"
Team:SydneyUni Australia/Modelling Conclusion
From 2013.igem.org
Jbergfield (Talk | contribs) |
|||
| (11 intermediate revisions not shown) | |||
| Line 1: | Line 1: | ||
| - | + | {{Team:SydneyUni_Australia/Style}} | |
| + | {{Team:SydneyUni_Australia/Header}} | ||
| - | + | == Conclusions: == | |
| - | + | *In our model we find that 1 mM of DCA is removed from solution within roughly 150 minutes when the DCA degrading cells are at a concentration of 2 x 10<sup>8</sup> cells/mL ([https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph1 graph 1] and [https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph5 graph 5]). | |
| - | + | *It is also evident that bacterial growth can occur ([https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph4 graph 4], [https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph8 graph 8] and [https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph9 graph 9]). This growth is due to the degradation of DCA to glycolate. We can also see that that bacterial growth correlates with glycolate accumulation (by comparing [https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph6 graph 6] and [https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph9 graph 9]). | |
| - | + | *The cytotoxic metabolic intermediate chloroactealdehyde does not accumulate to a significant concentration in either of the pathways and is consistently at a negligibly low concentration. We can see that chloroacetaldehyde reaches a maximum concentration of roughly 0.2 mM in both pathways ([https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph3 graph 3] and [https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph7 graph 7]). Chloroacetaldehyde is apparently metabolised very quickly; this concentration maximum is short lived, peaks at roughly 0.03 seconds and returns back to 0 mM by 0.5 seconds. It is expected that chloroacetaldehyde toxicity will not be a problem in our engineered cells. | |
| + | * We also conclude that the two pathways remove DCA at the same rate (by comparing [https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph1 graph 1] and [https://2013.igem.org/Team:SydneyUni_Australia/Modelling_Output#graph5 graph 5]). | ||
| - | == | + | == References:== |
[1] Krooshof, G. H., Ridder, I. S., Tepper, A. W., Vos, G. J., Rozeboom, H. J., Kalk, K. H., Dijkstra, B. W. & Janssen, D. B. (1998). Kinetic Analysis and X-ray Structure of Haloalkane Dehalogenase with a Modified Halide-Binding Site. <i>Biochemistry</i>, <b>37</b>(43), 15013-15023. | [1] Krooshof, G. H., Ridder, I. S., Tepper, A. W., Vos, G. J., Rozeboom, H. J., Kalk, K. H., Dijkstra, B. W. & Janssen, D. B. (1998). Kinetic Analysis and X-ray Structure of Haloalkane Dehalogenase with a Modified Halide-Binding Site. <i>Biochemistry</i>, <b>37</b>(43), 15013-15023. | ||
| Line 27: | Line 29: | ||
[6] Sinensky, M. I. (1974). Homeoviscous Adaption – A Homeostatic Process that Regulates the Viscosity of Membrane Lipids in <i>Escherichia coli</i>. <i>Proceedings from the National Academy of Science of the United States of America</i>, <b>71</b>(2), 522-525. | [6] Sinensky, M. I. (1974). Homeoviscous Adaption – A Homeostatic Process that Regulates the Viscosity of Membrane Lipids in <i>Escherichia coli</i>. <i>Proceedings from the National Academy of Science of the United States of America</i>, <b>71</b>(2), 522-525. | ||
| - | [7] CyberCell Database | + | [7] CyberCell Database. Retrieved from http://ccdb.wishartlab.com/CCDB/. |
| - | [8] | + | [8] Currie, R. C., Chiao, F. F., McKone, T. E. (1994) Intermedia Transfer Factors for Contaminants Found at Hazardous Waste Sites: 1,2 dichloroethane (DCA). Retrieved from http://www.dtsc.ca.gov/AssessingRisk/Upload/12dca.pdf |
| - | [9] | + | [9] Lord, J. M. (1972) Glycolate oxidoreductase in <i>Escherichia coli</i>. <i>Biochemica et Biophysica Acta</i> <b>267</b>:2, 227-327. |
| - | [10 | + | [10] Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M., Hartl, F. U., Kerner, M. J. & Frishman, D. (2008) Protein abundance profiling of the <i>Escherichia coli</i> cytosol. <i>BMC Genomics</i>, <b>9</b>:102. |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
{{Team:SydneyUni_Australia/Footer}} | {{Team:SydneyUni_Australia/Footer}} | ||
Latest revision as of 00:39, 29 October 2013
Conclusions:
- In our model we find that 1 mM of DCA is removed from solution within roughly 150 minutes when the DCA degrading cells are at a concentration of 2 x 108 cells/mL (graph 1 and graph 5).
