Team:Toulouse/Notebook/Calendar

From 2014.igem.org

(Difference between revisions)
 
(15 intermediate revisions not shown)
Line 14: Line 14:
<script type='text/javascript' src='http://ajax.googleapis.com/ajax/libs/jquery/1.9.0/jquery.min.js'></script>
<script type='text/javascript' src='http://ajax.googleapis.com/ajax/libs/jquery/1.9.0/jquery.min.js'></script>
-
<script type='text/javascript'> $(function(){  
+
<script type='text/javascript'> $(function(){ modelling
   $(window).scroll(function () {
   $(window).scroll(function () {
     if ($(this).scrollTop() > 250) {
     if ($(this).scrollTop() > 250) {
Line 34: Line 34:
   .title3{color:#7f8c8c; font-family:'Open Sans'; font-weight:400; font-size:16px; margin:0 0 20px 0; border:none;}
   .title3{color:#7f8c8c; font-family:'Open Sans'; font-weight:400; font-size:16px; margin:0 0 20px 0; border:none;}
 +
 +
.title4{color:#5a6060; font-family:'Open Sans'; font-weight:700; font-size:14px; margin:0 0 20px 0; border:none;}
   .texte{color:#5a6060; font-family:'Open Sans'; font-size:14px; margin:0 0 50px 0; line-height:24px; text-align: justify;}
   .texte{color:#5a6060; font-family:'Open Sans'; font-size:14px; margin:0 0 50px 0; line-height:24px; text-align: justify;}
Line 166: Line 168:
<p class="texte">
<p class="texte">
- iGEM competition presentation and explanations<br/>
- iGEM competition presentation and explanations<br/>
-
- Constitution of the team by interviewing different students from Université Paul Sabatier and INSA
+
- Constitution of the <a href="https://2014.igem.org/Team:Toulouse/Team">team</a> by interviewing different students from Université Toulouse III Paul Sabatier and INSA de Toulouse
</p>
</p>
-
<p class="texte" style="text-align:center"><B> The adventure begins for the 2014 Toulouse iGEM Team ! </B>
+
<p class="texte" style="text-align:center"><B> The adventure begins for the 2014 Toulouse iGEM Team!</B>
</p>
</p>
Line 180: Line 182:
- Thanks to weekly meetings, our team was able to discuss about new project ideas.
- Thanks to weekly meetings, our team was able to discuss about new project ideas.
<br/>
<br/>
-
- Many ideas were approached and debated regarding the feasibility thanks to the literature and supervisors including teachers and researchers
+
- Many ideas were approached and debated regarding the feasibility thanks to the literature and supervisors including teachers and researchers.<br>
<br/>
<br/>
This is a list of the main projects:  
This is a list of the main projects:  
Line 197: Line 199:
<div class="technology">June 2014: Choice of SubtiTree project</div>
<div class="technology">June 2014: Choice of SubtiTree project</div>
<div class="thelanguage">
<div class="thelanguage">
-
<p class="texte">The discussion has been long to estimate the practicability of our final project. By the end of June, most of the ideas were eliminated but two of them remained: controlling the cancer or saving the trees. It became easily clear that SubtiTree was successfully completed whether regarding the scientific part or the ethical aspect. Indeed, our knowledge in medicine was not sufficient enough to evaluate the consequences of a bacterium injection in the human body for <i>E. coli</i> cancer.</br>
+
<p class="texte">The discussion has been long to estimate the practicability of our final project. By the end of May, most of the ideas were eliminated but two of them remained: controlling the cancer or saving the trees. It became easily clear that SubtiTree was successfully completed whether regarding the scientific part or the ethical aspect. Indeed, our knowledge in medicine was not sufficient enough to evaluate the consequences of a bacterium injection in the human body for <i>E. coli</i> cancer.</br>
Therefore, the whole team agreed on focusing on a local issue as the preservation of the Canal du Midi plane trees. However, the final goal was based on the idea to allow our optimized bacteria to be efficient for all fungi infections in the environment.</br>
Therefore, the whole team agreed on focusing on a local issue as the preservation of the Canal du Midi plane trees. However, the final goal was based on the idea to allow our optimized bacteria to be efficient for all fungi infections in the environment.</br>
-
By this period, we evaluated our budget to approximately <B> k€ 40,000 </B>.
+
By this period, we evaluated our budget to approximately <B>€39,500</B>.
