Difference between revisions of "Team:Dundee Schools/Notebook"

 
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<ul class="submenu">
 
<ul class="submenu">
 
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Model">Modelling </a></li>
 
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Model">Modelling </a></li>
−
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Measurement">Medals</a></li>
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Medals">Medals</a></li>
 
                     </ul>
 
                     </ul>
 
                 </li>
 
                 </li>
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</div>
 
</div>
−
 
  
  
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<div class="content_wrapper">
 
<div class="content_wrapper">
−
 
  
  
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<h4 id="page_name"> Notebook </h4>
 
<h4 id="page_name"> Notebook </h4>
  
−
  <h3>Wet Team</h3>
+
  <h2>Wet Team</h2>
−
  <ul><h4>Week 1- Familiarising ourselves with the labs</h4>
+
 
−
   <li>Transformation + Overnight of PSBIC3
+
<h4>Week 1 - Familiarising ourselves with the labs</h4>
−
   <li>Mini Prep of PSBIC3</li>
+
  <p><ul>
−
   <li>Restriction Digest of PSB1C3</li>
+
   <p><li>Transformation + Overnight of pSBIC3</li>
 +
   <li>Mini Prep of pSBIC3</li>
 +
   <li>Restriction Digest of pSB1C3</li>
 
     <ul><h5>PCR’s:</h5>
 
     <ul><h5>PCR’s:</h5>
 
     <li>Hfq <i>E. coli</i>- Unsuccessful</li>
 
     <li>Hfq <i>E. coli</i>- Unsuccessful</li>
 
     <li>Hfq <i>Serratia</i>- Unsuccessful</li>
 
     <li>Hfq <i>Serratia</i>- Unsuccessful</li>
−
     <li>osmY- Unsuccessful</li>
+
     <li>OsmY- Unsuccessful</li>
 
     </ul>
 
     </ul>
−
   <li>Mini Prep of PSBIC3</li>
+
   <li>Mini Prep of pSBIC3</li>
−
   <li>Restriction Digest of PSB1C3</li>
+
   <li>Restriction Digest of pSB1C3</li>
 +
  </ul></p>
  
−
Week 2-
+
<h4>Week 2 - Carrying on with cloning</h4>
 +
  <p><ul>
 +
    <ul><h5>PCR’s:</h5>
 +
      <li>Hfq <i>E. coli</i>- Unsuccessful</li>
 +
      <li>Hfq <i>Serratia</i> – Unsuccessful</li>
 +
      <li>osmY- Unsuccessful</li>
 +
    </ul>
 +
    <ul><h5>3rd PCR set up:</h5>
 +
      <li>Hfq <i>E. coli</i> – Successful</li>
 +
      <li>Hfq <i>Serratia</i> – Unsuccessful</li>
 +
      <li>OsmY - Successful</li>
 +
    </ul>
 +
    <ul><h5>PCR’s:</h5>
 +
      <li>Hfq <i>Serratia</i> 2 at 49°C - Successful</li>
 +
      <li>Hfq <i>Serratia</i> 1 at 65°C - Successful</li>
 +
    </ul>
 +
    <li>Ligation into PSBIC3 and transformed</li>
 +
    <li>The 3 successful PCR’s were plated at concentrations of 2:1 and 3:1 with vector; no plates grew colonies</li>
 +
  </ul></p>
  
−
Carried on with cloning
+
<h4>Week 3 - Made our first BioBrick</h4>
 +
  <p><ul>
 +
  <li>Redid all 3 PCR’S – Hfq <i>E. coli</i> and osmY both worked. Hfq <i>Serratia</i> did not.</li>
 +
  <li>Colony PCR of the successful PCR’s, overnight, mini prep, sent away for sequencing and then stocked.</li>
 +
    <b>First 2 BioBricks made: OsmY + Hfq <i>E. coli</i></b>
 +
  <li>PCR of <i>osmY-hfq E. coli</i> fusion and PCR of <i>osmY-hfq Serratia</i> Fusion - successful</li>
 +
    <ul><li>Digested and Ligated etc.… sequenced then stocked.</li></ul>
 +
    <b>2 BioBricks made: osmY Hfq <i>E. coli</i> Fusion + osmY Hfq <i>Serratia</i> Fusion</b>
 +
  </ul></p>
  
