http://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&feed=atom&action=historyTeam:Cambridge/Modelling - Revision history2024-03-19T07:27:01ZRevision history for this page on the wikiMediaWiki 1.16.5http://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&diff=94176&oldid=prevXiaohu at 19:29, 29 October 20082008-10-29T19:29:23Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In the lab one can "simply" (Biologists clearly agree with this statement) put the sender and receiver device downstream of a p2 <del class="diffchange diffchange-inline">(here: p<sub>AIP</sub>) </del>promoter to recreate the agr-QS system with biobricks. For completeness, the entire model reads:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In the lab one can "simply" (Biologists clearly agree with this statement) put the sender and receiver device downstream of a p2 promoter to recreate the agr-QS system with biobricks. For completeness, the entire model reads:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>While we were not able to find data that would verify this estimate, we can consider the gram-negative ''E.coli''. In ideal conditions, ''E.coli'' grows to roughly (2-5) x 10<sup>9</sup> cells/ml in LB until it reaches stationary phase. Assuming that a single ''E.coli'' cell has a volume on the order of 1μm<sup>3</sup>, the cell density at stationary phase will be on the order of 10<sup>-3</sup> per unit volume. Assuming that growth in ideal conditions implies higher resulting cell densities, this number will be an upper limit to cell densities, and the ''E.coli''-QS system must be activated at roughly those densities (or slightly below). This validates that our guess of 5x10<sup>-3</sup> for the threshold density in agr-systems is in the correct order of magnitude.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>While we were not able to find data that would verify this estimate, we can consider the gram-negative ''E.coli''. In ideal conditions, ''E.coli'' grows to roughly (2-5) x 10<sup>9</sup> cells/ml in LB until it reaches stationary phase. Assuming that a single ''E.coli'' cell has a volume on the order of 1μm<sup>3</sup>, the cell density at stationary phase will be on the order of 10<sup>-3</sup> per unit volume. Assuming that growth in ideal conditions implies higher resulting cell densities, this number will be an upper limit to cell densities, and the ''E.coli''-QS system must be activated at roughly those densities (or slightly below). This validates that our guess of 5x10<sup>-3</sup> for the threshold density in agr-systems is in the correct order of magnitude.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Finally, it is interesting to note that we have arrived at this result by purely theoretical considerations. We have seen that the basal rate of expression plays a critical role in the system response. This in turn will be useful in informing possible design choices for engineered applications: To change the threshold density one can simply increase basal rates of expression, e.g. by constitutively expressing the agr-system in parallel to the agr-genes that are regulated by <del class="diffchange diffchange-inline">p<sub>AIP</sub></del>. As an example, if one was to increase basal expression rates (i.e. β) the threshold value would decrease. This makes it extremely interesting to engineered applications in Synthetic Biology.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Finally, it is interesting to note that we have arrived at this result by purely theoretical considerations. We have seen that the basal rate of expression plays a critical role in the system response. This in turn will be useful in informing possible design choices for engineered applications: To change the threshold density one can simply increase basal rates of expression, e.g. by constitutively expressing the agr-system in parallel to the agr-genes that are regulated by <ins class="diffchange diffchange-inline">p2</ins>. As an example, if one was to increase basal expression rates (i.e. β) the threshold value would decrease. This makes it extremely interesting to engineered applications in Synthetic Biology.</div></td></tr>
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</table>Xiaohuhttp://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&diff=91712&oldid=prevXiaohu at 16:51, 29 October 20082008-10-29T16:51:16Z<p></p>
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</table>Xiaohuhttp://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&diff=91620&oldid=prevXiaohu at 16:46, 29 October 20082008-10-29T16:46:21Z<p></p>
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</table>Xiaohuhttp://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&diff=91588&oldid=prevXiaohu at 16:43, 29 October 20082008-10-29T16:43:43Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''We are interested in using peptide-based quorum-sensing systems from gram-positive bacteria to create self-organising biological systems. We would like to demonstrate how to engineer multicellular biological systems that are capable of expressing spatial patterns of gene expression, such as with GFP, on a bacterial lawn. This would be a first step in the direction of engineering multicellular behaviour that will become immensely useful when thinking about further applications: Instead of using GFP in our patterns, we could use genes that increase cellular electric conductivity to arrive at self-assembling systems responding to electric input and output.'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''We are interested in using peptide-based quorum-sensing systems from gram-positive bacteria to create self-organising biological systems. We would like to demonstrate how to engineer multicellular biological systems that are capable of expressing spatial patterns of gene expression, such as with GFP, on a bacterial lawn. This would be a first step in the direction of engineering multicellular behaviour that will become immensely useful when thinking about further applications: Instead of using GFP in our patterns, we could use genes that increase cellular electric conductivity to arrive at self-assembling systems responding to electric input and output.'''</div></td></tr>
