Difference between revisions of "Team:Macquarie Australia/Experiment"

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<div class="panel">
 
<div class="panel">
 
   <p><ol>
 
   <p><ol>
−
<li> Using a sterile plastic loop, pick 10-12 large (2-3mm in diameter) colonies from the plate. Inoculate to 150mL of SOB medium in a 1L flask, and grow overnight at 18-22&#176;C, 200-250rpm. Alternatively, set up a starter culture (2ml) overnight and inoculate the large scale in the morning. Grow at 37&#176;C. </li>  
+
<li> Using a sterile plastic loop, pick 10-12 large (2-3 mm in diameter) colonies from the plate. Inoculate to 150 mL of SOB medium in a 1L flask, and grow overnight at 18-22&#176;C, 200-250rpm. Alternatively, set up a starter culture (2 mL) overnight and inoculate the large scale in the morning. Grow at 37&#176;C. </li>  
  
−
<li> A600 should be 0.2-0.8 when harvest. Preferably, cells should be in mid log phase with A600 ~ 0.5 </li>  
+
<li> A600 should be 0.2-0.8 when harvest. Preferably, cells should be in mid log phase with A600 ~0.5 </li>  
  
 
<li> Remove the flask from the incubator and place on ice for 10 minutes. FROM THIS STEP, KEEP THE CELLS ON ICE AS MUCH AS POSSIBLE!</li>  
 
<li> Remove the flask from the incubator and place on ice for 10 minutes. FROM THIS STEP, KEEP THE CELLS ON ICE AS MUCH AS POSSIBLE!</li>  
  
−
<li> Transfer the culture to a 15mL centrifuge tube and spin at 2500 x g for 10 min at 4&#176;C</li>  
+
<li> Transfer the culture to a 15 mL centrifuge tube and spin at 2500 x g for 10 min at 4&#176;C</li>  
  
 
<li> Pour off and discard the supernatant, and immediately place the tube on ice.</li>  
 
<li> Pour off and discard the supernatant, and immediately place the tube on ice.</li>  
  
−
<li> Resuspend your cells in 1mL of ice-cold TB buffer, make sure there are no clumps of cells left, but also treat your cells gently and keep them cold.</li>  
+
<li> Resuspend your cells in 1 mL of ice-cold TB buffer, make sure there are no clumps of cells left, but also treat your cells gently and keep them cold.</li>  
  
−
<li> Add ice-cold TB buffer to bring volume up to 1/5th of the original culture volume (~30mL in this case). Mix the tube by gently inverting 3 times.</li>  
+
<li> Add ice-cold TB buffer to bring volume up to 1/5th of the original culture volume (~30 mL in this case). Mix the tube by gently inverting 3 times.</li>  
  
 
<li> Incubate the tube on ice for 10 minutes.</li>  
 
<li> Incubate the tube on ice for 10 minutes.</li>  
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<li> Centrifuge at 2,500 x g for 7 minutes at 4&#176;C, discard the supernatant.</li>  
 
<li> Centrifuge at 2,500 x g for 7 minutes at 4&#176;C, discard the supernatant.</li>  
  
−
<li> Gently resuspend the cells in ~1/20th of the original culture volume of ice-cold TB buffer. NOTE: 1/20th is based on and OD600 of 0.5, so adjust volume accordingly. E.g. if the culture OD600 was 0.1 then resuspend in 1/100th of original volume.</li>  
+
<li> Gently resuspend the cells in ~1/20th of the original culture volume of ice-cold TB buffer. NOTE: 1/20th is based on an OD600 of 0.5, so adjust volume accordingly. E.g. if the culture OD600 was 0.1 then resuspend in 1/100th of original volume.</li>  
  
−
<li> Pre-chill 1.5ml Eppendorf tubes on ice. Add 930µl of your cell suspension, keeping the remainder on ice in the 15mL tube.</li>  
+
<li> Pre-chill 1.5 mL Eppendorf tubes on ice. Add 930 µL of your cell suspension, keeping the remainder on ice in the 15 mL tube.</li>  
  
−
<li> Add 70µl of DMSO to the 930µl of cell suspension. Mix gently by swirling, and place on ice. </li>  
+
<li> Add 70 µL of DMSO to the 930 µl of cell suspension. Mix gently by swirling, and place on ice. </li>  
  
