Team:Newcastle/Modeling/Stochastic

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Revision as of 19:02, 19 October 2009

Meetings Calendar

Stochastic Switch model

Our heads or tails stochastic switch is used in our system to a give decision to be a metal container and sequester Cadmium, or continue to normal vegetative life. This cell fate decision is given based on a number of parameters stochastically. Hin invertase which inverts a promoter is also included in the same region. Its expression is controlled by LacI controlled pspac promoter (inducable by IPTG) and XlyR controlled XylA promoter (Inducable by Xylose). LacI binds to pspac promoter and represses its expression whereas XylR binds to XylA promoter and represses its expression. When induced with IPTG, LacI falls off from the pspac promoter and when induced with Xylose, XylR falls of from XylA promoter and does not repress any more. The differences between LacI's and XylR's binding affinities to promoters and to their inducers effect the expression of Hin, hence the direction of the invertable region. When this region is oriented from left to right and pspac promoter is not repressed by LacI, sigA promoter in the invertable region expresses Rfp. When the region is oriented from right to the left, sigA promoter in the invertable region is also turned to right and express Gfp when its way is not blocked by XlyR bound to XylA promoter.

Hence Gfp and Rfp concentrations can be used as an indication of cell fate decisions and other downstream genes can be added after Rfp or Gfp to trigger those decisions.

This circuit can easily be controlled by IPTG and Xylose. As a third control, Arabinose can also be used. The orientation of the invertable region highly effect this decision and mainly the direction is changed by Hin protein. By doing so, its expression is also changed and this situation also adds to the stochasticity. Our stochastic switch has also modified version of ssrA degradation tag which requires sspB adaptor protein to get targetted for the degradatino by ClpXP system. Hence by controllling the expression of sspB by Arabinose (via araE promoter controlled by AraR), concentration of Hin can be controlled. Where necessary just a pulse of Hin can be created.

Here are the matlab files for our stochastic switch model, and below are some graphs which the model produced.

20 – 21 June 2009 - Europe workshop (London)
23 – 24 June 2009 - UK iGEM meetup (Edinburgh)
23 October Practice Presentation (Newcastle)
23 October T-shirts are ready
27 October Practice Presentation (Sunderland)
27 October Poster is ready
30 October – 2 November 2009 - Jamboree (Boston)

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 ==Stochastic Switch model==
-Our ''heads or tails'' stochastic switch is used in our system to a give decision to be a metal container and sequester Cadmium, or continue to normal vegetative life. This cell fate decision is given based on a number of parameters stochastically. Hin invertase which inverts a promoter is also included in the same region. Its expression is controlled by LacI controlled pspac promoter (inducable by IPTG) and XlyR controlled XylA promoter (Inducable by Xylose). LacI binds to pspac promoter and represses its expression whereas XylR binds to XylA promoter and represses its expression. When induced with IPTG, LacI falls of from the pspac promoter and when induced with Xylose, XylR falls of from XylA promoter and does not repress any more.  The differences between LacI's and XylR's binding affinities to promoters and to their inducers effect the expression of Hin, hence the direction of the invertable region. When this region is oriented from left to right and pspac promoter is not repressed by LacI, sigA promoter in the invertable region expresses Rfp. When the region is oriented from right to the left, sigA promoter in the invertable region is also turned to right and express Gfp when its way is not blocked by XlyR bound to XylA promoter.
+Our ''heads or tails'' stochastic switch is used in our system to a give decision to be a metal container and sequester Cadmium, or continue to normal vegetative life. This cell fate decision is given based on a number of parameters stochastically. Hin invertase which inverts a promoter is also included in the same region. Its expression is controlled by LacI controlled pspac promoter (inducable by IPTG) and XlyR controlled XylA promoter (Inducable by Xylose). LacI binds to pspac promoter and represses its expression whereas XylR binds to XylA promoter and represses its expression. When induced with IPTG, LacI falls off from the pspac promoter and when induced with Xylose, XylR falls of from XylA promoter and does not repress any more.  The differences between LacI's and XylR's binding affinities to promoters and to their inducers effect the expression of Hin, hence the direction of the invertable region. When this region is oriented from left to right and pspac promoter is not repressed by LacI, sigA promoter in the invertable region expresses Rfp. When the region is oriented from right to the left, sigA promoter in the invertable region is also turned to right and express Gfp when its way is not blocked by XlyR bound to XylA promoter.
 Hence Gfp and Rfp concentrations can be used as an indication of cell fate decisions and other downstream genes can be added after Rfp or Gfp to trigger those decisions.