http://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&feed=atom&action=historyTeam:Toulouse/Project/Spreading - Revision history2024-03-19T13:26:32ZRevision history for this page on the wikiMediaWiki 1.16.5http://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&diff=393456&oldid=prevEmeline at 03:02, 18 October 20142014-10-18T03:02:26Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">S. Dinant, J.L. Bonnemain, C. Girousse,and J. Kehr. <b> Phloem sap intricacy and interplay with aphid feeding.</b>C R Biol. 2010 Jun-Jul;333(6-7):504-15. doi: 10.1016/j.crvi.2010.03.008. Epub 2010 May 14.</p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">S. Dinant, J.L. Bonnemain, C. Girousse, and J. Kehr. <b> Phloem sap intricacy and interplay with aphid feeding.</b>C R Biol. 2010 Jun-Jul;333(6-7):504-15. doi: 10.1016/j.crvi.2010.03.008. Epub 2010 May 14.</p></li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte"> Z.N. Senwo, and M.A. Tabatabai. <b> Amino acid composition of soil organic matter.</b> Biology and Fertility of SoilsFebruary 1998, Volume 26, Issue 3, pp 235-242 </p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte"> Z.N. Senwo, and M.A. Tabatabai. <b> Amino acid composition of soil organic matter.</b> Biology and Fertility of SoilsFebruary 1998, Volume 26, Issue 3, pp 235-242 </p></li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen, and P. Stragier. <b> Plasmids for ectopic integration in <i>Bacillus subtilis</i>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen, and P. Stragier. <b> Plasmids for ectopic integration in <i>Bacillus subtilis</i>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td></tr>
</table>Emelinehttp://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&diff=393360&oldid=prevEmeline at 03:01, 18 October 20142014-10-18T03:01:46Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">S. Dinant, J.L. Bonnemain, C. Girousse, J. Kehr. <b> Phloem sap intricacy and interplay with aphid feeding.</b>C R Biol. 2010 Jun-Jul;333(6-7):504-15. doi: 10.1016/j.crvi.2010.03.008. Epub 2010 May 14.</p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">S. Dinant, J.L. Bonnemain, C. Girousse,<ins class="diffchange diffchange-inline">and </ins>J. Kehr. <b> Phloem sap intricacy and interplay with aphid feeding.</b>C R Biol. 2010 Jun-Jul;333(6-7):504-15. doi: 10.1016/j.crvi.2010.03.008. Epub 2010 May 14.</p></li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte"> Z.N. Senwo and M.A. Tabatabai. <b> Amino acid composition of soil organic matter.</b> Biology and Fertility of SoilsFebruary 1998, Volume 26, Issue 3, pp 235-242 </p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte"> Z.N. Senwo<ins class="diffchange diffchange-inline">, </ins>and M.A. Tabatabai. <b> Amino acid composition of soil organic matter.</b> Biology and Fertility of SoilsFebruary 1998, Volume 26, Issue 3, pp 235-242 </p></li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen and P. Stragier. <b> Plasmids for ectopic integration in <i>Bacillus subtilis</i>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen<ins class="diffchange diffchange-inline">, </ins>and P. Stragier. <b> Plasmids for ectopic integration in <i>Bacillus subtilis</i>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">G. Shang, X. Liu, D. Lu, J. Zhang, N. Li, C. Zhu, S. Liu, Q. Yu, Y. Zhao and L. Gu. <b> Structural insight into how <i>Pseudomonas aeruginosa</i> peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.</b> Biochem J. 2012 Dec 1;448(2):201-11. doi: 10.1042/BJ20120668.</p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">G. Shang, X. Liu, D. Lu, J. Zhang, N. Li, C. Zhu, S. Liu, Q. Yu, Y. Zhao<ins class="diffchange diffchange-inline">, </ins>and L. Gu. <b> Structural insight into how <i>Pseudomonas aeruginosa</i> peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.</b> Biochem J. 2012 Dec 1;448(2):201-11. doi: 10.1042/BJ20120668.</p></li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">W.Z. Hua, C. S. Yong and X.T. Ren. <b>Biology and chemistry of endophytes.</b> Nat. Prod. Rep., 2006, 23, 753–771, 753</p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">W.Z. Hua, C. S. Yong<ins class="diffchange diffchange-inline">, </ins>and X.T. Ren. <b>Biology and chemistry of endophytes.</b> Nat. Prod. Rep., 2006, 23, 753–771, 753</p></li></div></td></tr>
