Team:Newcastle/Modelling/SporulationTuning

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==KinA Expression Model==
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==Sporulation Tuning Model==
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Under normal conditions, LacI represses KinA.
 
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[[Image:TeamNewcastleKinAExpLacIKinA.png|110px|center]]
 
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However, in the presence of IPTG, KinA can be expressed, as IPTG binds to LacI, deactivating it. Equations (a) and (b) describes how IPTG binds to LacI, forming LacI*, which is the deactivated form of LacI
 
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[[Image:TeamNewcastleKinAExpLacIIPTG1.png|220px|center]]
 
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Over time, the deactivated form of LacI, LacI* may degrade. This is also taken into consideration while building the model.
 
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[[Image:TeamNewcastleKinAExpDeactivatedLacIDegradation.png|80px|center]]
 
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Protein synthesis requires two steps, transcription and translation, and is further illustrated in Figure 1, below.
 
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[[Image:TeamNewcastleKinAExpTranscriptiontranslation.png|300px|center]]
 
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<center>''Figure 1: Transcription and Translation''</center>
 
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Referring to Figure 1, the following equations can be written:
 
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;<u>Transcription of LacI,</u>
 
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[[Image:TeamNewcastleKinAExpLacITranscription.png|120px|center]]
 
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;<u>Translation of LacI,</u>
 
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[[Image:TeamNewcastleKinAExpLacITranslation.png|80px|center]]
 
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where mRNA_LacI is inducing the formation of LacI.
 
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;<u>Transcription of KinA,</u>
 
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[[Image:TeamNewcastleKinAExpKinATranscription.png|130px|center]]
 
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where LacI is repressing mRNA_KinA, therefore a lower concentration of LacI would result in a higher concentration of mRNA_KinA.
 
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;<u>Translation of KinA,</u>
 
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[[Image:TeamNewcastleKinAExpKinATranslation.png|80px|center]]
 
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where mRNA_KinA is inducing the formation of KinA.
 
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===Results===
 
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The above equations were modelled in COPASI, and the following graphs show the behaviour of the system over time at different IPTG concentrations.
 
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;<u>IPTG concentration = 1000 nmol/fl</u>
 
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[[Image:TeamNewcastleKinAExpPic1.png|center|500px]]
 
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<center>''Figure 1.1''</center>
 
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In Figure 1.1, at a IPTG concentration of 1000nmol/fl, due to the high concentration of LacI*, it is difficult to view the results for the other species, such as, KinA, LacI, mRNA_KinA, and mRNA_LacI as they are all concentrated at the bottom.
 
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[[Image:TeamNewcastleKinAExpPic2.png|center|500px]]
 
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<center>''Figure 1.2''</center>
 
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Figure 1.2 shows the behaviour of KinA, LacI, mRNA_KinA and mRNA_LacI more clearly, at the IPTG concentration of 1000nmol/flu.
 
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From Figure 1.1 and 1.2, it is observed that the concentration of LacI* is significantly higher than the other species when the IPTG concentration is set at 1000nmol/fl. Looking at Figure 1.2, while the concentration of KinA is increasing, it is still lower than that of LacI.
 
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;<u>IPTG concentration = 3000 nmol/fl</u>
 
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[[Image:TeamNewcastleKinAExpPic3.png|center|500px]]
 
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<center>''Figure 2.1''</center>
 
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Comparing Figure 1.1 and 2.1, though the IPTG concentration in Figure 2.1 is 3000nmol/fl, the LacI* concentration is not particularly different.
 
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[[Image:TeamNewcastleKinAExpPic4.png|center|500px]]
 
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<center>''Figure 2.2''</center>
 
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As the IPTG concentration increases from 1000 to 3000nmol/fl, the KinA concentration is greater than the LacI concentration. However, upon a closer look, the KinA concentration did not increase due to the higher IPTG concentration. The KinA concentration is now higher than the LacI concentration because the LacI concentration decreased.
 
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;<u>IPTG concentration = 5000 nmol/fl</u>
 
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[[Image:TeamNewcastleKinAExpPic5.png|center|500px]]
 
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<center>''Figure 3.1''</center>
 
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Once again, as obsered in Figure 1.1 and 2.1, the concentration of LacI* in Figure 3.1 seems to reach the similar concentrations although the concentration of IPTG has been increased in each case. This seems to say that the concentration of LacI* has reached a threshold concentration.
 
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[[Image:TeamNewcastleKinAExpPic6.png|500px|center]]
 
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<center>''Figure 3.2''</center>
 
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The KinA concentration in Figure 3.2 is greater than that of LacI once again. However, KinA concentration seems to be stagnant at approximately 90nmol/fl, while the LacI concentration constantly decreases with increased IPTG concentration. Therefore, the IPTG concentration only seems to affect the LacI concentration.
 
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Revision as of 16:11, 21 October 2009




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