Difference between revisions of "Team:Toulouse France/Collaborations"
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<div id="pageintro" class="hoc clear" style="padding:300px 0px;"> | <div id="pageintro" class="hoc clear" style="padding:300px 0px;"> | ||
| − | <center><p class="sec_title_trans">Collaborations and Meet | + | <center><p class="sec_title_trans">Collaborations and Meet Up</p></center> |
</div> | </div> | ||
| Line 50: | Line 50: | ||
<p class="texteb"> | <p class="texteb"> | ||
Our team decided to create protocol videos in order to help young scientists to manipulate. | Our team decided to create protocol videos in order to help young scientists to manipulate. | ||
| − | When people are working on <b> | + | When people are working on <b>Genetics engineering</b>, there are several <b>basic experiments</b> that have to be controlled. |
During our experiments, we filmed 4 steps of cloning: <b>PCR</b>, <b>digestion</b>, <b>ligation</b> and <b>transformation</b>. | During our experiments, we filmed 4 steps of cloning: <b>PCR</b>, <b>digestion</b>, <b>ligation</b> and <b>transformation</b>. | ||
| − | <br> | + | <br>Watching it, people could see how to manipulate safely. |
| − | We asked other igem teams to translate | + | We asked other igem teams to translate protocols in their mother tongue. |
| − | We obtained protocol videos in <b>English</b> with | + | We obtained protocol videos in <b>English</b> with <b><a href="https://2016.igem.org/Team:Imperial_College">Imperial College</a></b> team, |
in <b>Spanish</b> thanks to the <b><a href="https://2016.igem.org/Team:Tec-Monterrey">TEC-Monterrey</a></b> team, | in <b>Spanish</b> thanks to the <b><a href="https://2016.igem.org/Team:Tec-Monterrey">TEC-Monterrey</a></b> team, | ||
| − | in <b>Dutch</b> with | + | in <b>Dutch</b> with <b><a href="https://2016.igem.org/Team:Leiden">Leiden</a></b> team, |
| − | in <b>Chinese</b> with | + | in <b>Chinese</b> with <b><a href="https://2016.igem.org/Team:BIT">BIT</a></b> team, |
| − | in <b>Portuguese</b> thanks to | + | in <b>Portuguese</b> thanks to <b><a href="https://2016.igem.org/Team:USP-EEL-Brazil">EEL</a></b> team, |
| − | in <b>German</b> with | + | in <b>German</b> with <b><a href="https://2016.igem.org/Team:Hamburg">Hamburg</a></b> team and |
| − | in <b>French</b> with the collaboration of the <b><a href="https://2016.igem.org/Team:Bordeaux">Bordeaux</a></b> team. | + | in <b>French</b> with the collaboration of the <b><a href="https://2016.igem.org/Team:Bordeaux">Bordeaux</a></b> team. |
| − | We wrote the entire script | + | We wrote the entire script and we added some <b>guidance</b> in red (minutes for each paragraphs for instance). Teams had to translate and record the script. |
| − | Now, we possess | + | Now, we possess a lot of protocols explained in <b>six</b> different languages, accessible to everybody on <b>Youtube</b> and on our wiki. |
</p> | </p> | ||
</div> | </div> | ||
| Line 80: | Line 80: | ||
<div id="teamGallery2"> | <div id="teamGallery2"> | ||
<h2>Digestion</h2> | <h2>Digestion</h2> | ||
| − | <p>This video presents the protocol to do enzymatic digestion of a DNA sample. This technique is useful for usual clonings | + | <p>This video presents the protocol to do enzymatic digestion of a DNA sample. This technique is useful for usual clonings. </p> |
<div class="box"> | <div class="box"> | ||
| Line 265: | Line 265: | ||
<div id="teamGallery2"> | <div id="teamGallery2"> | ||
<h2>Ligation</h2> | <h2>Ligation</h2> | ||
| − | <p>When a DNA fragment is digested with | + | <p>When a DNA fragment is digested with digestion enzymes, it is possible to ligate its extremities with another digested fragment, if the extremities are cohesives. This method can be used to add an insert in a vector or a backbone. </p> |
| Line 437: | Line 437: | ||
<div id="teamGallery2"> | <div id="teamGallery2"> | ||
<h2>PCR</h2> | <h2>PCR</h2> | ||
| − | <p>PCR, or Polymerase Chain Reaction, is a technique that | + | <p>PCR, or Polymerase Chain Reaction, is a technique that amplify a DNA sequence by using primers and DNA polymerase. Throughout this video, you will see how to perform a PCR. A theoretical explanation of the way how PCR works ends the video. </p> |
| Line 612: | Line 612: | ||
<div id="teamGallery2"> | <div id="teamGallery2"> | ||
