Team:Southampton/Notebook

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link="#000099" alink="#000099" vlink="#990099"><div id="footerpush"></div>
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<ul class="cssMenu cssMenum">
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton">Home</a></li>
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<br>
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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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<br>
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<br>
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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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<br>
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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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<br>
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project">Project Description</a></li>
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<br>
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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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<div id="B02_"><a
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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"
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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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  onmouseover="image1.src=loadImage1.src;"
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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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  onmouseout="image1.src=staticImage1.src;"><img
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        <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]-->
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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/Protocols">Protocol Overview</a></li>
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<div id="C03_"><a
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Theory1">Protocol Theory</a></li>
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  href="https://2009.igem.org/Team:Southampton/Project"
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Transformation">Biobrick Transformation</a></li>
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  onmouseover="image2.src=loadImage2.src;"
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/ColonyPCR">Colony PCR</a></li>
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  onmouseout="image2.src=staticImage2.src;"><img
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/DoubleDigestion">DNA Double Digestion</a></li>
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  style="border: 0px solid ; width: 112px; height: 45px;" alt=""
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Gel">Gel Electrophoresis</a></li>
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  name="image2"
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Hfpcr">High Fidelity PCR</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>
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</div>
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<li class=" cssMenui"><a class="  cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/Ligation">Ligation</a></li>
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<div id="D04_"><a
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  href="https://2009.igem.org/Team:Southampton/Parts"
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/PlasmidPrep">Plasmid Preparation</a></li>
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  onmouseover="image3.src=loadImage3.src;"
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Project/Protocols/TA">TA Cloning</a></li>
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<!--[if lte IE 6]></td></tr></table></a><![endif]--></li>
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<div id="E05_"><a
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<li class=" cssMenui"><a class=" cssMenui" href="#">Biobrick Parts<![if gt IE 6]></a><![endif]><!--[if lte IE 6]><table><tr><td><![endif]-->
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  href="https://2009.igem.org/Team:Southampton/Team"
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<ul class=" cssMenum">
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  onmouseout="image4.src=staticImage4.src;"><img
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Parts/RPS">Rock Paper Scissors</a></li>
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</ul></li>
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<ul class=" cssMenum">
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<div id="F06_"> <a
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  href="https://2009.igem.org/Team:Southampton/Modeling"
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team/Advisors">Advisor Profiles</a></li>
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  onmouseover="image5.src=loadImage5.src;"
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team/Southampton">Southampton Profile</a></li>
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  onmouseout="image5.src=staticImage5.src;"><img
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<li class=" cssMenui"><a class=" cssMenui" href="https://2009.igem.org/Team:Southampton/Team/University">University Profile</a></li>
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<div id="G07_"><a
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<div id="J10_"> <img
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<div id="maintop"><img style="width: 975px; height: 24px;" id="bg"
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id="J10" src="http://img22.imageshack.us/img22/5245/j10osz.jpg"
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src="http://www.personal.soton.ac.uk/jeh2v07/images/maintop.gif" alt="" /></div>
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<div id="logobox">
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<img style="width: 63px; height: 63px;" alt="" src="http://www.personal.soton.ac.uk/jeh2v07/images/logobox.jpg" /></div>
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<div id="projectheading">
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<h1>Notebook</h1>
</div>
</div>
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<div id="wrap">
+
<div id="maincont">
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<div class="pagewrapper">
+
<div align="center">
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  <p>
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<div class="page">
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  <p>
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<div class="content"><!-- CONTENT -->
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  <br>
-
<h3> </h3><table style="text-align: left; width: 100%;"
+
  <br>
 +
  <br><div id="notebooktable">
 +
  <table style="text-align: left; width: 100%; background-color:#5d5d5d;"
  border="0" cellpadding="2" cellspacing="2">
  border="0" cellpadding="2" cellspacing="2">
   <tbody>
   <tbody>
     <tr>
     <tr>
-
       <td>
+
       <td width="30%"><h4>Week
-
      <h3><img
+
        Commencing</h4></td>
-
style="width: 100px; height: 100px;" alt="iGEM"
+
       <td width="70%"><h4>Summary Of The Week</h4></td>
-
src="http://img34.imageshack.us/img34/4945/igembox1.jpg"></h3>
+
-
      </td>
+
-
      <td>
+
-
       <h3>&gt;&gt; Welcome</h3>
+
-
      <p>Southampton University - Notebook</p>
+
-
      </td>
+
     </tr>
     </tr>
-
  </tbody>
 
