Team:Southampton/Notebook

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<title>University of Southampton
<title>University of Southampton
Wiki</title>
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  link="#000099" alink="#000099" vlink="#990099"><div id="footerpush"></div>
  link="#000099" alink="#000099" vlink="#990099"><div id="footerpush"></div>
<div id="banner"><img style="width: 975px; height: 276px;" id="banner"
<div id="banner"><img style="width: 975px; height: 276px;" id="banner"
-
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<div id="toolbar">
<div id="toolbar">
<ul class="cssMenu cssMenum">
<ul class="cssMenu cssMenum">
-
  <li class="cssMenui"><a class="cssMenui"
+
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton">Home</a></li>
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  href="https://2009.igem.org/Team:Southampton">Home</a></li>
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project"><span>Project</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]-->
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  <li class="cssMenui"><a class="cssMenui"
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-
  href="https://2009.igem.org/Team:Southampton/Project">Project</a></li>
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Aims">Project Aims</a></li>
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  <li class="cssMenui"><a class="cssMenui"
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Intro">Project Introduction</a></li>
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  href="https://2009.igem.org/Team:Southampton/Parts">Biobrick
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project">Project Description</a></li>
-
Parts</a></li>
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Achievements">Project Achievements</a></li>
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  <li class="cssMenui"><a class="cssMenui"
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Projection">Project Projection</a></li>
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  href="https://2009.igem.org/Team:Southampton/Team"><span>Team</span><!--[if gt IE 6]--></a><!--[endif]--><!--[if lte IE 6]><table><tr><td><![endif]-->
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Safety">Project Safety</a></li>
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    <ul class="cssMenum">
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Refer">References and Links</a></li>
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      <li class="cssMenui"><a class="cssMenui"
+
        <li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols"><span>Protocols</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]-->
-
  href="https://2009.igem.org/Team:Southampton/Team/Gallery">Gallery</a></li>
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<ul class=" cssMenum">
-
    </ul>
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols">Protocol Overview</a></li>
-
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Theory1">Protocol Theory</a></li>
-
  <li class="cssMenui"><a class="cssMenui"
+
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Transformation">Biobrick Transformation</a></li>
-
  href="https://2009.igem.org/Team:Southampton/Modeling">Modelling</a></li>
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/ColonyPCR">Colony PCR</a></li>
-
  <li class="cssMenui"><a class="cssMenui"
+
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/DoubleDigestion">DNA Double Digestion</a></li>
-
  href="https://2009.igem.org/Team:Southampton/Notebook">Notebook</a></li>
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Gel">Gel Electrophoresis</a></li>
-
  <li class="cssMenui"><a class="cssMenui"
+
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Hfpcr">High Fidelity PCR</a></li>
-
  href="https://2009.igem.org/Team:Southampton/Sponsors">Sponsors</a></li>
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/LBplates">LB Plates</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Ligation">Ligation</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Ligationtransformation">Ligation Transformation</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/PlasmidPrep">Plasmid Preparation</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/TA">TA Cloning</a></li>
 +
</ul>
 +
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
 +
</ul>
 +
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="#">Biobrick Parts<![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]-->
 +
<ul class=" cssMenum">
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Parts/GoL">Game of Life</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Parts/RPS">Rock Paper Scissors</a></li>
 +
</ul></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Team"><span>Team</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]-->
 +
<ul class=" cssMenum">
 +
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team">Team Profiles</a></li>
 +
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team/Advisors">Advisor Profiles</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Team/Southampton">Southampton Profile</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Team/University">University Profile</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Team/Gallery">Gallery</a></li>
 +
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 +
<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
 +
 +
            <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Modeling"><span>Modelling</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]-->
 +
<ul class=" cssMenum">
 +
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Modeling">Modelling Overview</a></li>
 +
        <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Modeling/GoL">Game Of Life</a></li>
 +
        <li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Modeling/RPS">Rock Paper Scissors</a></li>
 +
        <li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Modeling/Open">Open Access</a></li>
 +
</ul>
 +
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 +
             
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        <li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/HP"><span>Human Practices</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]-->
 +
<ul class=" cssMenum">
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/HP">Overview</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/HP/Outreach">Outreach</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/HP/igemexper">iGEM Experience</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/HP/Political">Political Awareness</a></li>
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/HP/Legacy">Our Legacy</a></li>
 +
</ul>
 +
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 +
   