−
* PCR’s:
+
<h4>Week 4 - Started to make gene fragments</h4>
 +
  <p><ul>
 +
  <li>PCR of Hfq <i>Serratia</i> - successful</li>
 +
    <ul><li>Sequenced and Stocked.</li></ul>
 +
    <b>1 Bio brick made: Hfq <i>Serratia</i></b>
 +
  <li>Gene fragments – EC-SRNA and sma-SRNA digested and ligated into pSBIC3</li>
 +
  <li>Digestion of Rhamnose promoter plasmid</li>
 +
  </ul></p>
  
−
o Hfq E.coli- Unsuccessful
+
<h4>Week 5 – Started to add Ha tags</h4>
 +
  <p><ul>
 +
    <ul><h5>Ligations:</h5>
 +
    <li>rbs-osmY-Hfq-<i>E. coli</i></li>
 +
    <li>rbs-osmY-Hfq-<i>Serratia</i></li>
 +
    <li>rbs-osmY-Hfq-<i>E. coli</i>- Ha Tag</li>
 +
    <li>rbs-osmY-Hfq-<i>Serratia</i>- Ha Tag</li>
 +
    </ul>
 +
    <ul><h5>PCR’s:</h5>
 +
    <li>rbs-osmY- Ha Tag - Successful</li>
 +
    <li>rbs-osmY-Hfq <i>E. coli</i>- Ha Tag- Successful</li>
 +
    <li>rbs-osmY-Hfq <i>Serratia</i>-Ha Tag – Successful</li>
 +
    </ul>
 +
  <li>All PCR’s transformed and overnighted.</li>
 +
  </ul></p>
  
−
o Hfq Serratia – Unsuccessful
+
<h4>Week 6 - Phage outbreak</h4>
 +
  <p><ul>
 +
    <ul><h5>Overnights of:</h5>
 +
    <li>rbs-osmY-Hfq- Ha tag</li>
 +
    <li>rbs-osmY-Hfq <i>E. coli</i>- Ha tag</li>
 +
    <li>rbs-osmY-Hfq <i>Serratia</i>- Ha tag</li>
 +
    </ul>
 +
  <li>Mini preps, sequencing and transformations of the above</li>
 +
  <li>Phage outbreak on Thursday; due to this all transformations were lost, but re-done the next day</li>
 +
  <li>All sent away for sequencing</li>
 +
  <li>Ec – SRNA and sma SRNA – both stocked.</li>
 +
  </ul></p>
  
−
o osmY- Unsuccessful
+
<h4>Week 7 - Western blots</h4>
 +
  <p><ul>
 +
  <li>We did our first western blot test with no timed samples.</li>
 +
  <li>We also completed a timed western blot by adding different concentrations of Rhamnose and taking samples every hour</li>
 +
    <ul><h5>Primers:</h5>
 +
    <li><i>fliC</i> for Ec-sRNA</li>
 +
    <li><i>virF</i> for Ec-sRNA</li>
 +
    </ul>
 +
  </ul></p>
  
−
* 3rd PCR set up:
+
<h4>Week 8 - Final week</h4>
 +
  <p><ul>
 +
  <li>Performed another Western Blot to get a much cleaner image for the whole cell</li>
 +
  <li>Overnights with Ec-SRNA <i>fliC</i> in MG1655 and Ec-SRNA <i>virF</i></li>
 +
  <li>Plates grew colonies – colony PCR with colonies.</li>
 +
  <li>Sent away for sequencing</li>
 +
  </ul></p>
  
