Difference between revisions of "Team:Dundee/Lab Book/Fingerprints"

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    <section id="about" class="row1">   
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          <a href="#section1" class="scroll"><span class="glyphicon glyphicon-briefcase"></span></a>
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          <h3>FluID</h3>
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          <p class="about-content">FluID is a cell free, all in one spray which will be used to detect and dinstiguish between body fluids found at crime scenes.</p>
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        <div class="col-lg-4">
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          <a href="#section2"><span class="glyphicon glyphicon-search" type="button"></span></a>
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          <h3>Chromate Biosensor</h3>
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          <p class="about-content">Our chromate biosensor is a device that will be used to detect stainless steel residues left behind on bones in blunt or sharp force trauma cases.</p>
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          <a href="#section3"><span class="glyphicon glyphicon-eye-open"></span></a>
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          <h3>Fingerprint Ageing</h3>
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          <p class="about-content">This device will search for the presence of a specifc component found in fingerprint deposits whose presence/absence will indicate approximate fingerprint age.</p>
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        </div>
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      </div>
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    </section>
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<!-- WEEK 1 -->
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        <div class="labtitle">Week Beginning 24/8/2015</div>
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          <p class="journal-summary-heading">Summary</p>
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        <p class="journal-content">Cloning of <i>LS</i> into the high expression vector pQE80-L was started this week.</p>
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            <span class="box-title">26/8: Amplification of <i>LS</i> for Cloning into pQE80-L</span>
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                <div id="collapsiblew1-1" class="collapse box-content">
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                  <p><b>Aim of Experiment:</b> To amplify <i>LS</i> for subsequent cloning into pQE80-L.</p>
 +
                  <p><b>Protocols Used:</b> <a data-toggle="modal" data-target="#PCR-modal" class="journal-protocol"> PCR</a></p>
 +
        <p><b>Results: </b> <a data-toggle="modal" data-target="#fp-figure1-modal" class="journal-protocol"> Figure 1</a> </p>
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                  <p><b>Next Steps:</b> The gel extracted PCR product will be digested and ligated into pQE80-L tomorrow.  </p>
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            <span class="box-title">27/8: Restriction Digests and Ligations of <i>LS</i> with pQE80-L</span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew1-2"></span>
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                <div id="collapsiblew1-2" class="collapse box-content">
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                  <p><b>Aim of experiment:</b> To set digest <i>LS</i> with BamHI and KpnI and set up ligations with the high expression vector pQE80-L. </p>
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                  <p><b>Protocols Used:</b> <a data-toggle="modal" data-target="#restrictiondigest-modal" class="journal-protocol">Restriction Digests</a> <a data-toggle="modal" data-target="#ligation-modal" class="journal-protocol"> Ligations</a> </p>
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        <p><b>Results:</b> N/A
 +
      <p><b>Next Steps:</b> Ligations will be left in the cold room over the weekend and transformed into M15pREP4 <i>E.coli</i> on Monday. </p>
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        </div>
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  </div>
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<!-- WEEK 2 -->
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        <div class="labtitle">Week Beginning 31/8/2015</div>
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        <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew2"></span>
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          <div class="box-content">
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          <p class="journal-summary-heading">Summary</p>
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        <p class="journal-content">Cloning of <i>LS</i> into pQE80-L was completed this week and cloning of <i>LS</i> into pSB1C3 was begun.</p>
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            <span class="box-title">31/8: Transformations of pQE80-L-<i>LS</i> into M15pREP4 <i>E.coli</i></span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew2-1"></span>
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                  <p><b>Aim of experiment:</b> To set up transformations of pQE80-L-<i>LS</i> into M15pREP4 <i>E.coli</i></p>
 +
                  <p><b>Protocols Used:</b> <a data-toggle="modal" data-target="#transformation-modal" class="journal-protocol">Transformations</a></p>
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        <p><b>Results:</b> N/A
 +
      <p><b>Next Steps:</b> If the transformations are successful, colonies will be selected for overnight cultures tomorrow. </p>
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            <span class="box-title">1/9: Overnight Cultures of M15pREP4 <i>E.coli</i> containing pQE80-L-<i>LS</i> </span>
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                  <p><b>Aim of experiment:</b> To set up overnight cultures of M15pREP4 <i>E.coli</i> containing pQE80-L-<i>LS</i>. </p>
 +
                  <p><b>Protocols Used:</b> <a data-toggle="modal" data-target="#onc-modal" class="journal-protocol">Overnight Cultures</a></p>
 +
        <p><b>Results:</b> N/A </p>
 +
      <p><b>Next Steps:</b> The overnight cultures will be miniprepped tomorrow.</p>
 +
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            <span class="box-title">2/9: Plasmid Purification of M15pREP4 <i>E.coli</i> Overnight Cultures containing pQE80-L-<i>LS</i> </span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew2-3"></span>
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                  <p><b>Aim of experiment:</b> To miniprep the M15pREP4 <i>E.coli</i> Overnight Cultures containing pQE80-L-<i>LS</i>. </p>
 +
                  <p><b>Protocols Used:</b> <a data-toggle="modal" data-target="#miniprep-modal" class="journal-protocol">Plasmid Purification</a></p>
 +
        <p><b>Results:</b> N/A </p>
 +
      <p><b>Next Steps:</b> The miniprep with highest concentration will be sent for sequencing. </p>
 +
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        </div>
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      <div class="row">
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      <div class="border-day">
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        <div class="box">
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            <span class="box-title">3/9: Amplification of <i>LS</i> for Cloning into pSB1C3</span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew2-4"></span>
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                <div id="collapsiblew2-4" class="collapse box-content">
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                  <p><b>Aim of experiment:</b> To amplify <i>LS</i> for cloning into pSB1C3.</p>
 +
                  <p><b>Protocols Used:</b> <a data-toggle="modal" data-target="#PCR-modal" class="journal-protocol">PCR</a></p>
 +
        <p><b>Results:</b> <a data-toggle="modal" data-target="#fp-figure2-modal" class="journal-protocol"> Figure 2</a>
 +
      <p><b>Next Steps:</b> The gel extracted PCR product will be digested tomorrow and ligations with pSB1C3 will be set up.  </p>
 +
                </div>
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      <div class="border-day">
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            <span class="box-title">19/6: Restriction Digests and Ligations of <i>LS</i> with pSB1C3</span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew2-5"></span>
