Team:Toulouse/Notebook/Protocols

From 2014.igem.org

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- Remove the supernatant
- Remove the supernatant
<br/>
<br/>
-
- Resuspend the pellet in 7.5 mL of 0.1M frozen CaCl<sub>2</sub>  
+
- Resuspend the pellet in 7.5 mL of 0.1 M frozen CaCl<sub>2</sub>  
<br/>
<br/>
-
- Centrifuge 10 minutes at 4500RPM
+
- Centrifuge 10 minutes at 4500 RPM
<br/>
<br/>
-
- Resuspend the pellet in 500µL of 0.1M CaCl<sub>2</sub>
+
- Resuspend the pellet in 500 µL of 0.1 M CaCl<sub>2</sub>
<br/>
<br/>
- Add glycerol to a final concentration of 15%
- Add glycerol to a final concentration of 15%
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- Thaw out the competent cell aliquotes for about  10 to 20 minutes
- Thaw out the competent cell aliquotes for about  10 to 20 minutes
<br/>
<br/>
-
- Add 20 to 100ng of plasmid or 3µL of kit plate DNA  
+
- Add 20 to 100 ng of plasmid or 3 µL of kit plate DNA  
<br/>
<br/>
-
<i>NB: for kit plate, resuspend the well in 10µL of sterile water</i>
+
<i>NB: for kit plate, resuspend the well in 10 µL of sterile water</i>
-
- Put the tubes 20 minutes in the ice
+
- Put the tubes 20 minutes in the ice </i>
<br/>
<br/>
-
- Put the tubes 2 minutes at 42°C in the water bath
+
- Put the tubes 2 minutes at 42°C in the water bath to create the thermic shock
<br/>
<br/>
-
- Put the tubes back in ice immediately to create the thermic shock
+
- Put the tubes back in ice immediately  
<br/>
<br/>
- Add 1mL of LB medium
- Add 1mL of LB medium
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- Put the tube 2 hours in the 37°C water bath (1 hour if it concerns an ampicillin resistant strain) to allow the phenotypic expression
- Put the tube 2 hours in the 37°C water bath (1 hour if it concerns an ampicillin resistant strain) to allow the phenotypic expression
<br/>
<br/>
-
- Centrifuge for 1 minute at 13000RPM
+
- Centrifuge for 1 minute at 13000 RPM
<br/>
<br/>
- Remove the supernatant  
- Remove the supernatant  
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- Resuspend in 250 µL of LB medium
- Resuspend in 250 µL of LB medium
<br/>
<br/>
-
- Streak the final mix on LB agar selective medium: 200µL on one plate, 50µL on the second plate
+
- Streak the final mix on LB agar selective medium: 200 µL on one plate, 50 µL on the second plate
  </p>
  </p>
   
   
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<br/>- Resuspend 4 to 12 colonies from the plate and name each colony taken on the tubes and on the plate (A, B, C, …)
<br/>- Resuspend 4 to 12 colonies from the plate and name each colony taken on the tubes and on the plate (A, B, C, …)
<br/>
<br/>
-
- Resuspend one colony per culture tube in 5mL of LB medium with antibiotic
+
- Resuspend one colony per culture tube in 5 mL of LB medium with antibiotic
<br/>
<br/>
- Let the culture grow overnight at 37°C in a shaking incubator</p>  
- Let the culture grow overnight at 37°C in a shaking incubator</p>  
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<br>
<br>
-
<br/><I>NB: It is possible to purify the plasmid with an alcaline lysis without any purification column. For 2 mL of culture, 200µL of buffer 1 is added to resuspend the pellet, 400µL of buffer 2 to allow the lysis of the cells and the denaturation of the protein and 300µL of buffer 3 to precipitate the DNA and the proteins. The solution is then centrifuged 10 minutes at 13 000 RPM.
+
<br/><i>NB: It is possible to purify the plasmid with an alcaline lysis without any purification column. For 2 mL of culture, 200 µL of buffer 1 is added to resuspend the pellet, 400 µL of buffer 2 to allow the lysis of the cells and the denaturation of the protein and 300 µL of buffer 3 to precipitate the DNA and the proteins. The solution is then centrifuged 10 minutes at 13 000 RPM.
