Difference between revisions of "Team:Exeter/Parts"

 
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         <div class="collapse navbar-collapse" id="myNavbar">
 
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<li><a id="links" style="margin:10px 0 30px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Project">Lab Project</a></li>
 
<li><a id="links" style="margin:10px 0 30px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Project">Lab Project</a></li>
 
     <li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Labbook">Lab Book</a></li>
 
     <li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Labbook">Lab Book</a></li>
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<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Safety">Safety</a></li>
  
 
   </ul>
 
   </ul>
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<li><a id="links" style="margin:10px 0 30px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Awards">Awards</a></li>
 
<li><a id="links" style="margin:10px 0 30px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Awards">Awards</a></li>
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<li><span style="margin:10px 0 30px 2px;padding:0;">Special pages</span></li>
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<li><span style="margin:10px 0 30px 2px;padding:0;"><u>Special pages</u></span></li>
 
<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/HP/Silver">HP Silver</a></li>
 
<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/HP/Silver">HP Silver</a></li>
 
<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/HP/Gold">HP Gold</a></li>
 
<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/HP/Gold">HP Gold</a></li>
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<a href="#section_2" class="banner_link col-xs-6 col-sm-3"><span class="oneline">KillerOrange</span></a>
 
<a href="#section_2" class="banner_link col-xs-6 col-sm-3"><span class="oneline">KillerOrange</span></a>
 
<a href="#section_3" class="banner_link col-xs-6 col-sm-3"><span class="oneline">Lysozyme</span></a>
 
<a href="#section_3" class="banner_link col-xs-6 col-sm-3"><span class="oneline">Lysozyme</span></a>
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                                <a href="#section_4" class="banner_link col-xs-6 col-sm-3"><span class="oneline">DNase</span></a>
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                 <h6>Name</h6>
 
                 <h6>Name</h6>
  
−
                 <p id="pp">pT7- E. coli optimised - KillerRed (EOKR)</p>
+
                 <p id="pp">pT7- <i>E. coli</i> optimised - KillerRed (EOKR)</p>
  
 
                 <h6>Description</h6>
 
                 <h6>Description</h6>
  
−
                 <p id="pp">KillerRed is a red fluorescent protein that generates reactive oxygen species after illumination with light between the wavelengths of 540-580nm[1].</p>
+
                 <p id="pp">KillerRed is a red fluorescent protein that generates reactive oxygen species after illumination with light between the wavelengths of 540-580 nm[1].</p>
  
 
                 <p id="pp">We further characterised this kill switch by illuminating induced cultures 24 hours after induction with IPTG as well as uninduced cultures. After 6 hours in the light box CFU’s were counted to determine if the kill switch was successful. This was also reproduced on cultures grown in a ministat for 120 and 168 hours to test how long the kill switch remains functional. The full protocol can be found <a href="https://2016.igem.org/Team:Exeter/Project#section_4">here</a> and the results can be found <a href="https://2016.igem.org/Team:Exeter/Project#section_2">here</a>. </p>
 
                 <p id="pp">We further characterised this kill switch by illuminating induced cultures 24 hours after induction with IPTG as well as uninduced cultures. After 6 hours in the light box CFU’s were counted to determine if the kill switch was successful. This was also reproduced on cultures grown in a ministat for 120 and 168 hours to test how long the kill switch remains functional. The full protocol can be found <a href="https://2016.igem.org/Team:Exeter/Project#section_4">here</a> and the results can be found <a href="https://2016.igem.org/Team:Exeter/Project#section_2">here</a>. </p>
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                 <p id="pp">Here we are submitting KillerRed as a composite part under a T7 promoter (BBa_I712074), an Elowitz ribosome binding site (BBa_B0034) and a double terminator (BBa_B0015).</p>
 
                 <p id="pp">Here we are submitting KillerRed as a composite part under a T7 promoter (BBa_I712074), an Elowitz ribosome binding site (BBa_B0034) and a double terminator (BBa_B0015).</p>
  
−
                 <p id="pp">The sequence for KillerRed protein coding region can be found here (BBa_K1141002)</p>
+
                 <p id="pp">The sequence for KillerRed protein coding region can be found here <a href="http://parts.igem.org/Part:BBa_K1914002">(BBa_K1141002)</a></p>
  
 
                 <h6>Biobrick Code</h6>
 
                 <h6>Biobrick Code</h6>
  
−
                 <p id="pp">BBa_K1914003</p>
+
                 <p id="pp"><a href="http://parts.igem.org/Part:BBa_K1914003">BBa_K1914003</a></p>
 +
 
