Difference between revisions of "Team:Pasteur Paris/Protocol"

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Line 144:

<td>Microbiology equipment</td>

<td>Materials always used in the lab </td>

−

+

</tr>

<tr>

<td>To reproduce (amplify) selected sections of DNA (inserts A1, A2, B1, B2, C1, C2, E1,E2).</td>

−

+

</tr>

<tr>

<td>Digestion</td>

<td>To linearize the different plasmids with appropriate enzymes. Perform restriction enzyme digestion in order to recover linear backbones of the plasmids. And chose the appropriate restriction sites based on the host plasmids. </td>

−

+

</tr>

<tr>

<td>Dephosphorylation</td>

−

<td>To reduce vector self-ligation and favor that of vector to insert instead.

+

<td>To reduce vector self-ligation and favor that of vector to insert instead. </td>

−

</td>

+

−

+

</tr>

<tr>

Line 166:

Line 165:

<td>To link an insert to its host plasmid before the transformation. This step happens after the digestion of the insert and the plasmid with the same restriction sites enzymes.

</td>

−

+

</tr>

<tr>

<td>Electrophoresis</td>

<td>To know the size of DNA fragments to check the efficiency of a digestion for instance.</td>

−

+

</tr>

<tr>

<td>Gel extraction kit</td>

<td>To get back the DNA purified thanks to the electrophoresis on agarose gel.</td>

−

+

</tr>

<tr>

<td>Transformation</td>

<td>To increase the amount of plasmid by transformation in competent cells. The amount of plasmid supplied is insufficient to perform all our future experiments.</td>

−

+

</tr>

<tr>

<td>Miniprep QIAGEN Kit</td>

<td> To extract DNA from a culture of bacteria</td>

−

+

</tr>

<tr>

<td>Harvest and culture</td>

<td>In order to obtain a large amount of plasmid, we need to grow the bacteria overnight.</td>

−

+

</tr>

<tr>

<td>Stab culture</td>

<td>To store a clone of bacteria to be used later.</td>

−

+

</tr>

<tr>

<td>IPTG induction</td>

<td>To increase the production of our protein which depends on this molecule.</td>

−

+

</tr>

<tr>

<td>Protein Purification Fast Protein Liquid Chromatography</td>

<td>To check if the His-tag works and if our protein has really been produced </td>

−

+

</tr>

<tr>

<td>Cellulose-binding Protocol</td>

<td>Verify that the C2 protein binds to cellulose.</td>

−

+

</tr>

Line 217:

Line 216:

<td>Silification & assay Protocol</td>

<td> Prepare a one pot mixture that will be compressed directly after incubation.</td>

−

+

−

+

</tr>

+

<tr>

+

<td>Model of the mechanical properties of the patch</td>

+

<td>Predict the influence of silification on the mechanical properties of the patch</td>

+

+

</tr>

+

<tr>

<td>Patch compression Protocol</td>

<td>Make a patch by compression with cellulose and the silicated C2 protein.</td>

−

+

</tr>

<tr>

<td>One pot mixture-Patch protocol</td>

<td> Prepare a one pot mixture that will be compressed directly after incubation.</td>

−

+

</tr>

<tr>

Line 233:

Line 237:

<td> The goal is to determine whether our immunoassay is effective. We want to ensure that our antibodies are well able to detect the presence or absence of viral proteins from Chikungunya and Yellow Fever viruses.

</td>

−

+

</tr>

Line 244:

Line 248:

</a>

You can also download all the protocols in one file here:

−

+

</div>

−

+

</div>

Experiments	Aim:	Download
Microbiology equipment	Materials always used in the lab
PCR	To reproduce (amplify) selected sections of DNA (inserts A1, A2, B1, B2, C1, C2, E1,E2).
Digestion	To linearize the different plasmids with appropriate enzymes. Perform restriction enzyme digestion in order to recover linear backbones of the plasmids. And chose the appropriate restriction sites based on the host plasmids.
Dephosphorylation	To reduce vector self-ligation and favor that of vector to insert instead.
Ligation	To link an insert to its host plasmid before the transformation. This step happens after the digestion of the insert and the plasmid with the same restriction sites enzymes.
Electrophoresis	To know the size of DNA fragments to check the efficiency of a digestion for instance.
Gel extraction kit	To get back the DNA purified thanks to the electrophoresis on agarose gel.
Transformation	To increase the amount of plasmid by transformation in competent cells. The amount of plasmid supplied is insufficient to perform all our future experiments.
Miniprep QIAGEN Kit	To extract DNA from a culture of bacteria
Harvest and culture	In order to obtain a large amount of plasmid, we need to grow the bacteria overnight.
Stab culture	To store a clone of bacteria to be used later.
IPTG induction	To increase the production of our protein which depends on this molecule.
Protein Purification Fast Protein Liquid Chromatography	To check if the His-tag works and if our protein has really been produced
Cellulose-binding Protocol	Verify that the C2 protein binds to cellulose.
Silification & assay Protocol	Prepare a one pot mixture that will be compressed directly after incubation.
Model of the mechanical properties of the patch	Predict the influence of silification on the mechanical properties of the patch
Patch compression Protocol	Make a patch by compression with cellulose and the silicated C2 protein.
One pot mixture-Patch protocol	Prepare a one pot mixture that will be compressed directly after incubation.
Antibody-binding Protocol	The goal is to determine whether our immunoassay is effective. We want to ensure that our antibodies are well able to detect the presence or absence of viral proteins from Chikungunya and Yellow Fever viruses.