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                <div id="collapsiblew2-5" class="collapse box-content">
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                  <p><b>Aim of experiment:</b> To digest the <i>LS</i> PCR product with EcoRI and PstI and then set up ligations with pSB1C3.</p>
 +
                  <p><b>Protocols Used:</b> <a data-toggle="modal" data-target="#restrictiondigest-modal" class="journal-protocol">Restriction Digests</a> <a data-toggle="modal" data-target="#ligation-modal" class="journal-protocol">Ligations</a></p>
 +
        <p><b>Results:</b> N/A
 +
      <p><b>Next Steps:</b> Ligations will be left over the weekend and transformed into JM110 <i>E.coli</i> on Monday. </p>
 +
                </div>
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        </div>
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        </div>
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      </div>
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        </div>
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  </div>
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  </div>
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<!-- WEEK 3 -->
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        <div class="labtitle">Week Beginning 7/9/15</div>
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        <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew3"></span>
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          <div class="box-content">
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          <p class="journal-summary-heading">Summary</p>
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 +
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        <p class="journal-content"> Cloning of <i>LS</i> into pSB1C3 was completed this week and sequencing confirmed it was successfully inserted into pQE80-L so overexpression assays were performed where LS was characterised via Western Blotting. </p>
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        <div id="collapsiblew3" class="collapse week-content">
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      <div class="border-day">
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            <span class="box-title">7/9: Transformations of pSB1C3-<i>LS</i> into JM110 <i>E.coli</i></span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew3-1"></span>
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                <div id="collapsiblew3-1" class="collapse box-content">
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                  <p><b>Aim of experiment:</b> To transform pSB1C3-<i>LS</i> into JM110 <i>E.coli</i>.</p>
 +
                  <p><b>Protocols Used: </b><a data-toggle="modal" data-target="#transformation-modal" class="journal-protocol"> Transformations</a></p>
 +
                  <p><b>Results:</b>N/A </p>
 +
<p><b>Next Steps:</b>If transformations are successful, overnight cultures will be set up tomorrow.</p>
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</div>
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        </div>
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      <div class="row">
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      <div class="border-day">
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            <span class="box-title">8/9: Overnight Cultures of JM110 <i>E.coli</i> containing pSB1C3-<i>LS</i></span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew3-2"></span>
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                <div id="collapsiblew3-2" class="collapse box-content">
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                  <p><b>Aim of experiment:</b> To set up overnight cultures of JM110 <i>E.coli</i> containing pSB1C3-<i>LS</i> from the transformations carried out yesterday.</p>
 +
                  <p><b>Protocols Used: </b><a data-toggle="modal" data-target="#onc-modal" class="journal-protocol"> Overnight Cultures</a></p>
 +
                  <p><b>Results:</b> N/A </p>
 +
<p><b>Next Steps:</b> The overnight cultures will be miniprepped and sent for sequencing tomorrow. </p>
 +
</div>
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      <div class="border-day">
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        <div class="box">
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            <span class="box-title">9/9: Plasmid Purification of the JM110 <i>E.coli</i> Overnight Cultures containing pSB1C3-<i>LS</i></i></span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew3-3"></span>
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                <div id="collapsiblew3-3" class="collapse box-content">
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                  <p><b>Aim of experiment:</b> To miniprep the JM110 <i>E.coli</i> Overnight Cultures containing pSB1C3-<i>LS</i>.</p>
 +
                  <p><b>Protocols Used: </b></p><a data-toggle="modal" data-target="#miniprep-modal" class="journal-protocol"> Plasmid Purification (QIAprep® Spin Miniprep Kit)</a></p>
 +
                  <p><b>Results:</b> N/A</p>
 +
<p><b>Next Steps:</b> The miniprep with the highest concentration will be sent for sequencing to confirm presence of insert. Sequencing for pQE80-L-<i>LS</i> came back correct so overexpression assays will be started tomorrow. </p>
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      <div class="border-day">
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            <span class="box-title">10/9: Overexpression Assays of <i>LS</i> </span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew3-4"></span>
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                <div id="collapsiblew3-4" class="collapse box-content">
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                  <p><b>Aim of experiment:</b> To set up overexpression assays of <i>LS</i> using different concentrations of IPTG.</p>
 +
                  <p><b>Protocols Used: </b><a data-toggle="modal" data-target="#sds-modal" class="journal-protocol"> Overexpression Assays</a> Note: Cultures were induced with 0 mM, 0.5 mM, 1 mM and 2 mM IPTG. The membrane for the blot was left blocking overnight.</p>
 +
                  <p><b>Results:</b> <a data-toggle="modal" data-target="#fp-figure3-modal" class="journal-protocol"> Figure 3 </a> </p>
 +
<p><b>Next Steps:</b> The gel shows a band corresponding to the expected size of LS. However, Western Blotting will confirm if it is indeed LS. </p>
 +
</div>
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      <div class="border-day">
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        <div class="box">
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            <span class="box-title">11/9: Characterisation of LS</span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew3-5"></span>
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                <div id="collapsiblew3-5" class="collapse box-content">
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                  <p><b>Aim of experiment:</b> To complete characterisation of LS via Western Blotting.</p>
 +
                  <p><b>Protocols Used: </b><a data-toggle="modal" data-target="#sds-modal" class="journal-protocol"> Westen Blotting</a> </p>
 +
                  <p><b>Results:</b><a data-toggle="modal" data-target="#fp-figure4-modal" class="journal-protocol"> Figure 4 </a></p>
 +
<p><b>Next Steps:</b> The blot shows that LS has been successfully detected at the expected size of 80 kDa. There is also partial degradation of the protein. Nevertheless, purification of LS will be started next week. </p>
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</div>
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        </div>
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    </div>
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  </div>
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  </div>
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<!-- WEEK 4 -->
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<div class="row">
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    <div class="border-week">
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    <div class="box">
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        <div class="labtitle">Week Beginning 14/9/15</div>
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        <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew4"></span>
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          <div class="box-content">
 +
          <p class="journal-summary-heading">Summary</p>
 +
           