 +
     
 +
        <li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Notebook">Notebook</a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]-->
 +
<ul class=" cssMenum">
 +
 
 +
<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Notebook">Notebook</a></li>
 +
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Notebook/Labbook">Lab Book</a></li>
 +
<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Notebook/Advisorblog">Advisor Blog</a></li>
 +
</ul>
 +
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 +
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    <li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Sponsors"><span>Acknowledgments</span><![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]-->
 +
<ul class=" cssMenum">
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Sponsors">Sponsors</a></li>
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Southampton">Team Southampton</a></li>
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       <td width="25%"><h4>Week
+
       <td width="30%"><h4>Week
         Commencing</h4></td>
         Commencing</h4></td>
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       <td width="75%"><h4>Summary Of The Week</h4></td>
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       <td width="70%"><h4>Summary Of The Week</h4></td>
     </tr>
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     <tr>
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         Digest&hellip;ligate&hellip;transform<br />
         Digest&hellip;ligate&hellip;transform<br />
         Digest&hellip;ligate&hellip;transform<br />
         Digest&hellip;ligate&hellip;transform<br />
-
         Shame none of them worked&hellip;<br />
+
         Shame none of them worked&hellip;
-
         On the plus side, our simulations are<br />
+
         On the plus side, our simulations are
         looking good!</h3></td>
         looking good!</h3></td>
     </tr>
     </tr>
     <tr>
     <tr>
       <td><h3>31st August 2009</h3></td>
       <td><h3>31st August 2009</h3></td>
-
       <td><h3>The team begins to feel pretty<br />
+
       <td><h3>The team begins to feel pretty
-
         demoralised as the second week of<br />
+
         demoralised as the second week of
-
         &lsquo;digest&hellip;ligate&hellip;transform&hellip;FAIL&rsquo;<br />
+
         &lsquo;digest&hellip;ligate&hellip;transform&hellip;FAIL&rsquo;
-
         commences.<br />
+
         commences.
-
         We decide to momentarily focus on building our &lsquo;novel&rsquo; biobrick.<br />
+
         We decide to momentarily focus on building our &lsquo;novel&rsquo; biobrick.
-
         Good news though, our simulations<br />
+
         Good news though, our simulations
-
         specific to RPS/GoL are complete. Now<br />
+
         specific to RPS/GoL are complete. Now
-
         to make them applicable to<br />
+
         to make them applicable to
-
         anything/everything else!<br />
+
         anything/everything else!
-
         Work starts on our synthetic biology<br />
+
         Work starts on our synthetic biology
-
         video&hellip;soon to be the most demanded<br />
+
         video&hellip;soon to be the most demanded
-
         on YouTube.<br />
+
         on YouTube.
-
         Our wiki page has been transformed.<br />
+
         Our wiki page has been transformed.
-
         Just you wait for the launch next week.<br />
+
         Just you wait for the launch next week.
-
         Mesmerising.<br />
+
         Mesmerising.
-
         We are warned about round two of<br />
+
         We are warned about round two of
-
         abandonment by team supervisor.<br />
+
         abandonment by team supervisor.
-
         &lsquo;Climbing&rsquo; is the new excuse. Not even<br />
+
         &lsquo;Climbing&rsquo; is the new excuse. Not even
         blaming the family this time!</h3></td>
         blaming the family this time!</h3></td>
     </tr>
     </tr>
     <tr>
     <tr>
       <td><h3>7th September 2009</h3></td>
       <td><h3>7th September 2009</h3></td>
-
       <td><h3>We think we have finally optimised our<br />
+
       <td><h3>We think we have finally optimised our
-
         digest&hellip;ligate technique. However,<br />
+
         digest&hellip;ligate technique. However,
-
         when we come to transform, we have a<br />
+
         when we come to transform, we have a
