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| - | ==KinA Expression Model== | + | ==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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| | {{:Team:Newcastle/Footer}} | | {{:Team:Newcastle/Footer}} |
| | {{:Team:Newcastle/Right}} | | {{:Team:Newcastle/Right}} |
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