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</table>Emelinehttp://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&diff=392522&oldid=prevEmeline at 02:55, 18 October 20142014-10-18T02:55:28Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">S. Dinant, J.L. Bonnemain, C. Girousse, J. Kehr. <b> Phloem sap intricacy and interplay with aphid feeding.</b>C R Biol. 2010 Jun-Jul;333(6-7):504-15. doi: 10.1016/j.crvi.2010.03.008. Epub 2010 May 14.</p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">S. Dinant, J.L. Bonnemain, C. Girousse, J. Kehr. <b> Phloem sap intricacy and interplay with aphid feeding.</b>C R Biol. 2010 Jun-Jul;333(6-7):504-15. doi: 10.1016/j.crvi.2010.03.008. Epub 2010 May 14.</p></li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte"> Z.N. Senwo and M.A. Tabatabai. <b> Amino acid composition of soil organic matter.</b> Biology and Fertility of SoilsFebruary 1998, Volume 26, Issue 3, pp 235-242 </p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte"> Z.N. Senwo and M.A. Tabatabai. <b> Amino acid composition of soil organic matter.</b> Biology and Fertility of SoilsFebruary 1998, Volume 26, Issue 3, pp 235-242 </p></li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen and P. Stragier <b> Plasmids for ectopic integration in <i>Bacillus subtilis</i>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen and P. Stragier<ins class="diffchange diffchange-inline">. </ins><b> Plasmids for ectopic integration in <i>Bacillus subtilis</i>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">G. Shang, X. Liu, D. Lu, J. Zhang, N. Li, C. Zhu, S. Liu, Q. Yu, Y. Zhao and L. Gu. <b> Structural insight into how <i>Pseudomonas aeruginosa</i> peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.</b> Biochem J. 2012 Dec 1;448(2):201-11. doi: 10.1042/BJ20120668.</p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">G. Shang, X. Liu, D. Lu, J. Zhang, N. Li, C. Zhu, S. Liu, Q. Yu, Y. Zhao and L. Gu. <b> Structural insight into how <i>Pseudomonas aeruginosa</i> peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.</b> Biochem J. 2012 Dec 1;448(2):201-11. doi: 10.1042/BJ20120668.</p></li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">W.Z. Hua, C. S. Yong and X.T. Ren <b>Biology and chemistry of endophytes.</b> Nat. Prod. Rep., 2006, 23, 753–771, 753</p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">W.Z. Hua, C. S. Yong and X.T. Ren<ins class="diffchange diffchange-inline">. </ins><b>Biology and chemistry of endophytes.</b> Nat. Prod. Rep., 2006, 23, 753–771, 753</p></li></div></td></tr>
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</table>Emelinehttp://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&diff=392434&oldid=prevEmeline at 02:54, 18 October 20142014-10-18T02:54:51Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen and P. Stragier <b> Plasmids for ectopic integration in <i>Bacillus subtilis</i>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen and P. Stragier <b> Plasmids for ectopic integration in <i>Bacillus subtilis</i>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">G. Shang, X. Liu, D. Lu, J. Zhang, N. Li, C. Zhu, S. Liu, Q. Yu, Y. Zhao and L. Gu. <b> Structural insight into how <i>Pseudomonas aeruginosa</i> peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.</b> Biochem J. 2012 Dec 1;448(2):201-11. doi: 10.1042/BJ20120668.</p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">G. Shang, X. Liu, D. Lu, J. Zhang, N. Li, C. Zhu, S. Liu, Q. Yu, Y. Zhao and L. Gu. <b> Structural insight into how <i>Pseudomonas aeruginosa</i> peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.</b> Biochem J. 2012 Dec 1;448(2):201-11. doi: 10.1042/BJ20120668.</p></li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">W.Z. Hua, C. S. Yong and X.T. Ren<b>Biology and chemistry of endophytes.</b> Nat. Prod. Rep., 2006, 23, 753–771, 753</p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">W.Z. Hua, C. S. Yong and X.T. Ren <b>Biology and chemistry of endophytes.</b> Nat. Prod. Rep., 2006, 23, 753–771, 753</p></li></div></td></tr>
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</table>Emelinehttp://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&diff=392110&oldid=prevEmeline at 02:52, 18 October 20142014-10-18T02:52:31Z<p></p>
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</table>Emelinehttp://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&diff=391928&oldid=prevEmeline at 02:51, 18 October 20142014-10-18T02:51:01Z<p></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p class="title1">Survival in the environment: <i><del class="diffchange diffchange-inline">B. </del>subtilis</i> that is proline auxotrophic</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="title1">Survival in the environment: <i><ins class="diffchange diffchange-inline">Bacillus </ins>subtilis</i> that is proline auxotrophic</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p class="texte">SubtiTree will live in sap tree, thus we will use an endophyte <I><del class="diffchange diffchange-inline">B. </del>subtilis</I> strain. In order to contain our bacteria in this </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="texte">SubtiTree will live in sap tree, thus we will use an endophyte <I><ins class="diffchange diffchange-inline">Bacillus </ins>subtilis</I> strain. In order to contain our bacteria in this </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>area during a short period of time, we think about modifying some of its survival characteristics. To turn the bacterium growth dependant on the presence </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>area during a short period of time, we think about modifying some of its survival characteristics. To turn the bacterium growth dependant on the presence </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>inside