</p>  
</p>  
Line 245: Line 247:
<p class="title3">Lab work:</p>
<p class="title3">Lab work:</p>
<p class="texte">
<p class="texte">
-
- E. coli transformation with BBA_J004450 (pSB1C3)
+
- <i>E. coli</i> transformation with BBA_J004450 (pSB1C3)
</p>
</p>
Line 266: Line 268:
<p class="texte">
<p class="texte">
- Beginning of the laboratory work to create our optimized bacterium <br/>
- Beginning of the laboratory work to create our optimized bacterium <br/>
-
- Research of sponsors and the communication thanks to the press
+
- Research of sponsors and communication thanks to the press
</p>  
</p>  
Line 276: Line 278:
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
-
- Participation at the BioSynSys conferences: presentation of SubtiTree<br/>
+
- Participation at the BioSynSys conferences: presentation of SubtiTree project<br/>
-
- We have put in place a newsletter system the first day of each month to keep all our sponsors and people who support us updated about the project, our financial state.
+
- We have put in place a newsletter system the first friday of each month to keep all our sponsors and people who support us updated about the project (financial, scientific and communication aspects).
</p>
</p>
Line 283: Line 285:
<p class="texte">
<p class="texte">
- Design of all the constructions needed with cloning and restriction enzymes to save some time and allow a better comprehension of our bacterium system </br>
- Design of all the constructions needed with cloning and restriction enzymes to save some time and allow a better comprehension of our bacterium system </br>
-
Problem: A problem was reported in the use of the CYP. Indeed, the biobrick is not expressed properly in <i>Bacillus subtilis</i> strain. Therefore we had to look at the literature to find a new fungicide called GAFP-1.<br/>
+
Problem: A problem was reported in the use of the CYP. Indeed, the BioBrick is not expressed properly in <i>Bacillus subtilis</i> strain. Therefore we had to look at the literature to find a new fungicide called GAFP-1.<br/>
-
- A bioreactor was conceived to reproduce the composition of the sap in the plane trees. The main goal was to identify the behavior of Bacillus strain in a medium composed of many different carbon sources.<br/>
+
- A bioreactor was conceived to reproduce the composition of the sap in the plane trees. The main goal was to identify the behavior of <i>Bacillus</i> strain in a medium composed of many different carbon sources.<br/>
- Competent cells and transformation practice using GFP and RFP.
- Competent cells and transformation practice using GFP and RFP.
</p>
</p>
Line 301: Line 303:
<div class="technology2">Week 5 (14-20 July)</div>
<div class="technology2">Week 5 (14-20 July)</div>
<div class="thelanguage2">
<div class="thelanguage2">
 +
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
- Our team was interviewed by many local newspapers such as 20minutes, Metronews, La Voix du Midi, La Dépêche but also by the local television channel France3 Midi-Pyrénées to present our draft to the community. Moreover, SubtiTree was approached in some radio programs like Virgin Radio Toulouse and France info.</br>
- Our team was interviewed by many local newspapers such as 20minutes, Metronews, La Voix du Midi, La Dépêche but also by the local television channel France3 Midi-Pyrénées to present our draft to the community. Moreover, SubtiTree was approached in some radio programs like Virgin Radio Toulouse and France info.</br>
Line 309: Line 312:
- GFP and RFP digestion amplified by miniprep and gel electrophoresis <br/>
