http://2007.igem.org/wiki/index.php?title=Paris/Perspectives&feed=atom&action=historyParis/Perspectives - Revision history2024-03-28T09:22:18ZRevision history for this page on the wikiMediaWiki 1.16.5http://2007.igem.org/wiki/index.php?title=Paris/Perspectives&diff=46390&oldid=prevDavid.bikard: /* System improvement through directed evolution */2007-10-27T00:52:54Z<p><span class="autocomment">System improvement through directed evolution</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>= System improvement through directed evolution =</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>= System improvement through directed evolution =</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The engineered <del class="diffchange diffchange-inline">MSB </del>may be further tuned by laboratory evolution. A key advantage of the system is that selection pressure could be tuned to either force faster reproduction (e.g., improving DAP production and/or export from the soma or alternatively for a more efficient use of DAP within the germline) or for improvement of soma-specific functions (see below). In other words, the soma-germline <del class="diffchange diffchange-inline">MSB </del>dichotomy provides us with the possibility to select for functions that are otherwise deleterious for the unicellular organism.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The engineered <ins class="diffchange diffchange-inline">SMB </ins>may be further tuned by laboratory evolution. A key advantage of the system is that selection pressure could be tuned to either force faster reproduction (e.g., improving DAP production and/or export from the soma or alternatively for a more efficient use of DAP within the germline) or for improvement of soma-specific functions (see below). In other words, the soma-germline <ins class="diffchange diffchange-inline">SMB </ins>dichotomy provides us with the possibility to select for functions that are otherwise deleterious for the unicellular organism.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Applications=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Applications=</div></td></tr>
</table>David.bikardhttp://2007.igem.org/wiki/index.php?title=Paris/Perspectives&diff=46385&oldid=prevDavid.bikard at 00:51, 27 October 20072007-10-27T00:51:21Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>SMB is composed of a germline and a soma. Germ cells are responsible for reproduction while the sterile somatic cells<del class="diffchange diffchange-inline">, unable generate a population independently by themselves</del>, are essential for the germline as the soma exports the DAP compound, supporting germline growth. The special feature of our system, the coexistence of two independent cell types, one dedicated to reproduction and the other sterile, makes it a potentially interesting tool for synthetic biology. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>SMB is composed of a germline and a soma. Germ cells are responsible for reproduction while the sterile somatic cells, are essential for the germline as the soma exports the DAP compound, supporting germline growth. The special feature of our system, the coexistence of two independent cell types, one dedicated to reproduction and the other sterile, makes it a potentially interesting tool for synthetic biology. </div></td></tr>
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</table>David.bikardhttp://2007.igem.org/wiki/index.php?title=Paris/Perspectives&diff=46364&oldid=prevAblindner: /* Project */2007-10-27T00:47:36Z<p><span class="autocomment">Project</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Project ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Project ===</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In an attempt to integrate all the proposed applications of the SMB, we <del class="diffchange diffchange-inline">daydream </del>of <del class="diffchange diffchange-inline">constructing is </del>Ecolight. Bringing together the synthetic organism (SMB), noxious compound synthesis ("metabolic plant"), and the security device. This would include optimizing the production of triglycerides in the soma cells of our synthetic multicellular bacterium. Soma isolation according to the "security device" would be included. The super triglycerides-producing-not-able-to-divide soma cells could then be ingested. The fatty acids they would store would be as many fatty acids you will not absorb! Eat fat, don't get fat! <br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In an attempt to integrate all the proposed applications of the SMB, we <ins class="diffchange diffchange-inline">advanced towards the construction </ins>of Ecolight. Bringing together the synthetic organism (SMB), noxious compound synthesis ("metabolic plant"), and the security device. This would include optimizing the production of triglycerides in the soma cells of our synthetic multicellular bacterium. Soma isolation according to the "security device" would be included. The super triglycerides-producing-not-able-to-divide soma cells could then be ingested. The fatty acids they would store would be as many fatty acids you will not absorb! Eat fat, don't get fat! <br></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>E.colight project is also made up with 2 independent parts. First we have to create the SMB to implement the secured module. Second E.coli has to absorb free fatty acid and to synthesize triglycerides in the cytoplasm.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>E.colight project is also made up with 2 independent parts. First we have to create the SMB to implement the secured module. Second E.coli has to absorb free fatty acid and to synthesize triglycerides in the cytoplasm.</div></td></tr>
