Team:Kent/diary

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      <caption>
      <strong>Content</strong>
      </caption>
      <tr>
        <td><div align="center"><a href="#week1">Week 1</a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week2">Week 2</a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week3">Week 3</a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week4">Week 4 </a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week5">Week 5 </a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week6">Week 6 </a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week7">Week 7</a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week8">Week 8</a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week9">Week 9</a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week10">Week 10</a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week11">Week 11</a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#week12">Week 12</a></div></td>
      </tr>
      <tr>
        <td><div align="center"><a href="#TOP">Top</a></div></td>
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    <table width="750px" border="0.5" align="center" cellspacing="5">
  <tr>
    <th scope="col"><h1 id="week1">Week 1</h1></th>
  </tr>
  <tr>
    <td><div>
      <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{134}" paraid="1459896294"><span xml:lang="EN-GB"><strong>Day 1 (25/06/14):</strong></span><strong> </strong></p>
    </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{138}" paraid="644007601"><span xml:lang="EN-GB">After a meeting with our advisors yesterday, we came into the lab this morning and began learning how to prepare competent cells</span><span xml:lang="EN-GB">. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{141}" paraid="132738343"><span xml:lang="EN-GB">We prepared:</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{146}" paraid="587698059"><span xml:lang="EN-GB">100mM CaCl</span><span xml:lang="EN-GB">2</span><span xml:lang="EN-GB"> – autoclaved</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{151}" paraid="759107298"><span xml:lang="EN-GB">100mM CaCl</span><span xml:lang="EN-GB">2</span><span xml:lang="EN-GB"> + 30% v/v glycerol – autoclaved</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{156}" paraid="2116064144"><span xml:lang="EN-GB">100ml LB media (1g </span><span xml:lang="EN-GB">Tryptone</span><span xml:lang="EN-GB">, 0.5g Yeast extract, 1g Sodium Chloride) - autoclaved</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{158}" paraid="1745966252"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{161}" paraid="1303440794"><span xml:lang="EN-GB">E.coli was added to 5ml of LB and incubated overnight at 37°</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{166}" paraid="1493432281"><span xml:lang="EN-GB">Pipette tips, conical flasks, bottles </span><span xml:lang="EN-GB">etc</span><span xml:lang="EN-GB"> were also autoclaved ready for tomorrow</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{171}" paraid="1444756520"><span xml:lang="EN-GB">Also discussed possible project ideas and booked a room</span><span xml:lang="EN-GB"> in the library</span><span xml:lang="EN-GB"> to discuss theses as a group tomorrow. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{173}" paraid="1653937830"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{176}" paraid="1788300743"><span xml:lang="EN-GB"><strong>Day 2 (26/06/14):</strong></span><strong> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{179}" paraid="482982637"><span xml:lang="EN-GB">Today we carried on with the preparation of the competent cells.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{197}" paraid="1922880316"><span xml:lang="EN-GB">E.coli that had been incubating overnight was inoculated into LB and grown at 37°C until the OD</span><span xml:lang="EN-GB">600</span><span xml:lang="EN-GB"> reached 0.4. Cells were then cooled in the cold room and then centrifuged at 3000rpm, 4°C for 8mins. Pellet was </span><span xml:lang="EN-GB">resuspended</span><span xml:lang="EN-GB"> in 100mM CaCl</span><span xml:lang="EN-GB">2</span><span xml:lang="EN-GB">, incubated on ice and centrifuged again. Pellet was again </span><span xml:lang="EN-GB">resuspended</span><span xml:lang="EN-GB"> in 100mM CaCl</span><span xml:lang="EN-GB">2</span><span xml:lang="EN-GB">, 30% v/v glycerol and divided into </span><span xml:lang="EN-GB">33 x </span><span xml:lang="EN-GB">100µl in </span><span xml:lang="EN-GB">eppendorfs</span><span xml:lang="EN-GB"> and stored at -80°C.</span><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{202}" paraid="1817585134"><span xml:lang="EN-GB">We began to prepare 100ml of LB agar (1g </span><span xml:lang="EN-GB">Tryptone</span><span xml:lang="EN-GB">,   0.5g Yeast extract, 1g Sodium Chloride, 2g agar), this was autoclaved   but we then discovered we had no Chloramphenicol so could not continue   preparing the plates. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{205}" paraid="831879479"><span xml:lang="EN-GB">We also spent a few hours discussing parts and looking through the registry, and discussing different ideas.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{207}" paraid="827165376"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{211}" paraid="869693238"><span xml:lang="EN-GB"><strong>Day 3 (27/06</strong></span><strong><span xml:lang="EN-GB">/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{214}" paraid="1691444929"><span xml:lang="EN-GB">Today we carried out the transformation of our competent E.coli cells. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{221}" paraid="1220684716"><span xml:lang="EN-GB">Firstly we prepared 500ml of LB agar (5g </span><span xml:lang="EN-GB">Tryptone</span><span xml:lang="EN-GB">, 2.5g Yeast extract, 5g Sodium chloride, 10g agar) and autoclaved. Once this had cooled we added 0.5ml (1:1000 </span><span xml:lang="EN-GB">dilution</span><span xml:lang="EN-GB">) of chloramphenicol and made the plates. These were then allowed to set. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{d5a72225-be32-4c30-ba6e-e2a957c7d332}{233}" paraid="1502297753"><span xml:lang="EN-GB">We then carried out the transformation by thawing four </span><span xml:lang="EN-GB">eppendorfs</span><span xml:lang="EN-GB"> of our competent cells on ice. 2µl of </span><span xml:lang="EN-GB">resuspended</span><span xml:lang="EN-GB"> DNA (GFP open reading frame), w</span><span xml:lang="EN-GB">as added to the competent cells, and 1µl of RFP control was added to the control competent cells. Cells</span><span xml:lang="EN-GB"> they were in</span><span xml:lang="EN-GB">cubated on ice for 30mins and</span><span xml:lang="EN-GB"> were then heat shocked in a 42°C water bath for 60s and place back on ice for 5mins.</span><span xml:lang="EN-GB"> 1ml of LB media was added to the cells and they were then incubated at   37°C for 2 hours. 50 and 100µl of the cells were plated on the LB agar   with chloramphenicol we had prepared and left to grow at room   temperature over the weekend. </span></p>
      </div></td>
  </tr>
  <tr>
    <td>&nbsp;</td>
  </tr>
  <tr>
      <th scope="col"><h1 id="week2">Week 2</h1></th>
  </tr>
  <tr>
    <td><div>
      <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{134}" paraid="395228389"><span xml:lang="EN-GB"><strong>Day 4 (30/06/14):</strong></span><strong> </strong></p>