- GFP and RFP digestion amplified by miniprep and gel electrophoresis <br/>
Problem: the digested GFP doesn’t appear on the gel contrary to RFP plasmid. We assumed a problem with the GFP miniprep. We tried the miniprep from the INSA Toulouse team from 2013 and the GFP plasmid was fully digested.<br/>
Problem: the digested GFP doesn’t appear on the gel contrary to RFP plasmid. We assumed a problem with the GFP miniprep. We tried the miniprep from the INSA Toulouse team from 2013 and the GFP plasmid was fully digested.<br/>
-
- Transformation and cryopreservation of biobricks BBa_K823002 (PlepA), BBa_K823003 (Pveg), BBa_K606061 (RBS SpoVG) and BBa_B0015 (double terminator), BBa_K823023 (pSBBS1C), BBa_K733013 (Pveg+ RBS) in <i>E. coli</i>.<br/>
+
- Transformation and cryopreservation of BioBricks BBa_K823002 (P<sub>lep</sub>A), BBa_K823003 (P<sub>veg</sub>), BBa_K606061 (RBS SpoVG) and BBa_B0015 (double terminator), BBa_K823023 (pSB<sub>BS</sub>1C), BBa_K733013 (P<sub>veg</sub> + RBS) in <i>E. coli</i>.<br/>
-
- Transformation of the Munich B. subtilis backbones<br/>
+
- Transformation of the Munich <i>B. subtilis</i> backbones<br/>
-
- Cloning of BBa_K606061 (RBS SpoVG) with BBa_K823003 (PvEG) and BBa_K823002 (PlepA)
+
- Cloning of BBa_K606061 (RBS SpoVG) with BBa_K823003 (P<sub>veg</sub>) and BBa_K823002 (P<sub>lepA</sub>)
</p>
</p>
Line 317: Line 320:
<p class="texte">
<p class="texte">
- Transformation of the Eurofins genes<br/>
- Transformation of the Eurofins genes<br/>
-
- Start assembling the biobricks for the fungicides<br/>
+
- Start assembling the BioBricks for the fungicides<br/>
- Check all the cloning
- Check all the cloning
</p>
</p>
Line 336: Line 339:
- PCR and migration on electrophoresis gel<br/>
- PCR and migration on electrophoresis gel<br/>
- Transformation BBA_1364003 (D4E1)  on pSB1C3 and BBA_1364002 (GAFP1) on pSB1C3<br/>
- Transformation BBA_1364003 (D4E1)  on pSB1C3 and BBA_1364002 (GAFP1) on pSB1C3<br/>
-
- Cloning BBA_1364002 (GAFP1) with BBa_B0015 (double terminator) and BBA_1364003 (D4E1) with BBa_K823003 (Pveg)
+
- Cloning BBA_1364002 (GAFP1) with BBa_B0015 (double terminator) and BBA_1364003 (D4E1) with BBa_K823003 (P<sub>veg</sub>)
</p>
</p>
Line 349: Line 352:
</div>
</div>
-
<div class="technology">August 2014 </div>
+
<div class="technology">August 2014</div>
<div class="thelanguage">
<div class="thelanguage">
<p class="title2">Main activities</p>
<p class="title2">Main activities</p>
Line 371: Line 374:
<p class="title3">Lab work: </p>
<p class="title3">Lab work: </p>
<p class="texte">
<p class="texte">
-
- Cloning BBa_K823003 (Pveg) + RFP and BBa_K823002 (PlepA) + RFP in pSBBs1C<br/>
+
- Cloning BBa_K823003 (P<sub>veg</sub>) + RFP and BBa_K823002 (P<sub>lepA</sub>) + RFP in pSB<sub>Bs</sub>1C<br/>
-
- Test of every pSBBs vector : BBa_K823021 (pSBBS1C-lacZ), BBa_K823022 (pSBBS4S), BBa_K823023 (pSBBS1C), minipreps and cryopreservation of the best clones<br/>
+
- Test of every pSB<sub>BS</sub> vector: BBa_K823021 (pSB<sub>BS</sub>1C-lacZ), BBa_K823022 (pSB<sub>BS</sub>4S), BBa_K823023 (pSB<sub>BS</sub>1C), minipreps and cryopreservation of the best clones<br/>
-
- Checking of BBA_1364002 (GAFP1)  + BBa_B0015 (double terminator) transformants (biobrick BBa_K1364007) and BBA_1364003 (D4E1)  + BBa_K823003 (Pveg) biobrick BBa_K1364009
+
- Checking of BBA_1364002 (GAFP1)  + BBa_B0015 (double terminator) transformants (BioBrick BBa_K1364007) and BBA_1364003 (D4E1)  + BBa_K823003 (P<sub>veg</sub>) BioBrick BBa_K1364009
<br/>
<br/>
-
- Cloning of BBA_1364003 (D4E1)  + pSBBS4S (BBa_K823022) and subculture of the colonies<br/>
+