-
60µL of isopropanol is added to the supernatant and the solution is centrifuged again. The pellet is then resuspended in 100µL of pH 7.4 TE buffer. A part of the contamination by the RNA can avoid by the addition of pH 7.4 TE buffer + 0.2 µL of RNAse.  
+
600 µL of isopropanol is added to the supernatant and the solution is centrifuged again. The pellet is then resuspended in 100 µL of pH 7.4 TE buffer. A part of the contamination by the RNA can avoid by the addition of pH 7.4 TE buffer + 0.2 µL of RNAse. </i>
<br>
<br>
-
<br> <b>Buffer 1:</b> Tris 10mM pH 8 + EDTA 1mM
+
<br> <b>Buffer 1:</b> Tris 10 mM pH 8 + EDTA 1mM
-
<br> <b>Buffer 2:</b> NaOH 2mM + SDS 1%
+
<br> <b>Buffer 2:</b> NaOH 2 mM + SDS 1%
-
<br> <b>Bufer 3:</b> A COOK 3M + A COOH 15%  
+
<br> <b>Buffer 3:</b> Potassium acetate 3 M + 15% glacial acetic acid
</I></p>
</I></p>
-
<p class="title1" id="select4"> Cloning </p>
+
<p class="title1" id="select4">Cloning </p>
<p class="texte">Cloning is the step after taking the competent cells, transforming the BioBricks and miniprep them.
<p class="texte">Cloning is the step after taking the competent cells, transforming the BioBricks and miniprep them.
<br>
<br>
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<p class="texte"><b>1) Digestion mix</b>
<p class="texte"><b>1) Digestion mix</b>
<br> For the vector :
<br> For the vector :
-
<br>- 5µL of miniprep plasmid  
+
<br>- 5 µL of miniprep plasmid  
<br>
<br>
-
- 2µL of each restriction enzymes
+
- 2 µL of each restriction enzymes
<br>
<br>
-
- 2µL of Green Buffer
+
- 2 µL of Green Buffer
<br>
<br>
-
- 9µL of Milli-Q water  
+
- 9 µL of Milli-Q water  
<br>
<br>
<br> For the insert :
<br> For the insert :
-
<br>- 10µL of miniprep plasmid  
+
<br>- 10 µL of miniprep plasmid  
<br>
<br>
-
- 2µL of each restriction enzymes
+
- 2 µL of each restriction enzymes
<br>
<br>
-
- 2µL of Green Buffer
+
- 2 µL of Green Buffer
<br>
<br>
-
- 4µL of Milli-Q water  
+
- 4 µL of Milli-Q water  
<br>
<br>
- Incubate 15 minutes at 37°C  
- Incubate 15 minutes at 37°C  
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- Prepare a 1% or 2% electrophoresis agarose gel with 0.5x TAE buffer
- Prepare a 1% or 2% electrophoresis agarose gel with 0.5x TAE buffer
<br>
<br>
-
- Put 20µL of sample + 6µL of marker (1kb for 1% gel and 100pb for 2%) into the well
+
- Put 20 µL of sample + 6 µL of marker (1 kb for 1% gel and 100 pb for 2%) into the well
<br>
<br>
-
- Migration for 30 min at 100V or 1hour at 50V
+
- Migration for 30 min at 100 V or 1 hour at 50V
<br>
<br>
- The revelation is made in BET (10 minutes). Then wash in water for 5 minutes
- The revelation is made in BET (10 minutes). Then wash in water for 5 minutes
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<br><br>3) Inactivation of the enzymes for the vector
<br><br>3) Inactivation of the enzymes for the vector
<br>There are two ways to inactivate the enzymes:
<br>There are two ways to inactivate the enzymes:
-
<br>- Use of DNA Clean up kit for the DNA fragment above 200pb
+
