Team:Toulouse/Notebook/Calendar

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/*Overview*/
/*Overview*/
.CropImg{
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<body>
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   <div style="margin:0 auto; width:960px;">
   <div style="margin:0 auto; width:960px;">
   <p style="color:#696969; padding-top:20px; font-size:16px; float:left;"> Notebook&nbsp;&nbsp;&nbsp;>&nbsp;&nbsp;&nbsp;Calendar</p>  
   <p style="color:#696969; padding-top:20px; font-size:16px; float:left;"> Notebook&nbsp;&nbsp;&nbsp;>&nbsp;&nbsp;&nbsp;Calendar</p>  
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       <div class="centering" style="padding-top: 85px; padding-bottom:40px;">
       <div class="centering" style="padding-top: 85px; padding-bottom:40px;">
-
<p class="title1">December 2013 – January 2014: Team selection</p>
+
<p style="font-size:1.3em; margin: 0 0 30px 0;"><a href="#" onClick="ddaccordion.expandall('technology'); return false">Expand all</a> | <a href="#" onClick="ddaccordion.collapseall('technology'); return false">Collapse all</a></p>
 +
 
 +
 
 +
<div class="technology">December 2013 – January 2014: Team selection</div>
 +
<div class="thelanguage">
<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<br/>
+
- Constitution of the <a href="http://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 Toulouse iGEM Team 2014! </B>
+
<p class="texte" style="text-align:center"><B> The adventure begins for the 2014 Toulouse iGEM Team!</B>
</p>
</p>
 +
 +
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology', 0); return false">Collapse</a></p>
 +
</div>
-
<p class="title1">January – June 2014: Projects brainstorming</p>
+
<div class="technology">January – June 2014: Projects brainstorming</div>
 +
<div class="thelanguage">
<p class="texte">
<p class="texte">
-
- Thanks to weekly meetings, our team was able to discuss about new project ideas and publications.
+
- 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:  
<br/>
<br/>
-
- Let's save our trees with SubtiTree: the purpose is to use <i>Bacillus subtilis</i> as an optimized bacterium to detect, target a fungi and secrete fungicides to destroy it
+
- Let's save our trees with SubtiTree: the purpose is to use <i>Bacillus subtilis</i> as an optimized bacterium to target and bind to a specific fungus and secrete fungicides to destroy it.
<br/>
<br/>
-
- <i>E. coli</i> cancer: the concept was to create a bacterium able to colonize specifically the hypoxic regions of the tumor. The oxygen-sensitive bacterium would not be able to develop in the healthy zones
+
- <i>E. coli</i> cancer: the concept was to create a bacterium able to colonize specifically the hypoxic regions of the tumor. The oxygen-sensitive bacterium would not be able to develop in the healthy zones.
-
<br/>
+
-
- Reduction of ruminants’ methane production: the goal is to reduce the production of methane by ingesting a microorganism in the animal’s rumen. This bacterium would be capable of reducing the quantity of metabolic hydrogen and eliminating the methanogenic Archaes population
+
<br/>
<br/>
 +
- Reduction of ruminants’ methane production: the goal is to reduce the production of methane by ingesting a microorganism in the animals' rumen. This bacterium would be able to reduce the quantity of metabolic hydrogen and eliminate the methanogenic Archaes population.
</p>
</p>
-
<p class="title1">June 2014: Choice of SubtiTree project</p>
+
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology', 1); return false">Collapse</a></p>
-
<p class="texte">The discussion has been long to estimate the practicabilty 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>
+
</div>
 +
 
 +
 
 +
<div class="technology">June 2014: Choice of SubtiTree project</div>
 +
<div class="thelanguage">
 +
<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> 40 k€ </B>.
+
By this period, we evaluated our budget to approximately <B>€39,500</B>.
</p>  
</p>  
-
<p class="title2">Week 1(16-22 June)</p>
+
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology', 2); return false">Collapse</a></p>
-
<p class="title3">Preparation period for the laboratory work:</p>
+
 