</table>Ablindnerhttp://2007.igem.org/wiki/index.php?title=Paris/Perspectives&diff=46352&oldid=prevAblindner: /* Metabolic engineering */2007-10-27T00:45:51Z<p><span class="autocomment">Metabolic engineering</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Metabolic engineering===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Metabolic engineering===</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>A bacterial multicellular organism could allow optimizing the production of compounds deleterious to the cell. If <del class="diffchange diffchange-inline">you attempt </del>to optimize the production of such a compound in a classical bacteria (E.coli for instance), trade off appears between the production of your compound and the growth of the cell. The synthetic organism could in part bypass this problem by partially decoupling growth from synthesis of the exogenous compound. It could indeed be modified so that only the soma produces the noxious molecule. If a mean exists to screen for maximum production of this molecule, you could then select the <del class="diffchange diffchange-inline">germ line </del>whose soma would have the best exocompound production yield. As long as the production doesn't impair too much the capacity of the soma to feed the <del class="diffchange diffchange-inline">germ line</del>, the optimization can go on. Thus, a <del class="diffchange diffchange-inline">tradeoff </del>also exists in this case, but it <del class="diffchange diffchange-inline">might </del>very well less stringent that in the wild type E.coli case. <del class="diffchange diffchange-inline">At least, this is worth testing. </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>A bacterial multicellular organism could allow optimizing the production of compounds deleterious to the cell. If <ins class="diffchange diffchange-inline">one attempts </ins>to optimize the production of such a compound in a classical bacteria (E.coli for instance), trade<ins class="diffchange diffchange-inline">-</ins>off appears between the production of your compound and the growth of the cell. The synthetic <ins class="diffchange diffchange-inline">multicellular </ins>organism could in part bypass this problem by partially decoupling growth from synthesis of the exogenous compound. It could indeed be modified so that only the soma produces the noxious molecule. If a mean exists to screen for maximum production of this molecule, you could then select the <ins class="diffchange diffchange-inline">germline </ins>whose soma would have the best exocompound production yield. As long as the production doesn't impair too much the capacity of the soma to feed the <ins class="diffchange diffchange-inline">germline</ins>, the optimization can go on. Thus, a <ins class="diffchange diffchange-inline">trade-off </ins>also exists in this case, but it <ins class="diffchange diffchange-inline">would </ins>very well less stringent that in the wild type E.coli case. </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Of course, all this is only possible if the germ line is not affected by the products released by the soma. Compounds that could be optimized in this way are thus constrained to molecules that can be noxious if <del class="diffchange diffchange-inline">acculated </del>in the cell, but that do not affect it too much if in the medium. For instance, if the product can be gradually filtered out of the medium.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Of course, all this is only possible if the germ line is not affected by the products released by the soma. Compounds that could be optimized in this way are thus constrained to molecules that can be noxious if <ins class="diffchange diffchange-inline">accumulated </ins>in the cell, but that do not affect it too much if in the medium. For instance, if the product can be gradually filtered out of the medium.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== E. Colight: towards a new slim diet == </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== E. Colight: towards a new slim diet == </div></td></tr>
</table>Ablindnerhttp://2007.igem.org/wiki/index.php?title=Paris/Perspectives&diff=46341&oldid=prevAblindner: /* Security device */2007-10-27T00:43:36Z<p><span class="autocomment">Security device</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>For details on proposed technical solutions to this challenge, [[Security device|SEE HERE]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>For details on proposed technical solutions to this challenge, [[Security device|<ins class="diffchange diffchange-inline">'''</ins>SEE HERE<ins class="diffchange diffchange-inline">'''</ins>]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Metabolic engineering===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Metabolic engineering===</div></td></tr>