- Cloning of BBA_1364003 (D4E1)  + pSB<sub>BS</sub>4S (BBa_K823022) and subculture of the colonies<br/>
- Cloning of BBa_K823003 (Pveg) + BBA_1364003 (D4E1)  with BBa_B0015 (double terminator)<br/>
- Cloning of BBa_K823003 (Pveg) + BBA_1364003 (D4E1)  with BBa_B0015 (double terminator)<br/>
-
- Cloning of BBa_K823003 (Pveg) + RFP (BBa_K1364017)  in pSBBS4S (BBa_K823022), subculture and minipreps<br/>
+
- Cloning of BBa_K823003 (Pveg) + RFP (BBa_K1364017)  in pSB<sub>BS</sub>4S (BBa_K823022), subculture and minipreps<br/>
-
- Cloning of BBa_K823002 (PlepA) + RFP (BBa_K1364016)  in pSBBs4S (BBa_K823022), subculture and minipreps<br/>
+
- Cloning of BBa_K823002 (PlepA) + RFP (BBa_K1364016)  in pSB<sub>BS</sub>4S (BBa_K823022), subculture and minipreps<br/>
- Cloning of BBa_1364018 (Strong Promotor + RFP)<br/>
- Cloning of BBa_1364018 (Strong Promotor + RFP)<br/>
-
- Cloning of BBA_1364003 (D4E1) + BBA_1364002 (GAFP1) + Promotor BBa_K823003 (Pveg) biobrick BBa_K1364012 with gel extraction for BBA_1364003 (D4E1) + BBA_1364002 (GAFP1)  and a PCR cleanup for BBa_K823003 (Pveg), subculture<br/>
+
- Cloning of BBA_1364003 (D4E1) + BBA_1364002 (GAFP1) + Promotor BBa_K823003 (P<sub>veg</sub>) BioBrick BBa_K1364012 with gel extraction for BBA_1364003 (D4E1) + BBA_1364002 (GAFP1)  and a PCR cleanup for BBa_K823003 (P<sub>veg</sub>), subculture<br/>
- Cloning BBa_K823003 (Pveg) + BBA_1364002 (GAFP1) + BBa_B0015 (double terminator) on pSBBS4S in <i>E. coli</i><br/>
- Cloning BBa_K823003 (Pveg) + BBA_1364002 (GAFP1) + BBa_B0015 (double terminator) on pSBBS4S in <i>E. coli</i><br/>
- Transformation of binding gene with <i>E. coli</i> competent cells<br/>
- Transformation of binding gene with <i>E. coli</i> competent cells<br/>
Line 390: Line 393:
</p>
</p>
-
<p class="title3">Weekly meeting with the instructors(08/01/2014)</p>
+
<p class="title3">Weekly meeting with the instructors (08/01/2014)</p>
<p class="texte">
<p class="texte">
- Possible problem with the restriction enzymes regarding the digestion: new recommendations
- Possible problem with the restriction enzymes regarding the digestion: new recommendations
Line 412: Line 415:
<p class="title3">Lab work:</p>
<p class="title3">Lab work:</p>
<p class="texte">
<p class="texte">
-
- Check the cloning of BBa_K823003 (Pveg)+BBA_1364002 (GAFP1) + BBa_B0015 (double terminator) on pSBBs4S and cryopreservation
+
- Check the cloning of BBa_K823003 (P<sub>veg</sub>)+BBA_1364002 (GAFP1) + BBa_B0015 (double terminator) on pSB<sub>BS</sub>4S and cryopreservation
<br/>
<br/>
-
- Transformation of BBa_K823003 (Pveg) +BBA_1364002 (GAFP1) + BBa_B0015 (double terminator)  (biobrick BBa_ K1364008) in BBa_K823022 (pSBBS4S)  
+
- Transformation of BBa_K823003 (P<sub>veg</sub>) + BBA_1364002 (GAFP1) + BBa_B0015 (double terminator)  (BioBrick BBa_ K1364008) in BBa_K823022 (pSB<sub>BS</sub>4S)  
<br/>
<br/>
-
- Cloning of BBa_K1364001, the binding gene + BBa_K823003 (Pveg) on pSB1C3 and pSBBS 4S
+
- Cloning of BBa_K1364001, the binding gene + BBa_K823003 (P<sub>veg</sub>) on pSB1C3 and pSB<sub>BS</sub>4S
<br/>
<br/>
-
Problem: the band is at 1500 bp instead of 1300 bp on the gel
+
Problem: the band is at 1500bp instead of 1300bp on the gel
<br/>
<br/>
-
- Cloning of BBa_K1162001 (EcAMP) + BBa_K823003 (Pveg) + BBa_K606061 (RBS SpoVG), miniprep, PCR and digestion  
+
- Cloning of BBa_K1162001 (EcAMP) + BBa_K823003 (P<sub>veg</sub>) + BBa_K606061 (RBS SpoVG), miniprep, PCR and digestion  
<br/>
<br/>
-
Problem: the fragment of DNA is too small (149 bp) to be seen on the gel and was probably lost during the PCR cleanup. Instead of that, we used the heat enzymes inactivation at 95°C for 15 minutes.  