−
o Hfq E.coli – Successful
 
  
−
o Hfq Serratia – Unsuccessful
 
  
−
o osmY - Successful
+
<h2>Dry Team</h2>
  
−
* PCR’s:
+
<h4>Week 1 -</h4>
−
 
+
  <p><ul>
−
o Hfq Serratia x 2 at 49 degrees - Successful
+
−
 
+
−
o Hfq Serratia x 1 at 65 degrees - Successful
+
−
 
+
−
* Ligation into PSBIC3 and transformed
+
−
 
+
−
* The 3 successful PCR’s were plated at concentrations of 2.1 and 3.1 with vector; no plates grew colonies
+
−
 
+
−
Week 3-
+
−
 
+
−
Made our first BioBrick
+
−
 
+
−
* Redid all 3 PCR’S – Hfq E.coli and osmY both worked. Hfq Serratia did not.
+
−
 
+
−
* Colony PCR of the successful PCR’s, overnight, mini prep, sent away for sequencing and then stocked.
+
−
 
+
−
First 2 BioBricks made: OsmY + Hfq E.coli
+
−
 
+
−
* PCR of osmY Hfq E.coli fusion and PCR of osmY Hfq Serratia Fusion - successful
+
−
 
+
−
Digested and Ligated etc.… sequenced then stocked.
+
−
 
+
−
2 BioBricks made: osmY Hfq E.coli Fusion + osmY Hfq Serratia Fusion
+
−
 
+
−
Week 4-
+
−
 
+
−
Started to make gene fragments
+
−
 
+
−
* PCR of Hfq Serratia - successful
+
−
 
+
−
* Sequenced and Stocked.
+
−
 
+
−
1 Bio brick made: Hfq Serratia
+
−
 
+
−
* Gene fragments – EC-SRNA and sma-SRNA digested and ligated into PSBIC3
+
−
 
+
−
* Digestion of Rhamnose promoter
+
−
 
+
−
Week 5 –
+
−
 
+
−
Started to add Ha tags
+
−
 
+
−
* Ligations:
+
−
 
+
−
o rbs-osmY-Hfq-E.coli
+
−
 
+
−
o rbs-osmY-Hfq-Serratia
+
−
 
+
−
o rbs-osmY-Hfq-E.coli- Ha Tag
+
−
 
+
−
o rbs-osmY-Hfq-Serratia- Ha Tag
+
−
 
+
−
* PCR’s:
+
−
 
+
−
o rbs-osmY- Ha Tag - Successful
+
−
 
+
−
o rbs-osmY-Hfq E.coli- Ha Tag- Successful
+
−
 
+
−
o rbs-osmY-Hfq Serratia-Ha Tag – Successful
+
−
 
+
−
All PCR’s transformed and overnighted.
+
−
 
+
−
Week 6-
+
−
 
+
−
Phage outbreak
+
−
 
+
−
* Overnights of:
+
−
 
+
−
o rbs-osmY-Hfq- Ha tag
+
−
 
+
−
o rbs-osmY-Hfq E.coli- Ha tag
+
−
 
+
−
o rbs-osmY-Hfq Serratia- Ha tag
+
−
 
+
−
* Mini preps, sequencing and transformations of the above
+
−
 
+
−
* Phage outbreak on Thursday; all transformations lost due to this re-done the next day
+
−
 
+
−
* All sent away for sequencing
+
−
 
+
−
* Ec – SRNA and sma SRNA – both stocked.
+
−
 
+
−
Week 7-
+
−
 
+
−
Western blot
+
−
 
+
−
* We did our first western blot test with no timed samples.
+
−
 
+
−
* We also completed a timed western blot by adding different concentrations of Rhamanose and taking samples every hour
+
−
 
+
−
* Primers:
+
−
 
+
−
o Fli C for Ec- sRNA
+
−
 
+
−
o Vir F for Ec-sRNA
+
−
 
+
−
Week 8-
+
−
 
+
−
Final week
+
−
 
+
−
* Performed another Western Blot to get a much cleaner image for the whole cell
+
−
 
