Team:Peking S/project/wire

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===Introduction to ‘Chemical Wire’ toolbox===
===Introduction to ‘Chemical Wire’ toolbox===
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Cell-cell communication-based multicellular networks provide an extended vista for synthetic biology. By compartmentalizing complex genetic circuits into separate engineered cells, the difficulty of the construction by layering elementary gates can be dramatically reduced, partly due to the insulation of crosstalk between modules, the suppression of noise by populationally averaging, and the reducing of metabolic burden in host cells. What’s more, cell-cell communication-based multicellular feature enables coordination and synchronization among cells in and between populations and facilitates the generation of reliable non-Boolean dynamics.
Cell-cell communication-based multicellular networks provide an extended vista for synthetic biology. By compartmentalizing complex genetic circuits into separate engineered cells, the difficulty of the construction by layering elementary gates can be dramatically reduced, partly due to the insulation of crosstalk between modules, the suppression of noise by populationally averaging, and the reducing of metabolic burden in host cells. What’s more, cell-cell communication-based multicellular feature enables coordination and synchronization among cells in and between populations and facilitates the generation of reliable non-Boolean dynamics.
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However, orthogonal ‘chemical wires’ that allow concurrent communication are far from sufficient, making developing a versatile ‘chemical wire’ toolbox for conducting a complex gene network more necessary. This year we are aiming to develop a ‘chemical wire’ toolbox, applicable for both Boolean and Non-Boolean gene networks.  
However, orthogonal ‘chemical wires’ that allow concurrent communication are far from sufficient, making developing a versatile ‘chemical wire’ toolbox for conducting a complex gene network more necessary. This year we are aiming to develop a ‘chemical wire’ toolbox, applicable for both Boolean and Non-Boolean gene networks.  
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As natural quorum sensing systems provide an excellent pool for developing ‘chemical wire’ toolbox, harvesting ‘chemical wires’ from the nature is a fast and affordable way. We selected and evaluated a recently reported quorum sensing system, CinI-CinR system from Rhizobium leguminosarum a candidate of our toolbox. An artificial QS system, PchAB-NahR system exploiting salicylate as signaling molecule was also built. Both of them were proved to owe promising performance.
 
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As natural quorum sensing systems provide an excellent pool for developing ‘chemical wire’ toolbox, harvesting ‘chemical wires’ from the nature is a fast and affordable way. We selected and evaluated a recently reported quorum sensing system, CinI-CinR system from'' Rhizobium leguminosarum'' as a candidate of our toolbox. An artificial QS system, PchAB-NahR system exploiting salicylate as signaling molecule was also built. Both of them were proved to owe promising performance.
<center>[[File:LB2cbbb.png|680px]]
<center>[[File:LB2cbbb.png|680px]]
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''For more details'', [https://2011.igem.org/Team:Peking_S/project/wire/harvest      ''click here'']
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[https://2011.igem.org/Team:Peking_S/project/wire/harvest      learn more]
 
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On the other hand, all of the quorum sensing systems currently exploited in synthetic biology exhibit transcriptional activation, which cannot provide negative feed back loops during cell-cell communication, and the conventional inverter, which was implemented by the repressor-operator pairs, has evident defects. We have developed a ‘from ground up’ approach to synthesize direct, fast and reliable signaling inverters for synthetic microbial consortia, harnessing the conditioned binding of quorum sensing regulators to their cognate DNA boxes to control the accessibility of RNA polymerase.
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On the other hand, all of the quorum sensing systems currently exploited in synthetic biology exhibit transcriptional activation, which cannot provide negative feed back loops during cell-cell communication, and the conventional switch that produces a negative feed back, which was implemented by the repressor-operator pairs, has evident defects. We have developed a ‘from ground up’ approach to synthesize direct, fast and reliable signaling inverters for synthetic microbial consortia, harnessing the conditioned binding of quorum sensing regulators to their cognate DNA boxes to control the accessibility of RNA polymerase.  
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<center>[[File:NN10.png|400px]]</center>
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''For more details'', [https://2011.igem.org/Team:Peking_S/project/wire/inverter      ''click here'']
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<center>[[File:NN10.png|400px]]</center>
 