−
<li> Aliquot 100µl of the competent cell/DMSO mixture into fresh microcentrifuge tubes. Label the tubes with: Date – Strain. Snap freeze with liquid nitrogen or dry ice. Store cells at -80&#176;C. </li>  
+
<li> Aliquot 100 µL of the competent cell/DMSO mixture into fresh microcentrifuge tubes. Label the tubes with: Date – Strain. Snap freeze with liquid nitrogen or dry ice. Store cells at -80&#176;C. </li>  
  
  
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<li> Obtain competent cells from -80&#176;C. </li>  
 
<li> Obtain competent cells from -80&#176;C. </li>  
  
−
<li> Defrost, then return on ice immediately. Always keep cells on ice up till Step 4. Pipette 50µl for each transformation. If you have 100ul aliquot, split into 2 tubes.</li>  
+
<li> Defrost, then return on ice immediately. Always keep cells on ice up till Step 4. Pipette 50 µL for each transformation. If you have 100 µL aliquot, split into 2 tubes.</li>  
  
−
<li> Add 2µl of plasmid DNA/ ligation mix to each tube. Incubate on ice for 10-15 min. </li>  
+
<li> Add 2 µL of plasmid DNA/ ligation mix to each tube. Incubate on ice for 10-15 min. </li>  
  
 
<li> Heat shock in 42&#176;C in block (or hot water in beaker with thermometer) for 45 seconds, then back on ice for 2 min.</li>  
 
<li> Heat shock in 42&#176;C in block (or hot water in beaker with thermometer) for 45 seconds, then back on ice for 2 min.</li>  
  
−
<li> Recovery- Add 500µl of SOC media to each tube, and incubate in the 37&#176;C shaker for 90 min and shaking 500 rpm (recovery- 30min for plasmid or 90min for ligation mix).</li>  
+
<li> Recovery- Add 500 µL of SOC media to each tube, and incubate in the 37&#176;C shaker for 90 min and shaking 500 rpm (recovery- 30min for plasmid or 90min for ligation mix).</li>  
  
−
<li> For each tube of cells, spread 20µl onto one LB plate with appropriate antibiotic, and 200µl onto a second plate, using aseptic technique. (Since colony counts have been so low we are currently only plating the 200µl.) Remember to label your plate properly (Your name, sample name, cell line, antibiotic, date)</li>  
+
<li> For each tube of cells, spread 20 µL onto one LB plate with appropriate antibiotic, and 200 µL onto a second plate, using aseptic technique. (Since colony counts have been so low we are currently only plating the 200 µL.) Remember to label your plate properly (Your name, sample name, cell line, antibiotic, date)</li>  
  
 
<li> Leave plates (with lid on) on bench or 37&#176;C incubator to dry out before sealing with parafilm (or use cling wrap for multiple plates). Place your plate upside-down in the 37&#176;C incubator.</li>  
 
<li> Leave plates (with lid on) on bench or 37&#176;C incubator to dry out before sealing with parafilm (or use cling wrap for multiple plates). Place your plate upside-down in the 37&#176;C incubator.</li>  
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   <p><ol>
 
   <p><ol>
  
−
<li> Digest the plasmid with EcoRI to created a linear plasmid and double digest with EcoRI and PstI to separate the gene and backbone (0.2µl enzyme is sufficient for single or double digest no need to adjust).  </li>  
+
<li> Digest the plasmid with EcoRI to created a linear plasmid and double digest with EcoRI and PstI to separate the gene and backbone (0.2 µL enzyme is sufficient for single or double digest no need to adjust).  </li>  
−
<li> When making up a master mix consider making up a 2X concentration then the correct DNA volume to reach 100ng with balance of H<sub>2</sub>O is added.  </li>  
+
<li> When making up a master mix consider making up a 2X concentration then the correct DNA volume to reach 100 ng with balance of H<sub>2</sub>O is added.  </li>  
 
<li>  Incubate the two restriction digest reactions at 37&#176;C for 30 minutes.  </li>  
 
<li>  Incubate the two restriction digest reactions at 37&#176;C for 30 minutes.  </li>  
  
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</br>
 
</br>
  
−
<h3> <i> E. coli </i> Hydrogen Production </h3>
+
<h3> <i>E. coli</i> Hydrogen Production </h3>
  
 
<button class="accordion">M9 Agar </button>
 
<button class="accordion">M9 Agar </button>
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</tr>  
 
</tr>  
 
<tr>  
 
<tr>  
−
<td> 1M MgSO4 </td> <td> 0.5 mL </td>  
+
<td> 1M MgSO<sub>4</sub> </td> <td> 0.5 mL </td>  
 