+
−
* Overnights with Ec-SRNA Fli C in MG1655 and Ec-SRNA Vir F
+
−
 
+
−
* Plates grew colonies – colony PCR with colonies.
+
−
 
+
−
* Sent away for sequencing
+
−
 
+
−
 
+
−
<br></br>
+
−
 
+
−
 
+
−
 
+
−
<h3>Dry Team</h3>
+
−
  <ul><b>Week 1-</b>
+
 
   <li>Started off discussing our topic of bacterial infections and brainstorming how we could target them; settled on RNA interference.</li>
 
   <li>Started off discussing our topic of bacterial infections and brainstorming how we could target them; settled on RNA interference.</li>
 
   <li>Split the team into 2 groups, wet team (Matthew, Bartosz, Albert) and dry team (Mia, Beth, Darryl).</li>
 
   <li>Split the team into 2 groups, wet team (Matthew, Bartosz, Albert) and dry team (Mia, Beth, Darryl).</li>
Line 590: Line 546:
 
   <li>Started with general research on our chosen infections (Cholera and Shigellosis)</li>
 
   <li>Started with general research on our chosen infections (Cholera and Shigellosis)</li>
 
   <li>Darryl started and completed learning basic HTML and CSS via tutorials on the site Codecadamy, then began the initial stages of the wiki so as to get to grips with it.</li>
 
   <li>Darryl started and completed learning basic HTML and CSS via tutorials on the site Codecadamy, then began the initial stages of the wiki so as to get to grips with it.</li>
−
   </ul>
+
   </ul></p>
−
<br></br>
+
  
−
  <ul><b>Week 2-</b>
+
<h4>Week 2 -</h4>
−
  <li>The dry team began to contact various people/organisations:  
+
  <p><ul>
−
    <ul><li>Colalife</li>
+
    <ul><p>Began to contact various people/organisations:</p>
 +
    <li>Colalife</li>
 
     <li>Mercy Ships</li>
 
     <li>Mercy Ships</li>
 
     <li>Water Aid</li>
 
     <li>Water Aid</li>
−
     <li>Lifeline Express</li></ul></li>
+
     <li>Lifeline Express</li>
 +
    </ul>
 
   <li>Had our first meeting about maths modelling and discussed how we could incorporate it into our project.</li>
 
   <li>Had our first meeting about maths modelling and discussed how we could incorporate it into our project.</li>
 
   <li>Further developed wiki.</li>
 
   <li>Further developed wiki.</li>
−
   </ul>
+
   </ul></p>
−
<br></br>
+
  
−
  <ul><b>Week 3-</b>
+
<h4>Week 3 -</h4>
 +
  <p><ul>
 
   <li>Had a phone call with Brian Walshe of Mercy Ships</li>  
 
   <li>Had a phone call with Brian Walshe of Mercy Ships</li>  
−
  <li>Started organisation for Northern meet up:
+
    <ul>Started organisation for Northern meet up:</p>
−
    <ul>
+
 
     <li>Began developing presentation content and layout</li>
 
     <li>Began developing presentation content and layout</li>
−
     <li>Work began on poster</li></ul></li>
+
     <li>Work began on poster</li>
−
   </ul>
+
    </ul>
−
<br></br>
+
   </ul></p>
  
−
  <ul><b>Week 4-</b>
+
<h4>Week 4 -</h4>
−
   <li>Spoke to Rob Porter (prof. of Microbiology) via email.</li>
+
  <p><ul>
 +
   <li>Spoke to Rob Porter (Prof. of clinical microbiology) via email.</li>
 
   <li>Planned a skype call with Simon Berry of Colalife.</li>
 
   <li>Planned a skype call with Simon Berry of Colalife.</li>
−
   <li>Contacted British red cross.</li>
+
   <li>Contacted British Red Cross.</li>
−
   </ul>
+
   </ul></p>
−
<br></br>
+
  
−
  <ul><b>Week 5-</b>
+
<h4>Week 5 -</h4>
 +
  <p><ul>
 
   <li>Attended the Edinburgh Northern meet up & presented our project there, to which we were met with excellent feedback.</li>
 
   <li>Attended the Edinburgh Northern meet up & presented our project there, to which we were met with excellent feedback.</li>
 