@@ Line 144: / Line 144: @@
        <td><strong>Microbiology equipment</strong></td>
        <td>Materials always used in the lab </td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/4/40/T--Pasteur_Paris--equipment.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/4/40/T--Pasteur_Paris--equipment.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
        <td><strong><p>PCR</p></strong></td>
        <td>To reproduce (amplify) selected sections of DNA (inserts A1, A2, B1, B2, C1, C2, E1,E2).</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/b/be/T--Pasteur_Paris--PCR_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/b/be/T--Pasteur_Paris--PCR_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
        <td><strong>Digestion</strong></td>
        <td>To linearize the different plasmids with appropriate enzymes. Perform restriction enzyme digestion in order to recover linear backbones of the plasmids. And chose the appropriate restriction sites based on the host plasmids. </td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/a/ab/T--Pasteur_Paris--Restriction_digestion_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/a/ab/T--Pasteur_Paris--Restriction_digestion_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
        <td><strong>Dephosphorylation</strong></td>
-       <td>To reduce vector self-ligation and favor that of vector to insert instead.
+       <td>To reduce vector self-ligation and favor that of vector to insert instead. </td>
-</td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/c/c0/T--Pasteur_Paris--dephosphorylation_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/c/c0/T--Pasteur_Paris--dephosphorylation_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
@@ Line 166: / Line 165: @@
        <td>To link an insert to its host plasmid before the transformation. This step happens after the digestion of the insert and the plasmid with the same restriction sites enzymes.
 </td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/6/6f/T--Pasteur_Paris--Ligation_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/6/6f/T--Pasteur_Paris--Ligation_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
        <td><strong>Electrophoresis</strong></td>
        <td>To know the size of DNA fragments to check the efficiency of a digestion for instance.</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/6/60/T--Pasteur_Paris--Gel_electrophoresis_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/6/60/T--Pasteur_Paris--Gel_electrophoresis_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
        <td><strong>Gel extraction kit</strong></td>
        <td>To get back the DNA purified thanks to the electrophoresis on agarose gel.</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/4/4e/T--Pasteur_Paris--Gel_extraction_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/4/4e/T--Pasteur_Paris--Gel_extraction_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
        <td><strong>Transformation</strong></td>
        <td>To increase the amount of plasmid by transformation in competent cells. The amount of plasmid supplied is insufficient to perform all our future experiments.</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/c/ca/T--Pasteur_Paris--Transformation_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/c/ca/T--Pasteur_Paris--Transformation_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
        <td><strong>Miniprep QIAGEN Kit</strong></td>
        <td> To extract DNA from a culture of bacteria</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/d/d5/T--Pasteur_Paris--Miniprep_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/d/d5/T--Pasteur_Paris--Miniprep_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
        <td><strong>Harvest and culture</strong></td>
        <td>In order to obtain a large amount of plasmid, we need to grow the bacteria overnight.</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/4/4b/T--Pasteur_Paris--Bacterial_culture_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/4/4b/T--Pasteur_Paris--Bacterial_culture_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
 <tr>
        <td><strong>Stab culture</strong></td>
        <td>To store a clone of bacteria to be used later.</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/b/b1/Stab_culture_Pasteur_Paris_2016.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/b/b1/Stab_culture_Pasteur_Paris_2016.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
        <td><strong>IPTG induction</strong></td>
        <td>To increase the production of our protein which depends on this molecule.</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/a/a4/T--Pasteur_Paris--Protein_induction_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/a/a4/T--Pasteur_Paris--Protein_induction_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
      <tr>
        <td><strong>Protein Purification Fast Protein Liquid Chromatography</strong></td>