 +
<br>
 +
<br>
  
 
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<h6>Name:</h6>
 
<h6>Name:</h6>
  
−
                 <p id="pp">pT7- E. coli optimised - KillerOrange (EOKO)</p>
+
                 <p id="pp">pT7- <i>E. coli</i> optimised - KillerOrange (EOKO)</p>
  
 
                 <h6>Description:</h6>
 
                 <h6>Description:</h6>
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                 <p id="pp">KillerOrange has an excitation maximum of 512 nm and emission maximum at 555 nm and its absorbance spectrum has two peaks, at 455 and 514 nm. <p>
 
                 <p id="pp">KillerOrange has an excitation maximum of 512 nm and emission maximum at 555 nm and its absorbance spectrum has two peaks, at 455 and 514 nm. <p>
  
−
                 <p id="pp">It is believed that was confers KillerOrange's ability to generate reactive oxygen species depends on a water-filler channel reaching the chromophore area from the end cap of the ß-barrel [3].</p>
+
                 <p id="pp">The mechanism by which KillerOrange kills cells isn’t fully understood yet. However, it is believed that KillerOrange's ability to generate reactive oxygen species depends on a water-filler channel reaching the chromophore area from the end cap of the ß-barrel [3].</p>
−
 
+
−
                <p id="pp">The mechanism by which KillerOrange kills cells isn’t fully understood yet[3]. </p>
+
  
 +
               
 
                 <p id="pp">We characterised this part in the same way as KillerRed (<a href="https://2016.igem.org/Team:Exeter/Project#section_4">protocol</a>), and the results of which can be found <a href="https://2016.igem.org/Team:Exeter/Project#section_2">here</a></p>
 
                 <p id="pp">We characterised this part in the same way as KillerRed (<a href="https://2016.igem.org/Team:Exeter/Project#section_4">protocol</a>), and the results of which can be found <a href="https://2016.igem.org/Team:Exeter/Project#section_2">here</a></p>
  
 
                 <p id="pp">Here we are submitting KillerOrange as a composite part under a T7 promoter (BBa_I712074), an Elowitz ribosome binding site (BBa_B0034) and a double terminator (BBa_B0015).</p>
 
                 <p id="pp">Here we are submitting KillerOrange as a composite part under a T7 promoter (BBa_I712074), an Elowitz ribosome binding site (BBa_B0034) and a double terminator (BBa_B0015).</p>
  
−
                 <p id="pp">The sequence for KillerOrange protein coding region can be found here (BBa_K1914000)</p>
+
                 <p id="pp">The sequence for KillerOrange protein coding region can be found here <a href="http://parts.igem.org/Part:BBa_K1914000">(BBa_K1914000)</a></p>
  
 
                 <h6> Biobrick Code </h6>
 
                 <h6> Biobrick Code </h6>
−
                 <p id="pp">BBa_K1914001</p>
+
                 <p id="pp"><a href="http://parts.igem.org/Part:BBa_K1914001">BBa_K1914001</a></p>
 +
 
 +
<br>
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<br>
  
 
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<div id="section_3" class="link_fix"></div>
 
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<div id="contentTitle">
 
<div id="contentTitle">
−
LysozymeC
+
Lysozyme
 
</div>
 
</div>
 
<h6>Name:</h6>
 
<h6>Name:</h6>
  
−
                 <p id="pp">pT7 Lysozyme C E.coli codon optimised, signal peptide, flag tag</p>
+
                 <p id="pp">pT7 Lysozyme <i>E. coli</i> codon optimised, signal peptide, flag tag</p>
  
 
                 <h6>Description:</h6>
 
                 <h6>Description:</h6>
  
−
                 <p id="pp">Lysozyme C from chicken egg white, attacks the cell wall in bacteria by hydrolysing the ß-1,4 linkages between N-acetylmuramic acid and N-acetylglucosamine of peptidoglycan [4].</p>
+
                 <p id="pp">Lysozyme from chicken egg white, attacks the cell wall in bacteria by hydrolysing the ß-1,4 linkages between N-acetylmuramic acid and N-acetylglucosamine of peptidoglycan [4].</p>
  
 
                 <p id="pp"> </p>
 
                 <p id="pp"> </p>
 
                 <p id="pp">Characterisation of this part involved using the Enzcheck assay kit which detects lysozyme activity as a measure of fluorescence as well as using the same protocol we used to characterise KillerRed (<a href="https://2016.igem.org/Team:Exeter/Project#section_4">protocol</a>)and the results of which can be found <a href="https://2016.igem.org/Team:Exeter/Project#section_2">here</a></p>
 
