http://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&feed=atom&action=historyTeam:TU Delft/19 July 2010 content - Revision history2024-03-29T07:14:33ZRevision history for this page on the wikiMediaWiki 1.16.5http://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&diff=48681&oldid=prevMvoges: /* Characterization of Anderson RBS sequences */2010-08-12T15:01:30Z<p><span class="autocomment">Characterization of Anderson RBS sequences</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To all samples with an end volume of 25 μL, 2.5 μL ligase buffer was added.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To all samples with an end volume of 25 μL, 2.5 μL ligase buffer was added.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In the likelihood that the abovementioned method will not yield desired transformants, a [[Team:TU_Delft/protocols/PCR|PCR amplification]] of E0240 was performed in three-fold. The resulting product over 1% agarose gel can be seen below. The PCR amplification product was subsequently digested using XbaI and PstI for later insertion into previously digested (SpeI and PstI) J23100(in J61002).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In the likelihood that the abovementioned method will not yield desired transformants, a [[Team:TU_Delft/protocols/PCR|PCR amplification]] of E0240 was performed in three-fold <ins class="diffchange diffchange-inline">in accordance with method 3</ins>. The resulting product over 1% agarose gel can be seen below. The PCR amplification product was subsequently digested using XbaI and PstI for later insertion into previously digested (SpeI and PstI) J23100(in J61002).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Team:TU_Delft/protocols/agarose_gel |1% Agarose gel]] of E0240 PCR product:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Team:TU_Delft/protocols/agarose_gel |1% Agarose gel]] of E0240 PCR product:</div></td></tr>
</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&diff=48679&oldid=prevMvoges: /* Characterization of Anderson RBS sequences */2010-08-12T14:59:47Z<p><span class="autocomment">Characterization of Anderson RBS sequences</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to continue progress made on the <del class="diffchange diffchange-inline">third </del>method, described in the blog of [https://2010.igem.org/Team:TU_Delft#page=pages/blog&blog=14_July_2010 July 14th] for the assembly of the reference construct J23100-B0032-E0040-B0015, the following [[Team:TU_Delft/protocols/restriction_enzyme_digestion_40| Digestions]] were performed:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to continue progress made on the <ins class="diffchange diffchange-inline">fourth </ins>method, described in the blog of [https://2010.igem.org/Team:TU_Delft#page=pages/blog&blog=14_July_2010 July 14th] for the assembly of the reference construct J23100-B0032-E0040-B0015, the following [[Team:TU_Delft/protocols/restriction_enzyme_digestion_40| Digestions]] were performed:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To all samples with an end volume of 25 μL, 2.5 μL ligase buffer was added.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To all samples with an end volume of 25 μL, 2.5 μL ligase buffer was added.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">Note: The above method is not exactly the proposed method #3, but a variation without PCR amplification of E0240. This is less elegant; while a re-ligation of the J61002 plasmid will result in colonies with red fluorescence, a re-ligation of the pSB1A2 plasmid containing E0240 cannot easily be screened against (or selected against as both contain ampicillin markers).</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the likelihood that the abovementioned method will not yield desired transformants, a [[Team:TU_Delft/protocols/PCR|PCR amplification]] of E0240 was performed in three-fold. The resulting product over 1% agarose gel can be seen below. The PCR amplification product was subsequently digested using XbaI and PstI for later insertion into previously digested (SpeI and PstI) J23100(in J61002).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In the likelihood that the abovementioned method will not yield desired transformants, a [[Team:TU_Delft/protocols/PCR|PCR amplification]] of E0240 was performed in three-fold. The resulting product over 1% agarose gel can be seen below. The PCR amplification product was subsequently digested using XbaI and PstI for later insertion into previously digested (SpeI and PstI) J23100(in J61002).</div></td></tr>
</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&diff=48517&oldid=prevMvoges: /* Characterization of Anderson RBS sequences */2010-08-12T12:14:19Z<p><span class="autocomment">Characterization of Anderson RBS sequences</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|2</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|2</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|1 μg E0240 <del class="diffchange diffchange-inline">+ </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|1 μg E0240</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|XbaI </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|XbaI </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|PstI </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|PstI </div></td></tr>
</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&diff=48516&oldid=prevMvoges: /* Characterization of Anderson RBS sequences */2010-08-12T12:11:49Z<p><span class="autocomment">Characterization of Anderson RBS sequences</span></p>
<table style="background-color: white; color:black;">