        <td>To check if the His-tag works and if our protein has really been produced </td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/0/07/T--Pasteur_Paris--FPLC_Protein_purification_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/c/c1/DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/0/07/T--Pasteur_Paris--FPLC_Protein_purification_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/1/1d/T--Pasteur_Paris--DownloadT--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
       <tr>
        <td><strong><p>Cellulose-binding Protocol</p></strong></td>
        <td>Verify that the C2 protein binds to cellulose.</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/e/e1/Protocol-cellulose-binding_Pasteur_Paris2016.pdf"><img src="https://static.igem.org/mediawiki/2016/1/19/Chemistry_T--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/e/e1/Protocol-cellulose-binding_Pasteur_Paris2016.pdf"><img src="https://static.igem.org/mediawiki/2016/1/15/T--Pasteur_Paris--Chemistry_T--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
@@ Line 217: / Line 216: @@
        <td><strong><p>Silification & assay Protocol</p></strong></td>
        <td> Prepare a one pot mixture that will be compressed directly after incubation.</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/2/2a/Protocol-silification-assay_Pasteur_Paris2016.pdf"><img src="https://static.igem.org/mediawiki/2016/1/19/Chemistry_T--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/2/2a/Protocol-silification-assay_Pasteur_Paris2016.pdf"><img src="https://static.igem.org/mediawiki/2016/1/15/T--Pasteur_Paris--Chemistry_T--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
+     <tr>
+     <td><strong><p>Model of the mechanical properties of the patch</p></strong></td>
+      <td>Predict the influence of silification on the mechanical properties of the patch</td>
+      <td> <center><a href="https://static.igem.org/mediawiki/2016/d/da/T--Pasteur_Paris--Mechanical_patch_properties_protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/7/76/T--Pasteur_Paris--Patch_T--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+    </tr>
+     <tr>
       <td><strong><p>Patch compression Protocol</p></strong></td>
        <td>Make a patch by compression with cellulose and the silicated C2 protein.</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/7/71/T--Pasteur_Paris--Patch_compression.pdf"><img src="https://static.igem.org/mediawiki/2016/2/2d/Patch_T--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/a/ac/Protocol-patch-compression_Pasteur_Paris.pdf"><img src="https://static.igem.org/mediawiki/2016/7/76/T--Pasteur_Paris--Patch_T--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
       <tr>
        <td><strong><p>One pot mixture-Patch protocol</p></strong></td>
        <td> Prepare a one pot mixture that will be compressed directly after incubation.</td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/8/89/Protocol-one-pot-mixture_Pasteur_Paris2016.pdf"><img src="https://static.igem.org/mediawiki/2016/2/2d/Patch_T--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/8/89/Protocol-one-pot-mixture_Pasteur_Paris2016.pdf"><img src="https://static.igem.org/mediawiki/2016/7/76/T--Pasteur_Paris--Patch_T--iGEM16_Pasteur_Paris--file.xxx.png" width="40%" alt=""></a></center></td>
      </tr>
       <tr>
@@ Line 233: / Line 237: @@
        <td> The goal is to determine whether our immunoassay is effective. We want to ensure that our antibodies are well able to detect the presence or absence of viral proteins from Chikungunya and Yellow Fever viruses.
 </td>
-       <td> <center><a href="https://static.igem.org/mediawiki/2016/2/21/T--Pasteur_Paris--Immunoassay_Protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/5/53/Antibody_Pasteur_PARIS_2016.png" width="40%" alt=""></a></center></td>
+       <td> <center><a href="https://static.igem.org/mediawiki/2016/2/21/T--Pasteur_Paris--Immunoassay_Protocol.pdf"><img src="https://static.igem.org/mediawiki/2016/f/f1/T--Pasteur_Paris--Antibody_Pasteur_PARIS_2016.png" width="40%" alt=""></a></center></td>
      </tr>
@@ Line 244: / Line 248: @@
 <p></a>
 You can also download all the protocols in one file here:</br></br>
-<center><a href="https://static.igem.org/mediawiki/2016/6/66/T--Pasteur_Paris--Protocols.pdf"><img src="https://static.igem.org/mediawiki/2016/a/a3/Protocols_Pasteur_Paris_2016.png" width="10%" alt=""></a></center></br></br></br></br></br></br></p>
+<center><a href="https://static.igem.org/mediawiki/2016/6/66/T--Pasteur_Paris--Protocols.pdf"><img src="https://static.igem.org/mediawiki/2016/3/3a/T--Pasteur_Paris--Protocols_Pasteur_Paris_2016.png" width="10%" alt=""></a></center></br></br></br></br></br></br></p>
 </div>
 <div class="text1">
-         <section><center><a href="#Science"><img src="https://static.igem.org/mediawiki/2016/b/b8/SCIENCE_PASTEUR_2016.png"class="image science"  alt=""></center></a></section>
+         <section><center><a href="#Science"><img src="https://static.igem.org/mediawiki/2016/c/c7/T--Pasteur_Paris--SCIENCE_PASTEUR_2016.png"class="image science"  alt=""></center></a></section>
 </div>