the tree (and therefore avoid spreading in the environment), we planned to use a <i>B.subtilis</i> strain that is proline auxotrophic. The bacterium</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>inside the tree (and therefore avoid spreading in the environment), we planned to use a <i>B. subtilis</i> strain that is proline auxotrophic. The bacterium</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> should then be unable to synthesize this essential amino acid. Proline is the most abundant amino acid in the phloem sap. If the bacterium is in the sap,</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> should then be unable to synthesize this essential amino acid. Proline is the most abundant amino acid in the phloem sap. If the bacterium is in the sap,</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> it should grow normally without any deficiency, but if it escapes from the tree and <i>a fortiori</i> from the sap, it will not be able to survive for a </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> it should grow normally without any deficiency, but if it escapes from the tree and <i>a fortiori</i> from the sap, it will not be able to survive for a </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> long time as proline is present only in very low quantities in the soil. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> long time as proline is present only in very low quantities in the soil. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br/> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br/> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Auxotrophic <i><del class="diffchange diffchange-inline">Bacillus </del>subtilis</i> strains already exist and are indexed in the databases BGSC (Bacillus Genetic Stock Center).</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Auxotrophic <i><ins class="diffchange diffchange-inline">B. </ins>subtilis</i> strains already exist and are indexed in the databases BGSC (Bacillus Genetic Stock Center).</p></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><p class="title1">Preventing sporulation of <i><del class="diffchange diffchange-inline">B. </del>subtilis</i></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="title1">Preventing sporulation of <i><ins class="diffchange diffchange-inline">Bacillus </ins>subtilis</i></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="texte"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="texte"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It is known that endophyte bacteria must sporulate to survive during the winter. We planned to limit Subtitree's lifespan to only one season.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It is known that endophyte bacteria must sporulate to survive during the winter. We planned to limit Subtitree's lifespan to only one season.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte"> Z.N. Senwo and M.A. Tabatabai. <b> Amino acid composition of soil organic matter.</b> Biology and Fertility of SoilsFebruary 1998, Volume 26, Issue 3, pp 235-242 </p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte"> Z.N. Senwo and M.A. Tabatabai. <b> Amino acid composition of soil organic matter.</b> Biology and Fertility of SoilsFebruary 1998, Volume 26, Issue 3, pp 235-242 </p></li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen and P. Stragier <b> Plasmids for ectopic integration in <i>Bacillus subtilis</i>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen and P. Stragier <b> Plasmids for ectopic integration in <i>Bacillus subtilis</i>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">G. Shang, X. Liu, D. Lu, J. Zhang, N. Li, C. Zhu, S. Liu, Q. Yu, Y. Zhao and L. Gu. <b> Structural insight into how Pseudomonas aeruginosa peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.</b> Biochem J. 2012 Dec 1;448(2):201-11. doi: 10.1042/BJ20120668.</p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">G. Shang, X. Liu, D. Lu, J. Zhang, N. Li, C. Zhu, S. Liu, Q. Yu, Y. Zhao and L. Gu. <b> Structural insight into how <ins class="diffchange diffchange-inline"><i></ins>Pseudomonas aeruginosa<ins class="diffchange diffchange-inline"></i> </ins>peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.</b> Biochem J. 2012 Dec 1;448(2):201-11. doi: 10.1042/BJ20120668.</p></li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">W.Z. Hua, C. S. Yong and X.T. Ren<b>Biology and chemistry of endophytes.</b> Nat. Prod. Rep., 2006, 23, 753–771, 753</p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">W.Z. Hua, C. S. Yong and X.T. Ren<b>Biology and chemistry of endophytes.</b> Nat. Prod. Rep., 2006, 23, 753–771, 753</p></li></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>
