
| - | |Leakage factor of Pci
| |
| - | | -
| |
| - | |Assumption
| |
| - | |-
| |
| - | |k<sub>tet</sub>
| |
| - | |6
| |
| - | |Dissociation constant of Ptet
| |
| - | |#m
| |
| - | |[[Team:TUDelft/Modeling_References|[10]]]
| |
| - | |-
| |
| - | |k<sub>ci</sub>
| |
| - | |20
| |
| - | |Dissociation constant of Pci
| |
| - | |#m
| |
| - | |[[Team:TUDelft/Modeling_References|[10]]]
| |
| - | |-
| |
| - | |k<sub>cUlp</sub>
| |
| - | |3
| |
| - | |Turnover rate of Ulp
| |
| - | |min<sup>-1</sup>
| |
| - | |[[Team:TUDelft/Modeling_References|[6]]]
| |
| - | |-
| |
| - | |n<sub>ci</sub>
| |
| - | |3
| |
| - | |Hills coefficient
| |
| - | | -
| |
| - | |[[Team:TUDelft/Modeling_References|[11]]]
| |
| - | |-
| |
| - | |n<sub>tet</sub>
| |
| - | |3
| |
| - | |Hills coefficient
| |
| - | | -
| |
| - | |[[Team:TUDelft/Modeling_References|[11]]]
| |
| - | |-
| |
| - | |s
| |
| - | |0 or 1
| |
| - | |Activation/Inactivation of T7 promoter
| |
| - | |Binary
| |
| - | |Assumption
| |
| - | |-
| |
| - | |s<sub>ci</sub>
| |
| - | |228
| |
| - | |Length of CI
| |
| - | |amino acids
| |
| - | |[[Team:TUDelft/Modeling_References|[12]]]
| |
| - | |-
| |
| - | |s<sub>PSU</sub>
| |
| - | |18 + 110
| |
| - | |Length of peptide plus SUMO
| |
| - | |amino acids
| |
| - | |[[Team:TUDelft/Modeling_References|[12]]]
| |
| - | |-
| |
| - | |s<sub>TET</sub>
| |
| - | |206
| |
| - | |Length of TET
| |
| - | |amino acids
| |
| - | |[[Team:TUDelft/Modeling_References|[13]]]
| |
| - | |-
| |
| - | |s<sub>Ulp</sub>
| |
| - | |233
| |
| - | |Length of Ulp1
| |
| - | |amino acids
| |
| - | |[[Team:TUDelft/Modeling_References|[13]]]
| |
| - | |-
| |
| - | |}
| |
| | </p> | | </p> |
| - |
| |
| - | <br>
| |
| - | <html>
| |
| - |
| |
| - |
| |
| - | <div style="margin-left:30px;margin-right:30px;float:left;display:inline-block;">
| |
| - | <h2 align="center">Results</h2>
| |
| - | <p align="justify">
| |
| - | TET and ULP must be set equal to zero (or a numerical equivalent). For CI the steady state value is
| |
| - | assumed as a starting condition as this is expressed before activation.
| |
| - | </p>
| |
| - | <br>
| |
| - | <center>
| |
| - | <img src="https://static.igem.org/mediawiki/2013/5/5d/Sumo.png">
| |
| - | <p>Figure 2: Simulation Results</p></div>
| |
| - | </center>
| |
| - | <br>
| |
| - |
| |
| - |
| |
| | </html> | | </html> |
"