+
Problem: the fragment of DNA is too small (149bp) to be seen on the gel and was probably lost during the PCR cleanup. Instead of that, we used the heat enzymes inactivation at 95°C for 15 minutes.  
<br/>
<br/>
-
- Cloning of Promotor + BBA_1364003 (D4E1)  + BBA_1364002 (GAFP1) in pSB1C3 and pSBBS4S and cryopreservation
+
- Cloning of Promotor + BBA_1364003 (D4E1)  + BBA_1364002 (GAFP1) in pSB1C3 and pSB<sub>BS</sub>4S and cryopreservation
<br/>
<br/>
- Elaboration of an efficient fungicide test protocol  
- Elaboration of an efficient fungicide test protocol  
Line 451: Line 454:
</p>
</p>
-
<p class="title2">Lab work:</p>
+
<p class="title3">Lab work:</p>
<p class="texte">
<p class="texte">
- Evaluation of the bacterial decrease rate from 10°C to 4°C with a sporuling strain of <i>B. subtilis</i>.
- Evaluation of the bacterial decrease rate from 10°C to 4°C with a sporuling strain of <i>B. subtilis</i>.
Line 457: Line 460:
- Chemotaxis test with different concentrations of glucose on a 0.3% agar.
- Chemotaxis test with different concentrations of glucose on a 0.3% agar.
<br/>
<br/>
-
- Miniprep of pSBBs4S with binding gene and transformation in <i>B. subtilis</i>.
+
- Miniprep of pSB<sub>B</sub>4S with binding gene and transformation in <i>B. subtilis</i>.
<br/>
<br/>
Problem: no digestion was visible on the gel => the cloning failed
Problem: no digestion was visible on the gel => the cloning failed
<br/>
<br/>
-
- Transformation of BBa_K1374010 (Pveg + RBS SpoVG + EcAMP) + BBa_K1364012 (RBS + Gafp1 + D4E1 + double terminator), subculture
+
- Transformation of BBa_K1374010 (P<sub>veg</sub> + RBS SpoVG + EcAMP) + BBa_K1364012 (RBS + GAFP1 + D4E1 + double terminator), subculture
<br/>
<br/>
-
- Subculture of <i>B. subtilis</i> clones transformed by BBa_K823003 (Pveg) + BBA_1364002 (GAFP1)  + BBa_B0015 (double terminator) in pSBBs4S, cryopreservation
+
- Subculture of <i>B. subtilis</i> clones transformed by BBa_K823003 (P<sub>veg</sub>) + BBA_1364002 (GAFP1)  + BBa_B0015 (double terminator) in pSB<sub>B</sub>4S, cryopreservation
<br/>
<br/>
- Fungicide test
- Fungicide test
Line 483: Line 486:
<p class="title3">Lab work:</p>
<p class="title3">Lab work:</p>
<p class="texte">
<p class="texte">
-
- Subculture and transformation in <i> B. subtilis </i> of BBa_K1364011 in pSBBS4S (BBa_K823022) and cloning of BBa_K1364011 on pSBBS1C (BBa_K823023).
+
- Subculture and transformation in <i> B. subtilis </i> of BBa_K1364011 in pSB<sub>BS</sub>4S (BBa_K823022) and cloning of BBa_K1364011 on pSB<sub>BS</sub>1C (BBa_K823023).
<br/>
<br/>
-
Problem: no clone had the insert on pSBBS1C => the cloning had to be done again
+
Problem: no clone had the insert on pSB<sub>BS</sub>1C => the cloning had to be done again
-
- Miniprep of BBa_K1364011 in BBa_K823023 (pSBBS1C) + Transformation in <i>B. subtilis</i>.
+
<br>- Miniprep of BBa_K1364011 in BBa_K823023 (pSB<sub>BS</sub>1C) + Transformation in <i>B. subtilis</i>.