   <li>Carried on working in the lab and progressing with our presentation.</li>
 
   <li>Carried on working in the lab and progressing with our presentation.</li>
 
   <li>Further development of poster.</li>
 
   <li>Further development of poster.</li>
−
   </ul>
+
   </ul></p>
−
<br></br>
+
  
−
  <ul><b>Week 6-</b>
+
<h4>Week 6 -</h4>
 +
  <p><ul>
 
   <li>Contacted British Pharmaceutical Society</li>
 
   <li>Contacted British Pharmaceutical Society</li>
−
   <li>Contacted Mark Mcculloch (Army Doctor)</li>
+
   <li>Contacted Mark McCulloch (Army Doctor)</li>
 
   <li>Carried on with making our poster for the UK meet up.</li>
 
   <li>Carried on with making our poster for the UK meet up.</li>
−
   </ul>
+
   </ul></p>
−
<br></br>
+
  
−
  <ul><b>Week 7-</b>
+
<h4>Week 7 -</h4>
 +
  <p><ul>
 
   <li>Set up meeting with Mark</li>
 
   <li>Set up meeting with Mark</li>
 
   <li>Finished poster</li>
 
   <li>Finished poster</li>
 
   <li>Carried on with our wiki content</li>
 
   <li>Carried on with our wiki content</li>
 
   <li>Received our FBI sunglasses and pens for the Jamboree.</li>
 
   <li>Received our FBI sunglasses and pens for the Jamboree.</li>
−
   </ul>
+
   </ul></p>
−
<br></br>
+
  
−
  <ul><b>Week 8-</b>
+
<h4>Week 8 -</h4>
 +
  <p><ul>
 
   <li>Attended the UK meet up in London – presented our talk and our poster to multiple UK iGEM teams.</li>
 
   <li>Attended the UK meet up in London – presented our talk and our poster to multiple UK iGEM teams.</li>
 
   <li>Got our hoodies and t-shirts for Boston.</li>
 
   <li>Got our hoodies and t-shirts for Boston.</li>
 
   <li>Had our agent photoshoot.</li>
 
   <li>Had our agent photoshoot.</li>
−
   </ul>
+
   </ul></p>
−
<br></br>
+
  
−
<p>Whilst we may now be back at school and so not working on our project full-time, we are still putting a large amount of time and effort into it. Wiki development continues both in its design and content, all of us continue to work on the presentation, other teams are still being collaborated with, people and organisations are still being contacted, videos are being planned and outreach to younger students is underway. Overall, things are still moving and the gears in our brains are still very much in motion towards our goal of having our project be the best that we can make it.
+
<p>
 
</p>
 
</p>
  

Latest revision as of 02:27, 20 October 2016

MENU ▤

Dundee Schools

Notebook

Wet Team

Week 1 - Familiarising ourselves with the labs

  • Transformation + Overnight of pSBIC3
  • Mini Prep of pSBIC3
  • Restriction Digest of pSB1C3
      • PCR’s:
    • Hfq E. coli- Unsuccessful
    • Hfq Serratia- Unsuccessful
    • OsmY- Unsuccessful
  • Mini Prep of pSBIC3
  • Restriction Digest of pSB1C3

Week 2 - Carrying on with cloning

      PCR’s:
    • Hfq E. coli- Unsuccessful
    • Hfq Serratia – Unsuccessful
    • osmY- Unsuccessful
      3rd PCR set up:
    • Hfq E. coli – Successful
    • Hfq Serratia – Unsuccessful
    • OsmY - Successful
      PCR’s:
    • Hfq Serratia 2 at 49°C - Successful
    • Hfq Serratia 1 at 65°C - Successful
  • Ligation into PSBIC3 and transformed
  • The 3 successful PCR’s were plated at concentrations of 2:1 and 3:1 with vector; no plates grew colonies

Week 3 - Made our first BioBrick

  • Redid all 3 PCR’S – Hfq E. coli and osmY both worked. Hfq Serratia did not.
  • Colony PCR of the successful PCR’s, overnight, mini prep, sent away for sequencing and then stocked.
    • First 2 BioBricks made: OsmY + Hfq E. coli
  • PCR of osmY-hfq E. coli fusion and PCR of osmY-hfq Serratia Fusion - successful
    • Digested and Ligated etc.… sequenced then stocked.
    2 BioBricks made: osmY Hfq E. coli Fusion + osmY Hfq Serratia Fusion

