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| <h2>Methodology</h2> | | <h2>Methodology</h2> |
| <p>Given the genetic circuits provided by LabPats team, we modelled the response functions of Plasmid1 and Plasmid 2. After generating the functional response models for both models, we ran a combinatorial analysis that tested the response of sfGFP expression across a range of RBS from RBS29-35, and performed sensitivity analysis. A combinatorial analysis requires changing one part and measuring the changing response of the model. In contrast, a sensitivity analysis measures the impact each part contributes to the response of the mode. The RBS in Plasmid 2 that was changed in the combinatorial analysis was the RBS downstream of J23117, as requested. Plasmid 1 and Plasmid 2 models were both simulated for 3600s. This timeframe is suitable as the models capture the transient and steady state responses of sfGFP. | | <p>Given the genetic circuits provided by LabPats team, we modelled the response functions of Plasmid1 and Plasmid 2. After generating the functional response models for both models, we ran a combinatorial analysis that tested the response of sfGFP expression across a range of RBS from RBS29-35, and performed sensitivity analysis. A combinatorial analysis requires changing one part and measuring the changing response of the model. In contrast, a sensitivity analysis measures the impact each part contributes to the response of the mode. The RBS in Plasmid 2 that was changed in the combinatorial analysis was the RBS downstream of J23117, as requested. Plasmid 1 and Plasmid 2 models were both simulated for 3600s. This timeframe is suitable as the models capture the transient and steady state responses of sfGFP. |
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| <h2>Results</h2> | | <h2>Results</h2> |
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| <h2>Discussion</h2> | | <h2>Discussion</h2> |
| <p>Results indicate that the greater the RBS strength, the greater the expression level of sfGFP. Therefore, from RBS29-35, RBS 35 and RBS34 offer the greatest levels of expression. They are followed by RBS29 and 30 which offer medium levels of expression, then RBS31 which offers low levels of expression, and finally RBS33 which offers a very low level of expression.</p> | | <p>Results indicate that the greater the RBS strength, the greater the expression level of sfGFP. Therefore, from RBS29-35, RBS 35 and RBS34 offer the greatest levels of expression. They are followed by RBS29 and 30 which offer medium levels of expression, then RBS31 which offers low levels of expression, and finally RBS33 which offers a very low level of expression.</p> |
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| <p>In practice, let us consider a case in Plasmid 2 where 1. the expression levels of sfGFP is not high enough despite using RBS34; and 2. PLasR is fixed because of its application in the circuit. Experimenters could change RBS34 to RBS35 to increase expression levels, however the resultant increase in sfGFP expression may not be enough. From the model we can identify that promoter strength has the greatest effect on response, therefore by changing J23117 to a stronger constitutive promoter such as J23114, we should be able to increase sfGFP expression levels significantly.</p> | | <p>In practice, let us consider a case in Plasmid 2 where 1. the expression levels of sfGFP is not high enough despite using RBS34; and 2. PLasR is fixed because of its application in the circuit. Experimenters could change RBS34 to RBS35 to increase expression levels, however the resultant increase in sfGFP expression may not be enough. From the model we can identify that promoter strength has the greatest effect on response, therefore by changing J23117 to a stronger constitutive promoter such as J23114, we should be able to increase sfGFP expression levels significantly.</p> |
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| <h2>Limitations of the Model</h2> | | <h2>Limitations of the Model</h2> |
| <p>Models of Plasmid 1 and Plasmid 2 represent a general understanding of the system; however, they are not without their limitations. As stated previously, the models are limited due to assumptions in Plasmid 1 about promoter strength and molecule interaction kinetics between LsrR and PLsr; and in Plasmid 2 assumptions about the molecule interaction kinetics between PLasR and LasR. To rectify these limitations further characterisation of PLsR and LsrR molecule, and PLasR and LasR molecule are needed.</p> | | <p>Models of Plasmid 1 and Plasmid 2 represent a general understanding of the system; however, they are not without their limitations. As stated previously, the models are limited due to assumptions in Plasmid 1 about promoter strength and molecule interaction kinetics between LsrR and PLsr; and in Plasmid 2 assumptions about the molecule interaction kinetics between PLasR and LasR. To rectify these limitations further characterisation of PLsR and LsrR molecule, and PLasR and LasR molecule are needed.</p> |
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| <h2>Our Applications</h2> | | <h2>Our Applications</h2> |
| <p> </p> | | <p> </p> |
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