Team:Aberdeen Scotland/parameters/invest 4

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[[Image:Input Model Graph 6.jpg|center|700px]]
[[Image:Input Model Graph 6.jpg|center|700px]]
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Knowing that the relationship between success with K LacI is quite uninteresting, our next plot will let us find another way of viewing the relationship between success, K tetR and K cI, and use our 4th dimension more cleverly
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[[Image:Input Model Graph 7.jpg|center|700px]]
[[Image:Input Model Graph 7.jpg|center|700px]]
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Knowing that the relationship between success with K<sub>LacI</sub> is quite uninteresting, our next plot will let us find another way of viewing the relationship between success, K <sub>TetR</sub> and K<sub>CI</sub>, and use our 4th dimension more cleverly
[[Image:Input Model Graph 8.jpg|center|700px]]
[[Image:Input Model Graph 8.jpg|center|700px]]
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[[Image:Input Model Graph 9.jpg|center|700px]]
[[Image:Input Model Graph 9.jpg|center|700px]]
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{{:Team:Aberdeen_Scotland/footer}}

Revision as of 14:08, 7 August 2009

University of Aberdeen iGEM 2009

The input dependant model

For this model, we no longer assume a trivial process of repression of lacI being liften and QS being turned on. The LacI repression is now a repression / induction hill function with a Kd of 1200 molecules per cell for IPGT forming IPGT lacI complexes. We assume IPGT leaks into the cell from outside. We only set the outside concentration of IPGT. For quorum sensing all we set is an elevated HSL concentration outside which is free to defuse in. We now include a feedback loop into the QS mechanism. To do this we attach a lux box onto the plasmid for producing luxR and luxI, like so:


Input Model Graph 1.jpg

However, we are taking the production strengths of this lux box to be reduced in comparison to our lux box for producing X, Y and cI. The strengths are

Production max for X, Y and cI = 0.44 pops

taken from the iGEM page of ***** and personal communication with **** on ****

Production min for X Y and cI = 0.013 pops

taken from *****

Production max for QS feedback = 0.002 pops

Production min for QS feedback = 0.00015 pops

These values are taken from the paper “ FIOADAOIDFJAOFJASDIOJASOIJADOAJSDAFOJAFOAJSD”

An important new parameter is KP. This is the dissociation constant for “P” activating the lux boxes. P is the luxR/HSL complex . To take a break from the wordy descriptions we will now show some small sections of results for this model, which should be easily interpretable after following the section about the Monte Carlo analysis


Outside levels of IPGT and HSL required for success

The outside levels of IPGT and HSL are the only two assumptions we make in this model, let’s see what these assumptions need to be in order to achieve success


Input Model Graph 2.jpg
Input Model Graph 3.jpg

So we need about 6000 molecules of both HSL and IPGT for success... although this will depend on our 3 old Kd values of KLacI KTetR KcI and our new one of KP. (P is the luxR HSL complex activating the lux boxes)

For this experiment the Kd values are


KLacI = 700 molecules per cell

KcI = 5000 molecules per cell

KtetR = 3000 molecules per cell

KP = 200 molecules per cell

For now we will take our outside levels of IPGT and HSL to be 10,000 molecules. Although we have not yet calculated physically appropriate values yet.

New relation between KTetR and KcI and KLacI

We studied this relationship in the simplified input model. Let’s now look at it again for the new input dependant one


Input Model Graph 5.jpg
Input Model Graph 6.jpg


Input Model Graph 7.jpg

Knowing that the relationship between success with KLacI is quite uninteresting, our next plot will let us find another way of viewing the relationship between success, K TetR and KCI, and use our 4th dimension more cleverly

Input Model Graph 8.jpg
Input Model Graph 9.jpg