Team:Imperial College London/Modelling/Output/Results and Conclusion

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Department of Bioengineering

Division of Molecular Biosciences

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Objectives; Detailed Description; Parameters & Constants; Results & Conclusion;Download MatLab Files;

Results & Conclusion

Changing time when catechol is added

If Catechol is added before t= 1000s, then the coloured output will reach its threshold value faster by simple production. If Catechol is added when t>1000s, then the coloured output will increase (marginally) faster through the amplification step in Model A. There does not seem to be a significant difference between the two models (Model preA and Model A). These observations are true for intial concentration of dioxygenase equal to 10^-5mol/dm³. However, we noticed that if the initial concentration is raised to 10^-4mol/dm³, then Model A can be more beneficial than Model preA after only 100 seconds. Hence, the question arises whether the concentration of protein in the cell can be as high as 10^-4mol/dm³. Our simple production model predicted that the concentration of protein could not reach such a high value. However, we decided to research more on ribosomal concentrations in bacteria to determine whether it is possible to establish such a high concentration in the cell. On the website E.coli Statistics [http://gchelpdesk.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi] it is stated that number of ribosomal proteins per cell is 900,000. In a cellular volume of order of 1μm³ = 10^-15dm³=10^-15L, the above number of ribosomes converts to 1.5×10^-3mol/L. This means that a concentration of 10^-4mol/dm³ is not completely out of scale.

Changing concentration of catechol added

There seem to be 3 regions of catechol concentration that influence the system in different ways. These regions are: c>1M, 1M>c>0.01M, 0.01M>c. The boundaries of these regions tend to vary depending on the choice of other initial conditions. The values given above apply to boundary conditions that are currently considered to be physiologically relevant. Varying the initial concentration of catechol within the highest region does not result in any change of colour output response (It is possible that all enzymes are occupied and the solution is over saturated with catechol). In the middle region the catechol concentration influences the amplfication. Amplification decreased when the concentration tends towards 0.01M. When this region is entered, there is no difference in output production by the two models.

Cell death

The coloured product of catechol kills cells by destroying the cell membrane. However, we do not know how quickly the cells will die. Therefore, we examined two different cases: immediate cell death and negligible cell death (i.e. cells death is negligible because it takes too long) Running the simluation in Matlab (not Simbiology!), our conclusions are:

Immediate cell death slows down production of coloured output. Depending on the threshold concentration this can delay the detectable response by a few minutes.
If Catechol is added before t=1000s, then cell death slows down the response considerably.
In case of cells being modelled as alive, the difference between the amplified and the simple production model is smaller than it is in case of cell death.

Since it appears that the time of cell death is important, we decided to discuss this issue with Wolf and Harriet. Referring to this paper [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6V78-4XXNV4Y-4-7&_cdi=5836&_user=217827&_pii=S0048969709011668&_orig=search&_coverDate=02%2F01%2F2010&_sk=995919994&view=c&wchp=dGLbVzz-zSkzk&_valck=1&md5=f8dca6227c29db659ddbeb588ad115e7&ie=/sdarticle.pdf (1)] we decided that cell death induced by catechool is a very slow process (we estimate that it will take a few hours) in comparison to the time scale that we are interested in (several seconds to minutes).

Output Amplification Model

File:Alive cells.png

Colour response model for cells being kept alive

File:Dead cells.png

Colour response model with the same parameters for cells being killed instantaneously by catechol

