Team:Edinburgh/Bacterial

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<p>In 2000, Elowitz and Leibler presented the first synthetic oscillatory system in E coli. Termed the repressilator, this combined three transcriptional repressor systems that were not naturally part of any oscillating system. This system oscillated but was not very precise (it had an oscillation period of 120 +/- 40min, and although mother cells transmitted their state to their daughters when dividing, the bacteria tended to get out of synchrony after time). Garcia-Ojalvo et al. (2004) presented a model of an improved repressilator which used quorum sensing to make the bacteria function as a single unit; Figure 1 shows a diagram of this system. Danino et al. (2009) produced an oscillating genetic circuit synchronised by quorum sensing, confirming that this method could be used to improve synthetic biological oscillators.</p><br>
<p>In 2000, Elowitz and Leibler presented the first synthetic oscillatory system in E coli. Termed the repressilator, this combined three transcriptional repressor systems that were not naturally part of any oscillating system. This system oscillated but was not very precise (it had an oscillation period of 120 +/- 40min, and although mother cells transmitted their state to their daughters when dividing, the bacteria tended to get out of synchrony after time). Garcia-Ojalvo et al. (2004) presented a model of an improved repressilator which used quorum sensing to make the bacteria function as a single unit; Figure 1 shows a diagram of this system. Danino et al. (2009) produced an oscillating genetic circuit synchronised by quorum sensing, confirming that this method could be used to improve synthetic biological oscillators.</p><br>
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<p>Figure 1: A quorum sensor synchronised repressilator as modelled by Garcia-Ojalvo et al (2004).</p><br></center>
<p>Figure 1: A quorum sensor synchronised repressilator as modelled by Garcia-Ojalvo et al (2004).</p><br></center>
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<p>The repressilator presented by Danino et al. in 2009 was not only advantageous in that it was more stable than the original Elowitz repressilator, but also in that the oscillation period could be controlled. The bacteria were grown in a trapping chamber, and when the flow rate through the main tube was increased or decreased, the quorum sensing molecule diffused away faster or slower, altering the oscillation period (see figure 2).</p><br>
<p>The repressilator presented by Danino et al. in 2009 was not only advantageous in that it was more stable than the original Elowitz repressilator, but also in that the oscillation period could be controlled. The bacteria were grown in a trapping chamber, and when the flow rate through the main tube was increased or decreased, the quorum sensing molecule diffused away faster or slower, altering the oscillation period (see figure 2).</p><br>
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<p>Figure 2: Danino et al. oscillator in flow chamber. By increasing or lowering the flow rate of water through the tube, the autoinducer (AI, which promotes transcription when bound to LuxR) diffuses more or less fast out of the chamber, allowing control of the oscillation rate.</p><br></center>
<p>Figure 2: Danino et al. oscillator in flow chamber. By increasing or lowering the flow rate of water through the tube, the autoinducer (AI, which promotes transcription when bound to LuxR) diffuses more or less fast out of the chamber, allowing control of the oscillation rate.</p><br></center>
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<a name="Diagram" id="Diagram"></a><h2>Diagram of mood lighting circuit</h2><br>
<a name="Diagram" id="Diagram"></a><h2>Diagram of mood lighting circuit</h2><br>
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<a name="PartList" id="PartList"></a><h2>List of parts needed</h2><br>
<a name="PartList" id="PartList"></a><h2>List of parts needed</h2><br>
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<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Core_repressilator" title="Core repressilator">Core repressilator</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Core_repressilator" title="Core repressilator">Core repressilator</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Blue_light_sensor" title="Blue light sensor">Blue light sensor</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Blue_light_sensor" title="Blue light sensor">Blue light sensor</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Blue_light_producer" title="Blue light producer">Blue light producer</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Blue_light_producer" title="Blue light producer">Blue light producer</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Green_light_sensor" title="Green light sensor">Green light sensor</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Green_light_sensor" title="Green light sensor">Green light sensor</a></p>
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<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Green_light_producer" title="Green light producer">Green light producer</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Green_light_producer" title="Green light producer">Green light producer</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Red_light_sensor" title="Red light sensor">Red light sensor</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Red_light_sensor" title="Red light sensor">Red light sensor</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Red_light_producer" title="Red light producer">Red light producer</a></p>
<p><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Red_light_producer" title="Red light producer">Red light producer</a></p>
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<a name="Alignment" id="Alignment"></a><h2>Alignment of spectra</h2><br>
<a name="Alignment" id="Alignment"></a><h2>Alignment of spectra</h2><br>
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Revision as of 10:16, 6 August 2010







Introduction: The original repressilator



In 2000, Elowitz and Leibler presented the first synthetic oscillatory system in E coli. Termed the repressilator, this combined three transcriptional repressor systems that were not naturally part of any oscillating system. This system oscillated but was not very precise (it had an oscillation period of 120 +/- 40min, and although mother cells transmitted their state to their daughters when dividing, the bacteria tended to get out of synchrony after time). Garcia-Ojalvo et al. (2004) presented a model of an improved repressilator which used quorum sensing to make the bacteria function as a single unit; Figure 1 shows a diagram of this system. Danino et al. (2009) produced an oscillating genetic circuit synchronised by quorum sensing, confirming that this method could be used to improve synthetic biological oscillators.




Figure 1: A quorum sensor synchronised repressilator as modelled by Garcia-Ojalvo et al (2004).



The repressilator presented by Danino et al. in 2009 was not only advantageous in that it was more stable than the original Elowitz repressilator, but also in that the oscillation period could be controlled. The bacteria were grown in a trapping chamber, and when the flow rate through the main tube was increased or decreased, the quorum sensing molecule diffused away faster or slower, altering the oscillation period (see figure 2).





Figure 2: Danino et al. oscillator in flow chamber. By increasing or lowering the flow rate of water through the tube, the autoinducer (AI, which promotes transcription when bound to LuxR) diffuses more or less fast out of the chamber, allowing control of the oscillation rate.






Alignment of spectra






References



Elowitz, M. B. and S. Leibler (2000). "A synthetic oscillatory network of transcriptional regulators." Nature 403(6767): 335-338.

Danino, T., O. Mondragon-Palomino, et al (2009). "A synchronized quorum of genetic clocks." Nature 463(7279): 326-330.

Garcia-Ojalvo, J., M. B. Elowitz, et al. (2004). "Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing." Proceedings of the National Academy of Sciences of the United States of America 101(30): 10955-10960.

A Levskaya, OD Weiner, WA Lim, CA Voigt (2009), "Spatiotemporal control of cell signalling using a light-switchable protein interaction." Nature Vol 461| 15 October 2009| doi:10.1038/nature08446

YI Wu, D Frey, OI Lungu, A Jaehrig, I Schlichting, et al. (2009) "A genetically encoded photoactivatable Rac controls the motility of living cells" Nature, 2009 Vol 461| 3 September 2009| doi:10.1038/nature08241

F Zhang, AM Aravanis, A Adamantidis, et al. (2007) "Circuit-breakers: optical technologies for probing neural signals and systems" Nature Reviews VOLUME 8 | AUGUST 2007 | 577