</table>Ablindnerhttp://2007.igem.org/wiki/index.php?title=Paris/Perspectives&diff=46338&oldid=prevAblindner: /* Security device */2007-10-27T00:42:45Z<p><span class="autocomment">Security device</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Security device===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Security device===</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We came up with the idea of modifying the synthetic organism in order to allow<del class="diffchange diffchange-inline">: </del>on demand, full differentiation of the <del class="diffchange diffchange-inline">germ line </del>into soma in a secured fashion. Why would we want to do that? This possibility is to be considered in the face of biohazard risks. Release of GM organisms in the environment poses ethical as well as technical questions. “Biological security” should be a prime concern in synthetic biology.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We came up with the idea of modifying the synthetic organism in order to allow<ins class="diffchange diffchange-inline">, </ins>on demand, <ins class="diffchange diffchange-inline">the </ins>full differentiation of the <ins class="diffchange diffchange-inline">germline </ins>into soma in a secured fashion. Why would we want to do that? </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This possibility is to be considered in the face of biohazard risks. Release of GM organisms in the environment poses ethical as well as technical questions. “Biological security” should be a prime concern in synthetic biology.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>If a task is to be transiently performed by a GM organism in the open environment, a major problem is persistence of the GM organism, with potential risks of proliferation and transgene dissemination. A possible solution, already used for some GM crops, is to render the organisms sterile. Can this solution be implemented for GM bacteria, in bioremediation systems for instance? Using a modified version of our SMB, the answer is yes. The SMB comprises two cell types, one being the soma, a group of cells that have a longer lifetime than wild type E.coli cells & are unable to replicate. The soma cells have the required characteristics for transient use in open environment. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>If a task is to be transiently performed by a GM organism in the open environment, a major problem is persistence of the GM organism, with potential risks of proliferation and transgene dissemination. A possible solution, already used for some GM crops, is to render the organisms sterile. Can this solution be implemented for GM bacteria, in bioremediation systems for instance? Using a modified version of our SMB, the answer is yes. The SMB comprises two cell types, one being the soma, a group of cells that have a longer lifetime than wild type E.coli cells & are unable to replicate. The soma cells have the required characteristics for transient use in open environment. </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><del class="diffchange diffchange-inline">A </del>next consideration is then: can full differentiation be induced in the SMB? In order to achieve this, two events should be initiated:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">The </ins>next consideration is then: can full differentiation be induced in the SMB? In order to achieve this, two events should be initiated:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Induction of a massive differentiation of the germ line into soma cell</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Induction of a massive differentiation of the germ line into soma cell</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Followed by selective death of the persistent germ line cells.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Followed by selective death of the persistent germ line cells.</div></td></tr>
</table>Ablindnerhttp://2007.igem.org/wiki/index.php?title=Paris/Perspectives&diff=46320&oldid=prevAblindner: /* System improvement through directed evolution */2007-10-27T00:40:29Z<p><span class="autocomment">System improvement through directed evolution</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>= System improvement through directed evolution =</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>= System improvement through directed evolution =</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;">The engineered MSB may be further tuned by laboratory evolution. A key advantage of the system is that selection pressure could be tuned to either force faster reproduction (e.g., improving DAP production and/or export from the soma or alternatively for a more efficient use of DAP within the germline) or for improvement of soma-specific functions (see below). In other words, the soma-germline MSB dichotomy provides us with the possibility to select for functions that are otherwise deleterious for the unicellular organism.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Applications=</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=Applications=</div></td></tr>