<h2>Transformation</h2> | <h2>Transformation</h2> | ||
| − | <p> | + | <p>A transformation is a method that allows to insert a plasmid in a <i> E. coli</i> bacteria. Several method to transform a bacteria exist, but we chose to use a thermal shock method for bacteria to become permeable. </p> |
<div class="box"> | <div class="box"> | ||
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<p class="texteb"> | <p class="texteb"> | ||
<center><img src="https://static.igem.org/mediawiki/2016/3/3e/Toulouse_France_erlenmeyers.jpg" style="margin-top:20px;"></center> | <center><img src="https://static.igem.org/mediawiki/2016/3/3e/Toulouse_France_erlenmeyers.jpg" style="margin-top:20px;"></center> | ||
| − | <br><br>In exchange for recording the script in English, we studied the optimal growth of | + | <br><br>In exchange for recording the script in English, we studied the optimal growth of Bacillus subtilis and Pseudomonas fluorescens for the <a href="https://2016.igem.org/Team:Imperial_College">Imperial London College team</a>. First, we did an experimental plan to observe if pH is in interaction with temperature. Finally, the conclusion was that pH and temperature were two independent parameters. We ran the experiments again, changing only one parameter. |
</p> | </p> | ||
<br><br> | <br><br> | ||
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<u><p class="title1" id="select1" style="text-align:center">3D conception</p></u> | <u><p class="title1" id="select1" style="text-align:center">3D conception</p></u> | ||
<p class="texteb"> | <p class="texteb"> | ||
| − | + | ||
| − | We did a 3D Conception of | + | We did a 3D Conception of the iGEM Bordeaux Team, on Blender. |
| − | + | <video width="490" height="275" controls> | |
| + | <source src="https://static.igem.org/mediawiki/2016/f/fa/Toulouse_France_logobordeau.mp4" type="video/mp4"> | ||
| + | Your browser does not support the video tag. | ||
| + | </video> | ||
We also did a 3D conception of their laboratory benching. | We also did a 3D conception of their laboratory benching. | ||
| − | + | ||
</p> | </p> | ||
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<p class="texteb"> | <p class="texteb"> | ||
| − | We want to thank <a href="https://2016.igem.org/Team:Aix-Marseille">Aix-Marseille team</a> for the great help they | + | We want to thank <a href="https://2016.igem.org/Team:Aix-Marseille">Aix-Marseille team</a> for the great help they give to us. |
The aim of the model they conceived for us is to assess the evolution of plasmids throughout the culture, | The aim of the model they conceived for us is to assess the evolution of plasmids throughout the culture, | ||
to determine which parameters can matter in the loss of those plasmids, | to determine which parameters can matter in the loss of those plasmids, | ||
| − | and to precise what are the probabilities for a | + | and to precise what are the probabilities for a bacteria to loose its plasmids during cell division. |
| − | As a plasmids can be a disadvantage for growth ( | + | As a plasmids can be a disadvantage for growth (energy spent into replicating processes) or a advantage |
| − | (protection against a toxin | + | (protection against a toxin) this question is hard to answer. |
| − | But in this situation, where one type of plasmid can influence on the presence of the other | + | But in this situation, where one type of plasmid can influence on the presence of the other type of plasmid in (and reciprocally) |
| − | in the same bacteria, the | + | in the same bacteria, the question become too tough to answer and only a mathematical model can resolve such a interrogation! |
<center> | <center> | ||
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<u><p class="title1" id="select1" style="text-align:center">Receipt of plasmids</p></u> | <u><p class="title1" id="select1" style="text-align:center">Receipt of plasmids</p></u> | ||
<p class="texteb"> | <p class="texteb"> | ||
| − | We want to thank the 2012 <a href="https://2012.igem.org/Team:LMU-Munich">Munich team</a> for sending us 4 different shuttle plasmids. One of these, | + | We want to thank the 2012 <a href="https://2012.igem.org/Team:LMU-Munich">Munich team</a> for sending us 4 different shuttle plasmids. One of these, pBs0k-p, was very useful because we used it for cloning in E.coli and Bacillus subtilis. |