 +
<div class="technology2">Week 1(16-22 June)</div>
 +
<div class="thelanguage2">
<p class="texte">
<p class="texte">
- Bibliography researches about our subject<br/>
- Bibliography researches about our subject<br/>
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- Increase in our communication strategy to find more sponsors specialized in environment and ecological matters <br/>
- Increase in our communication strategy to find more sponsors specialized in environment and ecological matters <br/>
- Support of Adisseo, Toulouse White Biotechnology, LISBP, INSA Toulouse<br/>
- Support of Adisseo, Toulouse White Biotechnology, LISBP, INSA Toulouse<br/>
-
- Organization of a weekly meeting each Friday with our supervisors to tackle any problem encountered<br/>
+
- Organization of a weekly meeting each Friday with our supervisors to tackle any problem encountered
</p>
</p>
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- Distribution of the non-scientific tasks regarding the wiki, communication, sponsorship, ethical problems, safety but also the lab work<br/>
- Distribution of the non-scientific tasks regarding the wiki, communication, sponsorship, ethical problems, safety but also the lab work<br/>
- Discussion about the different construction parts of the project<br/>
- Discussion about the different construction parts of the project<br/>
-
- Need to check the absence of stop codon in fungicides sequences
+
- Need to check the absence of stop codon in fungicides sequences<br/>
 +
- Ordering the list of necessary products for the laboratory and biobricks<br/>
 +
- Checking and validation of the genes sequences
</p>  
</p>  
   
   
-
<p class="title2">Week 2 (23-29 June)</p>
+
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 0); return false">Collapse</a></p>
-
<p class="title3">Preparation period for the laboratory work:</p>
+
</div>
-
<p class="texte">
+
-
- Ordering the list of necessary products for the laboratory and biobricks<br/>
+
-
- Checking and validation of the genes sequences<br/>
+
 +
 +
<div class="technology2">Week 2 (23-29 June)</div>
 +
<div class="thelanguage2">
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
-
- BioSynSyS conference work: powerpoint, logo in order to present our SubtiTree project to a whole audience of scientific and researchers (http://biosynsys2014.sciencesconf.org/)
+
- BioSynSyS conference work: powerpoint, logo in order to present our SubtiTree project to a whole audience of scientific and researchers
</p>
</p>
<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)<br/>
+
- <i>E. coli</i> transformation with BBA_J004450 (pSB1C3)
</p>
</p>
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- Check the mechanism of action of each fungicide to complete the ethical part
- Check the mechanism of action of each fungicide to complete the ethical part
</p>
</p>
 +
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 1); return false">Collapse</a></p>
 +
</div>
 +
</div>
 +
-
<p class="title1">July 2014</p>
+
<div class="technology">July 2014</div>
 +
<div class="thelanguage">
<p class="title2">Main activities</p>
<p class="title2">Main activities</p>
<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>  
-
<p class="title2">Week 3 (30 June -6 July) and Week 4 (7-13 July)</p>
+
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology', 3); return false">Collapse</a></p>
 +
 +
<div class="technology2">Week 3 (30 June -6 July) and Week 4 (7-13 July)</div>
 +
<div class="thelanguage2">
<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>
-
<p class="title3">Lab work: </p>
+
<p class="title3">Lab work:</p>
<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>
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</p>  
</p>  
   
   
-
<p class="title2">Week 5 (14-20 July)</p>
+
 
 +
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 2); return false">Collapse</a></p>
 +
</div>
 +
 
 +
<div class="technology2">Week 5 (14-20 July)</div>
 +
<div class="thelanguage2">
<p class="title3">Communication and financial support:</p>
<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>
-
- Support of ThermoFisher, New Englands BioLabs, Qiagen, Eurofins but also GenoToul, Labex Tulip, L’Université Paul Sabatier, CROUS.
+
- Support of ThermoFisher, New Englands BioLabs, Qiagen, Eurofins but also GenoToul, Labex Tulip, L’Université Paul Sabatier, CROUS.</p>
<p class="title3">Lab work:</p>
<p class="title3">Lab work:</p>
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- 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)<br/>
+
- Cloning of BBa_K606061 (RBS SpoVG) with BBa_K823003 (P<sub>veg</sub>) and BBa_K823002 (P<sub>lepA</sub>)
</p>
</p>
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<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>
-
<p class="title2">Week 6 (21 July-27 July)</p>
+
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 3); return false">Collapse</a></p>
 +
</div>
 +
 
 +
<div class="technology2">Week 6 (21 July-27 July)</div>
 +
<div class="thelanguage2">
 +
 
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
-
- Description of SubtiTree project and determination of the goodies for a crowdfunding campaign on Ulule website
+
- Description of SubtiTree project and determination of the goodies for a crowdfunding campaign on Ulule website</p>
<p class="title3">Lab work:</p>
<p class="title3">Lab work:</p>
<p class="texte">
<p class="texte">
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- 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)<br/>
+
- Cloning BBA_1364002 (GAFP1) with BBa_B0015 (double terminator) and BBA_1364003 (D4E1) with BBa_K823003 (P<sub>veg</sub>)
</p>
</p>
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<p class="texte">
<p class="texte">
- Research for plane tickets and hotels in Boston for the Giant Jamboree<br/>
- Research for plane tickets and hotels in Boston for the Giant Jamboree<br/>
-
- New idea: analyze the plane tree sap to determine the composition<br/>
+
- New idea: analyze the plane tree sap to determine its composition
</p>
</p>
-
<p class="title1">August 2014 </p>
+
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 4); return false">Collapse</a></p>
 +
</div>
 +
</div>
 +
 