    </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{137}" paraid="977121111"><span xml:lang="EN-GB">Over   the weekend our plates had been growing, both plates of GFP transformed   cells showed many colonies of E.coli. The two control plates both only   had a few colonies and their morphology was very different to the   colonies on the other plates. We therefore repeated the control plates. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{140}" paraid="194435965"><span xml:lang="EN-GB">We   picked a single colony from each plate we had grown and inoculated them   in glycerol stock and left them overnight to grow ready to carry out   the miniprep tomorrow. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{142}" paraid="533815414"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{145}" paraid="1791200343"><span xml:lang="EN-GB"><strong>Day 5 (01/07/14):</strong></span><strong> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{148}" paraid="15641373"><span xml:lang="EN-GB">This   morning we centrifuged our inoculated cells but no pellet was produced.   We found out this is because they should not have been inoculated in   glycerol stock. We therefore took two more colonies from the 100µl   plates and inoculated them in LB and left to grow overnight. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{151}" paraid="2109612571"><span xml:lang="EN-GB">As   we had no growth on our repeated control plates we also repeated the   transformation, using RFP for the controls and YFP for the non-controls.   These were left to incubate overnight at 37°C. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{156}" paraid="1176315658"><span xml:lang="EN-GB">In   the afternoon we had a meeting with Mark Shepherd, to discuss ideas. By   the end of the meeting we had decided to further research in</span><span xml:lang="EN-GB">to the production of esters in E</span><span xml:lang="EN-GB">.coli, but also to carry on researching into BMCs. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{158}" paraid="1257878848"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{161}" paraid="1682964116"><span xml:lang="EN-GB"><strong>Day 6 (02/07/14):</strong></span><strong> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{164}" paraid="1159511525"><span xml:lang="EN-GB">We   took two colonies from the 100µl plates of cells containing YFP and   inoculated them in LB media. These were left to grow overnight. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{167}" paraid="974373986"><span xml:lang="EN-GB">We   centrifuged the cells transformed with GFP that had been inoculated in   LB media overnight. Using the pellet of cells produced we followed the   miniprep protocol to obtain the plasmid DNA. </span> </p>
      </div>
      <div>
        <p paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{169}" paraid="1512959917"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{172}" paraid="783391684"><span xml:lang="EN-GB"><strong>Day 7 (03/07/14):</strong></span><strong> </strong></p>
      </div>
      <div>
        <p paraeid="{abd97193-cf09-445d-81c3-6e202dd6a423}{176}" paraid="1290615802"><span xml:lang="EN-GB">This morning we met to discuss ideas for the project. After the meeting with Mark Shepherd</span><span xml:lang="EN-GB"> we had spent the last few days researching the idea of targeting   antimicrobial peptides to BMCs to deliver them to the gut and for   treatment of gastroenteritis/other conditions, or alternatively using   E.coli to produce fragrances. We discussed the pros and cons of each   project and collectively decided to further research into using the   production of fragrances in E.coli as an environmentally friendly   alternative to their current industrial production. </span> </p>
      </div></td>
  </tr>
  <tr>
     <th scope="col"><h1 id="week3">Week 3</h1></th>
  </tr>
  <tr>
    <td id="week3"><div>
      <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{134}" paraid="1488196031"><strong><span xml:lang="EN-GB">Day 8 (07/07/14):</span> </strong></p>
    </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{137}" paraid="1306971499"><span xml:lang="EN-GB">Today   we met in the library to decide on which genes we wanted to try and   insert into plasmids. We decided upon S-linalool synthase, R-linalool   synthase, E-E-germacrene-B synthase, patchoulol synthase, R-limonene   synthase, zingiberne synthase and geraniol synthase. We found the   sequences for these and also began looking at what promoters and   terminators we could use. We also began looking at using light to   activate the synthesis of these genes. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{139}" paraid="1122231427"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{142}" paraid="1757446990"><strong><span xml:lang="EN-GB">Day 9 (08/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{145}" paraid="1563416506"><span xml:lang="EN-GB">Today   Taylor and Matt used the transformation efficiency kit to test the   efficiency of the competent cells we had made. These were plated and   left overnight to grow.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{151}" paraid="525288463"><span xml:lang="EN-GB">We   also had a meeting with Wei-Feng, and discussed the lab work we have   carried out so far, the enzymes we have selected to try and put into   plasmids, and the best methods to do this. Wei-Feng suggested using   Gibson assembly to do this. </span><span xml:lang="EN-GB">Wei-Feng also suggested disregarding any sequences that had been used in iGem before, as we would not be creating new </span><span xml:lang="EN-GB">biobricks</span><span xml:lang="EN-GB"> with them. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{153}" paraid="2054883895"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{156}" paraid="608617158"><strong><span xml:lang="EN-GB">Day 10 (09/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{159}" paraid="1866529131"><span xml:lang="EN-GB">This   morning we discovered that due to an error in carrying out the   transformation efficiency yesterday, cells had not grown on the plates. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{164}" paraid="1785317896"><span xml:lang="EN-GB">We also began designing primers for the sequences that we have chosen, and discussed using Gibson assembly as opposed to </span><span xml:lang="EN-GB">using the Biobrick method and what promoters to use.</span><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{166}" paraid="2123977607"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{169}" paraid="405531754"><strong><span xml:lang="EN-GB">Day 11 (10/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{173}" paraid="86038807"><span xml:lang="EN-GB">Today we narrowed down what </span><span xml:lang="EN-GB">sequences   we wanted to insert into plasmids to germacrene-b synthase, patchoulol   synthase, R-linalool synthase and zingiberne synthase. We started to   look at removing restriction sites from these sequences and optimizing   the sequences for expression in E.coli. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{176}" paraid="286609698"><span xml:lang="EN-GB">Matt and Claire also carried out again the transformation efficiency kit as it had not worked yesterday. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{178}" paraid="1642985070"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{181}" paraid="144556405"><strong><span xml:lang="EN-GB">Day 12 (11/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{184}" paraid="733164368"><span xml:lang="EN-GB">This morning we found again that the transformation efficiency had not worked as no colonies had grown on the plates. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{61987e03-a80b-4ecc-84b1-b9bbcd172a6c}{187}" paraid="1032607807"><span xml:lang="EN-GB">Ellie completed the optimization of the sequences with removal of restriction sites, and addition of prefixes and suffixes.</span></p>
      </div></td>
  </tr>
  <tr id="week4">
      <th scope="col"><h1 id="week4">Week 4</h1></th>
  </tr>
  <tr>
    <td id="week4"><div>
      <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{134}" paraid="851055362"><span xml:lang="EN-GB"><strong>Day 13 (14/07/14):</strong></span><strong> </strong></p>