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<td colspan='2' style="background-color: white; color:black;">Revision as of 12:11, 12 August 2010</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|T1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|T1</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|<del class="diffchange diffchange-inline">J23100-B0030</del>-I13401 </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">K081005</ins>-I13401 </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|pSB1A2</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|pSB1A2</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|T2</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|T2</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|<del class="diffchange diffchange-inline">J23100-B0030</del>-I13401 </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">K081005</ins>-I13401 </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|pSB1A2</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|pSB1A2</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
</table>Mvogeshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&diff=46544&oldid=prevNadinebongaerts: /* Ordered DNA + Solvent Tolerance and Hydrocarbon Sensing */2010-08-10T10:13:02Z<p><span class="autocomment">Ordered DNA + Solvent Tolerance and Hydrocarbon Sensing</span></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 10:13, 10 August 2010</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The frozen pellet of [https://2010.igem.org/Team:TU_Delft#page=pages/blog&blog=16_July_2010 last week] were isolated using [[Team:TU_Delft/protocols/birnboim_plasmid_isolation|Birnboim protocol]].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The frozen pellet of [https://2010.igem.org/Team:TU_Delft#page=pages/blog&blog=16_July_2010 last week] were isolated using [[Team:TU_Delft/protocols/birnboim_plasmid_isolation|Birnboim protocol]].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The following plasmid concentrations were obtained: </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The following plasmid concentrations were obtained <ins class="diffchange diffchange-inline">using the nanodrop</ins>: </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| style="color:black; background-color:white;" cellpadding="5" cellspacing="0" border="1"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| style="color:black; background-color:white;" cellpadding="5" cellspacing="0" border="1"</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''BioBrick'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''BioBrick'''</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''Concentration (ng/μL)'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''Concentration (ng/μL)'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">K398328T</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">AlkS and B0015</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">145.01</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">K398407T</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">PhPFDa and B0032</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">37.8</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">Control</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">pSB1T3 and B0015</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">71.65</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">K398300C</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">AlkS</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">24.54</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">Control</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">pSB1C3</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">93.86</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">K398200C</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">AlnA</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">4.23</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">K398000C</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">LadA</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<ins class="diffchange diffchange-inline">148.14</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|-</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|K398002C</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|RubA3</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|119.85</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|-</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|K398201C</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|OprG</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|161.28</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|-</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|K398400C</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|PhPFDa</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">|163.33</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
</table>Nadinebongaertshttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&diff=43398&oldid=prevEbrinkman at 20:05, 5 August 20102010-08-05T20:05:23Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''Buffer'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''Buffer'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''BSA'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|'''BSA'''</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|'''<del class="diffchange diffchange-inline">desired </del>fragment'''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|'''<ins class="diffchange diffchange-inline">Needed </ins>fragment'''</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|1</div></td></tr>