- It is also evident that bacterial growth can occur (graph 4, graph 8 and graph 9). This growth is due to the degradation of DCA to glycolate. We can also see that that bacterial growth correlates with glycolate accumulation (by comparing graph 6 and graph 9).
- The cytotoxic metabolic intermediate chloroactealdehyde does not accumulate to a significant concentration in either of the pathways and is consistently at a negligibly low concentration. We can see that chloroacetaldehyde reaches a maximum concentration of roughly 0.2 mM in both pathways (graph 3 and graph 7). Chloroacetaldehyde is apparently metabolised very quickly; this concentration maximum is short lived, peaks at roughly 0.03 seconds and returns back to 0 mM by 0.5 seconds. It is expected that chloroacetaldehyde toxicity will not be a problem in our engineered cells.
- We also conclude that the two pathways remove DCA at the same rate (by comparing graph 1 and graph 5).
References:
[1] Krooshof, G. H., Ridder, I. S., Tepper, A. W., Vos, G. J., Rozeboom, H. J., Kalk, K. H., Dijkstra, B. W. & Janssen, D. B. (1998). Kinetic Analysis and X-ray Structure of Haloalkane Dehalogenase with a Modified Halide-Binding Site. Biochemistry, 37(43), 15013-15023.
[2] Janecki, D. J., Bemis, K. G., Tegeler, T. J., Sanghani, P. C., Zhai, L., Hurley, T. D., Bosron, W. F. & Wang, M. (2007). A multiple reaction monitoring method for absolute quantification of the human liver alcohol dehydrogenase ADH1C1 isoenzyme. Analytical Biochemistry, 369(1), 18-26.
[3] Pandey, A. V. & Flück, C. E. (2013). NADPH P450 oxidoreductase: Structure, function, and pathology of diseases. Pharmacology & Therapeutics, 138(2), 229-254.
[4] van der Ploeg, J., Shmidt, M. P., Landa, A. S., & Janssen, D. B. (1994). Identification of Chloroacetaldehyde Dehydrogenase Involved in 1,2-Dichloroethane Degradation. Applied Environmental Microbiology 60(5), 1599-1605.
[5] van der Ploeg, J., van Hall, G. & Janssen, D. B. (1991) Characterization of the haloacid dehalogenase from Xanthobacter autotrophicus GJ10 and sequencing of the dhlB gene. Journal of Bacteriology, 173(24), 7925-33.
[6] Sinensky, M. I. (1974). Homeoviscous Adaption – A Homeostatic Process that Regulates the Viscosity of Membrane Lipids in Escherichia coli. Proceedings from the National Academy of Science of the United States of America, 71(2), 522-525.
[7] CyberCell Database. Retrieved from http://ccdb.wishartlab.com/CCDB/.
[8] Currie, R. C., Chiao, F. F., McKone, T. E. (1994) Intermedia Transfer Factors for Contaminants Found at Hazardous Waste Sites: 1,2 dichloroethane (DCA). Retrieved from http://www.dtsc.ca.gov/AssessingRisk/Upload/12dca.pdf
[9] Lord, J. M. (1972) Glycolate oxidoreductase in Escherichia coli. Biochemica et Biophysica Acta 267:2, 227-327.
[10] Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M., Hartl, F. U., Kerner, M. J. & Frishman, D. (2008) Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics, 9:102.
With thanks to:
