http://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&feed=atom&action=historyTeam:IPN-UNAM-Mexico/Project - Revision history2024-03-28T22:54:00ZRevision history for this page on the wikiMediaWiki 1.16.5http://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&diff=169647&oldid=prevLUIS DE JESUS at 06:54, 9 December 20092009-12-09T06:54:48Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Schematically we can see this description as:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Schematically we can see this description as:</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Curv ACT-INH.jpg |200px|center|Local activation & <del class="diffchange diffchange-inline">longe </del>range inhibition]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Curv ACT-INH.jpg |200px|center|Local activation & <ins class="diffchange diffchange-inline">long </ins>range inhibition]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># The coefficient rates of diffusion should be different.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># The coefficient rates of diffusion should be different.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># The starting distribution of morphogenes should not be completely homogeneous over the space.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># The starting distribution of morphogenes should not be completely homogeneous over the space.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># The Gierer and Mainhardt proposal: local activation and <del class="diffchange diffchange-inline">longe </del>range inhibition.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># The Gierer and Mainhardt proposal: local activation and <ins class="diffchange diffchange-inline">long </ins>range inhibition.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>When there is enough ''Lux AHL ''to achieve a second threshold, and if we supose that the ''tet'' promoter is not repressed, ''LuxR'' will be produced, forming a complex with ''Lux AHL'', ''LuxR ''+ ''AI ''which in turn will repress de double promoter. The <del class="diffchange diffchange-inline">Longe </del>range inhibition will take place.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>When there is enough ''Lux AHL ''to achieve a second threshold, and if we supose that the ''tet'' promoter is not repressed, ''LuxR'' will be produced, forming a complex with ''Lux AHL'', ''LuxR ''+ ''AI ''which in turn will repress de double promoter. The <ins class="diffchange diffchange-inline">Long </ins>range inhibition will take place.</div></td></tr>
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</table>LUIS DE JESUShttp://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&diff=160592&oldid=prevLUIS DE JESUS: /* The work of Turing */2009-10-21T23:57:45Z<p><span class="autocomment">The work of Turing</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Zebra.jpg|thumb|200px|zebra stripes pattern]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Zebra.jpg|thumb|200px|zebra stripes pattern]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[Image:Leopard.jpg|thumb|200px|<del class="diffchange diffchange-inline">zebra stripes </del>pattern]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[Image:Leopard.jpg|thumb|200px|<ins class="diffchange diffchange-inline">leopard spots </ins>pattern]]</div></td></tr>
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</table>LUIS DE JESUShttp://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&diff=160585&oldid=prevLUIS DE JESUS: /* The work of Turing */2009-10-21T23:57:20Z<p><span class="autocomment">The work of Turing</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===The work of Turing===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===The work of Turing===</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In 1952 Alan M. Turing in his classical paper called ''The chemical basis of morphogenesis '' he sugested that <del class="diffchange diffchange-inline">"...</del>a system of chemical substances, called morphogens, reacting together and diffusing through a tissue, is adequate to account for the main phenomena of morphogenesis." This system is amazing by its simplicity. With only two morphogens it's possible to reproduce nontrivial patterns that are similar to those of zebras or leopards.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In 1952 Alan M. Turing in his classical paper called ''The chemical basis of morphogenesis '' he sugested that a system of chemical substances, called morphogens, reacting together and diffusing through a tissue, is adequate to account for the main phenomena of morphogenesis." This system is amazing by its simplicity. With only two morphogens it's possible to reproduce nontrivial patterns that are similar to those of zebras or leopards.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Although there is not enough evidence of the existence of these morphogens in living organisms, the likeliness of the patterns obtained by theoretical means using this model with the ones found in nature is astonishing.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Although there is not enough evidence of the existence of these morphogens in living organisms, the likeliness of the patterns obtained by theoretical means using this model with the ones found in nature is astonishing.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Turing assumed that the morphogenes can react with each other and diffuse through cells. It is necessary that at the beginning there is a non-homogeneous distribuition of these morphogenes, which is often called chemical prepattern and can be given merely by random disturbances. An intuitive notion would tell us that the diffusion of the morphogenes starting from this chemical prepattern would led to a homogenous state of the system, but surprisingly the Turing proposal says that non-homgenous structures will arise, as a direct consequence of diffusion (the turing hyphotesis); reaching a stable state with regions with high concentrantions of one morphogen and regions with high concentration of the others. This non-homogeneous distribuition patterns of morphogens resembles those found in nature during some stages of morhpogenesis (from the gastrulation or the tentacle patterns on hydras to the jaguar spots).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Turing assumed that the morphogenes can react with each other and diffuse through cells. It is necessary that at the beginning there is a non-homogeneous distribuition of these morphogenes, which is often called chemical prepattern and can be given merely by random disturbances. An intuitive notion would tell us that the diffusion of the morphogenes starting from this chemical prepattern would led to a homogenous state of the system, but surprisingly the Turing proposal says that non-homgenous structures will arise, as a direct consequence of diffusion (the turing hyphotesis); reaching a stable state with regions with high concentrantions of one morphogen and regions with high concentration of the others. This non-homogeneous distribuition patterns of morphogens resembles those found in nature during some stages of morhpogenesis (from the gastrulation or the tentacle patterns on hydras to the jaguar spots).</div></td></tr>
</table>LUIS DE JESUShttp://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&diff=160444&oldid=prevIsui: /* The Activator-Inhibitor */2009-10-21T23:52:54Z<p><span class="autocomment">The Activator-Inhibitor</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The activator is autocathalyzed and it also triggers the formation of the inhibitor. Accordingly to its name, the inhibitor inhibits the production of the activator, leading to a simple but very rich dymamics (For more details on the acivator-inhibitor equations please go to [[Team:IPN-UNAM-Mexico/Modeling|modelling]] section). From the grass field and the fire analogy we can deduce that the diffusion coefficients of the fire should be slower than the grasshoppers one; if not the fire (activator) would spread completely in the area. This is an important fact that we mention again later.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The activator is autocathalyzed and it also triggers the formation of the inhibitor. Accordingly to its name, the inhibitor inhibits the production of the activator, leading to a simple but very rich dymamics (For more details on the acivator-inhibitor equations please go to [[Team:IPN-UNAM-Mexico/Modeling|modelling]] section). From the grass field and the fire analogy we can deduce that the diffusion coefficients of the fire should be slower than the grasshoppers one; if not the fire (activator) would spread completely in the area. This is an important fact that we mention again later.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>There are some variants of the classical Activator-Inhibitor system, like the Activator-Inhibitor with <del class="diffchange diffchange-inline">substrates</del>. Those systems describe the aditional <del class="diffchange diffchange-inline">existance </del>of a <del class="diffchange diffchange-inline">sustance </del>that is degraded or inactivated along time and the production of the activator is limited to its <del class="diffchange diffchange-inline">existance</del>. This kind of substrates can play the role of the inhibitor <del class="diffchange diffchange-inline">sometimes </del>and due to this duality we can model our project in several ways with no loss of generality.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>There are some variants of the classical Activator-Inhibitor system, like the Activator-Inhibitor with <ins class="diffchange diffchange-inline">Substrates</ins>. Those systems describe the aditional <ins class="diffchange diffchange-inline">existence </ins>of a <ins class="diffchange diffchange-inline">substance </ins>that is degraded or inactivated along <ins class="diffchange diffchange-inline">the </ins>time and the production of the activator is limited to its <ins class="diffchange diffchange-inline">availability</ins>. This kind of substrates can <ins class="diffchange diffchange-inline">sometimes </ins>play the role of the inhibitor<ins class="diffchange diffchange-inline">, </ins>and due to this duality we can model our project in several ways with no loss of generality.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==='''GENERAL CONDITIONS FOR PATTERN GENERATION'''===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==='''GENERAL CONDITIONS FOR PATTERN GENERATION'''===</div></td></tr>
</table>Isuihttp://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&diff=160086&oldid=prevIsui: /* Resuming */2009-10-21T23:42:25Z<p><span class="autocomment">Resuming</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>===<del class="diffchange diffchange-inline">Resuming</del>===</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>===<ins class="diffchange diffchange-inline">Synthesizing</ins>===</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The project of the IPN-UNAM-MEXICO team will provide biological evidence of a classical theoretical work of morphogenesis by means of synthetic biology. The biobricks synthetic network that we propose recover the qualitative requeriments to generate a spatiotemporal pattern because it recognize at least two differente morphogens ''Lux AHL'' and ''Las AHL'', they diffuse with different rates, we can give a non-homogeneous starting point to the area where the morphogens will interact and diffuse with IPTG and ATC; and in areas where there are enough substrates IPTG and ATC those zones can remain activated while in a farther place the inhibitory morphogen will predomain. Hence our biobricks system is of reaction-diffusion-substrate type.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The project of the IPN-UNAM-MEXICO team will provide biological evidence of a classical theoretical work of morphogenesis by means of synthetic biology. The biobricks synthetic network that we propose recover the qualitative requeriments to generate a spatiotemporal pattern because it recognize at least two differente morphogens ''Lux AHL'' and ''Las AHL'', they diffuse with different rates, we can give a non-homogeneous starting point to the area where the morphogens will interact and diffuse with IPTG and ATC; and in areas where there are enough substrates IPTG and ATC those zones can remain activated while in a farther place the inhibitory morphogen will predomain. Hence our biobricks system is of reaction-diffusion-substrate type.</div></td></tr>
</table>Isuihttp://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&diff=159524&oldid=prevLUIS DE JESUS: /* The Activator-Inhibitor */2009-10-21T23:25:29Z<p><span class="autocomment">The Activator-Inhibitor</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The activator is autocathalyzed and it also triggers the formation of the inhibitor. Accordingly to its name, the inhibitor inhibits the production of the activator, leading to a simple but very rich dymamics (For more details on the acivator-inhibitor equations please go to [[Team:IPN-UNAM-Mexico/Modeling|modelling]] section). From the grass field and the fire analogy we can deduce that the diffusion coefficients of the fire should be slower than the grasshoppers one; if not the fire (activator) would spread completely in the area. This is an important fact that we mention again later.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The activator is autocathalyzed and it also triggers the formation of the inhibitor. Accordingly to its name, the inhibitor inhibits the production of the activator, leading to a simple but very rich dymamics (For more details on the acivator-inhibitor equations please go to [[Team:IPN-UNAM-Mexico/Modeling|modelling]] section). From the grass field and the fire analogy we can deduce that the diffusion coefficients of the fire should be slower than the grasshoppers one; if not the fire (activator) would spread completely in the area. This is an important fact that we mention again later.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">There are some variants of the classical Activator-Inhibitor system, like the Activator-Inhibitor with substrates. Those systems describe the aditional existance of a sustance that is degraded or inactivated along time and the production of the activator is limited to its existance. This kind of substrates can play the role of the inhibitor sometimes and due to this duality we can model our project in several ways with no loss of generality.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==='''GENERAL CONDITIONS FOR PATTERN GENERATION'''===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==='''GENERAL CONDITIONS FOR PATTERN GENERATION'''===</div></td></tr>
</table>LUIS DE JESUShttp://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&diff=159225&oldid=prevLUIS DE JESUS: /* checar lode sustrato */2009-10-21T23:16:44Z<p><span class="autocomment">checar lode sustrato</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Inspired by the Gierer and Meinhardt work we designed a synthetic genetic network that acts as an Activator-Inhibitor with limiting substrates. Our proposal is that genes of the quorum system ''las'' will have the role of the Activator, while genes of the ''lux'' quorum system are going to be the Inhibitors and ''IPTG'' and ''ATC'' will be the substrates that will delimit de pattern. We explain each particular characteristics of reaction, diffusion and substrates in the following subsections.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Inspired by the Gierer and Meinhardt work we designed a synthetic genetic network that acts as an Activator-Inhibitor with limiting substrates. Our proposal is that genes of the quorum system ''las'' will have the role of the Activator, while genes of the ''lux'' quorum system are going to be the Inhibitors and ''IPTG'' and ''ATC'' will be the substrates that will delimit de pattern. We explain each particular characteristics of reaction, diffusion and substrates in the following subsections.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">==checar lode sustrato==</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Reaction - Diffusion===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Reaction - Diffusion===</div></td></tr>
</table>LUIS DE JESUShttp://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&diff=158074&oldid=prevIsui: /* 50px The Activator-Inhibitor system on biobricks: The dynamics */2009-10-21T22:44:45Z<p><span class="autocomment">50px The Activator-Inhibitor system on biobricks: The dynamics</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==[[Image:Month-icon.png | 50px]] The Activator-Inhibitor system on biobricks: The dynamics==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==[[Image:Month-icon.png | 50px]] The Activator-Inhibitor system on biobricks: The dynamics==</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The questions now is, how the <del class="diffchange diffchange-inline">biobricks </del>system works?, this subsection will answer this question starting from a prototypical point of view, the activator activates the inhibitor.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The questions now is, how the <ins class="diffchange diffchange-inline">BioBricks </ins>system works?, <ins class="diffchange diffchange-inline">in </ins>this subsection <ins class="diffchange diffchange-inline">we </ins>will answer this question starting from a prototypical point of view, the activator activates the inhibitor.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Later ''LuxI'' enzyme will be produced by the efect of ''LasR''+''PAI'' on its <del class="diffchange diffchange-inline">control </del>promoter, and ''Lux AHL'' will become released.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Later ''LuxI'' enzyme will be produced by the efect of ''LasR''+''PAI'' on its <ins class="diffchange diffchange-inline">controlling </ins>promoter, and ''Lux AHL'' will become released.</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>When there is enough ''Lux AHL ''to achieve a second threshold, <del class="diffchange diffchange-inline">an </del>if we supose that the ''tet'' promoter is not repressed, ''LuxR'' will be produced, forming a complex with ''Lux AHL'', ''LuxR ''+ ''AI ''which in turn will repress de double promoter. The Longe range inhibition will take place.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>When there is enough ''Lux AHL ''to achieve a second threshold, <ins class="diffchange diffchange-inline">and </ins>if we supose that the ''tet'' promoter is not repressed, ''LuxR'' will be produced, forming a complex with ''Lux AHL'', ''LuxR ''+ ''AI ''which in turn will repress de double promoter. The Longe range inhibition will take place.