Week 4 - Started to make gene fragments

  • PCR of Hfq Serratia - successful
    • Sequenced and Stocked.
    1 Bio brick made: Hfq Serratia
  • Gene fragments – EC-SRNA and sma-SRNA digested and ligated into pSBIC3
  • Digestion of Rhamnose promoter plasmid

Week 5 – Started to add Ha tags

      Ligations:
    • rbs-osmY-Hfq-E. coli
    • rbs-osmY-Hfq-Serratia
    • rbs-osmY-Hfq-E. coli- Ha Tag
    • rbs-osmY-Hfq-Serratia- Ha Tag
      PCR’s:
    • rbs-osmY- Ha Tag - Successful
    • rbs-osmY-Hfq E. coli- Ha Tag- Successful
    • rbs-osmY-Hfq Serratia-Ha Tag – Successful
  • All PCR’s transformed and overnighted.

Week 6 - Phage outbreak

      Overnights of:
    • rbs-osmY-Hfq- Ha tag
    • rbs-osmY-Hfq E. coli- Ha tag
    • rbs-osmY-Hfq Serratia- Ha tag
  • Mini preps, sequencing and transformations of the above
  • Phage outbreak on Thursday; due to this all transformations were lost, but re-done the next day
  • All sent away for sequencing
  • Ec – SRNA and sma SRNA – both stocked.

Week 7 - Western blots

  • We did our first western blot test with no timed samples.
  • We also completed a timed western blot by adding different concentrations of Rhamnose and taking samples every hour
      • Primers:
    • fliC for Ec-sRNA
    • virF for Ec-sRNA

Week 8 - Final week

  • Performed another Western Blot to get a much cleaner image for the whole cell
  • Overnights with Ec-SRNA fliC in MG1655 and Ec-SRNA virF
  • Plates grew colonies – colony PCR with colonies.
  • Sent away for sequencing

Dry Team

Week 1 -

  • Started off discussing our topic of bacterial infections and brainstorming how we could target them; settled on RNA interference.
  • Split the team into 2 groups, wet team (Matthew, Bartosz, Albert) and dry team (Mia, Beth, Darryl).
  • Decided what each team had to do for that week
  • Started with general research on our chosen infections (Cholera and Shigellosis)
  • Darryl started and completed learning basic HTML and CSS via tutorials on the site Codecadamy, then began the initial stages of the wiki so as to get to grips with it.

Week 2 -

      Began to contact various people/organisations:

    • Colalife
    • Mercy Ships
    • Water Aid
    • Lifeline Express
  • Had our first meeting about maths modelling and discussed how we could incorporate it into our project.
  • Further developed wiki.

Week 3 -

  • Had a phone call with Brian Walshe of Mercy Ships
      • Started organisation for Northern meet up:

    • Began developing presentation content and layout
    • Work began on poster

Week 4 -

  • Spoke to Rob Porter (Prof. of clinical microbiology) via email.
  • Planned a skype call with Simon Berry of Colalife.
  • Contacted British Red Cross.

Week 5 -

  • Attended the Edinburgh Northern meet up & presented our project there, to which we were met with excellent feedback.
  • Carried on working in the lab and progressing with our presentation.
  • Further development of poster.

Week 6 -

  • Contacted British Pharmaceutical Society
  • Contacted Mark McCulloch (Army Doctor)
  • Carried on with making our poster for the UK meet up.

Week 7 -

  • Set up meeting with Mark
  • Finished poster
  • Carried on with our wiki content
  • Received our FBI sunglasses and pens for the Jamboree.

Week 8 -

  • Attended the UK meet up in London – presented our talk and our poster to multiple UK iGEM teams.
  • Got our hoodies and t-shirts for Boston.
  • Had our agent photoshoot.