</p> | </p> | ||
<center><img src="" style="width:15%"></center> | <center><img src="" style="width:15%"></center> | ||
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<u><p class="title1" id="select1" style="text-align:center">Mailing of kit</p></u> | <u><p class="title1" id="select1" style="text-align:center">Mailing of kit</p></u> | ||
<p class="texteb"> | <p class="texteb"> | ||
| − | + | 2016 <a href="https://2016.igem.org/Team:Evry">Evry team</a> asked us to send a Ludox solution that was in our iGEM Kit. They stored their own solution at -20°C so it was not usable anymore. But it was important for them to participate to the InterLab project so we helped them. | |
</p> | </p> | ||
<center><img src="https://static.igem.org/mediawiki/2016/8/88/Toulouse_France_logoevry.jpg" style="width:15%"></center> | <center><img src="https://static.igem.org/mediawiki/2016/8/88/Toulouse_France_logoevry.jpg" style="width:15%"></center> | ||
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<u><p class="title1" id="select1" style="text-align:center">Protocol translation</p></u> | <u><p class="title1" id="select1" style="text-align:center">Protocol translation</p></u> | ||
<p class="texteb"> | <p class="texteb"> | ||
| − | 2016 <a href="https://2016.igem.org/Team:METU_HS_Ankara">METU HS Ankara</a> team wanted to create a database, which consists of different language protocols. They asked us to translate their | + | 2016 <a href="https://2016.igem.org/Team:METU_HS_Ankara">METU HS Ankara</a> team wanted to create a database, which consists of different language protocols. They asked us to translate their protocol in French. |
</p> | </p> | ||
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more about other brilliant projects. We met a lot of nice people from different teams and | more about other brilliant projects. We met a lot of nice people from different teams and | ||
| − | we sympathized a lot with every French | + | we sympathized a lot with every French team. |
<br> | <br> | ||
<br> | <br> | ||
| − | The organizers arranged two lectures during the weekend. | + | The organizers arranged two lectures during the weekend. First it dealt with the challenges |
and the risks of synthetic biology and the second talked about a new economic world. | and the risks of synthetic biology and the second talked about a new economic world. | ||
| Line 1,008: | Line 1,011: | ||
animated these round tables. One of our best memories was to meet the founder of iGEM: | animated these round tables. One of our best memories was to meet the founder of iGEM: | ||
| − | <b>Randy Rettberg</b>. It was an honor for us to speak with | + | <b>Randy Rettberg</b>. It was an honor for us to speak with this person and to explain our project. |
<br> | <br> | ||
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One day, on our Facebook page, we received a message from Itzel Guzman, iGEM TEC | One day, on our Facebook page, we received a message from Itzel Guzman, iGEM TEC | ||
| − | Monterrey team member. She was in Toulouse for a | + | Monterrey team member. She was in Toulouse for a semester and she asked us to meet us, |
| − | the iGEM Toulouse team. We discussed a long time | + | the iGEM Toulouse team. We discussed a long time on our project over a drink and we |
sympathized a lot! | sympathized a lot! | ||
Revision as of 19:10, 19 October 2016
Follow us @
Collaborations and Meet Up
Our Collaborations
Protocol videos
Our team decided to create protocol videos in order to help young scientists to manipulate.
When people are working on Genetics engineering, there are several basic experiments that have to be controlled.
During our experiments, we filmed 4 steps of cloning: PCR, digestion, ligation and transformation.
Watching it, people could see how to manipulate safely.
We asked other igem teams to translate protocols in their mother tongue.
We obtained protocol videos in English with Imperial College team,
in Spanish thanks to the TEC-Monterrey team,
in Dutch with Leiden team,
in Chinese with BIT team,
in Portuguese thanks to EEL team,
in German with Hamburg team and
in French with the collaboration of the Bordeaux team.
We wrote the entire script and we added some guidance in red (minutes for each paragraphs for instance). Teams had to translate and record the script.