<br/>
<br/>
-
- Cloning of BBA_1364003 (D4E1) , BBA_1364002 (GAFP1) , BBA_1364003 (D4E1) + BBA_1364002 (GAFP1)  on BBa_K823023 (pSBBS1C)  
+
- Cloning of BBA_1364003 (D4E1) , BBA_1364002 (GAFP1) , BBA_1364003 (D4E1) + BBA_1364002 (GAFP1)  on BBa_K823023 (pSB<sub>BS</sub>1C)  
<br/>
<br/>
-
- Transformation BBa_1364004 (in pSBBS4S in E.coli  
+
- Transformation BBa_1364004 (in pSB<sub>BS</sub>4S in <i>E. coli</i> )
<br/>
<br/>
-
- Cloning of BBa_K1364014 (Pveg + RBS SpoVG + EcAMP + GAFP1 +D4E1 + double terminator) in K823022 (pSBBS4S) and in BBa_K823023 (pSBBS1C), miniprep and digestion by restriction enzymes to see the size of the insert on a 1% gel
+
- Cloning of BBa_K1364014 (P<sub>veg</sub> + RBS SpoVG + EcAMP + GAFP1 + D4E1 + double terminator) in K823022 (pSB<sub>BS</sub>4S) and in BBa_K823023 (pSB<sub>BS</sub>1C), miniprep and digestion by restriction enzymes to see the size of the insert on a 1% gel
<br/>
<br/>
-
Problem: no clone had the insert on pSBBS1C => the cloning had to be done again
+
Problem: no clone had the insert on pSB<sub>BS</sub>1C => the cloning had to be done again
</p>
</p>
Line 512: Line 515:
- Cloning of BBa_K1364014 in BBa_K823022 and in BBa_K823023  
- Cloning of BBa_K1364014 in BBa_K823022 and in BBa_K823023  
<br/>
<br/>
-
- Cloning GAFP1 + BBa_K823023 (pSBBS1C) in <i>B. subtilis</i> with a change in the protocol: pre-induction of the culture with 0.125 µg/ml of chloramphenicol one hour after the addition of DNA, and let grow for another hour.
+
- Cloning GAFP1 + BBa_K823023 (pSB<sub>BS</sub>1C) in <i>B. subtilis</i> with a change in the protocol: pre-induction of the culture with 0.125 µg/ml of chloramphenicol one hour after the addition of DNA, and let grow for another hour.
<br/>
<br/>
Problem: no colony  
Problem: no colony  
<br/>
<br/>
-
- Liquid culture of Bacillus + BBA_1364002 (GAFP1); Bacillus + BBA_1364003 (D4E1) + BBA_1364002 (GAFP1) ; Bacillus + BBA_1364003 (D4E1) for future fungicide tests
+
- Liquid culture of <i>Bacillus subtilis</i> + BBA_1364002 (GAFP1); <i>Bacillus subtilis</i> + BBA_1364003 (D4E1) + BBA_1364002 (GAFP1) ; <i>Bacillus subtilis</i> + BBA_1364003 (D4E1) for future fungicide tests
<br/>
<br/>
-
- Miniprep of BBa_ K1364011 in BBa_ K823023 (pSBBs1C) and transformation in <i>Bacillus subtilis</i> strain.  
+
- Miniprep of BBa_ K1364011 in BBa_ K823023 (pSB<sub>BS</sub>1C) and transformation in <i>Bacillus subtilis</i> strain.  