<br>- Use of DNA Clean up kit for the DNA fragment above 200 pb
<br>- Heat inactivation at 95°C for 10 minutes.</p>
<br>- Heat inactivation at 95°C for 10 minutes.</p>
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<p class="texte"><b>1) Digestion mix</b>  
<p class="texte"><b>1) Digestion mix</b>  
<br>For each part, add:  
<br>For each part, add:  
-
<br>- 5µL of miniprep plasmid  
+
<br>- 5 µL of miniprep plasmid  
-
<br>- 1µL of each restriction enzymes
+
<br>- 1 µL of each restriction enzymes
-
<br>- 2µL of Green Buffer
+
<br>- 2 µL of Green Buffer
-
<br>- 9µL of Milli-Q water  
+
<br>- 9 µL of Milli-Q water  
<br>- Incubate 15 minutes at 37°C  
<br>- Incubate 15 minutes at 37°C  
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<b>2) Inactivation of the enzymes for the vector</b>
<b>2) Inactivation of the enzymes for the vector</b>
<br>There are two ways to inactivate the enzymes:
<br>There are two ways to inactivate the enzymes:
-
<br>- Use of DNA Clean up kit for the DNA fragment above 200pb
+
<br>- Use of DNA Clean up kit for the DNA fragment above 200 pb
<br>- Heat inactivation at 95°C for 10 minutes.</p>
<br>- Heat inactivation at 95°C for 10 minutes.</p>
<p class="title2">Second step</p>
<p class="title2">Second step</p>
<p class="title3">Ligation</p>
<p class="title3">Ligation</p>
-
<p class="texte">- Mix 10µL of insert + 4µL of vector + 2µL of 10x T4 buffer + 0.5µL of T4 ligase + 3.5µL of Milli-Q water
+
<p class="texte">- Mix 10 µL of insert + 4 µL of vector + 2 µL of 10x T4 buffer + 0.5 µL of T4 ligase + 3.5 µL of Milli-Q water
<br/>
<br/>
A control without insert must be made
A control without insert must be made
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<p class="title3">Transformation</p>
<p class="title3">Transformation</p>
<p class="texte">
<p class="texte">
-
- Take 5µL of the ligation mix for 50µL of competent cells and use the <a href="https://2014.igem.org/Team:Toulouse/Notebook/Protocols#select2">Toulouse iGEM Team 2014 transformation protocol</a>.
+
- Take 5µL of the ligation mix for 50 µL of competent cells and use the <a href="https://2014.igem.org/Team:Toulouse/Notebook/Protocols#select2">Toulouse iGEM Team 2014 transformation protocol</a>.
<br/>
<br/>
- Plate the solution on selective medium overnight at 37°C.</p>
- Plate the solution on selective medium overnight at 37°C.</p>
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<p class="title2">1) Colony PCR</p>
<p class="title2">1) Colony PCR</p>
<p class="texte">
<p class="texte">
-
- Add 0.5µL of plasmid + 25µL of DreamTAQ MasterMix + 2µL of each 10µM primer (VR and VF2) + H<sub>2</sub>0 qsp 25µL and take a colony.
+
- Add 0.5 µL of plasmid + 25 µL of DreamTAQ MasterMix + 2 µL of each 10 µM primer (VR and VF2) + H<sub>2</sub>0 qsp 25 µL and take a colony.
<br/>
<br/>
- Look for the number of necessary cycles and the proper temperature thanks to AmplifX or Serial Cloner 2.1 softwares.
- Look for the number of necessary cycles and the proper temperature thanks to AmplifX or Serial Cloner 2.1 softwares.