Now, we possess a lot of protocols explained in six different languages, accessible to everybody on Youtube and on our wiki.
Digestion
This video presents the protocol to do enzymatic digestion of a DNA sample. This technique is useful for usual clonings.
Ligation
When a DNA fragment is digested with digestion enzymes, it is possible to ligate its extremities with another digested fragment, if the extremities are cohesives. This method can be used to add an insert in a vector or a backbone.
PCR
PCR, or Polymerase Chain Reaction, is a technique that amplify a DNA sequence by using primers and DNA polymerase. Throughout this video, you will see how to perform a PCR. A theoretical explanation of the way how PCR works ends the video.
Transformation
A transformation is a method that allows to insert a plasmid in a E. coli bacteria. Several method to transform a bacteria exist, but we chose to use a thermal shock method for bacteria to become permeable.
Growth study of B. subtilis and P. fluorescens
In exchange for recording the script in English, we studied the optimal growth of Bacillus subtilis and Pseudomonas fluorescens for the Imperial London College team. First, we did an experimental plan to observe if pH is in interaction with temperature. Finally, the conclusion was that pH and temperature were two independent parameters. We ran the experiments again, changing only one parameter.
Results
Optimum Temperature (°C) |
Optimum pH |
Doubling time (minutes) |
|
Bacillus subtilis (WT 168) |
34-37 |
8 | 41 |
Pseudomonas fluorescens (SBW25) |
<29 |
7,5 | <80 |
Optimum temperatures and pH and the doubling times are summarized in the table for our two strains.
3D conception
We did a 3D Conception of the iGEM Bordeaux Team, on Blender. We also did a 3D conception of their laboratory benching.
Model of the plasmid loss
We want to thank Aix-Marseille team for the great help they give to us. The aim of the model they conceived for us is to assess the evolution of plasmids throughout the culture, to determine which parameters can matter in the loss of those plasmids, and to precise what are the probabilities for a bacteria to loose its plasmids during cell division. As a plasmids can be a disadvantage for growth (energy spent into replicating processes) or a advantage (protection against a toxin) this question is hard to answer. But in this situation, where one type of plasmid can influence on the presence of the other type of plasmid in (and reciprocally) in the same bacteria, the question become too tough to answer and only a mathematical model can resolve such a interrogation!
Receipt of plasmids
We want to thank the 2012 Munich team for sending us 4 different shuttle plasmids. One of these, pBs0k-p, was very useful because we used it for cloning in E.coli and Bacillus subtilis.
Mailing of kit
2016 Evry team asked us to send a Ludox solution that was in our iGEM Kit. They stored their own solution at -20°C so it was not usable anymore. But it was important for them to participate to the InterLab project so we helped them.
Protocol translation
2016 METU HS Ankara team wanted to create a database, which consists of different language protocols. They asked us to translate their protocol in French.
Meet Ups
The European Experience
The Evry and Ionis teams organized on the 1st and 2nd of July, a huge meeting that gathered
more than 11 European teams. In different rooms, each team had a space to hang its poster
and set up flyers and communication supports. We explained our project and discussed with
other iGEM members. Some helped us on different aspects like modeling and confinement
of our bacteria. When we were not on our stand, we walked around the rooms and learnt
more about other brilliant projects. We met a lot of nice people from different teams and
we sympathized a lot with every French team.
The organizers arranged two lectures during the weekend. First it dealt with the challenges
and the risks of synthetic biology and the second talked about a new economic world.
Different people, like CEOs of company, trainees, young workers, or research scientists
animated these round tables. One of our best memories was to meet the founder of iGEM:
Randy Rettberg. It was an honor for us to speak with this person and to explain our project.
We thank very much the organizing teams for these amazing days in Paris! It was for us an
enjoyable experience of what the Giant Jamboree will be in October.
Meeting with Itzel from TEC Monterrey team
One day, on our Facebook page, we received a message from Itzel Guzman, iGEM TEC
Monterrey team member. She was in Toulouse for a semester and she asked us to meet us,
the iGEM Toulouse team. We discussed a long time on our project over a drink and we
sympathized a lot!
We decided to collaborate together on the protocol videos (view more).
Website by Team iGEM Toulouse 2016