                 <p id="pp">Characterisation of this part involved using the Enzcheck assay kit which detects lysozyme activity as a measure of fluorescence as well as using the same protocol we used to characterise KillerRed (<a href="https://2016.igem.org/Team:Exeter/Project#section_4">protocol</a>)and the results of which can be found <a href="https://2016.igem.org/Team:Exeter/Project#section_2">here</a></p>
  
−
                 <p id="pp">Here we are submitting lysozymeC as a composite part under a T7 promoter (BBa_I712074), an Elowitz ribosome binding site (BBa_B0034) and a double terminator (BBa_B0015).</p>
+
                 <p id="pp">Here we are submitting lysozyme as a composite part under a T7 promoter (BBa_I712074), an Elowitz ribosome binding site (BBa_B0034) and a double terminator (BBa_B0015).</p>
  
−
                 <p id="pp">We have codon optimised the protein coding region, added a FLAG tag and signal peptide directing Lysozyme to the periplasm.The sequence for LysozymeC protein coding region can be found here (BBa_K1914004)</p>
+
                 <p id="pp">We have codon optimised the protein coding region, added a FLAG tag and exchanged the native signal peptide for one which is <i>E. coli</i> specific and directs Lysozyme to the periplasm [5]. The sequence for Lysozyme protein coding region can be found here <a href="http://parts.igem.org/Part:BBa_K1914004">(BBa_K1914004)</a></p>
  
 
                 <h6> Biobrick Code </h6>
 
                 <h6> Biobrick Code </h6>
  
−
                 <p id="pp">BBa_K1914005</p>
+
                 <p id="pp"><a href="http://parts.igem.org/Part:BBa_K1914005">BBa_K1914005</a></p>
 +
 
 +
<br>
 +
<br>
  
 
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<div class="col-xs-12" style="padding:0;margin:0;">
 
                     <img src="https://static.igem.org/mediawiki/2016/c/c5/T--Exeter--parts-LYSO_png.png" style="max-width:50%;margin:auto;display:block;">
 
                     <img src="https://static.igem.org/mediawiki/2016/c/c5/T--Exeter--parts-LYSO_png.png" style="max-width:50%;margin:auto;display:block;">
 +
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<br>
 
<br>
 
<br>
 
<br>
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<div>
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<a id="Section_link" href="#section_4" style="display:block;margin:20px auto 0 auto;width:14px;"><span style="color:#47BCC2;font-size: 25px;" class="glyphicon glyphicon-menu-down" aria-hidden="true"></span></a>
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<div id="contentTitle">
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DNase
 +
</div>
 +
<h6>Name:</h6>
 +
 +
                <p id="pp">DNase</p>
 +
 +
                <h6>Description:</h6>
 +
 +
                <p id="pp"> DNase was designed [6] as a DNA degrading kill switch aiming to prevent cross contamination of DNA</p>
 +
 +
               
 +
                <p id="pp"> A composite part containing DNase could not be created. This could be due to the need for a tightly regulating promoter to prevent DNase protein being produced before induction and destroying DNA.</p>
 +
 +
<br>
 +
<br>
 +
 +
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 +
                    <img src="https://static.igem.org/mediawiki/2016/0/06/T--Exeter--parts-DNase_png.png" style="max-width:50%;margin:auto;display:block;">
 +
<br>
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<br>
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</li>
 
</li>
 
                     <li>Blake, C.C.F., Koenig, D.F., Mair, G.A., North, A.C.T., Phillips, D.C. and Sarma, V.R., 1965. Structure of hen egg-white lysozyme: a three-dimensional Fourier synthesis at 2 Å resolution. Nature, 206(4986), pp.757-761.
 
                     <li>Blake, C.C.F., Koenig, D.F., Mair, G.A., North, A.C.T., Phillips, D.C. and Sarma, V.R., 1965. Structure of hen egg-white lysozyme: a three-dimensional Fourier synthesis at 2 Å resolution. Nature, 206(4986), pp.757-761.
 +
</li>
 +
                    <li>Fischer, B., Perry, B., Phillips, G., Sumner, I. and Goodenough, P., 1993. Physiological consequence of expression of soluble and active hen egg white lysozyme in Escherichia coli. Applied Microbiology and Biotechnology, 39, pp.537–540.
 +
</li>
 +
                    <li>Chen, C.Y., Lu, S.C. and Liao, T.H.,1998. Cloning, sequencing and expression of a cDNA encoding bovine pancreatic deoxyribonuclease I in Escherichia coli: purification and characterization of the recombinant enzyme. Gene, 206, pp.181–184.
 
</li>
 
</li>
 
                 </ol>
 
                 </ol>

Latest revision as of 20:24, 19 October 2016