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<p class="title2">2) Analytic digestion</p>
<p class="title2">2) Analytic digestion</p>
<p class="texte">
<p class="texte">
-
- Put a colony in 5mL of LB selective medium and wait for 6 hours
+
- Put a colony in 5 mL of LB selective medium and wait for 6 hours
<br/>
<br/>
- Make a purification thanks to the Miniprep kit
- Make a purification thanks to the Miniprep kit
<br/>
<br/>
-
- Mix 2µL of plasmid + 2µL of Fast Digest Green Buffer + 1µL of each enzyme +  Milli-Q water qsp 20µL
+
- Mix 2 µL of plasmid + 2 µL of Fast Digest Green Buffer + 1µL of each enzyme +  Milli-Q water qsp 20µL
<br/>
<br/>
-
- Wait 15 minutes at 37°C and put the mix on a 1% or 2% gel for 30 minutes at 100V.</p>
+
- Wait 15 minutes at 37°C and put the mix on a 1% or 2% gel for 30 minutes at 100 V.</p>
<p class="title2">3) Sequencing</p>
<p class="title2">3) Sequencing</p>
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<p class="texte">
<p class="texte">
<B> Day 0 </B>
<B> Day 0 </B>
-
<br/>- Streak out the <i>Bacillus</i> strain and plate this on an LB agar plate overnight at 37°C</p>
+
<br/>- Streak out the <i>B. subtilis</i> strain and plate this on an LB agar plate overnight at 37°C</p>
<p class="texte"><B> Day 1 </B>
<p class="texte"><B> Day 1 </B>
-
<br/>- Pick up a nice big colony of <I>B. Subtilis </I> strain and drop it in 2ml of completed 1x MC
+
<br/>- Pick up a nice big colony of <I>B. subtilis </I> strain and drop it in 2ml of completed 1x MC
<br/>
<br/>
- Grow at 37°C for 5 hours
- Grow at 37°C for 5 hours
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<p class="title1" id="select7">Test of the pSB<sub>BS</sub>4S plasmid integration in <i>Bacillus subtilis</i> genome on the threonine site</p>
<p class="title1" id="select7">Test of the pSB<sub>BS</sub>4S plasmid integration in <i>Bacillus subtilis</i> genome on the threonine site</p>
<p class="texte">
<p class="texte">
-
<br>- Plate the transformed <i>Bacillus strain</i> on a selective medium (LB + spectinomycin) overnight  
+
<br>- Plate the transformed <i>B. subtilis</i> strain on a selective medium (LB + spectinomycin) overnight  
<br>- The obtained clones are then plated on different media:  Medium Competence (Thr+), Medium Competence (Thr-) and LB + Spectinomycin.  
<br>- The obtained clones are then plated on different media:  Medium Competence (Thr+), Medium Competence (Thr-) and LB + Spectinomycin.  
<br>When the plasmid is integrated, the clone can grow on minimum medium with threonine and on LB + Spectinomycin but can not grow on the minimum medium without thronine.
<br>When the plasmid is integrated, the clone can grow on minimum medium with threonine and on LB + Spectinomycin but can not grow on the minimum medium without thronine.
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<center><img src="https://static.igem.org/mediawiki/2014/b/b1/Installation_1.gif" width="650px"></center>
<center><img src="https://static.igem.org/mediawiki/2014/b/b1/Installation_1.gif" width="650px"></center>
<p class="texte">
<p class="texte">
-
<br>- Put 200µl of the different chemoattractants in the wells of the ELISA plate and pipet 15µL of each with the multichannel pipette: galactose which represents our negative control, glucose which represents our positive control and N-acetylglucosamine (NAG). The volume in the tips must be marked.<br>
+
<br>- Put 200 µl of the different chemoattractants in the wells of the ELISA plate and pipet 15 µL of each with the multichannel pipette: galactose which represents our negative control, glucose which represents our positive control and N-acetylglucosamine (NAG). The volume in the tips must be marked.<br>
-
<br><i>NB: The NAG is the most important test because it is the monosaccharide which composes the chitin on Ceratocystis platani wall.</i><br>  
+
<br><i>NB: The NAG is the most important test because it is the monosaccharide which composes the chitin on <i>Ceratocystis platani</i> wall.</i><br>
-
<br>- Put the tips with chemoattractants in 300µL of the bacterial solution in exponential growth phase in the ELISA plate.
+
<br>- Put the tips with chemoattractants in 300 µL of the bacterial solution in exponential growth phase in the ELISA plate.
<br>- Let the installation settle for 1 hour at room temperature.
<br>- Let the installation settle for 1 hour at room temperature.
<br>- After an hour, put the volume of the tips on parafilm.  
<br>- After an hour, put the volume of the tips on parafilm.  
-
<br>- Each solution is diluted 1/10,000 and 100µL is spread on LA medium.
+
<br>- Each solution is diluted 1/10,000 and 100 µL is spread on LA medium.
