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| | __NOTOC__ | | __NOTOC__ |
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| + | ==Introduction == |
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| - | [[User:Jaroslaw Karcz|Jaroslaw Karcz]]. This is very confusing. A modelling page for infector detector and yet there is an entire section devoted to modelling, on the dry-lab drop-down menu. I have been working on ID there. I will continue to do so until I complete the modelling. See link below
| + | ==Implementation & Reaction Network== |
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| - | [https://2007.igem.org/Imperial/Dry_Lab/Modelling ID Modelling]
| + | ==Representative Model== |
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| + | ==Simulations== |
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| - | == Abstract == | + | ==Sensitivity Analysis?== |
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| - | == Graphs/Simulations ==
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| - | ==Approach==
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| - | Having generated the models for Infector Detector (applicable to both constructs) we intend to examine the behaviour of the system, w.r.t those state variables, which are experimentally manipulable.
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| - | Initially, we examine the behaviour of the system for a given set of parameters.
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| - | Our immediate goal is to obtain some intuition about the system; data analysis will in due course provide us with more biologically plausible parameters.
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| - | These can then be incorporated into the system model for a more representative output, which in turn allows for more realistic prediction/investigation. In other words, our initial approach is qualitative.
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| - | As described in the section on the development of the model, two models were established. However, these models are intimately connected. In fact, model 1 (link here), which is representative of the infinite energy case, is simply the limit case of the finite energy model, given by model 2. Model 2 approaches model 1, for greatly exaggerated initial energy (E<sub>0</sub>) and by setting the gene transcription cost, α<sub>i</sub> to zero.
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| - | Simulations are thus performed on the basis of the more representative model 2.
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| - | ===Investigations===
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| - | The following simulations were performed for both constructs, unless explicitly stated:
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| - | #[GFP] vs [AHL] - transfer function curve
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| - | #[GFP] vs time - varying [AHL]<sub>0</sub>
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| - | #[GFP] vs time - varying [P]<sub>0</sub>
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| - | #[GFP] vs time - varying [LuxR]<sub>0</sub> - Construct 2
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| - | ===Results===
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| - | ===='''1.'''====
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| - | [[Image: C1 GFP AHL.png |left|thumb|<b>Fig. 3</b>: Plot of [GFP] vs time for [AHL]<sub>0</sub> = 0.1nM, 1nM, 10nM & 100nM| 435px]]
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| - | [[Image: C2 GFP AHL.png |right|thumb|<b>Fig. 4</b>: Plot of [GFP] vs time for [AHL]<sub>0</sub> = 0.1nM, 1nM, 10nM & 100nM| 440px]]
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| - | ====<center>Discussion</center>====
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| - | It is evident from the above figures, that the response time of construct 1 (C1) is far greater than that of construct 2 (C2). C1 crosses some arbitrary threshold at approximately t = 80min, whereas C2 below 10min.
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| - | This is in line with our hypothesis, as we know steady-state has been forced upon the system in case of construct 2 - by flooding the system with purified LuxR.
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| - | Also the peak expression (max output) of GFP obtained for C1 is lower by approximately 50 percent. So, C2 produces a stronger output for corresponding [AHL].
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| - | However, although C2 is faster and generates a greater output, its energy consumption is far more pronounced. C1 thus has a greater lifespan.
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| - | ===='''2.'''====
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| - | [[Image: IC07 TransferFnc comp.png|thumb|left|440px]]
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| - | [[Image: IC07 TransferFnc2 comp.png|thumb|right|440px]]
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| - | ====<center>Discussion</center>====
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| - | The two figures above illustrate the response of both constructs after a specific t value. For both cases, the transfer function of C2 remains constant. However for C1, the sensitive AHL range decreases as t decreases (figure right - high t, left - low t). This is in line with our previous observation, where C1 longer response time compared to C2.
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| - | Also, it is clear that at lower concentrations of AHL, the output of both systems very close. As t increases, the concentration limit where both constructs have the same output can be increased by increasing t. This is because with more time, more LuxR is produced by C1 to allow a greater output compared to C2.
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| - | ===='''3.'''====
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| - | [[Image: C1_GFP_Po.png|left|thumb|<b>Fig. 5</b>: Plot of [GFP] vs time for varying [P]<sub>0</sub>| 420px]]
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| - | [[Image: C2_GFP_Po.png|right|thumb|<b>Fig. 6</b>: Plot of [GFP] vs time for varying [P]<sub>0</sub>| 420px]]
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| - | ====<center>Discussion</center>====
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| - | The above figures indicate the effect of increasing initial pLux promoter concentration ([P]<sub>0</sub>). The experiment involved varying ([P]<sub>0</sub>) and observing the concomitant effect on GFP expression. The following ([P]<sub>0</sub>) were utilized: 1, 2, 5, 10, 20 & 50nM.
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| - | It is clear that an increase in promoter concentration leads to reduction in response time (meaning that the same threshold is achieved in shorter time = more rapid response). This is a very prominent observation, particularly in the case of construct 1, in fig. x.
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| - | The increased promoter concentration also increases eventual maximum output of GFP = greater fluorescence = greater visual output. However, this effect is quite marginal. Evidently, this behaviour levels off (achieves saturation) with increased promoter concentration.
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| - | This behaviour is exhibited evidently in both constructs; however, the effect on C2 is quite interesting. Since we are increasing promoter concentration, there is increasing expenditure of energy. From previous analyses, we observed that for [P]<sub>0</sub> = 5, saturating behaviour for C2 (when initial [LuxR] was adjusted) occurred at [LuxR] ~ 10nM. For this concentration, the energy expenditure, was quite extensive. So that for the corresponding time lapse, only about a fifth of initial energy content remained.
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| - | In this experiment, the promoter concentration further depletes that energy, to such an extent that although a high expression peak (of GFP) is obtained (over 100000 arbitrary units), the lack of energy in the system, soon leads to degradation of [GFP] and visual output.
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| - | For C1, even though the promoter concentration is increased to the same extent, there is still residual energy, and so degradation of signal does not occur on the same time-scale as for C2.
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| - | ===='''4'''====
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| - | [[Image: C2 GFP LuxR1.png |left|thumb|<b>Fig. 5</b>: Plot of [GFP] vs time for varying [LuxR]<sub>0</sub>| 420px]]
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| - | [[Image: C2 GFP LuxR2.png |right|thumb|<b>Fig. 6</b>: Plot of [GFP] vs time for varying [LuxR]<sub>0</sub>| 420px]]
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| - | ====<center>Discussion</center>====
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| | == Equations == | | == Equations == |
| - | Link to [[Imperial/Dry_Lab/Modelling#Model_1|Equations to Construct 1]] in our Dry Lab page.
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| - | Link to [[Imperial/Dry_Lab/Modelling#Model_2|Equations to Construct 2]] in our Dry Lab page.
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| - | === Table of Parameters ===
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| - | Link to [[Imperial/Dry_Lab/Modelling#Model_Parameters|Table of Parameters]] in our Dry Lab page.
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| - | <center> [https://2007.igem.org/Imperial/Infector_Detector/Design << Design] | Modelling | [https://2007.igem.org/Imperial/Infector_Detector/Implementation Implementation >>]
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| - | </center>
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