</table>Emelinehttp://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&diff=391487&oldid=prevEmeline at 02:47, 18 October 20142014-10-18T02:47:38Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> long time as proline is present only in very low quantities in the soil. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> long time as proline is present only in very low quantities in the soil. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br/> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br/> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Auxotrophic <i><del class="diffchange diffchange-inline">B.</del>subtilis</i> strains already exist and are indexed in the databases BGSC (Bacillus Genetic Stock Center).</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Auxotrophic <i><ins class="diffchange diffchange-inline">Bacillus </ins>subtilis</i> strains already exist and are indexed in the databases BGSC (Bacillus Genetic Stock Center).</p></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><p class="title1">Preventing sporulation of <i>B. subtilis</i></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="title1">Preventing sporulation of <i>B. subtilis</i></p></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">S. Dinant, J.L. Bonnemain, C. Girousse, J. Kehr. <b> Phloem sap intricacy and interplay with aphid feeding.</b>C R Biol. 2010 Jun-Jul;333(6-7):504-15. doi: 10.1016/j.crvi.2010.03.008. Epub 2010 May 14.</p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">S. Dinant, J.L. Bonnemain, C. Girousse, J. Kehr. <b> Phloem sap intricacy and interplay with aphid feeding.</b>C R Biol. 2010 Jun-Jul;333(6-7):504-15. doi: 10.1016/j.crvi.2010.03.008. Epub 2010 May 14.</p></li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte"> Z.N. Senwo and M.A. Tabatabai. <b> Amino acid composition of soil organic matter.</b> Biology and Fertility of SoilsFebruary 1998, Volume 26, Issue 3, pp 235-242 </p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte"> Z.N. Senwo and M.A. Tabatabai. <b> Amino acid composition of soil organic matter.</b> Biology and Fertility of SoilsFebruary 1998, Volume 26, Issue 3, pp 235-242 </p></li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen and P. Stragier <b> Plasmids for ectopic integration in Bacillus subtilis.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">A.M. Guérout-Fleury, N. Frandsen and P. Stragier <b> Plasmids for ectopic integration in <ins class="diffchange diffchange-inline"><i></ins>Bacillus subtilis<ins class="diffchange diffchange-inline"></i></ins>.</b> Gene. 1996 Nov 21;180(1-2):57-61.</p></li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">G. Shang, X. Liu, D. Lu, J. Zhang, N. Li, C. Zhu, S. Liu, Q. Yu, Y. Zhao and L. Gu. <b> Structural insight into how Pseudomonas aeruginosa peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.</b> Biochem J. 2012 Dec 1;448(2):201-11. doi: 10.1042/BJ20120668.</p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">G. Shang, X. Liu, D. Lu, J. Zhang, N. Li, C. Zhu, S. Liu, Q. Yu, Y. Zhao and L. Gu. <b> Structural insight into how Pseudomonas aeruginosa peptidoglycanhydrolase Tse1 and its immunity protein Tsi1 function.</b> Biochem J. 2012 Dec 1;448(2):201-11. doi: 10.1042/BJ20120668.</p></li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">W.Z. Hua, C. S. Yong and X.T. Ren<b>Biology and chemistry of endophytes.</b> Nat. Prod. Rep., 2006, 23, 753–771, 753</p></li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li class="tree"><p class="texte">W.Z. Hua, C. S. Yong and X.T. Ren<b>Biology and chemistry of endophytes.</b> Nat. Prod. Rep., 2006, 23, 753–771, 753</p></li></div></td></tr>
</table>Emelinehttp://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&diff=371523&oldid=prevManon at 23:56, 17 October 20142014-10-17T23:56:46Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To control any unwanted long-term development of SubtiTree, our strain should therefore be unable to sporulate. Thus, during fall, when the sap become </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To control any unwanted long-term development of SubtiTree, our strain should therefore be unable to sporulate. Thus, during fall, when the sap become </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>less nutritious and the temperature is lower, the engineered bacterium will die and not pass through the following winter. This question has been studied in our</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>less nutritious and the temperature is lower, the engineered bacterium will die and not pass through the following winter. This question has been studied in our</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> <a= href "https://2014.igem.org/Team:Toulouse/Modelling" Modeling part<del class="diffchange diffchange-inline">> </del></a>.<br/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> <a= href "https://2014.igem.org/Team:Toulouse/Modelling"<ins class="diffchange diffchange-inline">> </ins>Modeling part </a>.<br/></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In addition, deleting all the engineered bacterial community every year puts a brake on the evolution due to random mutations,</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In addition, deleting all the engineered bacterial community every year puts a brake on the evolution due to random mutations,</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> thus allowing a better faith on the genetic constructions.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> thus allowing a better faith on the genetic constructions.</div></td></tr>