 +
 +
        <p class="journal-content">Purification of lanosterol synthase was started this week.</p>
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        <div id="collapsiblew4" class="collapse week-content">
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            <span class="box-title">14/9: Overnight Cultures of M15pREP4 <i>E.coli</i> containing pQE80-L-<i>LS</i></span>
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              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew4-1"></span>
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                  <p><b>Aim of Experiment:</b> To set up overnight cultures of M15pREP4 <i>E.coli</i> containing pQE80-L-<i>LS</i>.</p>
 +
                  <p><b>Protocols Used:</b> <a data-toggle="modal" data-target="#onc-modal" class="journal-protocol"> Overnight Cultures</a> Note: 150 ml cultures were set up.</p>
 +
        <p><b>Results: </b>N/A</p>
 +
                  <p><b>Next Steps:</b> The overnight cultures will be used to innoculate a 3 L day culture tomorrow.</p>
 +
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      <div class="border-day">
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            <span class="box-title">15/9: 3 L Day Cultures of M15pREP4 <i>E.coli</i> containing pQE80-L-<i>LS</i></span>
 +
              <span type="button" class="chevron_toggleable box-btn glyphicon glyphicon-chevron-down" data-toggle="collapse" data-target="#collapsiblew4-2"></span>
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                  <p><b>Aim of experiment:</b> To set up 3 L day cultures of M15pREP4 <i>E.coli</i> containing pQE80-L-<i>LS</i>.</p>
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                  <p><b>Protocols Used:</b> <a data-toggle="modal" data-target="#pp-modal" class="journal-protocol"> Protein Purification </a> Note: The protocol was stopped at Step 6- protein purification will be continued tomorrow. </p>
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        <p><b>Results:</b> N/A </p>
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      <p><b>Next Steps:</b> Affinity chromatography will be carried out tomorrow.</p>
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            <span class="box-title">16/9: Purification of LS</span>
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                  <p><b>Aim of experiment:</b> To continue purification of LS. </p>
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                  <p><b>Protocols Used:</b><a data-toggle="modal" data-target="#pp-modal" class="journal-protocol"> Protein Purification</a> Note: Protocol was stopped at Step 13.</p>
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        <p><b>Results:</b> <a data-toggle="modal" data-target="#fp-figure5-modal" class="journal-protocol"> Figure 5 </a> <a data-toggle="modal" data-target="#fp-figure6-modal" class="journal-protocol"> Figure 6 </a>
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      <p><b>Next Steps:</b> The SDS gel suggests that the peak observed in the affinity chromatography step may due to a smaller sized protein which has shown up strongly on the gel. However, there is still a band observable around the 75 kDa marker which may be LS. The samples will be pooled together and concentrated. A small sample will be blotted and then size exclusion chromaography can be performed. </p>
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Revision as of 15:56, 17 September 2015