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Resuming===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Resuming===</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The project of the IPN-UNAM-MEXICO team will provide biological evidence of a classical theoretical work of morphogenesis by means of synthetic biology. The biobricks synthetic network that we propose recover the qualitative requeriments to generate a spatiotemporal pattern because recognize at least two differente morphogens ''Lux AHL'' and ''Las AHL'', they diffuse with different rates, we can give a non-homogeneous starting point to the area where the morphogens will interact and diffuse with IPTG and ATC; and in areas where there are enough substrates IPTG and ATC those zones can remain activated while in a <del class="diffchange diffchange-inline">farter </del>place <del class="diffchange diffchange-inline">que inhibitor </del>morphogen will predomain. Hence our biobricks system is of reaction-diffusion-substrate type.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The project of the IPN-UNAM-MEXICO team will provide biological evidence of a classical theoretical work of morphogenesis by means of synthetic biology. The biobricks synthetic network that we propose recover the qualitative requeriments to generate a spatiotemporal pattern because <ins class="diffchange diffchange-inline">it </ins>recognize at least two differente morphogens ''Lux AHL'' and ''Las AHL'', they diffuse with different rates, we can give a non-homogeneous starting point to the area where the morphogens will interact and diffuse with IPTG and ATC; and in areas where there are enough substrates IPTG and ATC those zones can remain activated while in a <ins class="diffchange diffchange-inline">farther </ins>place <ins class="diffchange diffchange-inline">the inhibitory </ins>morphogen will predomain. Hence our biobricks system is of reaction-diffusion-substrate type.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For more information check de [[Team:IPN-UNAM-Mexico/Modeling | modeling]], [[Team:IPN-UNAM-Mexico/Modeling | parts]] and [[Team:IPN-UNAM-Mexico/Results | results]] sections.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>For more information check de [[Team:IPN-UNAM-Mexico/Modeling | modeling]], [[Team:IPN-UNAM-Mexico/Modeling | parts]] and [[Team:IPN-UNAM-Mexico/Results | results]] sections.</div></td></tr>
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</table>Isuihttp://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&diff=157781&oldid=prevIsui: /* Las AHL */2009-10-21T22:35:53Z<p><span class="autocomment">Las AHL</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This biobrick is a signaling proteing generator that is expected to controlled in two different ways, activated by ''LasR''+''PAI'' and repressed by ''LuxR''+''AI.'' It controls the expression of LasI enzyme and GFP in a polycistronic way.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This biobrick is a signaling proteing generator that is expected to <ins class="diffchange diffchange-inline">be </ins>controlled in two different ways, activated by ''LasR''+''PAI'' and repressed by ''LuxR''+''AI.'' It controls the expression of LasI enzyme and GFP in a polycistronic way.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Substrates===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Substrates===</div></td></tr>
</table>Isuihttp://2009.igem.org/wiki/index.php?title=Team:IPN-UNAM-Mexico/Project&diff=157719&oldid=prevIsui: /* 50pxReaction-Diffusion systems implemented on Biobricks */2009-10-21T22:33:55Z<p><span class="autocomment">50pxReaction-Diffusion systems implemented on Biobricks</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==[[Image:Month-icon.png | 50px]]Reaction-Diffusion systems implemented on Biobricks==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==[[Image:Month-icon.png | 50px]]Reaction-Diffusion systems implemented on Biobricks==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Inspired by the Gierer and <del class="diffchange diffchange-inline">Mainhardt </del>work we designed a synthetic genetic network that acts as an Activator-Inhibitor with limiting substrates. Our proposal is that the quorum system <del class="diffchange diffchange-inline">genes </del>''<del class="diffchange diffchange-inline">LAS</del>'' will have the role of the Activator, ''<del class="diffchange diffchange-inline">Lux</del>'' quorum system <del class="diffchange diffchange-inline">genes </del>are going to be the Inhibitors and ''IPTG'' and ''ATC'' will be the substrates that will delimit de pattern. We explain each particular characteristics of reaction, diffusion and substrates in the following subsections.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Inspired by the Gierer and <ins class="diffchange diffchange-inline">Meinhardt </ins>work we designed a synthetic genetic network that acts as an Activator-Inhibitor with limiting substrates. Our proposal is that <ins class="diffchange diffchange-inline">genes of </ins>the quorum system ''<ins class="diffchange diffchange-inline">las</ins>'' will have the role of the Activator, <ins class="diffchange diffchange-inline">while genes of the </ins>''<ins class="diffchange diffchange-inline">lux</ins>'' quorum system <ins class="diffchange diffchange-inline"> </ins>are going to be the Inhibitors and ''IPTG'' and ''ATC'' will be the substrates that will delimit de pattern. We explain each particular characteristics of reaction, diffusion and substrates in the following subsections.