</table>Manonhttp://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&diff=358112&oldid=prevJourdan at 21:48, 17 October 20142014-10-17T21:48:24Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="texte"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="texte"></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>While we have not constructed yet these modules, we definitely think that the <del class="diffchange diffchange-inline">measures that </del>we designed should render the use of SubtiTree acceptable </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>While we have not constructed yet these modules, we definitely think that the <ins class="diffchange diffchange-inline">elaborated strategies </ins>we designed should render the use of SubtiTree acceptable </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>in real conditions. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>in real conditions. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
</table>Jourdanhttp://2014.igem.org/wiki/index.php?title=Team:Toulouse/Project/Spreading&diff=358037&oldid=prevJourdan at 21:47, 17 October 20142014-10-17T21:47:38Z<p></p>
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<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><p class="texte">Our engineered bacterium is designed to be inoculated in a tree and to cure fungal diseases. To <del class="diffchange diffchange-inline">target </del>the <del class="diffchange diffchange-inline">possible </del>environmental issues resulting of <del class="diffchange diffchange-inline">using </del>a modified organism <del class="diffchange diffchange-inline">directly </del>on trees <del class="diffchange diffchange-inline">bordering </del>the Canal du Midi, our team worked on different aspects to ensure a safe use of SubtiTree. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="texte">Our engineered bacterium is designed to be inoculated in a tree and to cure fungal diseases. To <ins class="diffchange diffchange-inline">avoid </ins>the environmental issues </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The first objective is to avoid the spreading of our smart bacterium outside the tree. In other words, the purpose is to ensure that once SubtiTree is in the tree, it is unable to live anywhere else. Another issue concerns the horizontal transfers of the genetic material between different bacteria. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>resulting <ins class="diffchange diffchange-inline">from the use </ins>of a modified organism on <ins class="diffchange diffchange-inline">the </ins>trees <ins class="diffchange diffchange-inline">lining </ins>the Canal du Midi, our team worked on different aspects to ensure a safe use of</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Taking into account these <del class="diffchange diffchange-inline">issues</del>, we <del class="diffchange diffchange-inline">imagined three modules</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>SubtiTree. </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The first objective is to avoid the spreading of our smart bacterium outside <ins class="diffchange diffchange-inline">of </ins>the tree. In other words, the purpose is to ensure that once SubtiTree </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>is in the tree, it is unable to live anywhere else. Another issue concerns the horizontal transfers of the genetic material between different bacteria. </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Taking into account these <ins class="diffchange diffchange-inline">key points</ins>, we <ins class="diffchange diffchange-inline">elaborate different strategies</ins>.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></div></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><p class="title1">Survival in the environment: <del class="diffchange diffchange-inline">proline auxotroph </del><i>B. subtilis</i></p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="title1">Survival in the environment: <i>B. subtilis</i> <ins class="diffchange diffchange-inline">that is proline auxotrophic</ins></p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p class="texte">SubtiTree will live in sap tree, thus we will use an endophyte <I>B. subtilis</I> strain. In order to contain our bacteria in this area during a short period of time, we <del class="diffchange diffchange-inline">thought of </del>modifying some of its survival characteristics. To <del class="diffchange diffchange-inline">make </del>the bacterium growth dependant on the presence <del class="diffchange diffchange-inline">of </del>the tree (and therefore avoid spreading in the environment), we planned to use a <i>B.subtilis</i> strain <del class="diffchange diffchange-inline">auxotroph for </del>proline. The bacterium should then be unable to synthesize