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<img src="https://static.igem.org/mediawiki/2018/a/a3/T--RHIT--EQGEN.png" style="width:50%"> | <img src="https://static.igem.org/mediawiki/2018/a/a3/T--RHIT--EQGEN.png" style="width:50%"> | ||
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<h3> Simulations: </h3> | <h3> Simulations: </h3> | ||
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Table 1. List of values used in simulation parameters<br /> | Table 1. List of values used in simulation parameters<br /> | ||
− | <img src = "https://static.igem.org/mediawiki/2018/ | + | <img src = "https://static.igem.org/mediawiki/2018/4/49/T--RHIT--GenModParam.png" style="width:60%"> |
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<p>Figure 1 maps out the expression level of the free repressor protein AraC and Plasmid 1 genes, PETase and MHETase over 12 hours. The population of cells in the simulation was 1e+08. While free AraC protein, which would normally suppress expression, is relatively low there is a high expression of the objective proteins. The MHETase and PETase plots both follow the same trend, although, MHETase does decay slower than PETase and also reaches a higher maximum concentration. </p> | <p>Figure 1 maps out the expression level of the free repressor protein AraC and Plasmid 1 genes, PETase and MHETase over 12 hours. The population of cells in the simulation was 1e+08. While free AraC protein, which would normally suppress expression, is relatively low there is a high expression of the objective proteins. The MHETase and PETase plots both follow the same trend, although, MHETase does decay slower than PETase and also reaches a higher maximum concentration. </p> | ||
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<h3> Sensitivity Analysis: </h3> | <h3> Sensitivity Analysis: </h3> | ||
− | <p>In Table 1 | + | <p>In Table 1, there are three values that say they are estimated in the calculated column. This is due to the lack of comprehensive material on them, and that these values create realistic behavior of the system. There is a small range in each value where the system remains stable and biologically relevant, so these values were pulled from that range. The behavior of the system throughout the range is consistent with only slight variation on amounts. </p> |
<h3>References:</h3> | <h3>References:</h3> | ||
− | < | + | <ul> |
− | [1] D. Madar, E. Dekel, A. Bren and U. Alon. “Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli,” BMC Systems Biology. 2011. [Online]. | + | <li>[1] D. Madar, E. Dekel, A. Bren and U. Alon. “Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli,” BMC Systems Biology. 2011. [Online]. https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-111 </li> |
− | [2] L. Wang, Y. J. Zhou, D. Ji, and Z.K. Zhao, “An accurate method for estimation of the intracellular aqueous volume of Escherichia coli cells,” Journal of Microbiological Methods, 2013, p. 8. [Online]. | + | <li>[2] L. Wang, Y. J. Zhou, D. Ji, and Z.K. Zhao, “An accurate method for estimation of the intracellular aqueous volume of Escherichia coli cells,” Journal of Microbiological Methods, 2013, p. 8. [Online].http://bionumbers.hms.harvard.edu/bionumber.aspx?id=108813&ver=3&trm=e%20coli%20cell%20volume&org</li> |
− | + | <li>[3] H. Bremer and P. P. Dennis, “Modulation of chemical composition and other parameters of the cell by growth rate.” Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed. [Online]. Neidhardt, et al. eds. chapter 97, 1991, p. 1559. [Online]. http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=100059&ver=39</li> | |
− | [4] X. Zhang, T. Reeder, and R. Schleif. Transcription Activation Parameters at ara pBAD.” Journal of Molecular Biology. Vol 258, 1996, p. 14-24. [Online]. | + | <li>[4] X. Zhang, T. Reeder, and R. Schleif. Transcription Activation Parameters at ara pBAD.” Journal of Molecular Biology. Vol 258, 1996, p. 14-24. [Online]. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.417.6037&rep=rep1&type=pdf</li> |
− | [5] D. Kolodrubetz and R. Schleif. “Identifical of araC protein on two-dimensional gels, its in vivo instability and normal level.” Journal of Molecular Biology. Vol 149, issue 1, pp.133-139, 1981. [Online]. | + | <li>[5] D. Kolodrubetz and R. Schleif. “Identifical of araC protein on two-dimensional gels, its in vivo instability and normal level.” Journal of Molecular Biology. Vol 149, issue 1, pp.133-139, 1981. [Online]. https://www.sciencedirect.com/science/article/pii/0022283681902655 </li> |
− | [6] J.A. Mergerle, F. Georg, et al. “Timing and Dynamics of Single Cell Gene Expression in the Arabinose Utilization System.” Biophysical Journal. Vol. 95, Issue 4, pp.2103-2115, Aug 2008. [Online]. | + | <li>[6] J.A. Mergerle, F. Georg, et al. “Timing and Dynamics of Single Cell Gene Expression in the Arabinose Utilization System.” Biophysical Journal. Vol. 95, Issue 4, pp.2103-2115, Aug 2008. [Online]. https://www.sciencedirect.com/science/article/pii/S0006349508701681 </li> |
− | + | <li>[7] R. Schleif. “AraC protein, regulation of the L-arabinose operon in Escherichia coli, and the light switch mechanism of AraC action.” FEMS Microbiology Review. vol. 34, issue 5, September 2010, pp. 779-796. [Online]. https://academic.oup.com/femsre/article/34/5/779/797770</li> | |
− | [8] K. Martin, L. Huo, and R.Schleif. “The DNA Loop model for ara repression: AraC Protein occupies the proposed loop sites in vivo and repression-negative mutations lie in these same sites.” In USA Proceedings National Academy of Science. vol. 82, June 1986, pp. 3654-3658. [Available: | + | <li>[8] K. Martin, L. Huo, and R.Schleif. “The DNA Loop model for ara repression: AraC Protein occupies the proposed loop sites in vivo and repression-negative mutations lie in these same sites.” In USA Proceedings National Academy of Science. vol. 82, June 1986, pp. 3654-3658. [Available: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC323581/pdf/pnas00315-0095.pdf]</li> |
− | [9] “Part: pSB1C3.”iGEM Registry of Standard Biological Parts. Sept 2008. [Online]. | + | <li>[9] “Part: pSB1C3.”iGEM Registry of Standard Biological Parts. Sept 2008. [Online]. http://parts.igem.org/Part:pSB1C3</li> |
+ | </ul> | ||
</div> | </div> | ||
</html> | </html> |
Latest revision as of 20:22, 2 August 2018