Imperial/Infector Detector/F2620 Comparison

From 2007.igem.org

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|style="text-align: left;" |The graph above shows the transfer function of '''[AHL] <font color=red>input</font>''' vs '''rate of GFP synthesis <font color=red>output</font>'''. The graph shows the max rate of synthesis for each of the chassis; for ''in vivo'' this is the steady state reached after about 30 minutes and for ''in vitro'' it is the rate between 60 and 90 minutes which is the maximum rate before the energy limitations of the system cause the rate to drop. The blue line on corresponds to the range of AHL and the response of the ''in vitro'' chassis.<br>
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|style="text-align: left;" |The graph above shows the transfer function of '''[AHL] <font color=red>input</font>''' vs '''rate of GFP synthesis <font color=red>output</font>'''. The graph shows the follwoing:
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*''in vivo''(blue line) '''max rate of synthesis''' which is the steady state that is reached after about 30 minutes
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*''in vitro''(red line) '''max rate of synthesis''' which is the rate between 60 and 90 minutes which is the maximum rate before the energy limitations of the system cause the rate to drop. The dotted red line represents the expected transfer function for the lower AHL concentrations that we did not collected data points for.
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The key difference between the chassis is the rate of GFP synthesis which is lower in the ''in vitro'' chassis e.g. for 1000nM of AHL the rate of GFP synthesis ''in vivo'' is ~450 GFP molecules per sec per cell,'' ''in vitro'' has an equivalent value of 220 GFP molecules per second.<br>
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The key differences are between the chassis is the rate of GFP synthesis which is lower in the ''in vitro'' chassis e.g. for 1000nM of AHL the rate of GFP synthesis ''in vivo'' is ~450 GFP molecules per sec per cell,'' ''in vitro'' has an equivalent value of 220 GFP molecules per second.<br>
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The shape of the transfer function is very similar for both chassis, both begin to saturate at around 1000nM of AHL and the threshold of sensitivity is around 1nM AHL. It is very surprising that a construct works so similar in different chassis, showing the affect of the chassis is minimal to the constructs behavior.  
The shape of the transfer function is very similar for both chassis, both begin to saturate at around 1000nM of AHL and the threshold of sensitivity is around 1nM AHL. It is very surprising that a construct works so similar in different chassis, showing the affect of the chassis is minimal to the constructs behavior.  

Revision as of 23:47, 26 October 2007



Summary of Comparison

We thought to compare our in vitro characterisation to the characterisation of [http://partsregistry.org/Part:BBa_F2620 F2620] in vivo with the aim to highlight some of the differences between the chassis and investigate how the construct's characteristics may change between them. The [http://partsregistry.org/Part:BBa_F2620 F2620] is an ideal construct for comparison because of its detailed characterisation in vivo. The construct is the same as the construct 1 that was used for infecter detector, pTet-LuxR-pLux-GFPmut3b. The key results of the comparison were:

  • The creation of a new unit to allow comparison between in vitro and in vivo chassis.
  • That although we are changing the E.coli chassis from in vivo to in vitro the construct's characteristic response is independent of the chassis.

These are exciting findings, revealing the potential for the exploration of new chassis and the ability to use constructs in an exchangable manner.



IC2007 BF stage1 construct.PNG

The basis for comparison is to normalise the in vitro chassis on the number of plasmids to give a platform for comparison:
  • In Vitro - 4µg of DNA was added which for [http://partsregistry.org/Part:BBa_T9002 pTet-LuxR-pLux-GFPmut3b] is 904823007 plasmids
  • In Vivo - Each cell the plasmids number was estimated at 200 per cell

To compare we normalised the data of in vitro GFPmut3b molecules synthesised per 200 plasmids to allow some comparison to the in vivo data.

Of particular interest was to compare the:

  1. Rate of GFP synthesis of 100nM AHL
  2. Transfer Function.


In vitro in vivo comp.png
Comparison between in vivo and in vitro for rate of GFPmut3b synthesis for 100nM AHL. The in vivo chassis used was the bacterial strain MG1655 and the in vitro chassis was Promega Commercial S30 Cell Extract(60µl)


The graph shows the following:

  • in vivo has a maximal rate of 400-500 molecules of GFP synthesised per second per cell. In addition the rate reaches a steady state after around 30minutes and maintains it for the duration of the testing.
  • in vitro has the equivalent of 1400 molecules of GFP synthesised per second per cell equivalent, the cell equilavent being based upon the normalization of DNA plasmids. Interestingly the in vitro chassis does not reach a steady state, in fact it decreases in rate of synthesis after 90 minutes and keeps decreasing until rate is zero at around 360 minutes.

Key Difference:

  • GFP Synthesis - The life of synthesis of in vitro is about 90 minutes, compared to in vivo that has a life span of days. The differences is that in vitro has a burst of expression giving a high but short rate of GFP synthesis. In vivo is a slower rate but more prolonged rate of synthesis.
  • Intial Rate of Synthesis - The initial rate of GFP synthesis is slower for in vitro. This is thought to be due to LuxR levels, which in vivo are at steady state but in vitro has to produce the LuxR upon addition of DNA.

Interestingly the values of rate of synthesis are in the same order magnitude of hundreds, this suggesting that the normalisation we are using to compare these chassis is valid.

Transfer Function


Comparison of transfer function.PNG
The graph above shows the transfer function of [AHL] input vs rate of GFP synthesis output. The graph shows the follwoing:
  • in vivo(blue line) max rate of synthesis which is the steady state that is reached after about 30 minutes
  • in vitro(red line) max rate of synthesis which is the rate between 60 and 90 minutes which is the maximum rate before the energy limitations of the system cause the rate to drop. The dotted red line represents the expected transfer function for the lower AHL concentrations that we did not collected data points for.


The key differences are between the chassis is the rate of GFP synthesis which is lower in the in vitro chassis e.g. for 1000nM of AHL the rate of GFP synthesis in vivo is ~450 GFP molecules per sec per cell, in vitro has an equivalent value of 220 GFP molecules per second.
The shape of the transfer function is very similar for both chassis, both begin to saturate at around 1000nM of AHL and the threshold of sensitivity is around 1nM AHL. It is very surprising that a construct works so similar in different chassis, showing the affect of the chassis is minimal to the constructs behavior.

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