 +
<div class="technology">August 2014</div>
 +
<div class="thelanguage">
<p class="title2">Main activities</p>
<p class="title2">Main activities</p>
<p class="texte">
<p class="texte">
- Finishing the cloning for the different parts of the bacterium<br/>
- Finishing the cloning for the different parts of the bacterium<br/>
-
- Putting in place the fungicides, binding and chemotaxis tests<br/>
+
- Putting in place the fungicides, binding and chemotaxis tests
</p>  
</p>  
-
<p class="title2">Week 7 (28 July-3 August)</p>
+
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 +
 
 +
 
 +
<div class="technology2">Week 7 (28 July-3 August)</div>
 +
<div class="thelanguage2">
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
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<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) biobirck 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 296: Line 390:
- Spreading of BBa_K1162001 (EcAMP), miniprep and digestion<br/>
- Spreading of BBa_K1162001 (EcAMP), miniprep and digestion<br/>
Problem: the digestion did not work => Issue with the quantity of DNA in the miniprep is assumed<br/>
Problem: the digestion did not work => Issue with the quantity of DNA in the miniprep is assumed<br/>
-
- First experience of chemotaxis with a glucose chemo-attractant<br/>
+
- First experience of chemotaxis with a glucose chemo-attractant
</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 305: Line 399:
- Discussion about EcAMP cloning which presents some issues
- Discussion about EcAMP cloning which presents some issues
<br/>
<br/>
-
- Discussion about the transfer of pSB1C3 from E. coli to Bacillus strain
+
- Discussion about the transfer of pSB1C3 from <i>E. coli</i> to <i>B. subtilis</i> strain
</p>  
</p>  
   
   
-
<p class="title2">Week 8 (04-10 August)</p>
+
 
 +
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 5); return false">Collapse</a></p>
 +
</div>
 +
 
 +
 
 +
<div class="technology2">Week 8 (04-10 August)</div>
 +
<div class="thelanguage2">
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
Line 315: 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  
<br/>
<br/>
-
- Test of the fungus growth on PDA medium + test of growth for Bacillus subtilis liquid culture on PDA
+
- Test of the fungus growth on PDA medium + test of growth for <i>B. subtilis</i> liquid culture on PDA
</p>
</p>
Line 338: Line 438:
- Ask iGEM headquarters if all the biobricks must be on pSB1C3 plasmid
- Ask iGEM headquarters if all the biobricks must be on pSB1C3 plasmid
<br/>
<br/>
-
- Use another strain of E. coli (DH5-1 instead of DH5 alpha) to have a faster growth
+
- Use another strain of <i>E. coli</i> (DH5-1 instead of DH5 alpha) to have a faster growth
<br/>
<br/>
-
- Check which quantity of Bacillus subtilis is necessary to naturally destroy the fungus
+
- Check which quantity of <i>B. subtilis</i> is necessary to naturally destroy the fungus
</p>
</p>
-
<p class="title2">Week 9 (11-17 August)</p>
+
 
 +
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 6); return false">Collapse</a></p>
 +
</div>
 +
 
 +
<div class="technology2">Week 9 (11-17 August)</div>
 +
<div class="thelanguage2">
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
Line 349: 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 Bacillus subtilis.
+
- Evaluation of the bacterial decrease rate from 10°C to 4°C with a sporuling strain of <i>B. subtilis</i>.
<br/>
<br/>
-
- Chemotaxis test with different concentration 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>Bacillus 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 Bacillus subtilis 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
</p>
</p>
-
<p class="title2">Week 10 (18-24 August)</2>
+
 
 +
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 7); return false">Collapse</a></p>
 +
</div>
 +
 
 +
<div class="technology2">Week 10 (18-24 August)</div>
 +
<div class="thelanguage2">
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
Line 376: Line 486:
<p class="title3">Lab work:</p>
<p class="title3">Lab work:</p>
<p class="texte">
<p class="texte">
-
- Subculture and transformation in Bacillus subtilis 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>
-
<p class="title2">Week 11 (25- 31 August)</p>
+
 
 +
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 8); return false">Collapse</a></p>
 +
</div>
 +
 