-
</table>
 
-
<br><table style="text-align: left; width: 100%;"
 
-
border="0" cellpadding="2" cellspacing="2">
 
-
  <tbody>
 
     <tr>
     <tr>
-
       <td><h4>Week
+
       <td><h3>20th July 2009</h3></td>
-
Commencing</h4></td>
+
       <td><h3>&lsquo;Brainstorming&rsquo;
-
       <td><h4>Summary Of The Week</h4></td>
+
        becomes our key word.<br>
 +
        We scrutinise various ideas before deciding on &lsquo;Game of
 +
        Life&rsquo; and &lsquo;Rock Paper Scissors&rsquo;.<br>
 +
        Numerous hours were spent on the registry of parts finding approved
 +
        Biobrick parts.<br>
 +
        We become absolute pros at filling out COSHH forms. You just have to
 +
        work through the cramp.</h3></td>
     </tr>
     </tr>
     <tr>
     <tr>
-
       <td>20th July 2009</td>
+
       <td><h3>27th July 2009</h3></td>
-
       <td>&lsquo;Brainstorming&rsquo;
+
       <td><h3>Work begins on our wiki
-
becomes our key word.<br>
+
        page and logo design.<br>
-
We scrutinise various ideas before deciding on &lsquo;Game of
+
        We create a very exciting &lsquo;cluster map&rsquo; on our
-
Life&rsquo; and &lsquo;Rock Paper Scissors&rsquo;.<br>
+
        wiki. One cluster so far: Southampton.<br>
-
Numerous hours were spent on the registry of parts finding approved
+
        We finalise our plasmid diagrams and Biobrick parts. <br>
-
Biobrick parts.<br>
+
        The team mugshot was taken.<br>
-
We become absolute pros at filling out COSHH forms. You just have to
+
        We went from lab protocol amateurs to experts within the week.<br>
-
work through the cramp.</td>
+
        The team supervisor abandoned us for 7 days. &lsquo;Family
 +
        holiday&rsquo; was the excuse. We soldiered on.</h3></td>
     </tr>
     </tr>
     <tr>
     <tr>
-
       <td>27th July 2009</td>
+
       <td><h3>3rd August 2009</h3></td>
-
       <td>Work begins on our wiki
+
       <td><h3>The hard works
-
page and logo design.<br>
+
        begins&hellip;<br>
-
We create a very exciting &lsquo;cluster map&rsquo; on our
+
        DNA Biobricks were transformed, starter cultures made and plasmid
-
wiki. One cluster so far: Southampton.<br>
+
        maxiprep performed.<br>
-
We finalise our plasmid diagrams and Biobrick parts. <br>
+
        Our Southampton iGEM logo is nearly finalised.&nbsp; <br>
-
The team mugshot was taken.<br>
+
        Cluster map update: 9 different hits including Canada, Turkey, Poland,
-
We went from lab protocol amateurs to experts within the week.<br>
+
        Japan and Netherlands.<br>
-
The team supervisor abandoned us for 7 days. &lsquo;Family
+
        Work commences on the simulations.<br>
-
holiday&rsquo; was the excuse. We soldiered on.</td>
+
        One man down :( . Apparently going to hospital is the new excuse for
 +
        getting out of labs.</h3></td>
     </tr>
     </tr>
     <tr>
     <tr>
-
       <td>3rd August 2009</td>
+
       <td><h3>10th August 2009</h3></td>
-
       <td>The hard works
+
       <td><h3>Man back :) , he just
-
begins&hellip;<br>
+
        could not stay away.<br>
-
DNA Biobricks were transformed, starter cultures made and plasmid
+
        Note to self:<br>
-
maxiprep performed.<br>
+
        1) In the plasmid maxiprep: Turns out it does make a difference if you
-
Our Southampton iGEM logo is nearly finalised.&nbsp; <br>
+
        accidently put the white column on top of the blue, instead of the
-
Cluster map update: 9 different hits including Canada, Turkey, Poland,
+
        other way round&hellip;<br>
-
Japan and Netherlands.<br>
+
        2) Adding B0034 to B0015 and centrifuging them together does not, in
-
Work commences on the simulations.<br>
+
        fact, bode well.<br>
-
One man down :( . Apparently going to hospital is the new excuse for
+
        3) The nanodrop only works when the switch is turned to
-
getting out of labs.</td>
+
  &lsquo;on&rsquo;.<br>
 +
        Exciting times, having been all maxiprepped out, we started a new
 +
        protocol: Digestion. <br>
 +
        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.<br>
 +
        Cluster map update: <br>
 +
        UK (i.e. Southampton) &ndash; 57<br>
 +
        Rest of world &ndash; 30<br>
 +
        Still a bit of room for improvement&hellip;</h3></td>
     </tr>
     </tr>
     <tr>
     <tr>