Fingerprint Aging

Lab Book

FluID

FluID is a cell free, all in one spray which will be used to detect and dinstiguish between body fluids found at crime scenes.

Chromate Biosensor

Our chromate biosensor is a device that will be used to detect stainless steel residues left behind on bones in blunt or sharp force trauma cases.

Fingerprint Ageing

This device will search for the presence of a specifc component found in fingerprint deposits whose presence/absence will indicate approximate fingerprint age.

Week Beginning 24/8/2015

Summary

Cloning of LS into the high expression vector pQE80-L was started this week.

26/8: Amplification of LS for Cloning into pQE80-L

Aim of Experiment: To amplify LS for subsequent cloning into pQE80-L.

Protocols Used: PCR

Results: Figure 1

Next Steps: The gel extracted PCR product will be digested and ligated into pQE80-L tomorrow.

27/8: Restriction Digests and Ligations of LS with pQE80-L

Aim of experiment: To set digest LS with BamHI and KpnI and set up ligations with the high expression vector pQE80-L.

Protocols Used: Restriction Digests Ligations

Results: N/A

Next Steps: Ligations will be left in the cold room over the weekend and transformed into M15pREP4 E.coli on Monday.

Week Beginning 31/8/2015

Summary

Cloning of LS into pQE80-L was completed this week and cloning of LS into pSB1C3 was begun.

31/8: Transformations of pQE80-L-LS into M15pREP4 E.coli

Aim of experiment: To set up transformations of pQE80-L-LS into M15pREP4 E.coli

Protocols Used: Transformations

Results: N/A

Next Steps: If the transformations are successful, colonies will be selected for overnight cultures tomorrow.

1/9: Overnight Cultures of M15pREP4 E.coli containing pQE80-L-LS

Aim of experiment: To set up overnight cultures of M15pREP4 E.coli containing pQE80-L-LS.

Protocols Used: Overnight Cultures

Results: N/A

Next Steps: The overnight cultures will be miniprepped tomorrow.

2/9: Plasmid Purification of M15pREP4 E.coli Overnight Cultures containing pQE80-L-LS

Aim of experiment: To miniprep the M15pREP4 E.coli Overnight Cultures containing pQE80-L-LS.