<br>- The plates are then incubated overnight at 37°C.</p>
<br>- The plates are then incubated overnight at 37°C.</p>
<p class="title2">Binding test</p>
<p class="title2">Binding test</p>
-
<p class="texte"><I>CBB (Chitin Binding Buffer):</I>
+
<p class="texte"><i>CBB (Chitin Binding Buffer):</i>
-
<br>- 500mM NaCl
+
<br>- 500 mM NaCl
-
<br>- 20mM Tris-HCl
+
<br>- 20 mM Tris-HCl
-
<br>- 1mM EDTA
+
<br>- 1 mM EDTA
<br>- 0,05% Triton X-100, 25°C, pH=8
<br>- 0,05% Triton X-100, 25°C, pH=8
</p>
</p>
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<p class="texte">
<p class="texte">
CAUTION : all the lab equipment must be desinfected before and after the manipulations with the fungi. <br>
CAUTION : all the lab equipment must be desinfected before and after the manipulations with the fungi. <br>
-
<br>Three different fungus strains were used : <I>Aspergillus brasiliensis, Aspergillus nidulans and Trichoderma reesei</I>
+
<br>Three different fungus strains were used : <i>Aspergillus brasiliensis</i>, <i>Aspergillus nidulans</i> and <i>Trichoderma reesei</i>
<br>- The conidia can be taken by adding one drop of Tween 80 on the fungus plate.
<br>- The conidia can be taken by adding one drop of Tween 80 on the fungus plate.
<br>- Then the drop is mixed with 1mL of sterile water in an Eppedorf.
<br>- Then the drop is mixed with 1mL of sterile water in an Eppedorf.
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<br>- The plates containing 10,000 conidia and the soaked pads are then put at room temperature for a few days according to the growth speed of the fungi. Controls are also realized with wild type strains or copper sulfate at 10 and 20mg/mL.
<br>- The plates containing 10,000 conidia and the soaked pads are then put at room temperature for a few days according to the growth speed of the fungi. Controls are also realized with wild type strains or copper sulfate at 10 and 20mg/mL.
</p>
</p>
 +
<p class= "texte">
 +
<b> Sap-like Medium (250 mL) (see references)</b>: <br>
 +
 +
2,5g de tryptone
 +
 +
<br>1,25g de YE
 +
 +
<br>2,5g de NaCl
 +
 +
<br>Glucose : 1,175g
 +
 +
<br>Fructose : 1,125g
 +
 +
<br>Sucrose : 0,125g
 +
 +
<br>Inositol : 0,084 g
<p class="title2">Fungicide test: <i>in planta</i> assay</p>
<p class="title2">Fungicide test: <i>in planta</i> assay</p>
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The next step begins with the preparation of the fungal samples. Fungal culture is crushed and mixed with PDB (Potato Dextrose Broth). Then the mix passes through a 100 µm filter (to remove large aggregates) and  through a 40 µm filter. The caught hyphae are mixed with PDB for 24 to 48 hours until it reaches an OD of 2.5 at 600nm. The previously seeded leaves are taken from the plant using a scalpel and placed in boxes above wet absorbent paper (leaves are kept alive for a week). Above each leaf, 5µl of the fungal suspension is deposited (using beveled tips because it is too viscous). As control, we kept inoculated leaves without fungus and leaves with only fungus. Pictures are taken at different times. All the plants are destroyed by autoclaving.
The next step begins with the preparation of the fungal samples. Fungal culture is crushed and mixed with PDB (Potato Dextrose Broth). Then the mix passes through a 100 µm filter (to remove large aggregates) and  through a 40 µm filter. The caught hyphae are mixed with PDB for 24 to 48 hours until it reaches an OD of 2.5 at 600nm. The previously seeded leaves are taken from the plant using a scalpel and placed in boxes above wet absorbent paper (leaves are kept alive for a week). Above each leaf, 5µl of the fungal suspension is deposited (using beveled tips because it is too viscous). As control, we kept inoculated leaves without fungus and leaves with only fungus. Pictures are taken at different times. All the plants are destroyed by autoclaving.
</p>
</p>
-
 
+
<br>
 +
<p class="texte">
 +
<b>References</b><br>
 +
Véronique Amiard, Annette Morvan-Bertrand, Jean-Bernard Cliquet, Jean-Pierre Billard,
 +
Claude Huault, Jonas P. Sandström, and Marie-Pascale Prud’homme. <b>Carbohydrate and amino
 +
acid composition in phloem sap of Lolium perenne L. before and after defoliation</b>. Can. J. Bot.
 +
Vol. 82: 1594–1601, 2004.</p>
  </div>
  </div>

Latest revision as of 03:37, 18 October 2014