this essential amino acid. Proline is the most abundant amino acid in the phloem sap. If the bacterium is in the sap, it should grow normally without any deficiency, but if it escapes from the tree and <i>a fortiori</i> from the sap, it will not be able to survive for a long time <del class="diffchange diffchange-inline">(</del>proline is present only in very low quantities in the <del class="diffchange diffchange-inline">ground)</del>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="texte">SubtiTree will live in sap tree, thus we will use an endophyte <I>B. subtilis</I> strain. In order to contain our bacteria in this </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>area during a short period of time, we <ins class="diffchange diffchange-inline">think about </ins>modifying some of its survival characteristics. To <ins class="diffchange diffchange-inline">turn </ins>the bacterium growth dependant on the presence </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">inside </ins>the tree (and therefore avoid spreading in the environment), we planned to use a <i>B.subtilis</i> strain <ins class="diffchange diffchange-inline">that is </ins>proline <ins class="diffchange diffchange-inline">auxotrophic</ins>. The bacterium</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>should then be unable to synthesize this essential amino acid. Proline is the most abundant amino acid in the phloem sap. If the bacterium is in the sap,</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>it should grow normally without any deficiency, but if it escapes from the tree and <i>a fortiori</i> from the sap, it will not be able to survive for a </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>long time <ins class="diffchange diffchange-inline">as </ins>proline is present only in very low quantities in the <ins class="diffchange diffchange-inline">soil</ins>. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br/> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br/> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Auxotroph </del><i>B.<del class="diffchange diffchange-inline">sutbilis</del></i> strains already exist and are indexed in databases <del class="diffchange diffchange-inline">as </del>BGSC (Bacillus Genetic Stock Center)<del class="diffchange diffchange-inline">, therefore they should be easy to find</del>.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Auxotrophic </ins><i>B.<ins class="diffchange diffchange-inline">subtilis</ins></i> strains already exist and are indexed in <ins class="diffchange diffchange-inline">the </ins>databases BGSC (Bacillus Genetic Stock Center).</p></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><p class="title1">Preventing sporulation of <i>B. subtilis</i></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="title1">Preventing sporulation of <i>B. subtilis</i></p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="texte"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="texte"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>It is known that endophyte bacteria must sporulate to survive <del class="diffchange diffchange-inline">to </del>winter. <del class="diffchange diffchange-inline">In order to limit the spreading of our bacterium, we </del>planned to limit <del class="diffchange diffchange-inline">its </del>lifespan to only one season. The bacteria should be injected in spring, grow during the summer and finally should die in the fall.<br\> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>It is known that endophyte bacteria must sporulate to survive <ins class="diffchange diffchange-inline">during the </ins>winter. <ins class="diffchange diffchange-inline">We </ins>planned to limit <ins class="diffchange diffchange-inline">Subtitree's </ins>lifespan to only one season.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><i>B. subtilis</i> is a <del class="diffchange diffchange-inline">sporing </del>bacterium: sporulation enables the microorganism to resist very harsh conditions and to spread from tree to tree.<br/> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>The bacteria should be injected in spring, grow during the summer and finally should</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>To control any unwanted long-term development of SubtiTree, our strain should therefore be <del class="diffchange diffchange-inline">deficient for sporulating. We USED or COULD USE a <I>B.subtilis</I> strain deficient in the late genes for sporulation</del>. Thus, during fall, when the sap become less nutritious and the temperature is <del class="diffchange diffchange-inline">low</del>, the engineered bacterium will die and not pass through the following winter.<br/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>die in the fall.<br\> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In addition, deleting all the engineered bacterial community every year puts a brake on the evolution due to random <del class="diffchange diffchange-inline">mutation</del>, thus allowing a better faith on the genetic constructions.