    </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{137}" paraid="833587014"><span xml:lang="EN-GB">Today   we repeated the transformation efficiency protocol again with cells   that we knew were definitely competent, to see if the problem was with   the cells we were using or with our carrying out of the protocol. These   were left to incubate overnight at 37°C. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{140}" paraid="802771287"><span xml:lang="EN-GB">We   also carried on working on our sequences, and started looking into how   much it will cost to order our sequence. As our sequences are quite long   we looked into whether it will be cheaper to order the sequences in   parts or as one long sequence. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{143}" paraid="1136664201"><span xml:lang="EN-GB">As   a group we discussed ideas for the wiki, and Taylor and Alex carried on   working on this. Claire designed a poster for Alex and Ellie to take to   Sheffield on Friday. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{145}" paraid="1647407736"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{148}" paraid="1123808943"><strong><span xml:lang="EN-GB">Day 14 (15/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{152}" paraid="926310474"><span xml:lang="EN-GB">When we took the transformation efficiency plates out of the freezer this morning we found that </span><span xml:lang="EN-GB">once   again we had no colonies. We discussed reasons for this, and prepared   an agarose gel to check that the plasmid was present in the DNA samples   we are using.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{155}" paraid="1612404698"><span xml:lang="EN-GB">We also prepared a number of agar plates and agar plates with Chloramphenicol.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{158}" paraid="106865345"><span xml:lang="EN-GB">Taylor   and Alex carried on working on the wiki, using the idea of a   minimalistic design that we had agreed upon. We also decided that we   like the logo that Rosie has designed, but that it needs some   changes/improvements. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{161}" paraid="401202528"><span xml:lang="EN-GB">We   met with our supervisors, and discussed sequences, lab work, the wiki   and future events. We decided that due to the budget we will initially   only order one sequence. We decided as a team that zingiberne synthase   would be the enzyme we would like to use first.  </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{163}" paraid="23142116"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{166}" paraid="1052431569"><strong><span xml:lang="EN-GB">Day 15 (16/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{171}" paraid="1121718767"><span xml:lang="EN-GB">We carried out agarose gel electrophoresis on the GFP plasmids we had obtained in the miniprep.   However due to an error in the preparation of the gel this was   unsuccessful. We also left a sample of E.coli cells in freshly prepared   LB at 37°</span><span xml:lang="EN-GB">C over</span><span xml:lang="EN-GB"> night to grow.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{174}" paraid="1790367813"><span xml:lang="EN-GB">Taylor   carried on working on the Wiki, and Rosie and Alex carried on working   on the logo. We also filled out the iGem safety forms and a proposal for   a workshop we could hold at the YSB conference in September. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{178}" paraid="1199014465"><span xml:lang="EN-GB">As   a group we discussed whether or not to use the enzyme patchoulol   synthase as we have found out that the current production of patchouli   oil is done is quite a sustainable way. </span><span xml:lang="EN-GB">We   decided that using patchoulol synthase probably isn&rsquo;t the best idea and   to look into alternative enzymes we could use instead. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{180}" paraid="647478961"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{183}" paraid="483802667"><strong><span xml:lang="EN-GB">Day 16 (17/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{186}" paraid="871709124"><span xml:lang="EN-GB">Today   we completed the poster and presentation for the Sheffield meet up. We   also carried on working on the logo design, adding in some of the iGem   colours. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{189}" paraid="802468588"><span xml:lang="EN-GB">The   zingiberne synthase sequence was finalised and sent to Wei-Feng to be   ordered, and we design the Biobrick we will make with this sequence,   including the promoter, ribosome binding site and terminator.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{e80698e6-4051-4df9-ac50-e1dba26bed1e}{192}" paraid="1434102252"><span xml:lang="EN-GB">In   the lab Brogan and Rosie prepared some more competent cells, and also   carried out agarose gel electrophoresis of the plasmid we obtained from   the mini-prep, to check the plasmid was present. Unfortunately when   viewed under UV, only the DNA marker was present, showing the plasmid   was not present in the sample. </span></p>
      </div></td>
  </tr>
  <tr>
  <th scope="col"><h1 id="week5">Week 5</h1></th>
  </tr>
  <tr>
    <td id="week5"><div>
      <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{134}" paraid="2023929638"><strong><span xml:lang="EN-GB">Day 17 (21/07/14):</span> </strong></p>
    </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{137}" paraid="1032743607"><span xml:lang="EN-GB">Today   we took a colony of GFP transformed cells and inoculated them in LB   media. These were left to grow overnight at 37°C ready to be used in the   miniprep   procedure tomorrow. We also transformed the new competent cells we had   made with YFP, and left these to grow overnight also at 37°C on   chloramphenicol agar plates. An agarose gel was also prepared ready to   carry agarose gel electrophoresis tomorrow with the plasmid we hope to   obtain from the miniprep, to check the plasmid is present. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{142}" paraid="1018332894"><span xml:lang="EN-GB">We finalised the zingiberne synthase and alpha-</span><span xml:lang="EN-GB">farnesene</span><span xml:lang="EN-GB"> sequences, so that they could be ordered and we can then begin to assemble our Biobrick. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{144}" paraid="1897818383"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{147}" paraid="846534638"><strong><span xml:lang="EN-GB">Day 18 (22/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{152}" paraid="476422979"><span xml:lang="EN-GB">Today we carried out the miniprep   of the GFP transformed cells that had been growing overnight to obtain   the GFP plasmid from them. This plasmid was the run on the agarose gel   we had prepared yesterday. </span><span xml:lang="EN-GB">Unfortunately whilst running this gel began to melt.</span><span xml:lang="EN-GB"> We also used spectrometry to determine the concentration of plasmid we had obtained, and we had a high concentration.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{155}" paraid="1561249105"><span xml:lang="EN-GB">We   also sent emails to five different local and national newspapers to   begin trying to spread the word about synthetic biology. We also emailed   an iGem team from Paris and Sheffield iGem about collaborations. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{158}" paraid="1317443958"><span xml:lang="EN-GB">We also met with our supervisors and discussed the ordering of sequences, Boston trip, outreach and other iGem events.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{161}" paraid="460379653"><span xml:lang="EN-GB">Ellie, Claire and Lisa developed sequences for R-linalool synthase and Patchoulol synthase. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{164}" paraid="277642939"><strong><span xml:lang="EN-GB">Day 19 (23/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{168}" paraid="1781464574"><span xml:lang="EN-GB">Today our sequence for zingiberne synthase was ordered. It will hopefully arrive in eight days. </span><span xml:lang="EN-GB">We confirmed the sequences for patchoulol synthase and R-linalool synthase, and found parts in the repository that we need to order. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{171}" paraid="2024243066"><span xml:lang="EN-GB">Taylor   carried on developing the wiki, creating a &lsquo;landing page&rsquo; that people   will see when they look at our site until it is completed.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{174}" paraid="1197049315"><span xml:lang="EN-GB">Brogan and Rosie found quotes for hotels and flights for Boston, and also emailed newspapers and planned outreach.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{176}" paraid="1509802971"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{179}" paraid="1498221699"><strong><span xml:lang="EN-GB">Day 20 (24/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{184}" paraid="1103689184"><span xml:lang="EN-GB">This   morning we decided upon a constitutive promoter, a ribosome binding   site and a terminator that we wanted to transform. This is so we will   have these ready when our sequence for zingiberne synthase arrives. We </span><span xml:lang="EN-GB">also decided to transform limone</span><span xml:lang="EN-GB">ne synthase (from the iGem kit), so we can practice doing the restriction digests and ligations. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{187}" paraid="1402306312"><span xml:lang="EN-GB">We   prepared chloramphenicol of the correct concentration, and then   prepared agar plates with chloramphenicol to grow our transformed cells   on. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{194}" paraid="1538826682"><span xml:lang="EN-GB">We then carried out the four transformations, </span><span xml:lang="EN-GB">using   parts BBa_J23108 (promoter), BBa_J1742111 (limonene synthase),   BBa_B0015 (terminator) and BBa_B0030 (RBS) from the plates in our kit.   We</span><span xml:lang="EN-GB"> </span><span xml:lang="EN-GB"> </span><span xml:lang="EN-GB">plated each transformation twice and left to incubate overnight at 37°C.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{196}" paraid="1600906645"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{199}" paraid="1509183098"><strong><span xml:lang="EN-GB">Day 21 (25/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{202}" paraid="1807016814"><span xml:lang="EN-GB">This morning we counted the plates of transformed cells that we had been growing overnight.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{205}" paraid="2060559782"><span xml:lang="EN-GB">BBa_J23108: 0 colonies, 0 colonies</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{209}" paraid="1330459754"><span xml:lang="EN-GB">BBa_B0030</span><span xml:lang="EN-GB">: 0 colonies, 1 colony</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{212}" paraid="738179030"><span xml:lang="EN-GB">BBa_J1742111: 8 colonies, 7 colonies</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{215}" paraid="886640191"><span xml:lang="EN-GB">BBa_B0015: 2 colonies, 8 colonies</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{218}" paraid="112071768"><span xml:lang="EN-GB">As there was no real growth for the promoter or RBS we will retransform these next week. We will miniprep the limonene synthase and terminator transformations next week as well.</span></p>
        <p paraeid="{3e7180f1-cd7c-4091-82b0-c58dd5d3e31a}{218}" paraid="112071768">&nbsp;</p>
      </div></td>
  </tr>
  <tr>
  <th scope="col"><h1 id="week6">Week 6</h1></th>
  </tr>
  <tr>
    <td id="week6"><div>
      <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{134}" paraid="1637948415"><strong><span xml:lang="EN-GB">Day 22 (28/07/2014):</span> </strong></p>
    </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{138}" paraid="809024919"><span xml:lang="EN-GB">Today   we found a new constitutive promoter and ribosome binding site to   transform. These are parts BBa_J23109 (promoter) and BBa_B0032 (RBS). </span><span xml:lang="EN-GB">These were transformed, plated, and left to grow overnight at 37°C. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{143}" paraid="640732948"><span xml:lang="EN-GB">We selected a colony of the E.</span><span xml:lang="EN-GB">coli transformed with part BBa_</span><span xml:lang="EN-GB">1742111   (limonene synthase) and part BBa_B0015 (terminator) and inoculated   these in LB. These were also left at 37°C overnight to grow ready to   carry out the miniprep tomorrow.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{145}" paraid="435991489"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{148}" paraid="1903943814"><strong><span xml:lang="EN-GB">Day 23 (29/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{151}" paraid="501125030"><span xml:lang="EN-GB">Today   we found that colonies had grown on the plates transformed with part   BBa_B0032 (RBS) yesterday, but no colonies on the plates transformed   with part BBa_J23109. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{154}" paraid="798412720"><span xml:lang="EN-GB">A colony of BBa_B0032 (RBS) transformed E.coli cells was inoculated in LB media and left to grow overnight at 37°C.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{157}" paraid="745758440"><span xml:lang="EN-GB">We   selected another new constitutive promoter, part BBa_J23119 and carried   out the transformation of this, as well as retransforming part   BBa_J23109. These were both plated and left at 37°C overnight to grow.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{162}" paraid="986300787"><span xml:lang="EN-GB">We carr</span><span xml:lang="EN-GB">ied out a miniprep of part BBa_</span><span xml:lang="EN-GB">1742111   (limonene synthase) transformed cells and part BBa_B0015 (terminator)   transformed cells that had been grown up overnight. The plasmid obtained   from these was stored at -20°C.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{165}" paraid="854554059"><span xml:lang="EN-GB">We   also had a meeting with Wei-Feng and Luca, in which we discussed the   planning of Boston and YSB 2.0, our ordered sequence and general lab   work. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{168}" paraid="562356250"><span xml:lang="EN-GB">We also skyped Paris Bettencourt and discussed a possible collaboration between the teams.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{170}" paraid="504571833"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{173}" paraid="1549072177"><strong><span xml:lang="EN-GB">Day 24 (30/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{176}" paraid="738537875"><span xml:lang="EN-GB">We   had a lot of growth of both promoters, parts BBa_J23109 and BBa_J23119,   however we realised this is as they had been grown on plates with no   chloramphenicol and therefore transformed colonies had not been selected   for. We therefore transformed both of these parts again, plated these   and left them to grow overnight at 37°C. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{182}" paraid="1988400682"><span xml:lang="EN-GB">We had been growing</span><span xml:lang="EN-GB"> up overnight E.coli cells transformed with part BBa_B0032 (RBS). We carried out </span><span xml:lang="EN-GB">a miniprep</span><span xml:lang="EN-GB"> of these and collected the plasmid. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{191}" paraid="2007582770"><span xml:lang="EN-GB">Plasmi</span><span xml:lang="EN-GB">d obtained from the </span><span xml:lang="EN-GB">minipreps</span><span xml:lang="EN-GB"> of the E.coli ce</span><span xml:lang="EN-GB">lls transformed with parts BBa_</span><span xml:lang="EN-GB">1742111   (limonene synthase), BBa_B0015 (terminator) and BBa_B0032 (RBS), was   then ran on an agarose gel to check if the plasmid is present. </span><span xml:lang="EN-GB">All three plasmids were present. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{193}" paraid="293576996"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{196}" paraid="407317384"><strong><span xml:lang="EN-GB">Day 25 (31/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{200}" paraid="1643841837"><span xml:lang="EN-GB">Colonies of E.coli transformed with parts BBa_J23109 and BBa_J23119 had both </span><span xml:lang="EN-GB">grown overnight. Colonies were selected and inoculated into 5ml of LB to grow at 37°C overnight.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{204}" paraid="1305318975"><span xml:lang="EN-GB">We   performed a single restriction digest of limonene synthase plasmid   using the enzyme EcoR1, another single restriction digest using the   enzyme Pst1, and a double restriction digest using both enzymes. The   fragments obtained from these digests were then run on an agarose gel. </span><span xml:lang="EN-GB">However, these digests did not work.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{206}" paraid="828635537"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{209}" paraid="1659195174"><strong><span xml:lang="EN-GB">Day 26 (01/07/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{214}" paraid="88134459"><span xml:lang="EN-GB">E.coli transformed with the promoter parts BBa_J23109 and BBa_J23119 that had been grown up overnight were </span><span xml:lang="EN-GB">minipreped</span><span xml:lang="EN-GB">, and the plasmid obtained from each stored at -20°C. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{218}" paraid="75157945"><span xml:lang="EN-GB">As   yesterday&rsquo;s digest of limonene synthase had not gone correctly, this   was repeated today. Limonene synthase gene in the plasmid backbone   psb1C3 was digested singly with EcoR1 and Pst1, and doubly with both   enzymes. This was then run on the gel again and the </span><span xml:lang="EN-GB">correct parts had been obtained, although there had been a problem with the gel so this will be repeated on Monday. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{82a3cf11-59e1-4fd5-9c2d-c49f590058bc}{221}" paraid="1734506924"><span xml:lang="EN-GB">Taylor and Alex have also carried on designing and coding the wiki. </span></p>
      </div></td>
  </tr>
  <tr>
  <th scope="col"><h1 id="week7">Week 7</h1></th>
  </tr>
  <tr>
    <td id="week89"><div>
      <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{134}" paraid="211437433"><strong><span xml:lang="EN-GB">Day 27 (04/08/14):</span> </strong></p>
    </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{137}" paraid="1508648882"><span xml:lang="EN-GB">We   carried out a restriction digest using just EcoR1, just Pst1 and using   both enzymes on parts BBa_J23109 (promoter), BBa_J23119 (promoter),   BBa_B0032 (RBS), BBa_174211 (limonene synthase), and BBa_B0015   (terminator). </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{140}" paraid="152449167"><span xml:lang="EN-GB">We   than ran the digests on agarose gels to check the correct size parts   had been obtained. Due to running out of time the gels were not able to   be left running long enough and therefore when imaged the bands had not   separated. We will therefore repeat this work tomorrow.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{142}" paraid="288393445"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{145}" paraid="1384140484"><strong><span xml:lang="EN-GB">Day 28 (05/08/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{148}" paraid="1356889166"><span xml:lang="EN-GB">We   carried out a restriction digest using just EcoR1, just Pst1 and using   both enzymes on parts BBa_J23109 (promoter), BBa_J23119 (promoter),   BBa_B0032 (RBS), BBa_174211 (limonene synthase), and BBa_B0015   (terminator). </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{151}" paraid="626219183"><span xml:lang="EN-GB">We   then ran the digests on agarose gels to check the correct size parts   had been obtained. These all showed the expected bands so the   restriction digest had worked. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{154}" paraid="345576015"><span xml:lang="EN-GB">We   also had a meeting with our supervisors in which we discussed upcoming   deadlines, London YSB 2.0 planning, Boston travel, outreach and   collaborations and lab work. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{157}" paraid="1869713770"><span xml:lang="EN-GB">Taylor carried on working on the wiki, creating the template design that the information will then be loaded onto.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{159}" paraid="80841581"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{162}" paraid="1943596970"><strong><span xml:lang="EN-GB">Day 29 (06/08/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{165}" paraid="1965945902"><span xml:lang="EN-GB">Today we prepared two agarose gels that we can run a digested limonene synthase plasmid on tomorrow.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{171}" paraid="2107144267"><span xml:lang="EN-GB">We carried out a transformation of parts BBa_174211 (limonene synthase) and BBa_</span><span xml:lang="EN-GB">B0015   (terminator), into competent E.coli cells. We also revitalised our   colonies BBa_J23109 (promoter), BBa_J23119 (promoter) and BBa_B0032   (RBS) transformed cells be </span><span xml:lang="EN-GB">replating</span><span xml:lang="EN-GB"> them. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{174}" paraid="698563606"><span xml:lang="EN-GB">We   also compiled an inventory of all of the cells, plasmids, enzymes etc.   that we have in stock, so that we can make/order more before we run   out. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{177}" paraid="1585853767"><span xml:lang="EN-GB">Taylor also uploaded our wiki template so we can start to upload information onto it.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{180}" paraid="67581119"><span xml:lang="EN-GB">A   double restriction digest of limonene synthase plasmids was carried out   using the enzymes EcoR1 and Pst1. These were left to incubate overnight   at room temperature.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{182}" paraid="1135918820"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{185}" paraid="1275223379"><strong><span xml:lang="EN-GB">Day 30 (07/08/14):</span> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{190}" paraid="895879210"><span xml:lang="EN-GB">The digested limonene synthase plasmid was </span><span xml:lang="EN-GB">ran</span><span xml:lang="EN-GB"> on two agarose gels to separate the psb1C3 backbone from the limonene   synthase part. The bands were then visualised and cut out of the gel. A   DNA gel extraction kit was used to extract the DNA from the gel. This   DNA was then stored at -20°C.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{5e4f41c7-9c8a-495d-9e6d-4bf1ef133d98}{197}" paraid="1098926057"><span xml:lang="EN-GB">We inoculated cells transformed yesterday with </span><span xml:lang="EN-GB">parts  BBa</span><span xml:lang="EN-GB">_J23109 (promoter), BBa_J23119 (promoter), BBa_B0032 (RBS), </span><span xml:lang="EN-GB">BBa_174211 (limonene synthase) and BBa_B0015 (terminator)</span><span xml:lang="EN-GB"> in LB and left overnight at 37°C.</span></p>
      </div></td>
  </tr>
  <tr>
    <td id="week8"><div align="center" id="week8">
      <h1>Week 8</h1>
    </div></td>