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<center>''Figure 3: The mechanism of AHL repressible promoter.'' </center>
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With candidates harvested from nature or re-designed from the natural counterpart, we started to characterize them, specially focusing on their orthogonality, dose response, time dependence (signaling speed) and their ability to coordinate cell population.  
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<center>[[File:signalingOrthogonal.png|450px]]</center>
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''For more details'', [https://2011.igem.org/Team:Peking_S/project/wire/matrix    ''click here'']
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[https://2011.igem.org/Team:Peking_S/project/wire/inverter      learn more]
 
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== Reference ==
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With candidates harvested from nature or re-designed from the natural counterpart, we started to characterize them, specially focusing on their orthogonality, dose response, time dependence (signaling speed) and their ability to coordinate cell population.
 
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[1] Li, B. You, L. Synthetic biology: Division of logic labour. Nature 469, 171–172 (2011).
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<center>[[File:signalingOrthogonal.png|300px]]</center>
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[2] Marguet, P. Balagadde F. Tan C. You L. Biology by design: reduction and synthesis of cellular components and behaviour. JR Soc Interface 4, 607–623 (2007).
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[3] Voigt, C.A. Genetic parts to program bacteria. Curr Opin Biotechnol 17, 548–557 (2006).
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[4] Clancy, K, Voigt, C.A. Programming cells: towards an automated 'Genetic Compiler'. Curr Opin Biotechnol 21, 572–581 (2010) .
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[https://2011.igem.org/Team:Peking_S/project/wire/matrix    learn more]
 
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Chemical Wire Toolbox


Introduction|Harvesting ‘Chemical Wires’ From Nature|Synthesizing Quorum Sensing Inverters|Orthogonal Activating Matrix


Introduction to ‘Chemical Wire’ toolbox


Cell-cell communication-based multicellular networks provide an extended vista for synthetic biology. By compartmentalizing complex genetic circuits into separate engineered cells, the difficulty of the construction by layering elementary gates can be dramatically reduced, partly due to the insulation of crosstalk between modules, the suppression of noise by populationally averaging, and the reducing of metabolic burden in host cells. What’s more, cell-cell communication-based multicellular feature enables coordination and synchronization among cells in and between populations and facilitates the generation of reliable non-Boolean dynamics.


However, orthogonal ‘chemical wires’ that allow concurrent communication are far from sufficient, making developing a versatile ‘chemical wire’ toolbox for conducting a complex gene network more necessary. This year we are aiming to develop a ‘chemical wire’ toolbox, applicable for both Boolean and Non-Boolean gene networks.


As natural quorum sensing systems provide an excellent pool for developing ‘chemical wire’ toolbox, harvesting ‘chemical wires’ from the nature is a fast and affordable way. We selected and evaluated a recently reported quorum sensing system, CinI-CinR system from Rhizobium leguminosarum as a candidate of our toolbox. An artificial QS system, PchAB-NahR system exploiting salicylate as signaling molecule was also built. Both of them were proved to owe promising performance.

LB2cbbb.png

For more details, click here


On the other hand, all of the quorum sensing systems currently exploited in synthetic biology exhibit transcriptional activation, which cannot provide negative feed back loops during cell-cell communication, and the conventional inverter, which was implemented by the repressor-operator pairs, has evident defects. We have developed a ‘from ground up’ approach to synthesize direct, fast and reliable signaling inverters for synthetic microbial consortia, harnessing the conditioned binding of quorum sensing regulators to their cognate DNA boxes to control the accessibility of RNA polymerase.

NN10.png

For more details, click here


With candidates harvested from nature or re-designed from the natural counterpart, we started to characterize them, specially focusing on their orthogonality, dose response, time dependence (signaling speed) and their ability to coordinate cell population.

SignalingOrthogonal.png

For more details, click here


Reference

[1] Li, B. You, L. Synthetic biology: Division of logic labour. Nature 469, 171–172 (2011).

[2] Marguet, P. Balagadde F. Tan C. You L. Biology by design: reduction and synthesis of cellular components and behaviour. JR Soc Interface 4, 607–623 (2007).

[3] Voigt, C.A. Genetic parts to program bacteria. Curr Opin Biotechnol 17, 548–557 (2006).

[4] Clancy, K, Voigt, C.A. Programming cells: towards an automated 'Genetic Compiler'. Curr Opin Biotechnol 21, 572–581 (2010) .


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