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</table>Xiaohuhttp://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&diff=91560&oldid=prevXiaohu at 16:42, 29 October 20082008-10-29T16:42:00Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''We are interested in using peptide-based quorum-sensing systems from gram-positive bacteria to create self-organising biological systems. We would like to demonstrate how to engineer multicellular biological systems that are capable of expressing spatial patterns of gene expression, such as with GFP, on a bacterial lawn. This would be a first step in the direction of engineering multicellular behaviour that will become immensely useful when thinking about further applications: Instead of using GFP in our patterns, we could use genes that increase cellular electric conductivity to arrive at self-assembling systems responding to electric input and output.'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''We are interested in using peptide-based quorum-sensing systems from gram-positive bacteria to create self-organising biological systems. We would like to demonstrate how to engineer multicellular biological systems that are capable of expressing spatial patterns of gene expression, such as with GFP, on a bacterial lawn. This would be a first step in the direction of engineering multicellular behaviour that will become immensely useful when thinking about further applications: Instead of using GFP in our patterns, we could use genes that increase cellular electric conductivity to arrive at self-assembling systems responding to electric input and output.'''</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[4] [Canton+Labno, 2008] Refinement and standardization of synthetic biological parts and devices</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[4] [Canton+Labno, 2008] Refinement and standardization of synthetic biological parts and devices</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[5] [Meinhard, 1992] Rep. Prog. Phys., Pattern formation in biology: a comparison of models and experiments</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*[5] [Meinhard, 1992] Rep. Prog. Phys., Pattern formation in biology: a comparison of models and experiments</div></td></tr>
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</table>Xiaohuhttp://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&diff=86890&oldid=prevXiaohu at 09:11, 29 October 20082008-10-29T09:11:20Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''We are interested in using peptide-based quorum-sensing systems from gram-positive bacteria to create self-organising biological systems. We would like to demonstrate how to engineer multicellular biological systems that are capable of expressing spatial patterns of gene expression, such as with GFP, on a bacterial lawn. This would be a first step in the direction of engineering multicellular behaviour that will become immensely useful when thinking about further applications: Instead of using GFP in our patterns, we could use genes that increase cellular electric conductivity to arrive at self-assembling systems responding to electric input and output.'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''We are interested in using peptide-based quorum-sensing systems from gram-positive bacteria to create self-organising biological systems. We would like to demonstrate how to engineer multicellular biological systems that are capable of expressing spatial patterns of gene expression, such as with GFP, on a bacterial lawn. This would be a first step in the direction of engineering multicellular behaviour that will become immensely useful when thinking about further applications: Instead of using GFP in our patterns, we could use genes that increase cellular electric conductivity to arrive at self-assembling systems responding to electric input and output.'''</div></td></tr>
</table>Xiaohuhttp://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&diff=86873&oldid=prevXiaohu at 09:08, 29 October 20082008-10-29T09:08:28Z<p></p>
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</table>Xiaohuhttp://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&diff=83054&oldid=prevTasslehoff at 22:53, 28 October 20082008-10-28T22:53:17Z<p></p>
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</table>Tasslehoffhttp://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&diff=83053&oldid=prevTasslehoff at 22:52, 28 October 20082008-10-28T22:52:59Z<p></p>
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</table>Tasslehoffhttp://2008.igem.org/wiki/index.php?title=Team:Cambridge/Modelling&diff=83040&oldid=prevXiaohu at 22:51, 28 October 20082008-10-28T22:51:28Z<p></p>
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