-
       <td>10thAugust 2009</td>
+
       <td><h3>17th August 2009</h3></td>
-
       <td>Man back :) , he just
+
       <td><h3>We are granted
-
could not stay away.<br>
+
        permission to start an outreach project &hellip;hold tight folks,
-
Note to self:<br>
+
        more details coming soon.<br>
-
1) In the plasmid maxiprep: Turns out it does make a difference if you
+
        Our team diminishes further - apparently &lsquo;working at
-
accidently put the white column on top of the blue, instead of the
+
        home&rsquo; is the new &lsquo;working&hellip;at
-
other way round&hellip;<br>
+
        work&rsquo;.<br>
-
2) Adding B0034 to B0015 and centrifuging them together does not, in
+
        Our PCRs FINALLY work. Maybe practise really does make perfect.<br>
-
fact, bode well.<br>
+
        We perform our last ever Maxiprep&hellip;sob.<br>
-
3) The nanodrop only works when the switch is turned to
+
        Don&rsquo;t panic though, we are moving onto bigger and better
-
&lsquo;on&rsquo;.<br>
+
        protocols; Ligation.<br>
-
Exciting times, having been all maxiprepped out, we started a new
+
        It&rsquo;s nearly week six, and we have finally mastered the art of
-
protocol: Digestion. <br>
+
        making and loading a gel. It&rsquo;s &lsquo;simple&rsquo;
-
After much deliberation and input from the entire team, our logo is
+
        they say. Obviously not. <br>
-
finally finished. It was worth the wait. I mean look at it. Genius.<br>
+
        An exciting wall chart appears in our office.<br>
-
Cluster map update: <br>
+
        Cluster map update: UK &ndash; 92. Really must stop checking the
-
UK (i.e. Southampton) &ndash; 57<br>
+
        cluster map so often&hellip;</h3></td>
-
Rest of world &ndash; 30<br>
+
-
Still a bit of room for improvement&hellip;</td>
+
     </tr>
     </tr>
     <tr>
     <tr>
-
       <td>17th August 2009</td>
+
       <td><h3>25th August 2009</h3></td>
-
       <td>We are granted
+
       <td><h3>We perfect a pattern:<br />
-
permission to start an outreach project &hellip;hold tight folks,
+
        Digest&hellip;ligate&hellip;transform<br />
-
more details coming soon.<br>
+
        Digest&hellip;ligate&hellip;transform<br />
-
Our team diminishes further - apparently &lsquo;working at
+
        Digest&hellip;ligate&hellip;transform<br />
-
home&rsquo; is the new &lsquo;working&hellip;at
+
        Shame none of them worked&hellip;
-
work&rsquo;.<br>
+
        On the plus side, our simulations are
-
Our PCRs FINALLY work. Maybe practise really does make perfect.<br>
+
        looking good!</h3></td>
-
We perform our last ever Maxiprep&hellip;sob.<br>
+
    </tr>
-
Don&rsquo;t panic though, we are moving onto bigger and better
+
    <tr>
-
protocols; Ligation.<br>
+
      <td><h3>31st August 2009</h3></td>
-
It&rsquo;s nearly week six, and we have finally mastered the art of
+
      <td><h3>The team begins to feel pretty
-
making and loading a gel. It&rsquo;s &lsquo;simple&rsquo;
+
        demoralised as the second week of
-
they say. Obviously not. <br>
+
        &lsquo;digest&hellip;ligate&hellip;transform&hellip;FAIL&rsquo;
-
An exciting wall chart appears in our office.<br>
+
        commences.
-
Cluster map update: UK &ndash; 92. Really must stop checking the
+
        We decide to momentarily focus on building our &lsquo;novel&rsquo; biobrick.
-
cluster map so often&hellip;</td>
+
        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&hellip;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.
 +
        &lsquo;Climbing&rsquo; is the new excuse. Not even
 +
        blaming the family this time!</h3></td>
 +
    </tr>
 +
    <tr>
 +
      <td><h3>7th September 2009</h3></td>
 +
      <td><h3>We think we have finally optimised our
 +
        digest&hellip;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
 +
        &lsquo;behind the scenes&rsquo; such as content for
 +
        our wiki. It&rsquo;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 &lsquo;fun&rsquo; 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&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>
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+
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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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