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">==checar lode sustrato==</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Reaction - Diffusion===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Reaction - Diffusion===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We suppose the existence of two morphogenes, represented by ''Lux'' <del class="diffchange diffchange-inline">and </del>''Las'' <del class="diffchange diffchange-inline">, </del>''AI'' <del class="diffchange diffchange-inline">and </del>''PAI'' lactones respectively. This <del class="diffchange diffchange-inline">substances </del>are very small and travel <del class="diffchange diffchange-inline">throw </del>the membrane<del class="diffchange diffchange-inline">, and diffuse fast </del>in the media. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We suppose the existence of two morphogenes, represented by ''Lux''<ins class="diffchange diffchange-inline">, </ins>''Las'' <ins class="diffchange diffchange-inline">and </ins>''AI''<ins class="diffchange diffchange-inline">, </ins>''PAI'' lactones respectively. This <ins class="diffchange diffchange-inline">compounds </ins>are very small and travel <ins class="diffchange diffchange-inline">through </ins>the membrane <ins class="diffchange diffchange-inline">rapidly diffusing </ins>in the media. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We used two promoters, one inducible by ''LasR''+''PAI'' ([http://www.partsregistry.org/Part:Bba_R0079 Bba_R0079]) and the other double controlled ([http://www.partsregistry.org/Part:Bba_RK091146 Bba_K091146]), repressed by ''LuxR''+''AI ''and induced by ''LasR''+''PAI''<del class="diffchange diffchange-inline"><nowiki>; </del>in our genetic network <del class="diffchange diffchange-inline">we gave </del>the cell the <del class="diffchange diffchange-inline">posibility </del>of <del class="diffchange diffchange-inline">responde to a gradient of </nowiki></del>''PAI'' and ''AI ''<del class="diffchange diffchange-inline">and express </del>''GFP''.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We used two promoters, one inducible by ''LasR''+''PAI'' ([http://www.partsregistry.org/Part:Bba_R0079 Bba_R0079]) and the other double controlled ([http://www.partsregistry.org/Part:Bba_RK091146 Bba_K091146]), repressed by ''LuxR''+''AI ''and induced by ''LasR''+''PAI''<ins class="diffchange diffchange-inline">. </ins>in our genetic network the cell <ins class="diffchange diffchange-inline">will differentially respond to the different concentrations in </ins>the <ins class="diffchange diffchange-inline">gradients </ins>of ''PAI'' and ''AI'' <ins class="diffchange diffchange-inline">by expressing different levels of </ins>''GFP''.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We used <del class="diffchange diffchange-inline">too </del>a constitutive ''Lac'' <del class="diffchange diffchange-inline">Inverter, </del>to control the production of ''LasR'' with ''IPTG''<del class="diffchange diffchange-inline">, </del>a constitutive ''Tet'' inverter that <del class="diffchange diffchange-inline">controls </del>''LuxR'' with ''<del class="diffchange diffchange-inline">ATC</del>. ''<del class="diffchange diffchange-inline">These </del>inverters <del class="diffchange diffchange-inline">provides </del>a good way to <del class="diffchange diffchange-inline">control the systems and </del>make <del class="diffchange diffchange-inline">it </del>more sensitive <del class="diffchange diffchange-inline">for </del>parameters <del class="diffchange diffchange-inline">adjust</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We <ins class="diffchange diffchange-inline">also </ins>used a constitutive ''Lac'' <ins class="diffchange diffchange-inline">inverter that allows us </ins>to control the production of ''LasR'' with ''IPTG'' <ins class="diffchange diffchange-inline">and </ins>a constitutive ''Tet'' inverter that <ins class="diffchange diffchange-inline">allows us to control </ins>''LuxR'' with ''<ins class="diffchange diffchange-inline">aTc</ins>. ''<ins class="diffchange diffchange-inline">The controlling system of </ins>inverters <ins class="diffchange diffchange-inline">provide </ins>a good way to make more sensitive <ins class="diffchange diffchange-inline">the </ins>parameters <ins class="diffchange diffchange-inline">adjustment</ins>.</div></td></tr>
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</table>Isui