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

Line 437: Line 437:
 
  <h3>Wet Team</h3>
 
  <h3>Wet Team</h3>
  
−
<h4>Week 1 - Familiarising ourselves with the labs</h4>
+
<h4>Week 1 - Familiarising ourselves with the labs</h4>
 
   <p><ul>
 
   <p><ul>
 
   <p><li>Transformation + Overnight of PSBIC3</li>
 
   <p><li>Transformation + Overnight of PSBIC3</li>
Line 451: Line 451:
 
   </ul></p>
 
   </ul></p>
  
−
  <ul><h4>Week 2 - Carrying on with cloning</h4>
+
<h4>Week 2 - Carrying on with cloning</h4>
−
    <p><ul><h5>PCR’s:</h5>
+
  <p><ul>
 +
    <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>
Line 470: Line 471:
 
   </ul></p>
 
   </ul></p>
  
−
<br></br>
+
<h4>Week 3 - Made our first BioBrick</h4>
−
 
+
  <p><ul>
−
  <ul><h4>Week 3 - Made our first BioBrick</h4>
+
 
   <li>Redid all 3 PCR’S – Hfq <i>E. coli</i> and osmY both worked. Hfq <i>Serratia</i> did not.</li>
 
   <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>
 
   <li>Colony PCR of the successful PCR’s, overnight, mini prep, sent away for sequencing and then stocked.</li>
Line 479: Line 479:
 
     <ul><li>Digested and Ligated etc.… sequenced then stocked.</li></ul>
 
     <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>
 
     <b>2 BioBricks made: osmY Hfq <i>E. coli</i> Fusion + osmY Hfq <i>Serratia</i> Fusion</b>
−
   </ul>
+
   </ul></p>
  
−
<br></br>
+
<h4>Week 4 - Started to make gene fragments</h4>
−
 
+
  <p><ul>
−
  <ul><h4>Week 4 - Started to make gene fragments</h4>
+
 
   <li>PCR of Hfq <i>Serratia</i> - successful</li>
 
   <li>PCR of Hfq <i>Serratia</i> - successful</li>
 
     <ul><li>Sequenced and Stocked.</li></ul>
 
     <ul><li>Sequenced and Stocked.</li></ul>
Line 489: Line 488:
 
   <li>Gene fragments – EC-SRNA and sma-SRNA digested and ligated into PSBIC3</li>
 
   <li>Gene fragments – EC-SRNA and sma-SRNA digested and ligated into PSBIC3</li>
 
   <li>Digestion of Rhamnose promoter</li>
 
   <li>Digestion of Rhamnose promoter</li>
−
   </ul>
+
   </ul></p>
  
−
<br></br>
+
<h4>Week 5 – Started to add Ha tags</h4>
−
 
+
  <p><ul>
−
  <ul><h4>Week 5 – Started to add Ha tags</h4>
+
 
     <ul><h5>Ligations:</h5>
 
     <ul><h5>Ligations:</h5>
 
     <li>rbs-osmY-Hfq-<i>E. coli</i></li>
 
     <li>rbs-osmY-Hfq-<i>E. coli</i></li>
Line 506: Line 504:
 
     </ul>
 
     </ul>
 
   <li>All PCR’s transformed and overnighted.</li>
 
   <li>All PCR’s transformed and overnighted.</li>
−
   </ul>
+
   </ul></p>
  
−
<br></br>
+
<h4>Week 6 - Phage outbreak</h4>
−
 
+
  <p><ul>
−
  <ul><h4>Week 6 - Phage outbreak</h4>
+
 
     <ul><h5>Overnights of:</h5>
 
     <ul><h5>Overnights of:</h5>
 
     <li>rbs-osmY-Hfq- Ha tag</li>
 
     <li>rbs-osmY-Hfq- Ha tag</li>
Line 520: Line 517:
 