-
         distinct lack of competent cells. Whose<br />
+
         distinct lack of competent cells. Whose
-
         authorisation do we need? The project<br />
+
         authorisation do we need? The project
-
         supervisor. And where is he? Turkey.<br />
+
         supervisor. And where is he? Turkey.
-
         Splendid.<br />
+
         Splendid.
-
         Instead, we concentrate on more<br />
+
         Instead, we concentrate on more
-
         &lsquo;behind the scenes&rsquo; such as content for<br />
+
         &lsquo;behind the scenes&rsquo; such as content for
-
         our wiki. It&rsquo;s going well, and we are<br />
+
         our wiki. It&rsquo;s going well, and we are
-
         collecting information fast.<br />
+
         collecting information fast.
-
         Progress is also being made with<br />
+
         Progress is also being made with
-
         regard to the video, the script is almost<br />
+
         regard to the video, the script is almost
-
         complete, and filming is due to start<br />
+
         complete, and filming is due to start
-
         early next week. Now, who wants to be<br />
+
         early next week. Now, who wants to be
-
         in it?<br />
+
         in it?
-
         To fill the lack of time spent in the labs,<br />
+
         To fill the lack of time spent in the labs,
-
         we decided to do a &lsquo;fun&rsquo; side project, to<br />
+
         we decided to do a &lsquo;fun&rsquo; side project, to
-
         optimize SYBR gold gels. It failed. Yes,<br />
+
         optimize SYBR gold gels. It failed. Yes,
-
         an experiment with no use other than<br />
+
         an experiment with no use other than
         to fill time, failed. Time to go home&hellip;</h3></td>
         to fill time, failed. Time to go home&hellip;</h3></td>
 +
    </tr>
 +
    <tr>
 +
      <td><h3>14th September 2009</h3></td>
 +
      <td><h3>The competent cells finally arrive and we are all frantically busy in labs again. Has anything been successful yet? No.
 +
One of our post grad supervisors makes some dodgy minimal media. As in, it was cloudy and brown. ‘It’s okay he said, they will set clear…’
 +
Meanwhile, our other supervisor threw our ligation products out, only to root around the bin and find that they had kept the right ones in the first place… we look up to our supervisors, we really do. Our first iGEM romance becomes apparent. We’re just surprised it’s taken this long to occur!
 +
Our project supervisor returns sporting the most fantastic suit. Just imagine, beige chinos, brown shoes, white shirt, gold tie and black, velvet jacket. Stunning.
 +
 +
</h3></td>
 +
    </tr>
 +
<tr>
 +
      <td><h3>21st September 2009</h3></td>
 +
      <td><h3>So, onto the final week, and what do we have to show for our iGEM experience?
 +
We performed TA cloning on our novel biobricks; pTac and GFP. This is good news, as it is the first (and only) successful ligation so far…
 +
We have a final meeting and farewell with a few refreshments…it starts off well as one of our supervisors walks in and immediately says ‘so, we’re celebrating failure now are we?!’ That didn’t hurt at all. Much.
 +
The wiki is nearly completed, the outreach projects have been successful, and the simulations are ready to be uploaded for the world to see. It’s a shame about the lab work, it really is.
 +
Last ever cluster map update: 26 different countries totalling nearly 400 visits…we just won’t mention how many of those were from the UK (ahem….Southampton).
 +
Finally, our project supervisor drops one last bombshell…he’s not joining us in America.
 +
Guess the excuse this time…
 +
</h3></td>
     </tr>
     </tr>
   </tbody>
   </tbody>
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<h5>| <a href="#">Top</a> |&nbsp; &nbsp;&nbsp;&nbsp;
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Parts | Team | Modelling | Notebook | Sponsors
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&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;
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&nbsp;&nbsp;&nbsp;
&nbsp;&nbsp;&nbsp;
University of
University of
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Southampton iGEM 2009
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Southampton iGEM 2009</h5>
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Latest revision as of 19:58, 21 October 2009