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><i>B. subtilis</i> is a <ins class="diffchange diffchange-inline">spore-forming </ins>bacterium: sporulation enables the microorganism to resist <ins class="diffchange diffchange-inline">to </ins>very harsh conditions and </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>to spread from tree to tree.<br/> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>To control any unwanted long-term development of SubtiTree, our strain should therefore be <ins class="diffchange diffchange-inline">unable to sporulate</ins>. Thus, during fall, when the sap become </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>less nutritious and the temperature is <ins class="diffchange diffchange-inline">lower</ins>, the engineered bacterium will die and not pass through the following winter<ins class="diffchange diffchange-inline">. This question has been studied in our</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 class="diffchange diffchange-inline"> <a= href "https://2014.igem.org/Team:Toulouse/Modelling" Modeling part> </a></ins>.<br/></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In addition, deleting all the engineered bacterial community every year puts a brake on the evolution due to random <ins class="diffchange diffchange-inline">mutations</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 class="diffchange diffchange-inline"> </ins>thus allowing a better faith on the genetic constructions.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></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><p class="texte">These two <del class="diffchange diffchange-inline">first characteristics of SubtiTree demonstrate that it should be </del>an annual bacterium, growing only in sap tree. By combining them, they should prevent any long term colonization of any other ecological niche than <del class="diffchange diffchange-inline">the </del>plane trees</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="texte">These two <ins class="diffchange diffchange-inline">strategies aim to make <i>B. subtilis</i> </ins>an annual bacterium, growing only in <ins class="diffchange diffchange-inline">the </ins>sap tree. By combining them, </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>they should prevent any long term colonization of any other ecological niche than plane trees<ins class="diffchange diffchange-inline">.</ins></p></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: #eee; color:black; font-size: smaller;"><div><p class="title1">Gene transfer: toxin-antitoxin system</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="title1">Gene transfer: toxin-antitoxin system</p></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><p class="texte">We also wondered about horizontal <del class="diffchange diffchange-inline">genes transfer</del>. The goal of this module is to prevent horizontal transfers between bacteria and any exchange of synthetic genetic material that could be dangerous between wild type organisms and optimized organisms.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p class="texte">We also wondered about horizontal <ins class="diffchange diffchange-inline">gene transfers</ins>. The goal of this module is to prevent horizontal transfers between bacteria </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><br>We thought about a system limiting such transfers: a toxin-antitoxin module. It involves the addition of two genes to the bacterium: a gene encoding for a toxin (for example <i>tse2</i>) and a gene encoding for the antitoxin (<i>tsi1</i>), placing them in <del class="diffchange diffchange-inline">an opposite way on </del>the genome. The large <del class="diffchange diffchange-inline">space </del>between them prevents simultaneous transfers: if the optimized bacterium transfers the gene encoding for the toxin, the probability that the gene encoding for the antitoxin may be transferred simultaneously is <del class="diffchange diffchange-inline">really </del>low <del class="diffchange diffchange-inline">since they are located far away from each other</del>.<br/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>and any exchange of synthetic genetic material that could be dangerous between wild type organisms and optimized organisms.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Therefore, if <del class="diffchange diffchange-inline">anther </del>host bacterium receives the gene encoding for the toxin, it will be unable to survive since it will not possess the antitoxin. If it receives the antitoxin only, it will not be useful for the bacterium, and will not affect it.