</tr>
 
</tr>
 
<tr>  
 
<tr>  
−
<td> 1M CaCl2 </td> <td> 0.05 mL </td>  
+
<td> 1M CaCl<sub>2</sub> </td> <td> 0.05 mL </td>  
 
</tr>  
 
</tr>  
 
<tr>  
 
<tr>  
−
<td> 1M MgSO4 </td> <td> 0.5 mL </td>  
+
<td> 1M MgSO<sub>4</sub> </td> <td> 0.5 mL </td>  
 
</tr>
 
</tr>
 
<tr>  
 
<tr>  
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</tr>  
 
</tr>  
 
<tr>  
 
<tr>  
−
<td> 0.2 M Fe(NH4)SO4 </td> <td> 125 uL </td>  
+
<td> 0.2 M Fe(NH<sub>4</sub>)SO<sub>4</sub> </td> <td> 125 uL </td>  
 
</tr>  
 
</tr>  
 
<tr>  
 
<tr>  
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</table>
 
</table>
  
−
<p> Top up to 500 mL with Sterile Milli-Q H2O. </p>
+
<p> Top up to 500 mL with Sterile Milli-Q H<sub>2</sub>O. </p>
 
   
 
   
 
                                         </ol></p>
 
                                         </ol></p>
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<div class="panel">
 
<div class="panel">
 
   <p><ol>
 
   <p><ol>
−
<li> Add 2 mL of M9 media to a 15 mL tube with a colony of transformed <i> E. coli </i> for an overnight culture, 37&#176;C and shaking. </li>
+
<li> Add 2 mL of M9 media to a 15 mL tube with a colony of transformed <i>E. coli</i> for an overnight culture, 37&#176;C and shaking. </li>
 
<li> Measure the OD600 and dilute to get an OD of 0.1. </li>
 
<li> Measure the OD600 and dilute to get an OD of 0.1. </li>
 
<li> Grow cells up to OD600 0.5. </li>
 
<li> Grow cells up to OD600 0.5. </li>

Revision as of 23:54, 27 October 2017


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Preparation of E. coli

  1. Using a sterile plastic loop, pick 10-12 large (2-3 mm in diameter) colonies from the plate. Inoculate to 150 mL of SOB medium in a 1L flask, and grow overnight at 18-22°C, 200-250rpm. Alternatively, set up a starter culture (2 mL) overnight and inoculate the large scale in the morning. Grow at 37°C.
  2. A600 should be 0.2-0.8 when harvest. Preferably, cells should be in mid log phase with A600 ~0.5
  3. Remove the flask from the incubator and place on ice for 10 minutes. FROM THIS STEP, KEEP THE CELLS ON ICE AS MUCH AS POSSIBLE!
  4. Transfer the culture to a 15 mL centrifuge tube and spin at 2500 x g for 10 min at 4°C
  5. Pour off and discard the supernatant, and immediately place the tube on ice.
  6. Resuspend your cells in 1 mL of ice-cold TB buffer, make sure there are no clumps of cells left, but also treat your cells gently and keep them cold.
  7. Add ice-cold TB buffer to bring volume up to 1/5th of the original culture volume (~30 mL in this case). Mix the tube by gently inverting 3 times.
  8. Incubate the tube on ice for 10 minutes.
  9. Centrifuge at 2,500 x g for 7 minutes at 4°C, discard the supernatant.
  10. Gently resuspend the cells in ~1/20th of the original culture volume of ice-cold TB buffer. NOTE: 1/20th is based on an OD600 of 0.5, so adjust volume accordingly. E.g. if the culture OD600 was 0.1 then resuspend in 1/100th of original volume.
  11. Pre-chill 1.5 mL Eppendorf tubes on ice. Add 930 µL of your cell suspension, keeping the remainder on ice in the 15 mL tube.
  12. Add 70 µL of DMSO to the 930 µl of cell suspension. Mix gently by swirling, and place on ice.
  13. Aliquot 100 µL of the competent cell/DMSO mixture into fresh microcentrifuge tubes. Label the tubes with: Date – Strain. Snap freeze with liquid nitrogen or dry ice. Store cells at -80°C.