<br/>
<br/>
-
- Fungicide test of BBa_K1364011 in pSBBs4S, Promotor + BBA_1364002 (GAFP1) + Terminator (biobrick BBa_K1364008) in pSBBS4S, Promotor + BBA_1364003 (D4E1) + Terminator (biobrick BBa_K1364009) in pSBBS4S, Promotor + BBA_1364002 (GAFP1) + BA_1364003 (D4E1)  + Terminator ( biobrick BBa_K1364013) in pSBBS4S
+
- Fungicide test of BBa_K1364011 in pSB<sub>BS</sub>4S, Promotor + BBA_1364002 (GAFP1) + Terminator (BioBrick BBa_K1364008) in pSB<sub>BS</sub>4S, Promotor + BBA_1364003 (D4E1) + Terminator (BioBrick BBa_K1364009) in pSB<sub>BS</sub>4S, Promotor + BBA_1364002 (GAFP1) + BA_1364003 (D4E1)  + Terminator (BioBrick BBa_K1364013) in pSB<sub>BS</sub>4S
<br/>
<br/>
- Transformation of a new vector PKL 190 (threonine integrative) in <i>Bacillus</i> strain  
- Transformation of a new vector PKL 190 (threonine integrative) in <i>Bacillus</i> strain  
Line 540: Line 543:
   
   
<div class="technology">September 2014</div>
<div class="technology">September 2014</div>
-
<div class ="thelanguage"><p class="title2">Main activities</p>
+
<div class ="thelanguage">
 +
<p class="title2">Main activities</p>
<p class="texte">
<p class="texte">
- Finish the tests of the different modules
- Finish the tests of the different modules
Line 563: Line 567:
<p class="title3">Lab work:</p>
<p class="title3">Lab work:</p>
<p class="texte">
<p class="texte">
-
- Chemotaxis test and modelling
+
- Chemotaxis test and modeling
<br/>
<br/>
- Fungicides tests on EcAMP-A,  EcAMP-B, EcAMP-C, EcAMP-D, MaxiOpA, MaxiOpB, MaxiOpC, MaxiOpD from 2ml of overnight cultures. Only with 25000 conidia with both fungi.
- Fungicides tests on EcAMP-A,  EcAMP-B, EcAMP-C, EcAMP-D, MaxiOpA, MaxiOpB, MaxiOpC, MaxiOpD from 2ml of overnight cultures. Only with 25000 conidia with both fungi.
<br/>
<br/>
-
- PCR on pSBBS4S + BBa_K1162001 (EcAMP)  
+
- PCR on pSB<sub>BS</sub>4S + BBa_K1162001 (EcAMP)  
<br/>
<br/>
Problem: failed on both diluted plasmid and colony
Problem: failed on both diluted plasmid and colony
Line 596: Line 600:
- PCR on D4E1 colony with different primers
- PCR on D4E1 colony with different primers
<br/>- Culture and miniprep of EcAMP to get more DNA + analytic digestion  
<br/>- Culture and miniprep of EcAMP to get more DNA + analytic digestion  
-
<br/>- Transformation of K1364014+K1364006 in E. coli  
+
<br/>- Transformation of K1364014 + K1364006 in <i>E. coli</i>
-
<br/>- Transformation of GAFP1 + D4E1, GAFP1 and  EcAMP+GAFP1+D4E1 on <i>B. subtilis</i> + colony PCR + threonine test
+
<br/>- Transformation of GAFP1 + D4E1, GAFP1 and  EcAMP + GAFP1 + D4E1 on <i>B. subtilis</i> + colony PCR + threonine test
-
<br/>NB: good results for the maxi operon and GAFP1 but not for GAFP1 + D4E1 CA
+
<br/><i>NB: good results for the maxi operon and GAFP1 but not for GAFP1 + D4E1</i>
-
<br/>- Cloning of K606013+pEX_K4, 823022+PlepA_RFP, 823022+ Pveg_RFP
+
<br/>- Cloning of K606013 + pEX_K4, 823022 + P<sub>lepA</sub>_RFP, 823022 + P<sub>veg</sub>_RFP
<br/>- Chemotaxis tests: different times of LB + agar addition in the LB medium (after 3 minutes, 5 minutes, 8 minutes, 10 minutes…) are performed => No difference of the results after spreading on the plates.
<br/>- Chemotaxis tests: different times of LB + agar addition in the LB medium (after 3 minutes, 5 minutes, 8 minutes, 10 minutes…) are performed => No difference of the results after spreading on the plates.
<br/>- New test of chemotaxis: capillary between two Eppendorf tubes
<br/>- New test of chemotaxis: capillary between two Eppendorf tubes
Line 621: Line 625:
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
-
- Support of two French city halls: Mairie de Montréal, Mairie de Ventenac en Minervois.
+
- Support of two French city halls: Mairie de Montréal and Mairie de Ventenac en Minervois.
-
<br/>- First interview by the French national radio France Inter which will be aired on October 12th.
+
<br/>- First interview by the French national radio France Inter which will be aired on October 19<sup>th</sup>.
<br/>- Beginning of the organization of the Toulouse iGEM team acknowledgement day: the purpose is to present the project to the students and give a feedback on the competition to the sponsors.
<br/>- Beginning of the organization of the Toulouse iGEM team acknowledgement day: the purpose is to present the project to the students and give a feedback on the competition to the sponsors.