</table>Ablindnerhttp://2007.igem.org/wiki/index.php?title=Paris/Perspectives&diff=46222&oldid=prevAblindner at 00:25, 27 October 20072007-10-27T00:25:19Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>SMB is composed of a <del class="diffchange diffchange-inline">germ line </del>and a soma. Germ cells are responsible for reproduction while the sterile somatic cells, unable generate a population independently by themselves, are essential for the <del class="diffchange diffchange-inline">germ line. The </del>soma exports <del class="diffchange diffchange-inline">Dap </del>compound, supporting <del class="diffchange diffchange-inline">germ line </del>growth. The special feature of our system, the coexistence of two independent cell types, one dedicated to reproduction and the other sterile, makes it a potentially interesting tool for synthetic biology. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>SMB is composed of a <ins class="diffchange diffchange-inline">germline </ins>and a soma. Germ cells are responsible for reproduction while the sterile somatic cells, unable generate a population independently by themselves, are essential for the <ins class="diffchange diffchange-inline">germline as the </ins>soma exports <ins class="diffchange diffchange-inline">the DAP </ins>compound, supporting <ins class="diffchange diffchange-inline">germline </ins>growth. The special feature of our system, the coexistence of two independent cell types, one dedicated to reproduction and the other sterile, makes it a potentially interesting tool for synthetic biology. </div></td></tr>
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</table>Ablindnerhttp://2007.igem.org/wiki/index.php?title=Paris/Perspectives&diff=46150&oldid=prevEismoustique: /* E. Colight: towards a new slim diet */2007-10-27T00:11:14Z<p><span class="autocomment">E. Colight: towards a new slim diet</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Project ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Project ===</div></td></tr>
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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">Finally, </del>the <del class="diffchange diffchange-inline">last part </del>of <del class="diffchange diffchange-inline">our project would be to bring </del>together the synthetic organism, <del class="diffchange diffchange-inline">the optimization of a </del>compound <del class="diffchange diffchange-inline">noxious to the bacteria</del>, and the security device. <del class="diffchange diffchange-inline">To do so, we'd like to optimize </del>the production of triglycerides in the soma cells of our synthetic <del class="diffchange diffchange-inline">organism</del>. <del class="diffchange diffchange-inline">We </del>would <del class="diffchange diffchange-inline">then </del>be <del class="diffchange diffchange-inline">able to differentiate all the germ line of the synthetic organism into soma in a secured way</del>. <del class="diffchange diffchange-inline">Those </del>super triglycerides-producing-not-able-to-divide cells could then be ingested. The fatty acids they would <del class="diffchange diffchange-inline">stock </del>would be as many fatty acids you will not absorb! Eat fat, don't get fat! <br></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">In an attempt to integrate all </ins>the <ins class="diffchange diffchange-inline">proposed applications </ins>of <ins class="diffchange diffchange-inline">the SMB, we daydream of constructing is Ecolight. Bringing </ins>together the synthetic organism <ins class="diffchange diffchange-inline">(SMB)</ins>, <ins class="diffchange diffchange-inline">noxious </ins>compound <ins class="diffchange diffchange-inline">synthesis ("metabolic plant")</ins>, and the security device. <ins class="diffchange diffchange-inline"> This would include optimizing </ins>the production of triglycerides in the soma cells of our synthetic <ins class="diffchange diffchange-inline">multicellular bacterium</ins>. <ins class="diffchange diffchange-inline">Soma isolation according to the "security device" </ins>would be <ins class="diffchange diffchange-inline">included</ins>. <ins class="diffchange diffchange-inline">The </ins>super triglycerides-producing-not-able-to-divide <ins class="diffchange diffchange-inline">soma </ins>cells could then be ingested. The fatty acids they would <ins class="diffchange diffchange-inline">store </ins>would be as many fatty acids you will not absorb! Eat fat, don't get fat! <br></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>E.colight project is also made up with 2 independent parts. First we have to create the SMB to implement the secured module. Second E.coli has to absorb free fatty acid and to synthesize triglycerides in the cytoplasm.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>E.colight project is also made up with 2 independent parts. First we have to create the SMB to implement the secured module. Second E.coli has to absorb free fatty acid and to synthesize triglycerides in the cytoplasm.</div></td></tr>
</table>Eismoustiquehttp://2007.igem.org/wiki/index.php?title=Paris/Perspectives&diff=46094&oldid=prevEismoustique at 00:00, 27 October 20072007-10-27T00:00:10Z<p></p>
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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;">== Another biomedical applications ==</del></div></td><td colspan="2"> </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;">Crohn disease and hemorrhagic recto-colitis are both autoimmune diseases located in the intestine. These diseases are thought to be caused by tolerance disruption of the body to its intestinal flora leading to abnormal inflammatory reponses. For example proinflammatory cytokines are produced and generate intestine lesions responsible of clinical symptoms. New therapies are now targeting inflammatory cytokines. We could also imagine producing IL10 or IL11 in our secured SMB. These anti-inflammatory cytokines could also limit the extension of inflammatory lesions.<br><br></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>'''References:''' <br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''References:''' <br></div></td></tr>
</table>Eismoustique