  1. Obtain competent cells from -80°C.
  2. Defrost, then return on ice immediately. Always keep cells on ice up till Step 4. Pipette 50 µL for each transformation. If you have 100 µL aliquot, split into 2 tubes.
  3. Add 2 µL of plasmid DNA/ ligation mix to each tube. Incubate on ice for 10-15 min.
  4. Heat shock in 42°C in block (or hot water in beaker with thermometer) for 45 seconds, then back on ice for 2 min.
  5. Recovery- Add 500 µL of SOC media to each tube, and incubate in the 37°C shaker for 90 min and shaking 500 rpm (recovery- 30min for plasmid or 90min for ligation mix).
  6. For each tube of cells, spread 20 µL onto one LB plate with appropriate antibiotic, and 200 µL onto a second plate, using aseptic technique. (Since colony counts have been so low we are currently only plating the 200 µL.) Remember to label your plate properly (Your name, sample name, cell line, antibiotic, date)
  7. Leave plates (with lid on) on bench or 37°C incubator to dry out before sealing with parafilm (or use cling wrap for multiple plates). Place your plate upside-down in the 37°C incubator.



BioBrick Transformation

  1. Harvest cells- Reserving 500 uL of culture for glycerol stock the remainder can be used for miniprep. Overnight culture - centrifuge 1 min to pellet cells. (Pour off supernatant and centrifuge more in the same tube. Keep quantities equal across your tubes to aid centrifuge balance. It is unnecessary to use all culture).
  2. Resuspend- 200 µL (this solution is refrigerated due to RNase).
  3. Lyse- 200 µL (gentle inversions < 5min) followed by precipitate/neutralize- 350 µL (gentle inversions).
  4. Centrifuge- 10 min (to pellet debris).
  5. Prepare columns- (cut lids off and label columns) 500 µL (column prep solution) - centrifuge 1 min.
  6. Collect DNA- pass lysate through column - centrifuge 1 min.
  7. Wash columns 750 µL - centrifuge 45 s (discard flow through) and centrifuge another 90 s.
  8. Elute DNA into labelled Eppendorf tubes. 30 µL - centrifuge 1 min. Retaining the elution and centrifuge through a 2nd time collects more DNA.
  9. Nanodrop to determine DNA concentration and label accordingly. (Use Miniprep elution solution as blank).

  1. Digest Upstream Part with EcoRI-HF and SpeI.
  2. Digest Downstream Part with XbaI and PstI.
  3. Digest the Destination Plasmid with EcoRI-HF and PstI: The Destination Plasmid should also have a different antibiotic resistance marker from both the plasmid containing the Upstream Part and the plasmid containing the Downstream Part to avoid the need to purify the Upstream and Downstream Parts.
  4. Incubate all 3 restriction digest reactions at 37°C for 60 min, then heat inactivate at 80°C for 20 minutes.
  5. Ligate the Upstream and Downstream Parts into the digested Destination Plasmid.
  6. Incubate the ligation mix at 16°C for 15 min, 30°C for 30 min, 37°C for 15 min, then heat inactivate at 80°C for 20 min.

  1. Digest the plasmid with EcoRI to created a linear plasmid and double digest with EcoRI and PstI to separate the gene and backbone (0.2 µL enzyme is sufficient for single or double digest no need to adjust).
  2. When making up a master mix consider making up a 2X concentration then the correct DNA volume to reach 100 ng with balance of H2O is added.
  3. Incubate the two restriction digest reactions at 37°C for 30 minutes.



E. coli Hydrogen Production

    Ingredient Volume
    M9 Minimal salt (5X) 100 mL
    RO water 400 mL

    Autoclave then add the following filter sterilised ingredients:

    Trace Elements 5 mL
    1M MgSO4 0.5 mL
    1M CaCl2 0.05 mL
    1M MgSO4 0.5 mL
    20% cas amino acid 2.5 mL
    0.2 M Fe(NH4)SO4 125 uL
    2% Thiamine 125 uL

    Top up to 500 mL with Sterile Milli-Q H2O.

  1. Add 2 mL of M9 media to a 15 mL tube with a colony of transformed E. coli for an overnight culture, 37°C and shaking.
  2. Measure the OD600 and dilute to get an OD of 0.1.
  3. Grow cells up to OD600 0.5.
  4. Induce with IPTG (1:1000) and add 20 mM glucose.
  5. Grow anaerobically for 24 hours, 37°C and shaking.

  1. Add 2 mL of diluted induced culture with an OD600 0.4. Dilute with M9 media, with glucose and IPTG.
  2. Close tightly with plunger.
  3. Leave electrode to measure for 48 hours.