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

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</style>
  
−
<head>
+
 
−
  <meta name="viewport" content="width=device-width, initial-scale=1">
+
 
−
  <title>Dundee Schools: Notebook</title>
+
 
 +
<!--- THIS IS WHERE THE HTML BEGINS --->
 +
 
 +
 
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<!-- This tells the browser that your page is responsive -->
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<div class="collapsable_menu_control"> MENU ▤ </div>
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+
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+
−
}
+
  
−
li .a:hover, .dropdown:hover .dropbtn {
+
<li class="menu_item"> <a href="https://2016.igem.org/Team:Dundee_Schools">HOME </a> </li>
−
    background-color:#a8bce1;
+
−
    color:black;
+
−
    list-style-type:none;
+
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+
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+
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+
  
−
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−
.dropdown-content .a {
+
<li class="menu_item"> <div class="icon plus"></div> TEAM
−
    color:white;
+
<ul class="submenu">
−
    margin:0px;
+
<li> <a href=" https://2016.igem.org/Team:Dundee_Schools/Team"> Meet the Agents  </a> </li>
−
    padding:1.5vh .25vw .5vh .25vw;
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Collaborations"> Collaborations </a> </li>
−
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+
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−
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−
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+
−
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+
−
}
+
  
−
.dropdown-content .a:hover {
+
<li class="menu_item"> <div class="icon plus"></div> PROJECT 
−
    background-color:#a8bce1;
+
<ul class="submenu">
−
    color:black;
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Description">  Description </a></li>
−
    list-style-type:none;
+
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−
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+
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−
}
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Proof"> Proof of Concept </a></li>
 +
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Results"> Results </a></li>
 +
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Notebook"> Notebook </a></li>
 +
                    </ul>
 +
                </li>
  
−
.dropdown:hover .dropdown-content {
+
<li class="menu_item"> <div class="icon plus"></div> PARTS 
−
    display:block;
+
<ul class="submenu">
−
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+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Parts">Parts </a></li>
−
    list-style-type:none;
+
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−
    opacity:1; filter:alpha(opacity=100);
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Composite_Part"> Composite Parts </a></li>
−
}
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Part_Collection"> Part Collection </a></li>
 +
                    </ul>
 +
                </li>
  
−
</style>
 
  
−
<!--HTML-->
+
<li class="menu_item"> <a href="https://2016.igem.org/Team:Dundee_Schools/Safety"> SAFETY </a> </li>
  
−
<!--navigation bar-->
 
−
<div id="nav_bar"></div>
 
−
  <p style="position:fixed;float:right;height:3vh;width:auto;color:white;margin:1.5vh 2vw 0vh 40vw;font-weight:bold;font-size:3vh;">DUNDEE SCHOOLS: FIGHTING BACTERIAL INFECTIONS</p>
 
−
<ul class="ul">
 
−
<img id="logos" src="https://static.igem.org/mediawiki/2016/2/20/T--Dundee_Schools--nav_logos.png"/>
 
−
  <li><a style="height:2.5vh;width:auto;float:right;margin:6vh 2vw 0vh 0vw;padding:1vh .5vw 1vh .5vw;font-size:2.5vh;display:inline;" class="a" class="active" href="https://2016.igem.org/Team:Dundee_Schools/Attributions">ATTRIBUTIONS</a></li>
 
−
  <li class="dropdown">
 
−
    <a class="a" href="#" class="dropbtn">PARTS</a>
 
−
    <div class="dropdown-content">
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Parts">Parts</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Basic">Basic</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Composite">Composite</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Part_collection">Collection</a>
 
−
    </div>
 
−
  </li>
 
−
  <li class="dropdown">
 
−
    <a class="a" href="#" class="dropbtn">LAB WORK</a>
 
−
    <div class="dropdown-content">
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Experiments">Experiments</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Results">Results</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Safety">Safety</a>
 
−
    </div>
 
−
  </li>
 
−
  <li class="dropdown">
 
−
    <a class="a" href="#" class="dropbtn">HUMAN PRACTICES</a>
 
−
    <div class="dropdown-content">
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Human_Practices">Human Practices</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/HP/Silver">Silver</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/HP/Gold">Gold</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Integrated_Practices">Integrated Practices</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Engagement">Engagement</a>
 
