# IGEM:IMPERIAL/2006/project/Oscillator/project browser/Test Sensing Predator Construct/Modelling

### From OpenWetWare

< IGEM:IMPERIAL | 2006 | project | Oscillator | project browser | Test Sensing Predator Construct(Difference between revisions)

Current revision (10:13, 29 October 2006) (view source) (→Predator Test Construct) |
|||

Line 24: | Line 24: | ||

</div> | </div> | ||

<br style="clear:both"> | <br style="clear:both"> | ||

- | = | + | __NOTOC__ |

- | + | ==Model assumptions and relevance== | |

- | * | + | *General assumptions on gene expression modelling: |

- | * | + | **Quasi-steady state hypothesis on mRNA expression. |

+ | **Gene activation can be approximated by [http://en.wikipedia.org/wiki/Hill_equation Hill equations]. | ||

- | + | *Assumptions linked to the quorum sensing: | |

+ | **As a first approximation, we assume that luxR and AHL molecules form a heterodimer (even if it has been found that the complex formed is more complicated). | ||

+ | **The degradation rate of luxR and aiiA is mainly due to the growth dilution. | ||

- | + | ==Model description of the oscillator== | |

- | + | ||

- | + | ||

+ | '''[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/Modelling Full derivation of the above equations.]''' | ||

- | + | ==Model description of the growth of the predator== | |

+ | *mathematical description of the predator growth and death: | ||

+ | **<math>\frac{d[luxR]}{dt} = \frac{c * [AHL] * [luxR]}{(c0 + [AHL] * [luxR])} - gd * [luxR]</math> | ||

+ | **<math>\frac{d[aiiA]}{dt} = \frac{c * [AHL] * [luxR]}{(c0 + [AHL] * [luxR])} - gd * [aiiA]</math> | ||

- | + | *insert a graphical representation if possible (e.g. CellDesigner display) | |

- | + | *link to SBML file or matlab. | |

- | + | ||

- | + | ||

+ | ==Model variables and parameters for the growth of the predator== | ||

+ | (list all the variables and parameters of the model in a table, specifying if their values are known, unknown, to be measured.) | ||

- | ''' | + | {| border="1" width="100%" |

- | + | | style="background:lightblue" colspan="5"| '''Variables''' | |

- | + | |- style="background:lightgrey" | |

- | + | !Name !! Description !! Initial Value !! Confidence !! Reference | |

- | + | ||

- | ! Name !! Value | + | |

|- | |- | ||

- | + | |width="100"| AHL || homoserine lactone acting as the prey-molecule || 0|| depends how good is the control of the prey positive feedback || links | |

- | | 0 | + | |

|- | |- | ||

- | + | |width="100"| luxR || molecule acting as the sensing module for the predator || 0|| to be measured as we might have to deal with some leakage of the promoter || links | |

- | | 0 | + | |

|- | |- | ||

- | + | |width="100"| aiiA || molecule acting as the killing module of the prey for the predator || 0 || to be measured as we might have to deal with some leakage of the promoter || links | |

- | | | + | |

- | | | + | |

- | + | ||

- | | 0 | + | |

- | + | ||

|} | |} | ||

- | |||

- | + | {| border="1" width="100%" | |

- | '''Parameters | + | | style="background:lightblue" colspan="5"| '''Parameters''' |

- | + | |- style="background:lightgrey" | |

- | + | ! Name !! Description !! Value !! Confidence !! Reference | |

- | + | ||

- | + | ||

- | ! Name !! Value | + | |

|- | |- | ||

- | + | |width="100"| c || maximum synthesis rate of the pLux promoter || to be characterized || to be measured || links | |

- | | | + | |

|- | |- | ||

- | + | |width="100"| c0 || dissociation constant according to Hill eq || to be characterized|| to be measured || links | |

- | | | + | |

|- | |- | ||

- | + | |width="100"| gd || growth dilution || to be characterized || to be measured || links | |

- | | | + | |

- | | | + | |

- | + | ||

- | | | + | |

- | + | ||

|} | |} | ||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | |||

- | + | ==Characterization== | |

- | + | *Parameters c & c0 for characterization have to be extracted. | |

+ | *gd[luxR] and gd[aiiA] can be controlled by the chemostat. |

## Current revision

Super Parts | Predator Construct | |||
---|---|---|---|---|

Actual Part | ||||

Sub Parts | <bbpart>R0062</bbpart> | <bbpart>B0034</bbpart> | <bbpart>C0062</bbpart> | <bbpart>I13504</bbpart> |

- Specifications
- Design
**Modelling**- Implementation
- Testing/Validation

## Model assumptions and relevance

- General assumptions on gene expression modelling:
- Quasi-steady state hypothesis on mRNA expression.
- Gene activation can be approximated by Hill equations.

- Assumptions linked to the quorum sensing:
- As a first approximation, we assume that luxR and AHL molecules form a heterodimer (even if it has been found that the complex formed is more complicated).
- The degradation rate of luxR and aiiA is mainly due to the growth dilution.

## Model description of the oscillator

**Full derivation of the above equations.**

## Model description of the growth of the predator

- mathematical description of the predator growth and death:

- insert a graphical representation if possible (e.g. CellDesigner display)
- link to SBML file or matlab.

## Model variables and parameters for the growth of the predator

(list all the variables and parameters of the model in a table, specifying if their values are known, unknown, to be measured.)

Variables
| ||||

Name | Description | Initial Value | Confidence | Reference |
---|---|---|---|---|

AHL | homoserine lactone acting as the prey-molecule | 0 | depends how good is the control of the prey positive feedback | links |

luxR | molecule acting as the sensing module for the predator | 0 | to be measured as we might have to deal with some leakage of the promoter | links |

aiiA | molecule acting as the killing module of the prey for the predator | 0 | to be measured as we might have to deal with some leakage of the promoter | links |

Parameters
| ||||

Name | Description | Value | Confidence | Reference |
---|---|---|---|---|

c | maximum synthesis rate of the pLux promoter | to be characterized | to be measured | links |

c0 | dissociation constant according to Hill eq | to be characterized | to be measured | links |

gd | growth dilution | to be characterized | to be measured | links |

## Characterization

- Parameters c & c0 for characterization have to be extracted.
- gd[luxR] and gd[aiiA] can be controlled by the chemostat.