<br/></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><br>We thought about a system limiting such transfers: a toxin-antitoxin module. It involves the addition of two genes to the bacterium: a gene encoding </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>for a toxin (for example <i>tse2</i><ins class="diffchange diffchange-inline">, placed next to the engineered genetic modules</ins>) and a gene encoding for the antitoxin (<i>tsi1</i>), placing them <ins class="diffchange diffchange-inline">far away from each other </ins>in the genome. The large <ins class="diffchange diffchange-inline">intergenic region</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 class="diffchange diffchange-inline"> </ins>between them prevents simultaneous transfers: if the optimized bacterium transfers the gene encoding for the toxin, the probability that the gene </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>encoding for the antitoxin may be transferred simultaneously is <ins class="diffchange diffchange-inline">very </ins>low.<br/></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Therefore, if <ins class="diffchange diffchange-inline">another </ins>host bacterium receives the gene encoding for the toxin, it will be unable to survive since it will not possess the antitoxin. </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>If it receives the antitoxin only, it will not be useful for the bacterium, and will not affect it.<br/></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In summary, since a simultaneous transfer is dimly probable, the bacterium will either die because of the toxin or live while expressing the antitoxin. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In summary, since a simultaneous transfer is dimly probable, the bacterium will either die because of the toxin or live while expressing the antitoxin. </div></td></tr>
<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;"></p></del></div></td><td colspan="2"> </td></tr>
<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;"></del></div></td><td colspan="2"> </td></tr>
<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;"><p class="texte">Our synthetic genes are not the only problem in the design of SubtiTree. One of the side effects of our cloning method is the persistence of antibiotic resistance genes. This is incompatible with the introduction of SubtiTree in the environment. It is possible to delete this resistance in chromosome.</del></div></td><td colspan="2"> </td></tr>
<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;"><br></del></div></td><td colspan="2"> </td></tr>
<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;">While we have not constructed yet these modules, we definitely think that the measures that we designed should render the use of SubtiTree acceptable in the environment. </del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></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><p class="title1">Using integrative plasmids</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="title1">Using integrative plasmids</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="texte"></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="texte"></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">All </del>our constructions are carried by integrative plasmids. Consequently, our different genetic modules should be integrated into the bacterium genome. The integration in the genome is more stable as the constructions are less likely to be transferred to other microorganisms. In addition to that, the expression of our genetic modules would not be dependent on a selective pressure, allowing a high level of transcription <i>in planta</i>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">One of the side effects of our cloning method is the persistence of antibiotic resistance genes. This is incompatible with the introduction </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 class="diffchange diffchange-inline">in the tree, and with the stability of our constructs. To avoid this, all </ins>our constructions are carried by integrative plasmids. Consequently, our different</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>genetic modules should be integrated into the bacterium genome. The integration in the genome is more stable as the constructions are less likely to be </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>transferred to other microorganisms. In addition to that, the expression of our genetic modules would not be dependent on a selective pressure, </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"> </ins>allowing a high level of transcription <i>in planta</i>. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></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 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;"><p class="texte"></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;"><br></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;">While we have not constructed yet these modules, we definitely think that the measures that we designed should render the use of SubtiTree acceptable </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;">in real conditions. </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;"></p></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="title1">References</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p class="title1">References</p></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>
</table>Jourdan