Team:WITS-CSIR SA/Project/Modelling
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+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA">Home</a></li> | ||
+ | <li><a href="#" class="dir">Project</a> | ||
+ | <ul> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Project/Concept">Overview</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Characterization">Characterization</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Project/Modelling">Modelling</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Collaboration/Index">Collaboration</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Project/Notebook">Lab notebook</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Project/Applications">Potential applications</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Project/Achievements">Achievements</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Project/Protocols">Protocols</a></li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Parts">Parts submitted</a></li> | ||
+ | <li><a href="./" class="dir">Outreach</a> | ||
+ | <ul> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Outreach/SciBono">Scibono experience</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Outreach/Forum">Synthetic biology forum</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Outreach/Survey">Survey</a></li> | ||
+ | </ul> | ||
+ | </li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Project/Safety">Safety</a></li> | ||
+ | |||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/Diary/Gallery">Gallery</a></li> | ||
+ | <li><a href="./" class="dir">About us</a> | ||
+ | <ul> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/AboutUs/MeetTheTeam">Meet the team</a></li> | ||
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+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/AboutUs/Attributions">Attributions</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/AboutUs/Acknowledgements">Acknowledgements</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/AboutUs/MeetOurBugs">Meet our bugs!</a></li> | ||
+ | <li><a href="https://2011.igem.org/Team:WITS-CSIR_SA/AboutUs/ContactUs">Contact us</a></li> | ||
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<p>The Wits CSIR iGEM team intend to use a riboswitch to reprogram the chemotactic behavior of <i>E.coli</i>. The project includes engineering the attraction of the bacteria to theophylline[1]. CheZ is an important protein controlling the chemotaxis of bacteria. They used a theophylline riboswitch to control the expression of CheZ in CheZ deletion mutants in order to engineer the bacteria's movement towards theophylline[1]. We're using a riboswitch sensitive to theophylline to control the expression of CheZ. In the absence of theophylline, the start codon is covered so the translation of the strand cannot occur. In the presence of theophylline, the conformation of the riboswitch changes and the ribosome binding site is exposed[1]. Thus, the higher the concentration of the theophylline, the more will enter the cell resulting in the up regulation of CheZ expression. This will increase the frequency of directed movement[1].</p> | <p>The Wits CSIR iGEM team intend to use a riboswitch to reprogram the chemotactic behavior of <i>E.coli</i>. The project includes engineering the attraction of the bacteria to theophylline[1]. CheZ is an important protein controlling the chemotaxis of bacteria. They used a theophylline riboswitch to control the expression of CheZ in CheZ deletion mutants in order to engineer the bacteria's movement towards theophylline[1]. We're using a riboswitch sensitive to theophylline to control the expression of CheZ. In the absence of theophylline, the start codon is covered so the translation of the strand cannot occur. In the presence of theophylline, the conformation of the riboswitch changes and the ribosome binding site is exposed[1]. Thus, the higher the concentration of the theophylline, the more will enter the cell resulting in the up regulation of CheZ expression. This will increase the frequency of directed movement[1].</p> | ||
<p>The theophylline riboswitch can be modeled in three differential equations [2].</p> | <p>The theophylline riboswitch can be modeled in three differential equations [2].</p> | ||
- | <p><center>M | + | <p><center>M ?= a?(T)-?M</center></p> |
- | <p><center>(CheZ) | + | <p><center>(CheZ) ?= ßMT(P)-?CheZ</center></p> |
- | <p><center>T | + | <p><center>T ?= ?(P_ext )CheZ-dT</center></p> |
- | <p>M, CheZ and T respectively stands for the concentration of CheZ mRNA, the concentration of protein CheZ and the concentration of theophylline. The constants | + | <p>M, CheZ and T respectively stands for the concentration of CheZ mRNA, the concentration of protein CheZ and the concentration of theophylline. The constants a,ß,?,? and d are all positive, and respectively denote the CheZ-promoter transcription rate, the CheZ-mRNA translation rate and the mRNA, CheZ and theophylline degradation-plus-dilution-rates. ?(Text) is the theophylline transport rate per unit CheZ concentration. It is a function of number of theophylline receptors and external theophylline concentration. The function ?(T) and T(T) denote the theophylline-governed regulation ay the transcriptional and translation levels respectively (equation below [2]). KF is the equilibrium constant at transcriptional level and KT is the equilibrium constant at translation level.</p> |
- | <p><center> | + | <p><center>F(T)= K_F/(K_F+T)</center></p> |
- | <p><center> | + | <p><center>T(T)= K_T/(K_T+T)</center></p> |
- | <p>Varying the parameter | + | <p>Varying the parameter ?(Text) of above model could help us to understand how the number of receptors and external theophylline concentration effect the intracellular concentration of theothyline and hence the expression level of CheZ. The results are shown in Fig 1 and Fig 2 below. In addition, the response curve of CheZ against theophylline concentration with different theophylline transport rate was illustrated in Fig 3.</p> |
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+ | <p>[2] C. Rao, J. Kirby, A. Arkin, Design and Diversity in Bacterial Chemotaxis: A Comparative Study in Escherichia coli and Bacillus subtilis, PloS Biology, Issue 2, Vol 2, pp. 239 – 252, February 2004.</p> | ||
<p>[1] P. Spiro, J. Parkinson, H., Othmer, A model of excitation and adaptation in bacterial chemotaxis, Proceedings of the Nation Academy of Sciences, United States of America, Biochemistry, Vol 94, pp. 7263 – 7268, July 1997.</p> | <p>[1] P. Spiro, J. Parkinson, H., Othmer, A model of excitation and adaptation in bacterial chemotaxis, Proceedings of the Nation Academy of Sciences, United States of America, Biochemistry, Vol 94, pp. 7263 – 7268, July 1997.</p> | ||
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