−
    </div>
 
−
  </li>
 
−
  <li class="dropdown">
 
−
    <a class="a" href="#" class="dropbtn">PROJECT</a>
 
−
    <div class="dropdown-content">
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Description">Description</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Design">Design</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Proof">Proof of concept</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Notebook">Notebook</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Medals">Medals</a>
 
−
    </div>
 
−
  </li>
 
−
  <li class="dropdown">
 
−
    <a class="a" href="#" class="dropbtn">TEAM</a>
 
−
    <div class="dropdown-content">
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Team">Meet the agents</a>
 
−
      <a class="a" href="https://2016.igem.org/Team:Dundee_Schools/Collaborations">Collaborations</a>
 
−
    </div>
 
−
  </li>
 
−
  <li><a style="height:2.5vh;width:auto;float:right;margin:6vh 0vw 0vh 0vw;padding:1.25vh .5vw 1.25vh .5vw;font-size:2.5vh;" class="a" class="active" href="https://2016.igem.org/Team:Dundee_Schools">HOME</a></li>
 
−
</ul>
 
  
 +
<li class="menu_item"> <a href="https://2016.igem.org/Team:Dundee_Schools/Attributions"> ATTRIBUTIONS </a></li>
  
−
<h2>Notebook</h2>
 
  
−
<h3>Wet Team</h3>
+
<li class="menu_item"> <div class="icon plus"></div> HUMAN PRACTICES
−
  <p><b>Week 1-</b>
+
<ul class="submenu">
−
Familiarising ourselves with the labs
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Human_Practices"> Human Practices </a></li>
−
• Transformation + Overnight of PSBIC3
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/HP/Silver"> Silver </a></li>
−
• Mini Prep of PSBIC3
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/HP/Gold">Gold </a></li>
−
• Restriction Digest of PSB1C3
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Integrated_Practices"> Integrated Practices </a></li>
−
• PCR’s:
+
<li> <a href="https://2016.igem.org/Team:Dundee_Schools/Engagement"> Engagement </a></li>
−
o Hfq E.coli- Unsuccessful
+
                    </ul>
−
o Hfq Serratia- Unsuccessful
+
                </li>
−
o osmY- Unsuccessul
+
−
• Mini Prep of PSBIC3
+
−
• Restriction Digest of PSB1C3
+
  
 +
 +
<li class="menu_item"> <div class="icon plus"></div> AWARDS
 +
<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/Measurement">Medals</a></li>
 +
                    </ul>
 +
                </li>
 +
</ul>
 +
 +
</div>
 +
 +
 +
 +
 +
 +
<div class="content_wrapper">
 +
 +
 +
 +
<h1 id="team_name"> Dundee Schools </h1>
 +
<h4 id="page_name"> Notebook </h4>
 +
 +
<h3>Wet Team</h3>
 +
  <ul><h4>Week 1- Familiarising ourselves with the labs</h4>
 +
  <li>Transformation + Overnight of PSBIC3
 +
  <li>Mini Prep of PSBIC3</li>
 +
  <li>Restriction Digest of PSB1C3</li>
 +
    <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>
 +
  <li>Mini Prep of PSBIC3</li>
 +
  <li>Restriction Digest of PSB1C3</li>
  
 
Week 2-
 
Week 2-
 +
 
Carried on with cloning
 
Carried on with cloning
−
• PCR’s:  
+
 
−
o Hfq E.coli- Unsuccessful
+
* PCR’s:
−
o Hfq Serratia – Unsuccessful
+
 
−
o osmY- Unsuccessful  
+
o Hfq E.coli- Unsuccessful
−
• 3rd PCR set up:
+
 
−
o Hfq E.coli – Successful
+
o Hfq Serratia – Unsuccessful
−
o Hfq Serratia – Unsuccessful
+
 
−
o osmY - Successful
+
o osmY- Unsuccessful
−
• PCR’s:
+
 
−
o Hfq Serratia x 2 at 49 degrees - Successful
+
* 3rd PCR set up:
−
o Hfq Serratia x 1 at 65 degrees - Successful
+
 
−
• Ligation into PSBIC3 and transformed
+
o Hfq E.coli – Successful
−
• The 3 successful PCR’s were plated at concentrations of 2.1 and 3.1 with vector; no plates grew colonies  
+
 
 +
o Hfq Serratia – Unsuccessful
 +
 
 +
o osmY - Successful
 +
 
 +
* PCR’s:
 +
 
 +
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-
 
Week 3-
 +
 
Made our first BioBrick
 
Made our first BioBrick
−
• Redid all 3 PCRS’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.
+
* 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
 
First 2 BioBricks made: OsmY + Hfq E.coli
  
−
• PCR of osmY Hfq E.coli fusion and PCR of osmY Hfq Serratia Fusion - successful
+
* PCR of osmY Hfq E.coli fusion and PCR of osmY Hfq Serratia Fusion - successful
 +
 
 
Digested and Ligated etc.… sequenced then stocked.
 