</table>Ebrinkmanhttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&diff=40505&oldid=prevJcnossen: /* Characterization of Anderson RBS sequences */2010-08-03T12:45:55Z<p><span class="autocomment">Characterization of Anderson RBS sequences</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Characterization of Anderson RBS sequences==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Characterization of Anderson RBS sequences==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h5>Assembly of reference construct</h5></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h5>Assembly of reference construct</h5></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[https://2010.igem.org/Team:TU_Delft#/blog<del class="diffchange diffchange-inline">?</del>blog=16_July_2010 Friday's] ligation products, ligation control and digestion control were [https://2010.igem.org/Team:TU_Delft/protocols/transformation transformed] into chemically competent Top10 cells and incubated on ampicillin plates. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[https://2010.igem.org/Team:TU_Delft#<ins class="diffchange diffchange-inline">page=pages</ins>/blog<ins class="diffchange diffchange-inline">&</ins>blog=16_July_2010 Friday's] ligation products, ligation control and digestion control were [https://2010.igem.org/Team:TU_Delft/protocols/transformation transformed] into chemically competent Top10 cells and incubated on ampicillin plates. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| style="color:black; background-color:white;" cellpadding="5" cellspacing="0" border="1"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| style="color:black; background-color:white;" cellpadding="5" cellspacing="0" border="1"</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 481:</td>
<td colspan="2" class="diff-lineno">Line 481:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to continue progress made on the third method, described in the blog of [https://2010.igem.org/Team:TU_Delft#/blog<del class="diffchange diffchange-inline">?</del>blog=14_July_2010 July 14th] for the assembly of the reference construct J23100-B0032-E0040-B0015, the following [[Team:TU_Delft/protocols/restriction_enzyme_digestion_40| Digestions]] were performed:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to continue progress made on the third method, described in the blog of [https://2010.igem.org/Team:TU_Delft#<ins class="diffchange diffchange-inline">page=pages</ins>/blog<ins class="diffchange diffchange-inline">&</ins>blog=14_July_2010 July 14th] for the assembly of the reference construct J23100-B0032-E0040-B0015, the following [[Team:TU_Delft/protocols/restriction_enzyme_digestion_40| Digestions]] were performed:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| style="color:black; background-color:white;" cellpadding="5" cellspacing="0" border="1"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| style="color:black; background-color:white;" cellpadding="5" cellspacing="0" border="1"</div></td></tr>
</table>Jcnossenhttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&diff=40501&oldid=prevJcnossen: /* Ordered DNA + Solvent Tolerance and Hydrocarbon Sensing */2010-08-03T12:44:55Z<p><span class="autocomment">Ordered DNA + Solvent Tolerance and Hydrocarbon Sensing</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Ordered DNA + Solvent Tolerance and Hydrocarbon Sensing==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Ordered DNA + Solvent Tolerance and Hydrocarbon Sensing==</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The frozen pellet of [https://2010.igem.org/Team:TU_Delft/<del class="diffchange diffchange-inline">16_July_2010_content </del>last week] were isolated using [[Team:TU_Delft/protocols/birnboim_plasmid_isolation|Birnboim protocol]].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The frozen pellet of [https://2010.igem.org/Team:TU_Delft<ins class="diffchange diffchange-inline">#page=pages</ins>/<ins class="diffchange diffchange-inline">blog&blog=16_July_2010 </ins>last week] were isolated using [[Team:TU_Delft/protocols/birnboim_plasmid_isolation|Birnboim protocol]].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The following plasmid concentrations were obtained: </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The following plasmid concentrations were obtained: </div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 42:</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Because not all [https://2010.igem.org/Team:TU_Delft/<del class="diffchange diffchange-inline">14_July_2010_content </del>ligation mixes] resulted in transformants were repeated the [[Team:TU_Delft/protocols/transformation|transformation]] with the overnight ligated reactions.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Because not all [https://2010.igem.org/Team:TU_Delft<ins class="diffchange diffchange-inline">#page=pages</ins>/<ins class="diffchange diffchange-inline">blog&blog=14_July_2010 </ins>ligation mixes] resulted in transformants were repeated the [[Team:TU_Delft/protocols/transformation|transformation]] with the overnight ligated reactions.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Alkane degradation==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Alkane degradation==</div></td></tr>
</table>Jcnossenhttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&diff=39986&oldid=prevEbrinkman at 19:32, 2 August 20102010-08-02T19:32:09Z<p></p>
<table style="background-color: white; color:black;">