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> University of Southampton Wiki

Notebook




Week Commencing

Summary Of The Week

20th July 2009

‘Brainstorming’ becomes our key word.
We scrutinise various ideas before deciding on ‘Game of Life’ and ‘Rock Paper Scissors’.
Numerous hours were spent on the registry of parts finding approved Biobrick parts.
We become absolute pros at filling out COSHH forms. You just have to work through the cramp.

27th July 2009

Work begins on our wiki page and logo design.
We create a very exciting ‘cluster map’ on our wiki. One cluster so far: Southampton.
We finalise our plasmid diagrams and Biobrick parts.
The team mugshot was taken.
We went from lab protocol amateurs to experts within the week.
The team supervisor abandoned us for 7 days. ‘Family holiday’ was the excuse. We soldiered on.

3rd August 2009

The hard works begins…
DNA Biobricks were transformed, starter cultures made and plasmid maxiprep performed.
Our Southampton iGEM logo is nearly finalised. 
Cluster map update: 9 different hits including Canada, Turkey, Poland, Japan and Netherlands.
Work commences on the simulations.
One man down :( . Apparently going to hospital is the new excuse for getting out of labs.

10th August 2009

Man back :) , he just could not stay away.
Note to self:
1) In the plasmid maxiprep: Turns out it does make a difference if you accidently put the white column on top of the blue, instead of the other way round…
2) Adding B0034 to B0015 and centrifuging them together does not, in fact, bode well.
3) The nanodrop only works when the switch is turned to ‘on’.
Exciting times, having been all maxiprepped out, we started a new protocol: Digestion.
After much deliberation and input from the entire team, our logo is finally finished. It was worth the wait. I mean look at it. Genius.
Cluster map update:
UK (i.e. Southampton) – 57
Rest of world – 30
Still a bit of room for improvement…

17th August 2009

We are granted permission to start an outreach project …hold tight folks, more details coming soon.
Our team diminishes further - apparently ‘working at home’ is the new ‘working…at work’.
Our PCRs FINALLY work. Maybe practise really does make perfect.
We perform our last ever Maxiprep…sob.
Don’t panic though, we are moving onto bigger and better protocols; Ligation.
It’s nearly week six, and we have finally mastered the art of making and loading a gel. It’s ‘simple’ they say. Obviously not.
An exciting wall chart appears in our office.
Cluster map update: UK – 92. Really must stop checking the cluster map so often…

25th August 2009

We perfect a pattern:
Digest…ligate…transform
Digest…ligate…transform
Digest…ligate…transform
Shame none of them worked… On the plus side, our simulations are looking good!

31st August 2009

The team begins to feel pretty demoralised as the second week of ‘digest…ligate…transform…FAIL’ commences. We decide to momentarily focus on building our ‘novel’ biobrick. Good news though, our simulations specific to RPS/GoL are complete. Now to make them applicable to anything/everything else! Work starts on our synthetic biology video…soon to be the most demanded on YouTube. Our wiki page has been transformed. Just you wait for the launch next week. Mesmerising. We are warned about round two of abandonment by team supervisor. ‘Climbing’ is the new excuse. Not even blaming the family this time!

7th September 2009

We think we have finally optimised our digest…ligate technique. However, when we come to transform, we have a distinct lack of competent cells. Whose authorisation do we need? The project supervisor. And where is he? Turkey. Splendid. Instead, we concentrate on more ‘behind the scenes’ such as content for our wiki. It’s going well, and we are collecting information fast. Progress is also being made with regard to the video, the script is almost complete, and filming is due to start early next week. Now, who wants to be in it? To fill the lack of time spent in the labs, we decided to do a ‘fun’ side project, to optimize SYBR gold gels. It failed. Yes, an experiment with no use other than to fill time, failed. Time to go home…

14th September 2009

The competent cells finally arrive and we are all frantically busy in labs again. Has anything been successful yet? No. One of our post grad supervisors makes some dodgy minimal media. As in, it was cloudy and brown. ‘It’s okay he said, they will set clear…’ Meanwhile, our other supervisor threw our ligation products out, only to root around the bin and find that they had kept the right ones in the first place… we look up to our supervisors, we really do. Our first iGEM romance becomes apparent. We’re just surprised it’s taken this long to occur! Our project supervisor returns sporting the most fantastic suit. Just imagine, beige chinos, brown shoes, white shirt, gold tie and black, velvet jacket. Stunning.

21st September 2009

So, onto the final week, and what do we have to show for our iGEM experience? We performed TA cloning on our novel biobricks; pTac and GFP. This is good news, as it is the first (and only) successful ligation so far… We have a final meeting and farewell with a few refreshments…it starts off well as one of our supervisors walks in and immediately says ‘so, we’re celebrating failure now are we?!’ That didn’t hurt at all. Much. The wiki is nearly completed, the outreach projects have been successful, and the simulations are ready to be uploaded for the world to see. It’s a shame about the lab work, it really is. Last ever cluster map update: 26 different countries totalling nearly 400 visits…we just won’t mention how many of those were from the UK (ahem….Southampton). Finally, our project supervisor drops one last bombshell…he’s not joining us in America. Guess the excuse this time…

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