Digested and Ligated etc.… sequenced then stocked.
  
 
2 BioBricks made: osmY Hfq E.coli Fusion + osmY Hfq Serratia Fusion
 
2 BioBricks made: osmY Hfq E.coli Fusion + osmY Hfq Serratia Fusion
  
−
Week 4-  
+
Week 4-
−
Started to make gene fragments
+
−
• PCR of Serratia - successful
+
−
• Sequenced and Stocked.
+
  
−
1 Bio brick made: Hfq Serratia  
+
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 –
  
−
• Gene fragments –  EC-SRNA and sma-SRNA digested and ligated into PSBIC3
 
−
• Digestion of Rhamnose promoter
 
−
Week 5 –
 
 
Started to add Ha tags
 
Started to add Ha tags
−
• Ligations:
+
 
−
o rbs-osmY-Hfq-E.coli
+
* Ligations:
−
o rbs-osmY-Hfq-Serratia
+
 
−
o rbs-osmY-Hfq-E.coli- Ha Tag
+
o rbs-osmY-Hfq-E.coli
−
o rbs-osmY-Hfq-Serratia- Ha Tag
+
 
−
• PCR’s:  
+
o rbs-osmY-Hfq-Serratia
−
o rbs-osmY- Ha Tag - Successful  
+
 
−
o rbs-osmY-Hfq E.coli- Ha Tag- Successful
+
o rbs-osmY-Hfq-E.coli- Ha Tag
−
o rbs-osmY-Hfq Serratia-Ha Tag – Successful
+
 
 +
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.
 
All PCR’s transformed and overnighted.
 +
 
Week 6-
 
Week 6-
 +
 
Phage outbreak
 
Phage outbreak
−
• Overnights of:  
+
 
−
o rbs-osmY-Hfq- Ha tag
+
* Overnights of:
−
o rbs-osmY-Hfq E.coli- Ha tag
+
 
−
o rbs-osmY-Hfq Serratia- Ha tag  
+
o rbs-osmY-Hfq- 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
+
o rbs-osmY-Hfq E.coli- Ha tag
−
• All sent away for sequencing
+
 
−
• Ec – SRNA and sma SRNA – both stocked.
+
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-
 
Week 7-
 +
 
Western blot
 
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
+
* We did our first western blot test with no timed samples.
−
• Primers:
+
 
−
o Fli C for Ec- sRNA  
+
* We also completed a timed western blot by adding different concentrations of Rhamanose and taking samples every hour
−
o Vir F for Ec-sRNA
+
 
 +
* Primers:
 +
 
 +
o Fli C for Ec- sRNA
 +
 
 +
o Vir F for Ec-sRNA
  
 
Week 8-
 
Week 8-
 +
 
Final week
 
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
+
* Performed another Western Blot to get a much cleaner image for the whole cell
−
• Plates grew colonies – colony PCR with colonies.
+
 
−
• Sent away for sequencing  
+
* Overnights with Ec-SRNA Fli C in MG1655 and Ec-SRNA Vir F
−
</p>
+
 
 +
* Plates grew colonies – colony PCR with colonies.
 +
 
 +
* Sent away for sequencing
  
  
 
<br></br>
 
<br></br>
 +
 +
 +
 
  <h3>Dry Team</h3>
 
  <h3>Dry Team</h3>
−
  <p>
 
 
   <ul><b>Week 1-</b>
 
   <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>
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<br></br>
 
<br></br>
  
−
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>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.
 
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Revision as of 04:30, 19 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- Carried on with cloning * PCR’s: o Hfq E.coli- Unsuccessful o Hfq Serratia – Unsuccessful o osmY- Unsuccessful * 3rd PCR set up: o Hfq E.coli – Successful o Hfq Serratia – Unsuccessful o osmY - Successful * PCR’s: 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

    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-
    • The dry team 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.


    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.