<br/>- Final design of the wiki
<br/>- Final design of the wiki
Line 629: Line 633:
<p class="title3">Lab work:</p>
<p class="title3">Lab work:</p>
<p class="texte">
<p class="texte">
-
- Threonine tests for the BBa_K1364014 maxi operon (EcAMP1 – GAFP1 – D4E1) and mini operon BBa_K1364013 (GAFP1-D4E1)
+
- Threonine tests for the BBa_K1364014 maxi operon (EcAMP1 – GAFP1 – D4E1) and mini operon BBa_K1364013 (GAFP1 - D4E1)
<br/>- Colony PCR on the mini operon BBa_K1364013 (GAFP1 - D4E1)
<br/>- Colony PCR on the mini operon BBa_K1364013 (GAFP1 - D4E1)
<br/>- Colony PCR on BBa_K1364011 on BBa_K823022 (pSBBS4S)
<br/>- Colony PCR on BBa_K1364011 on BBa_K823022 (pSBBS4S)
<br/>- Chemotaxis test with wild type <i>B. subtilis</i> strain using Imperial College protocol
<br/>- Chemotaxis test with wild type <i>B. subtilis</i> strain using Imperial College protocol
-
<br/>- Tansformation of BBa_K1364011 + BBa_K823022 (pSBBS4S) in <i>B. subtilis</i>
+
<br/>- Tansformation of BBa_K1364011 + BBa_K823022 (pSB<sub>BS</sub>4S) in <i>B. subtilis</i>
<br/>- Culture of fungi with fungicides
<br/>- Culture of fungi with fungicides
<br/>- Sequencing of plasmids containing the fungicides
<br/>- Sequencing of plasmids containing the fungicides
</p>
</p>
-
<p class="title3">Weekly meeting with the instructors(09/18/2014)</p>  
+
<p class="title3">Weekly meeting with the instructors (09/18/2014)</p>  
<p class="texte">
<p class="texte">
- Sequencing worked for D4E1 and GAFP1 and the mini operon BBa_K1364013 (GAFP1-D4E1).
- Sequencing worked for D4E1 and GAFP1 and the mini operon BBa_K1364013 (GAFP1-D4E1).
<br/>- The next step is to sequence the maxi operon (EcAMP1 – GAFP1 – D4E1).
<br/>- The next step is to sequence the maxi operon (EcAMP1 – GAFP1 – D4E1).
<br/>- Try different approaches for the chemotaxis:
<br/>- Try different approaches for the chemotaxis:
-
<br/>- New protocol with the capillary assay with a new system made by a glassblower.
+
<br/>New protocol with the capillary assay with a new system made by a glassblower.
-
<br/>- Make the Imperial College test again by testing 3 different solutions: chitin, N-acetylglucosamine and another carbon source.
+
<br/>Make the Imperial College test again by testing 3 different solutions: chitin, N-acetylglucosamine and another carbon source.
<br/>- Decrease the number of conidia and temperature for the fungicide test.
<br/>- Decrease the number of conidia and temperature for the fungicide test.
</p>
</p>
Line 656: Line 660:
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
-
- New support of Sallèles d’Aude, Ventenac en Minervois, Labastide d'Anjou, Montréal city halls but also the Département de l'Hérault.
+
- New support of Sallèles d’Aude and Labastide d'Anjou city halls but also the Département de l'Hérault.
<br/>- Payment of the plane tickets.
<br/>- Payment of the plane tickets.
-
<br/>- Acknowledgement day (4th December): contact with catering service, reservation of the amphitheater, list of guests…
+
<br/>- Acknowledgement day (4<sup>th</sup> December): contact with catering service, reservation of the amphitheater, list of guests…
<br/>- Order of the T shirt for the Jamboree! We look awesome with them!
<br/>- Order of the T shirt for the Jamboree! We look awesome with them!
</p>
</p>
Line 682: Line 686:
<p class="title2">Main activites</p>
<p class="title2">Main activites</p>
<p class="texte">
<p class="texte">
-
- Preparation of the wiki every day... all day long...so hard to work on it, especially at night!
+
- Preparation of the wiki every day... all day long... so hard to work on it, especially at night!
<br/>- Preparation of the poster and the presentation for the Giant Jamboree with our instructors
<br/>- Preparation of the poster and the presentation for the Giant Jamboree with our instructors
<br/>
<br/>

Latest revision as of 00:48, 18 October 2014