 +
<div class="technology2">Week 11 (25- 31 August)</div>
 +
<div class="thelanguage2">
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
Line 400: 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 Bacillus subtilis 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 Bacillus subtilis 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 Bacillus strain  
+
- Transformation of a new vector PKL 190 (threonine integrative) in <i>Bacillus</i> strain  
</p>
</p>
Line 421: Line 536:
- Objectives : chemotaxis, binding and fungicides tests have to be performed again
- Objectives : chemotaxis, binding and fungicides tests have to be performed again
</p>  
</p>  
 +
 +
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 9); return false">Collapse</a></p>
 +
</div>
 +
</div>
 +
   
   
-
<p class="title1"> September 2014</p>
+
<div class="technology">September 2014</div>
 +
<div class ="thelanguage">
<p class="title2">Main activities</p>
<p class="title2">Main activities</p>
<p class="texte">
<p class="texte">
Line 434: Line 555:
</p>  
</p>  
-
<p class="title2">Week 12 (1-7 September)</p>
+
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology', 5); return false">Collapse</a></p>
 +
 
 +
<div class="technology2">Week 12 (1-7 September)</div>
 +
<div class="thelanguage2">
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
Line 443: 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 458: Line 582:
- The first sequencing was not successful => new sequencing with one primer/tube<br/>
- The first sequencing was not successful => new sequencing with one primer/tube<br/>
- Chemotaxis test: increase the concentration in bacterium, try a new protocol by capillarity<br/>
- Chemotaxis test: increase the concentration in bacterium, try a new protocol by capillarity<br/>
-
- End of the binding test: IT WORKS PERFECTLY! SubtiTree has the good phenotype and presents a better binding property than the wild type Bacillus subtilis strain.<br/>
+
- End of the binding test: IT WORKS PERFECTLY! SubtiTree has the good phenotype and presents a better binding property than the wild type <i>Bacillus subtilis</i> strain.<br/>
- Fungicides test: contaminants with the fungus. Need to ask for another culture of our fungi.
- Fungicides test: contaminants with the fungus. Need to ask for another culture of our fungi.
</p>
</p>
-
<p class="title2">Week 13 (8- 14 September)</p>
+
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 10); return false">Collapse</a></p>
 +
</div>
 +
 
 +
<div class="technology2">Week 13 (8- 14 September)</div>
 +
<div class="thelanguage2">
<p class="title3">Communication and financial support:</p>
<p class="title3">Communication and financial support:</p>
<p class="texte">
<p class="texte">
Line 472: 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 Bacillus subtilis + 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 490: Line 618:
</p>
</p>
-
<p class="title2">Week 14 (15 - 21 September)</p>
+
<p style="text-align:right;font-size:1.3em;"><a href="#" class="collapseLink" onClick="ddaccordion.collapseone('technology2', 11); return false">Collapse</a></p>
 +
</div>
 +
 
 +
<div class="technology2">Week 14 (15 - 21 September)</div>
 +
<div class="thelanguage2">
<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 iGEM Toulouse 2014 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
</p>
</p>
Line 501: 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>Bacillus 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 Bacillus subtilis
+
<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>
-
<p class="title2">Week 15 (22 - 28 September)</p>
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<div class="technology2">Week 15 (22 - 28 September)</div>
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<div class="thelanguage2">
<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 city hall.
+
- 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!
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- Last experiments regarding chemotaxis tests.
- Last experiments regarding chemotaxis tests.
</p>
</p>
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<p class="title3">Weekly meeting with the instructors(09/26/2014)</p>  
<p class="title3">Weekly meeting with the instructors(09/26/2014)</p>  
<p class="texte">
<p class="texte">
- Focus on the wiki design and writing.
- Focus on the wiki design and writing.
-
<br/>- Start making the power point presentation for Boston and the poster.
+
<br/>- Start making the power point presentation for the Giant Jamboree and the poster.
-
<br/>- Division of responsibilities for all the non-scientific work.
+
<br/>- Division of responsibilities for the non-scientific work.
</p>
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<p class="title1">October 2014</p>
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<div class="technology">October 2014</div>
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<div class="thelanguage">
<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 this even 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 Jamboree with our instructors
+
<br/>- Preparation of the poster and the presentation for the Giant Jamboree with our instructors
<br/>
<br/>
- Daily presentations in front of the laboratory teachers to repeat again and again and again… let’s get ready for the Jamboree!
- Daily presentations in front of the laboratory teachers to repeat again and again and again… let’s get ready for the Jamboree!
</p>  
</p>  
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Latest revision as of 00:48, 18 October 2014