  </tr>
  <tr>
    <td id="week8"><div>
      <p align="justify" paraeid="{fc59b7b9-285a-46ed-affc-9c50e4a2fd60}{134}" paraid="1688410318"><span xml:lang="EN-GB"><strong>Day 32 (11/08/14):</strong></span><strong> </strong></p>
    </div>
      <div>
        <p align="justify" paraeid="{fc59b7b9-285a-46ed-affc-9c50e4a2fd60}{137}" paraid="371083845"><span xml:lang="EN-GB">Double digest run on all parts, left overnight for gels. Gels were also prepared.</span> </p>
      </div>

      <div>
        <p align="justify" paraeid="{fc59b7b9-285a-46ed-affc-9c50e4a2fd60}{142}" paraid="827182974"><span xml:lang="EN-GB"><strong>Day 33 (12/08/14):</strong></span><strong> </strong></p>
      </div>

      <div>
        <p align="justify" paraeid="{fc59b7b9-285a-46ed-affc-9c50e4a2fd60}{149}" paraid="2135918219"><span xml:lang="EN-GB">All parts were run on </span><span xml:lang="EN-GB">gels,</span><span xml:lang="EN-GB"> gels were then extracted and frozen. This gave us a bulk store for assembly.</span> </p>
      </div>

      <div>
        <p align="justify" paraeid="{fc59b7b9-285a-46ed-affc-9c50e4a2fd60}{154}" paraid="72648302"><span xml:lang="EN-GB"><strong>Day 34 (13/08/14):</strong></span><strong> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{fc59b7b9-285a-46ed-affc-9c50e4a2fd60}{163}" paraid="436805571"><span xml:lang="EN-GB">Pcr</span><span xml:lang="EN-GB"> for limonene synthase, gel run to check if the </span><span xml:lang="EN-GB">pcr</span><span xml:lang="EN-GB"> had worked, </span><span xml:lang="EN-GB">pcr</span><span xml:lang="EN-GB"> purification run so we have more of our plasmid for assembly</span><span xml:lang="EN-GB">.</span> </p>
      </div>

      <div>
        <p align="justify" paraeid="{fc59b7b9-285a-46ed-affc-9c50e4a2fd60}{168}" paraid="1349397305"><span xml:lang="EN-GB"><strong>Day 35 (14/08/14):</strong></span><strong> </strong></p>
      </div>

      <div>
        <p align="justify" paraeid="{fc59b7b9-285a-46ed-affc-9c50e4a2fd60}{177}" paraid="1994548117"><span xml:lang="EN-GB">Pcr</span><span xml:lang="EN-GB"> gel rerun as there was a fault with the gel, </span><span xml:lang="EN-GB">pcr</span><span xml:lang="EN-GB"> purification and double digest on the limonene synthase ready for ligation back into the plasmid backbone</span><span xml:lang="EN-GB">.</span> </p>
      </div>

      <div>
        <p align="justify" paraeid="{fc59b7b9-285a-46ed-affc-9c50e4a2fd60}{182}" paraid="930499557"><span xml:lang="EN-GB"><strong>Day 36 (15/08/14):</strong></span><strong> </strong></p>
      </div>

      <div>
        <p align="justify" paraeid="{fc59b7b9-285a-46ed-affc-9c50e4a2fd60}{188}" paraid="1575717935"><span xml:lang="EN-GB">Double digest of the limonene synthase backbone, gel run of the double digest and gel extraction</span><span xml:lang="EN-GB">.</span> </p>
      </div>
</td>
  </tr>
  <tr>
    <td id="week9"><div align="center" id="week9">
      <h1>Week 9</h1>
    </div></td>
  </tr>
  <tr>
    <td id="week122"><div>
      <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{144}" paraid="1684732928"><span xml:lang="EN-GB"><strong>Day 37 (18/08/14):</strong></span> </p>
    </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{148}" paraid="1800436943"><span xml:lang="EN-GB">Ligation of limonene synthase and backbone, transformation of ligated product, run a gel of ligation</span><span xml:lang="EN-GB">.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{150}" paraid="1359512319"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{153}" paraid="584453046"><span xml:lang="EN-GB"><strong>Day 38 (19/08/14):</strong></span><strong> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{155}" paraid="1396181651"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{158}" paraid="1048161974"><span xml:lang="EN-GB">Today   we had a meeting with our supervisors. We discussed arrangements for   YSB 2.0, Boston and also our progress in the lab. We discussed how we   can continue being productive in the lab until our genes arrive.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{160}" paraid="539958566"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{163}" paraid="75687180"><span xml:lang="EN-GB"><strong>Day 39 (20/08/14):</strong></span><strong> </strong></p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{165}" paraid="977741178"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{168}" paraid="1198569094"><span xml:lang="EN-GB">Today   we digested parts BBa_J23109 and BBa_J23119 to remove them from the   psb1C3 backbone with chloramphenicol resistance. These were then ligated   into a plasmid backbone with tetracycline resistance.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{171}" paraid="1958588102"><span xml:lang="EN-GB">Limonene synthase vector with RBS was ligated onto a backbone with ampicillin resistance.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{175}" paraid="885138769"><span xml:lang="EN-GB">Plasmids of both promoters (BBa_J23109 and BBa_J23119) and limonene synthase</span><span xml:lang="EN-GB"> (BBa_I742111) were transformed into E.coli cells and left to grow overnight at 37°C.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{178}" paraid="682183532"><span xml:lang="EN-GB">Chloramphenicol, ampicillin and tetracycline plates were made.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{180}" paraid="1898385857"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{183}" paraid="1591463249"><span xml:lang="EN-GB"><strong>Day 40 (21/08/14):</strong></span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{185}" paraid="327050150"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{188}" paraid="772318322"><span xml:lang="EN-GB">Yesterday&rsquo;s   transformations of limonene synthase and promoters J23109 and J23119   were unsuccessful as we had no colonies on any of the plates. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{191}" paraid="1134048075"><span xml:lang="EN-GB">Digestions   were again carried out of limonene synthase with RBS (BBa_I742111) and   both promoters (BBa_J23109 and BBa_J23119). Ligations were then carried   out of limonene synthase onto an ampicillin resistant backbone and both   promoters onto a tetracycline resistant backbone. Transformations were   carried out of each part into E.coli. These were plated and left   overnight at 37°C. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{194}" paraid="1504103654"><span xml:lang="EN-GB">Ampicillin, tetracycline and chloramphenicol agar plates were made. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{198}" paraid="252146966"><span xml:lang="EN-GB">A PCR reaction was set up and left to run overnight to amplify </span><span xml:lang="EN-GB">a digested promoter.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{200}" paraid="154204247"><span xml:lang="EN-GB"> </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{203}" paraid="257330352"><span xml:lang="EN-GB"><strong>Day 41 (22/08/14):</strong></span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{208}" paraid="356955112"><span xml:lang="EN-GB">Yesterday&rsquo;s transformations of limonene synthase and promoters J23109 and J23119 were </span><span xml:lang="EN-GB">again </span><span xml:lang="EN-GB">unsuccessful as we had no colonies on any of the plates. </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{211}" paraid="627504426"><span xml:lang="EN-GB">Ampicillin, tetracycline and chloramphenicol agar plates were made.