@@ Line 6: / Line 6: @@
   <a href="https://2010.igem.org/wiki/index.php?title=Team:Imperial_College_London/Modelling/Output/Objectives"><b>Objectives</b></a>; <a href="https://2010.igem.org/Team:Imperial_College_London/Modelling/Output/Detailed_Description"><b>Detailed Description</b></a>; <a href="https://2010.igem.org/Team:Imperial_College_London/Modelling/Output/Parameters_and_Constants"><b>Parameters & Constants</b></a>; <a href="https://2010.igem.org/Team:Imperial_College_London/Modelling/Output/Results_and_Conclusion"><b>Results & Conclusion</b></a>;<a href="https://2010.igem.org/Team:Imperial_College_London/Modelling/Output/Download_MatLab_Files"><b>Download MatLab Files</b></a>;
 </html>
+|}
+{| style="width:900px;background:#f5f5f5;text-align:justify;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:25px;" cellspacing="20"
+|style="font-family: helvetica, arial, sans-serif;font-size:2em;color:#ea8828;"|Output Amplification Model
+|-
+<html><h2>Results & Conclusion</h2></html>
+*'''Changing time when catechol is added'''
+If Catechol is added before t= 1000s, then the coloured output will reach its threshold value faster by simple production. If Catechol is added when t>1000s, then the coloured output will increase (marginally) faster through the amplification step in Model A. There does not seem to be a significant difference between the two models (Model preA and Model A). These observations are true for intial concentration of dioxygenase equal to <html>10<sup>-5</sup>mol/dm<sup>3</sup></html>. However, we noticed that if the initial concentration is raised to <html>10<sup>-4</sup>mol/dm<sup>3</sup></html>, then Model A can be more beneficial than Model preA after only 100 seconds.
+Hence, the question arises whether the concentration of protein in the cell can be as high as <html>10<sup>-4</sup>mol/dm<sup>3</sup></html>. Our simple production model predicted that the concentration of protein could not reach such a high value. However, we decided to research more on ribosomal concentrations in bacteria to determine whether it is possible to establish such a high concentration in the cell.
+On the website E.coli Statistics [http://gchelpdesk.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi] it is stated that number of ribosomal proteins per cell is 900,000.
+In a cellular volume of order of <html>1&mu;m<sup>3</sup> = 10<sup>-15</sup>dm<sup>3</sup>=10<sup>-15</sup>L</html>, the above number of ribosomes converts to <html>1.5&times;10<sup>-3</sup>mol/L</html>. This means that a concentration of <html>10<sup>-4</sup>mol/dm<sup>3</sup></html> is not completely out of scale.
+*'''Changing concentration of catechol added'''
+There seem to be 3 regions of catechol concentration that influence the system in different ways. These regions are: c>1M, 1M>c>0.01M, 0.01M>c. The boundaries of these regions tend to vary depending on the choice of other initial conditions. The values given above apply to boundary conditions that are currently considered to be physiologically relevant. Varying the initial concentration of catechol within the highest region does not result in any change of colour output response (It is possible that all enzymes are occupied and the solution is over saturated with catechol). In the middle region the catechol concentration influences the amplfication. Amplification decreased when the concentration tends towards 0.01M. When this region is entered, there is no difference in output production by the two models.
+*'''Cell death'''
+The coloured product of catechol kills cells by destroying the cell membrane.
+However, we do not know how quickly the cells will die.
+Therefore, we examined two different cases: immediate cell death and negligible cell death (i.e. cells death is negligible because it takes too long)
+Running the simluation in Matlab (not Simbiology!), our conclusions are:
+#Immediate cell death slows down production of coloured output. Depending on the threshold concentration this can delay the detectable response by a few minutes.
+#If Catechol is added before t=1000s, then cell death slows down the response considerably.
+#In case of cells being modelled as alive, the difference between the amplified and the simple production model is smaller than it is in case of cell death.
+Since it appears that the time of cell death is important, we decided to discuss this issue with Wolf and Harriet. Referring to this paper [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6V78-4XXNV4Y-4-7&_cdi=5836&_user=217827&_pii=S0048969709011668&_orig=search&_coverDate=02%2F01%2F2010&_sk=995919994&view=c&wchp=dGLbVzz-zSkzk&_valck=1&md5=f8dca6227c29db659ddbeb588ad115e7&ie=/sdarticle.pdf (1)] we decided that cell death induced by catechool is a very slow process (we estimate that it will take a few hours) in comparison to the time scale that we are interested in (several seconds to minutes).
+{|
+|-
+|[[Image:Alive_cells.png|500px|thumb|center|alt=A|Colour response model for cells being kept alive]]
+|
+[[Image:Dead_cells.png|500px|thumb|center|alt=A|Colour response model with the same parameters for cells being killed instantaneously by catechol ]]
 |}