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Biobricks in production: K398007T, K398008T, K398009T, K398010T, K398016T, K398017T & K398018T</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Biobricks in production: K398007T, K398008T, K398009T, K398010T, K398016T, K398017T & K398018T</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><h4</del>>Digestion<del class="diffchange diffchange-inline"></h4></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">====</ins>>Digestion<ins class="diffchange diffchange-inline">====</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Team:TU_Delft/protocols/restriction_enzyme_digestion| Digestion reactions]]:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Team:TU_Delft/protocols/restriction_enzyme_digestion| Digestion reactions]]:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 280:</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><h4></del>Ligation<del class="diffchange diffchange-inline"></h4></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">====</ins>Ligation<ins class="diffchange diffchange-inline">====</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The digestion products were [[Team:TU_Delft/protocols/ligation|ligated]] over night:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The digestion products were [[Team:TU_Delft/protocols/ligation|ligated]] over night:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 355:</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Since last weeks attempt to construct the inducible protomer R0011 with RBS B0032 failed, we decided to take a different approach. Instead of doing the standard 2 parts assembly, we amplify the promoter by PCR digest it and ligate in the plasmid that contains the RBS which has only be cut open at the left side. By doing so we do not risk losing the super small DNA fragments like the RBS. The problem is that we cannot use antibiotics selection. So we need to determine that by colony PCR and sequencing.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Since last weeks attempt to construct the inducible protomer R0011 with RBS B0032 failed, we decided to take a different approach. Instead of doing the standard 2 parts assembly, we amplify the promoter by PCR digest it and ligate in the plasmid that contains the RBS which has only be cut open at the left side. By doing so we do not risk losing the super small DNA fragments like the RBS. The problem is that we cannot use antibiotics selection. So we need to determine that by colony PCR and sequencing.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><h4></del>PCR Amplification<del class="diffchange diffchange-inline"></h4></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">====</ins>PCR Amplification<ins class="diffchange diffchange-inline">====</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>R0011 was [[Team:TU_Delft/protocols/PCR|amplified]] with the universal primers G00100 and G00101. The product was put on [[Team:TU_Delft/protocols/agarose_gel|1% agarose gel]]:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>R0011 was [[Team:TU_Delft/protocols/PCR|amplified]] with the universal primers G00100 and G00101. The product was put on [[Team:TU_Delft/protocols/agarose_gel|1% agarose gel]]:</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 387:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The PCR band is about 300 bps long. R0011 itself is just 55 bp, but the flanking primer regions are about 100 bp each.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The PCR band is about 300 bps long. R0011 itself is just 55 bp, but the flanking primer regions are about 100 bp each.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline"><h4></del>Digestion<del class="diffchange diffchange-inline"></h4></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">====</ins>Digestion<ins class="diffchange diffchange-inline">====</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The PCR product of promotor R0011 was cut with EcoRI and SpeI and the RBS containing plasmid has been cut open with EcoRI and Xbal for 2.5 hours at 37 °C. This deviates from the standard biobrick assembly, thus is not completely as described in our [[Team:TU_Delft/protocols/restriction_enzyme_digestion|digestion protocol]].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The PCR product of promotor R0011 was cut with EcoRI and SpeI and the RBS containing plasmid has been cut open with EcoRI and Xbal for 2.5 hours at 37 °C. This deviates from the standard biobrick assembly, thus is not completely as described in our [[Team:TU_Delft/protocols/restriction_enzyme_digestion|digestion protocol]].</div></td></tr>
</table>Ebrinkmanhttp://2010.igem.org/wiki/index.php?title=Team:TU_Delft/19_July_2010_content&diff=39886&oldid=prevEbrinkman at 18:54, 2 August 20102010-08-02T18:54:31Z<p></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 18:54, 2 August 2010</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|PstI</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|PstI</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|2 (BioLabs)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|2 (BioLabs)</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|✓<del class="diffchange diffchange-inline">) </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|✓</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|‘X–rubA3–P’</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|‘X–rubA3–P’</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|ALDH + XbaI + PstI</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|ALDH + XbaI + PstI</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|1521, 1618, 705</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|1521, 1618, 705</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>|<font color=limegreen><del class="diffchange diffchange-inline">&#10004;</del></font></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>|<font color=limegreen><ins class="diffchange diffchange-inline">✓</ins></font></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|Originally in a Kan backbone which gives an extra fragment of 800 bp when cut, rest of the backbone and the fragment both ~ 1500, so overlap</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|Originally in a Kan backbone which gives an extra fragment of 800 bp when cut, rest of the backbone and the fragment both ~ 1500, so overlap</div></td></tr>
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</table>Ebrinkman