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{214}" paraid="1294002486"><span xml:lang="EN-GB">Transformations of the following were carried out:</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{218}" paraid="870800454"><span xml:lang="EN-GB">-</span><span xml:lang="EN-GB">limonene synthase with RBS on an ampicillin resistant backbone, </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{69dbc1dc-187e-4eef-9180-2a31af17ae93}{104}" paraid="659678966" xml:lang="EN-US"><span xml:lang="EN-GB">-</span><span xml:lang="EN-GB">promoters J23109 and J23119 on a tetracycline resistant backbone,</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{226}" paraid="232220310"><span xml:lang="EN-GB">-</span><span xml:lang="EN-GB">promoters J23109 and J23119 on a chloramphenicol resistant backbone, </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{230}" paraid="943877229"><span xml:lang="EN-GB">-</span><span xml:lang="EN-GB">RBS on a chloramphenicol resistant backbone, </span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{234}" paraid="1385669810"><span xml:lang="EN-GB">-</span><span xml:lang="EN-GB">a light inducible promoter on a chloramphenicol resistant backbone,</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{238}" paraid="1231030221"><span xml:lang="EN-GB">-</span><span xml:lang="EN-GB">A backbone</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{241}" paraid="1969166"><span xml:lang="EN-GB">These were plated on the appropriate agar plates and left to grow over the weekend at room temperature.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{246}" paraid="1366388828"><span xml:lang="EN-GB">The PCR product was purified and ran on an agarose gel. However when </span><span xml:lang="EN-GB">visualised under UV no promoter</span><span xml:lang="EN-GB"> could be seen on the gel. It is possible the promoter was lost during purification due to its small size.</span> </p>
      </div>
      <div>
        <p align="justify" paraeid="{c8b4a4c9-f082-4c27-84bf-cb4567ce29d8}{249}" paraid="1635329309"><span xml:lang="EN-GB">Our gene R-linalool synthase arrived! This was amplified using PCR. </span></p>
      </div></td>
  </tr>
  <tr>
    <td id="week13">&nbsp;</td>
  </tr>
  <tr>
      <td id="week10"><h1 align="center">Week 10</h1></td>
    </td>
  </tr>
  <tr>
    <td id="week15"><div align="justify"><strong>Day 42 (26/08/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week16"><div align="justify">We had a number of successful transformations from Friday. We had colonies of promoter J23109 on a tetracycline resistant backbone, promoter J23119 on a chloramphenicol resistant backbone, RBS on a chloramphenicol resistant backbone and limonene synthase on an ampicillin resistant backbone. Colonies of these were selected and inoculated in LB to grow up overnight to be minipreped tomorrow. <br>
      We also inoculated a sample of untransformed E.coli into LB and left to grow up overnight ready to make competent tomorrow. <br>
      We ran an agarose gel to check that the PCR of R-linalool had been successful. Bands were seen so it had been. <br>
      We also carried out another transformation of the blue light promoter.</div></td>
  </tr>
  <tr>
    <td id="week17">&nbsp;</td>
  </tr>
  <tr>
    <td id="week18"><div align="justify"><strong>Day 43 (27/08/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week19"><div align="justify">We carried out a PCR reaction of R-linalool and then ran this on a gel. When ran on a gel there were no bands for R-linalool showing this had been unsuccessful. <br>
      We carried out the miniprep of both promoters, J23109 and J23119, limonene synthase and RBS. <br>
      We prepared competent cells using the cells that had been grown up overnight. <br>
      We also carried out a Gibson assembly reaction to insert R-linalool into a chloramphenicol backbone. These were transformed into E.coli, plated on chloramphenicol agar and left to grow overnight at 37°C.</div></td>
  </tr>
  <tr>
    <td id="week20">&nbsp;</td>
  </tr>
  <tr>
    <td id="week21"><div align="justify"><strong>Day 44 (28/08/14):</strong></div></td>
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  <tr>
    <td id="week22"><div align="justify">The transformation of R-linalool in a chloramphenicol backbone had been successful, with colonies having grown. Colonies were selected and grown up in LB containing chloramphenicol. Colonies were also replated. <br>
      Plasmid of limonene synthase on an ampicillin backbone was digested using EcoR1 and Pst1, and ran on a gel to check we had the correct product. This was successful as the correct bands were obtained. <br>
      Promoters J23109 and J23119 were digested and ligated into a tetracycline resistant backbone. These were plated on agar and left to grow overnight at 37°C.</div></td>
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    <td id="week23">&nbsp;</td>
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    <td id="week24"><strong>Day 45 (29/08/14):</strong></td>
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    <td id="week25"><div align="justify">The ligation of promoters J23109 and J23119 onto a tetracycline backbone was unsuccessful, and therefore we carried out a digestion of J23119 again. We then re-ligated it into tetracycline and left to grow overnight again at 37°C. <br>
      The minipreped R-linalool plasmid was digested, and the fragments ran on an agarose gel to check if the correct fragments had been obtained. This was successful so we now have a BioBrick with R-linalool inserted. <br>
      We also carried out a transformation efficiency test on the competent cells we prepared on Wednesday.</div></td>
  </tr>
  <tr>
    <td id="week26">&nbsp;</td>
  </tr>
  <tr>
      <td id="week11"><h1 align="center">Week 11</h1></td>
</td>
  </tr>
  <tr>
    <td id="week28"><div align="justify"><strong>Day 46 (1/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week29"><div align="justify">London YSB 2.0</div></td>
  </tr>
  <tr>
    <td id="week30">&nbsp;</td>
  </tr>
  <tr>
    <td id="week31"><div align="justify"><strong>Day 47 (2/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week32"><div align="justify">Rosie and Lisa at London YSB 2.0.<br>
      We carried out double digests of limonene synthase, promoter J23119, TET backbone. <br>
      We carried out a ligation of promoter J23119 with limonene synthase onto a tetracycline backbone. These were transformed into E.coli and grown on agar overnight at 37°C. <br>
      We transformed a promoter + RBS part on a chloramphenicol backbone into E.coli, and grew these up overnight at 37°C.</div></td>
  </tr>
  <tr>
    <td id="week33">&nbsp;</td>
  </tr>
  <tr>
    <td id="week34"><div align="justify"><strong>Day 48 (3/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week35"><div align="justify">Today we carried out double digests of limonene synthase on an ampicillin backbone, R-linalool on a chloramphenicol backbone, promoter J23119 on a chloramphenicol backbone, TET and AMP backbones. <br>
      Limonene synthase was ligated to promoter J23119 and onto a tetracycline resistant backbone, using 3A assembly. This was transformed into E.coli, spread on agar plates and left to grow overnight at 37°C. <br>
      R-linalool was ligated onto a ampicillin resistant backbone, transformed into E.coli, spread on agar plates and left to grow overnight at 37°C. <br>
      Colonies that had been transformed with promoter and RBS were inoculated in LB and grown up overnight at 37°C. <br>
      E.coli was transformed with a blue light promoter and also with RFP on a tetracycline resistant backbone. These were plated on agar and left to grow overnight at 37°C</div></td>
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  <tr>
    <td id="week36">&nbsp;</td>
  </tr>
  <tr>
    <td id="week37"><div align="justify"><strong>Day 49 (4/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week38"><div align="justify">We had colonies grown of the assembly of promoter J23119 with limonene synthase onto a TET backbone, and of the light promoter. We had a lawn of colonies of R-linalool onto ampicillin suggesting this had been contaminated. We had no growth of RFP on a TET backbone. <br>