Protocols Used: Plasmid Purification

Results: N/A

Next Steps: The miniprep with highest concentration will be sent for sequencing.

3/9: Amplification of LS for Cloning into pSB1C3

Aim of experiment: To amplify LS for cloning into pSB1C3.

Protocols Used: PCR

Results: Figure 2

Next Steps: The gel extracted PCR product will be digested tomorrow and ligations with pSB1C3 will be set up.

19/6: Restriction Digests and Ligations of LS with pSB1C3

Aim of experiment: To digest the LS PCR product with EcoRI and PstI and then set up ligations with pSB1C3.

Protocols Used: Restriction Digests Ligations

Results: N/A

Next Steps: Ligations will be left over the weekend and transformed into JM110 E.coli on Monday.

Week Beginning 7/9/15

Summary

Cloning of LS into pSB1C3 was completed this week and sequencing confirmed it was successfully inserted into pQE80-L so overexpression assays were performed where LS was characterised via Western Blotting.

7/9: Transformations of pSB1C3-LS into JM110 E.coli

Aim of experiment: To transform pSB1C3-LS into JM110 E.coli.

Protocols Used: Transformations

Results:N/A

Next Steps:If transformations are successful, overnight cultures will be set up tomorrow.

8/9: Overnight Cultures of JM110 E.coli containing pSB1C3-LS

Aim of experiment: To set up overnight cultures of JM110 E.coli containing pSB1C3-LS from the transformations carried out yesterday.

Protocols Used: Overnight Cultures

Results: N/A

Next Steps: The overnight cultures will be miniprepped and sent for sequencing tomorrow.

9/9: Plasmid Purification of the JM110 E.coli Overnight Cultures containing pSB1C3-LS

Aim of experiment: To miniprep the JM110 E.coli Overnight Cultures containing pSB1C3-LS.

Protocols Used:

Plasmid Purification (QIAprep® Spin Miniprep Kit)

Results: N/A

Next Steps: The miniprep with the highest concentration will be sent for sequencing to confirm presence of insert. Sequencing for pQE80-L-LS came back correct so overexpression assays will be started tomorrow.

10/9: Overexpression Assays of LS

Aim of experiment: To set up overexpression assays of LS using different concentrations of IPTG.

Protocols Used: Overexpression Assays Note: Cultures were induced with 0 mM, 0.5 mM, 1 mM and 2 mM IPTG. The membrane for the blot was left blocking overnight.

Results: Figure 3

Next Steps: The gel shows a band corresponding to the expected size of LS. However, Western Blotting will confirm if it is indeed LS.

11/9: Characterisation of LS

Aim of experiment: To complete characterisation of LS via Western Blotting.

Protocols Used: Westen Blotting

Results: Figure 4

Next Steps: The blot shows that LS has been successfully detected at the expected size of 80 kDa. There is also partial degradation of the protein. Nevertheless, purification of LS will be started next week.

Week Beginning 14/9/15

Summary

Purification of lanosterol synthase was started this week.

14/9: Overnight Cultures of M15pREP4 E.coli containing pQE80-L-LS

Aim of Experiment: To set up overnight cultures of M15pREP4 E.coli containing pQE80-L-LS.

Protocols Used: Overnight Cultures Note: 150 ml cultures were set up.

Results: N/A

Next Steps: The overnight cultures will be used to innoculate a 3 L day culture tomorrow.

15/9: 3 L Day Cultures of M15pREP4 E.coli containing pQE80-L-LS

Aim of experiment: To set up 3 L day cultures of M15pREP4 E.coli containing pQE80-L-LS.

Protocols Used: Protein Purification Note: The protocol was stopped at Step 6- protein purification will be continued tomorrow.

Results: N/A

Next Steps: Affinity chromatography will be carried out tomorrow.

16/9: Purification of LS

Aim of experiment: To continue purification of LS.

Protocols Used: Protein Purification Note: Protocol was stopped at Step 13.

Results: Figure 5 Figure 6

Next Steps: The SDS gel suggests that the peak observed in the affinity chromatography step may due to a smaller sized protein which has shown up strongly on the gel. However, there is still a band observable around the 75 kDa marker which may be LS. The samples will be pooled together and concentrated. A small sample will be blotted and then size exclusion chromaography can be performed.