   <li>All sent away for sequencing</li>
 
   <li>All sent away for sequencing</li>
 
   <li>Ec – SRNA and sma SRNA – both stocked.</li>
 
   <li>Ec – SRNA and sma SRNA – both stocked.</li>
−
   </ul>
+
   </ul></p>
  
−
<br></br>
+
<h4>Week 7 - Western blots</h4>
−
 
+
  <p><ul>
−
  <ul><h4>Week 7 - Western blots</h4>
+
 
   <li>We did our first western blot test with no timed samples.</li>
 
   <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>
 
   <li>We also completed a timed western blot by adding different concentrations of Rhamnose and taking samples every hour</li>
Line 531: Line 527:
 
     <li>Vir F for Ec-sRNA</li>
 
     <li>Vir F for Ec-sRNA</li>
 
     </ul>
 
     </ul>
−
   </ul>
+
   </ul></p>
  
−
<br></br>
+
<h4>Week 8 - Final week</h4>
−
 
+
  <p><ul>
−
  <ul><h4>Week 8 - Final week</h4>
+
 
   <li>Performed another Western Blot to get a much cleaner image for the whole cell</li>
 
   <li>Performed another Western Blot to get a much cleaner image for the whole cell</li>
 
   <li>Overnights with Ec-SRNA Fli C in MG1655 and Ec-SRNA Vir F</li>
 
   <li>Overnights with Ec-SRNA Fli C in MG1655 and Ec-SRNA Vir F</li>
 
   <li>Plates grew colonies – colony PCR with colonies.</li>
 
   <li>Plates grew colonies – colony PCR with colonies.</li>
 
   <li>Sent away for sequencing</li>
 
   <li>Sent away for sequencing</li>
−
   </ul>
+
   </ul></p>
  
  
−
<br></br>
 
 
<br></br>
 
<br></br>
−
 
  
 
  <h3>Dry Team</h3>
 
  <h3>Dry Team</h3>
  
−
  <ul><h4>Week 1 -</h4>
+
<h4>Week 1 -</h4>
 +
  <p><ul>
 
   <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 555: Line 549:
 
   <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>
+
<h4>Week 2 -</h4>
−
 
+
   <p><ul>
−
   <ul><h4>Week 2 -</h4>
+
     <ul><p>Began to contact various people/organisations:</p>
−
     <ul><p>The dry team began to contact various people/organisations:</p>
+
 
     <li>Colalife</li>
 
     <li>Colalife</li>
 
     <li>Mercy Ships</li>
 
     <li>Mercy Ships</li>
Line 568: Line 561:
 
   <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>
+
<h4>Week 3 -</h4>
−
 
+
   <p><ul>
−
   <ul><h4>Week 3 -</h4>
+
 
   <li>Had a phone call with Brian Walshe of Mercy Ships</li>  
 
   <li>Had a phone call with Brian Walshe of Mercy Ships</li>  
 
     <ul><p>Started organisation for Northern meet up:</p>
 
     <ul><p>Started organisation for Northern meet up:</p>
Line 578: Line 570:
 
     <li>Work began on poster</li>
 
     <li>Work began on poster</li>
 
     </ul>
 
     </ul>
−
   </ul>
+
   </ul></p>
  
−
<br></br>
+
<h4>Week 4 -</h4>
−
 
+
   <p><ul>
−
   <ul><h4>Week 4 -</h4>
+
 
   <li>Spoke to Rob Porter (prof. of Microbiology) via email.</li>
 
   <li>Spoke to Rob Porter (prof. of 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>
+
<h4>Week 5 -</h4>
−
 
+
   <p><ul>
−
   <ul><h4>Week 5 -</h4>
+
 
   <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>
+
<h4>Week 6 -</h4>
−
 
+
   <p><ul>
−
   <ul><h4>Week 6 -</h4>
+
 
   <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>
+
<h4>Week 7 -</h4>
−
 
+
   <p><ul>
−
   <ul><h4>Week 7 -</h4>
+
 
   <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>
+
<h4>Week 8 -</h4>
−
 
+
   <p><ul>
−
   <ul><h4>Week 8 -</h4>
+
 
   <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>
  
 
<p>
 
<p>

Revision as of 09:15, 19 October 2016

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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 Serratiax 2 at 49°C - Successful
    • Hfq Serratiax 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

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:
    • Fli C for Ec- sRNA
    • 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



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 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.