IGEM:IMPERIAL/2006/project/Oscillator/project browser/Test Sensing Predator Construct: Difference between revisions

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=Predator Test Construct=
==Motivation==
==Motivation==


The purpouse for building and testing this part is so we can test the predator cell in isolation to determine the Production rates of the proteins involved in the predator cell. The Aiia gene has been replaced with GFP. This allows us to directly mesure the production rate of a protein which is located in the place of GFP in our final system.
*The purpouse for building and testing this part is so we can characterize the production of AHL-lactonase
 
*The Aiia gene has been replaced with GFP to allow direct measurement of protein production
From this data we can create a transfer function where AHL is the input and GFP the output. We then make the assumpion that aiiA is transcribed at the same rate as GFP. This allpws us determine paremeters for our model.
*From this data we can create a transfer function where AHL is the input and GFP the output  
*Making the assumpion that AHL-lactonase is transcribed at the same rate as GFP we can use the transfer curve to extract parameters to allow characterization of the sensing part of the predator
*In this part the AiiA gene has been replaced with the reporter gene GFP to allow the measurement of the production of GFP as a function of AHL.
*The part will be used to form the sensing part of the final predator construct
*The resulting transfer curve will be used to extract parameters Vmax and Kd to characterize the part and for use in our modelling.
*The part will form the receiver of the final predator construct
[[Image:R0062 logo.png|40px]][[Image:B0034 logo.png|40px]][[Image:C0062 logo.png|40px]][[Image:B0034 logo.png|40px]]


==Parts Interface==
==Parts Interface==
This Part is designed to mimic the predator sensing part to get parameters for the model. It will give us an idea of the expression of aiiA.


{| border="0" width="100% align="center"
{| border="0" width="100% align="center"
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! style="background:#66CC99"| INPUTS !!style="background:#FF3333"| OUTPUTS  
! style="background:#66CC99"| INPUTS !!style="background:#FF3333"| OUTPUTS  
|-
|-
| AHL || GFP  
| AHL || AHL-lactonase & fluctuating [AHL]
 
|}
||
[[Image:PredatorAtDeviceLevel.png|thumbnail|right|350px|Predator construct at the device level.]]
|-
|
{| border="1" cellpadding="15" width="100%"
|-
! style="background:#66CC99"| INPUTS !!style="background:#FF3333"| OUTPUTS
|-
| AHL || AHL-lactonase
|}
||
[[Image:Predsenspart.png|thumbnail|right|350px|Predator sensing test construct.]]
|-
|
{| border="1" cellpadding="15" width="100%"
|-
! style="background:#66CC99"| INPUTS !!style="background:#FF3333"| OUTPUTS
|-
| AHL || GFP
|}
|}
||
||
[[]]
[[Image:Predsensingblackbox.png|thumbnail|right|350px|Predator sensing test construct.]]
|}
|}
[[Image:IGEM IMPERIAL PreadatorConstructSystemIcon.png|thumbnail|left|350px|Predator construct at the system level.]][[Image:PredatorAtDeviceLevel.png|thumbnail|right|350px|Predator construct at the device level.]]


==Expected behavior and performances==
==Expected behavior and performances==
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! style="background:lightgrey" width="100pt" |Properties !! colspan="2" | Specifications
! style="background:lightgrey" width="100pt" |Properties !! colspan="2" | Specifications
|-
|-
| Input Range(s)|| colspan="2" | Input range of the prey should at least match the dynamic range of the prey.
| Input Range(s)|| colspan="2" | [0.01nm,10000nm]
|-
| rowspan="2"| Output Range(s)|| colspan="2" | Output range of the prey should at least match the dynamic range of the prey.
|-
|-
| colspan="2" | Output range of the predator to be defined.
| Output Range(s)|| colspan="2" | <font color=red>'''?'''</font>
|-
|-
| Transfer function(s) || [[Image:IGEM_IMPERIAL_TransferFunctionPredator1.png|250px]] <br> Transfer function inspired by the pure Lotka-Volterra equations, growth predator = C*prey_population_*predator_population|| [[Image:IGEM_IMPERIAL_TransferFunctionPredator2.png|250px]] <br>Transfer function inspired by the pure Lotka-Volterra equations, prey killing = B*prey_population_*predator_population.
| Transfer function(s) || [[Image:016transfercurve.png|250px]]  
|-
|-
| Robustness || colspan="2" | Device should work for at least 10 cycles of the oscillator to match system level oscillator specifications.
| Robustness || colspan="2" | Device should work for at least 10 cycles of the oscillator to match system level oscillator specifications.

Latest revision as of 07:21, 29 October 2006

Super Parts Predator Construct
Actual Part
Sub Parts <bbpart>R0062</bbpart> <bbpart>B0034</bbpart> <bbpart>C0062</bbpart> <bbpart>I13504</bbpart>


Motivation

  • The purpouse for building and testing this part is so we can characterize the production of AHL-lactonase
  • The Aiia gene has been replaced with GFP to allow direct measurement of protein production
  • From this data we can create a transfer function where AHL is the input and GFP the output
  • Making the assumpion that AHL-lactonase is transcribed at the same rate as GFP we can use the transfer curve to extract parameters to allow characterization of the sensing part of the predator
  • The part will be used to form the sensing part of the final predator construct

Parts Interface

INPUTS OUTPUTS
AHL AHL-lactonase & fluctuating [AHL]
Predator construct at the device level.
INPUTS OUTPUTS
AHL AHL-lactonase
Predator sensing test construct.
INPUTS OUTPUTS
AHL GFP
Predator sensing test construct.

Expected behavior and performances

System level specifications
Properties Specifications
Input Range(s) [0.01nm,10000nm]
Output Range(s) ?
Transfer function(s)
Robustness Device should work for at least 10 cycles of the oscillator to match system level oscillator specifications.
Variability Variability at the device population level (day to day, device to device) should be as low as possible.
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