      Colonies of the limonene synthase assembly and of the light promoter were selected and inoculated in LB. These were left to grow overnight at 37°C. <br>
      E.coli that had been transformed with promoter and RBS and grown up overnight were miniprepped, and the plasmid stored at -20°C.</div></td>
  </tr>
  <tr>
    <td id="week39">&nbsp;</td>
  </tr>
  <tr>
    <td id="week40"><div align="justify"><strong>Day 50 (5/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week41"><div align="justify">A double digest of R-linalool on a chloramphenicol backbone was carried out, and R-linalool was ligated onto an ampicillin resistant backbone. This was then transformed into E.coli, plated on ampicillin agar plates and left to grow overnight at 37°C. <br>
      R-linalool was also assembled onto a kanamycin resistant backbone using Gibson assembly. <br>
      E.coli that had been transformed with the limonene synthase assembly and with the light promoter and grown up overnight were miniprepped, and the plasmid obtained stored at -20°C.</div></td>
  </tr>
  <tr>
    <td id="week42">&nbsp;</td>
  </tr>
  <tr>
    <td id="week43"><div align="justify"><strong>Day 51 (7/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week44"><div align="justify">Colonies of E.coli transformed with R-linalool on an ampicillin resistant backbone were selected, and inoculated in LB. These were left to grow up overnight at 37°C.</div></td>
  </tr>
  <tr>
    <td id="week45">&nbsp;</td>
  </tr>
  <tr>
      <td id="week12"><h1 align="center">Week 12</h1></td>
    </td>
  </tr>
  <tr>
    <td id="week47"><div align="justify"><strong>Day 52 (8/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week48"><div align="justify">We carried out a miniprep of E.coli that had been transformed with R-linalool on an ampicillin backbone to obtain the plasmid. <br>
      We then carried out a double digest using EcoR1 and Pst1 of the limonene synthase assembly and R-linalool on an ampicillin resistant backbone. These were run on agarose gels to check we had the correct assemblies. The gels showed that the digests had not worked correctly. <br>
      We also carried out a PCR reaction of the tetracycline and ampicillin resistant backbones to amplify the amount we had. <br>
      E.coli cells were inoculated in LB and grown up overnight to be made competent tomorrow. <br>
      We met with Lee to discuss human practices and the Medway Research Festival. We designed a questionnaire, and discussed the presentation we would give. </div></td>
  </tr>
  <tr>
    <td id="week49">&nbsp;</td>
  </tr>
  <tr>
    <td id="week50"><div align="justify"><strong>Day 53 (9/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week51"><div align="justify">Today we prepared another batch of competent cells. <br>
      We carried out a PCR purification of the plasmid backbones, Amp, Tet, Cam and Kan that had been amplified yesterday. <br>
      We also had a meeting with Wei-Feng, who suggested testing the enzymes we were using to ensure they are functioning properly. </div></td>
  </tr>
  <tr>
    <td id="week52">&nbsp;</td>
  </tr>
  <tr>
    <td id="week53"><div align="justify"><strong>Day 54 (10/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week54"><div align="justify">Today we attended the Medway research festival. We hosted a stall and presented our poster to many other scientists, researchers from a number of disciplines and members of the public. We also gathered responses to the survey we created. From other people at the festival we gathered ideas about the best and worst case scenarios of our project, and barriers that prevent scientists interacting with MPs and scientific policy makers. </div></td>
  </tr>
  <tr>
    <td id="week55">&nbsp;</td>
  </tr>
  <tr>
    <td id="week56"><div align="justify"><strong>Day 55 (11/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week57"><div align="justify">E.coli were transformed with RFP plasmid on backbones with AMP, TET, CAM and KAN resistance. This were plated on the appropriate agar and grown up overnight at 37°C. <br>
      To test the functioning of the enzymes we ran a series of digests of the limonene synthase plasmid on a gel. These were single digest with EcoR1, single digest with Pst1 and double digests with EcoR1 and Pst1. These showed that the EcoR1 enzyme was not functioning. </div></td>
  </tr>
  <tr>
    <td id="week58">&nbsp;</td>
  </tr>
  <tr>
    <td id="week59"><div align="justify"><strong>Day 56 (12/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week60"><div align="justify">Our zingiberne synthase gene finally arrived today! As we had ordered this gene in a plasmid we carried out a double digest using EcoR1 and Pst1 and ran these on an agarose gel to check the digest had worked and that we had the correct part. This worked so we are now able to start the assembly of the zingiberne synthase BioBrick. <br>
      We also moved out of the teaching labs where we have been working and into a research lab in preparation for the start of term.</div></td>
  </tr>
  <tr>
    <td id="week61">&nbsp;</td>
  </tr>
  <tr>
    <td id="week13"><h1 align="center">Week 13</h1></td>
  </tr>
  <tr>
    <td id="week65"><div align="justify"><strong>Day 57 (15/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week62"><div align="justify">Today we carried out double digests of Limonene synthase, promoter J23119, R-linalool and TET backbone. <br>
      We carried out 3A assembly of promoter and limonene synthase onto a TET backbone. These were transformed into E.coli, plated and left to grow overnight at 37°C. <br>
      R-linalool was assembled onto an AMP backbone using Gibson assembly. These were transformed into E.coli, plated and left to grow overnight at 37°C.</div></td>
  </tr>
  <tr>
    <td id="week63">&nbsp;</td>
  </tr>
  <tr>
    <td id="week66"><div align="justify"><strong>Day 58 (16/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week67"><div align="justify">We had no growth of the limonene synthase assembly, but we did have colonies of growth of R-linalool on the ampicillin resistant backbone. Colonies of R-linalool were selected, inoculated in LB media and respreads on fresh plates and left to grow overnight at 37°C. <br>
      To check if the limonene synthase gene had assembled with the promoter and just not transformed we ran the assembly product on an agarose gel. When we viewed the gel there was no DNA present. <br>
      We also made fresh agar plates containing ampicillin and tetracycline. <br>
      Zingiberne synthase and tetracycline backbone were both digested ready to carry out a Gibson assembly.</div></td>
  </tr>
  <tr>
    <td id="week68">&nbsp;</td>
  </tr>
  <tr>
    <td id="week69"><div align="justify"><strong>Day 60 (18/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week70"><p align="justify">Promoter + RBS and R-linalool on a CAM resistant backbone that had been grown up overnight were miniprepped. We carried out a double digest on the miniprep material and ran these on a gel to ensure the correct parts had been obtained. </p></td>
  </tr>
  <tr>
    <td id="week71">&nbsp;</td>
  </tr>
  <tr>
    <td id="week72"><div align="justify"><strong>Day 61 (19/09/14):</strong></div></td>
  </tr>
  <tr>
    <td id="week73"><div align="justify">We carried out 3A assembly of promoter + RBS onto R-linalool and promoter onto limonene synthase. These were plated on agar and left at 37°C overnight to grow. <br>
      We also used PCR to amplify the amount of the three antibiotic resistant backbones we are using.</div></td>
  </tr>
    </table>

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