http://2013.igem.org/wiki/index.php?title=Team:UNITN-Trento/Notebook/Labposts/08/37&feed=atom&action=historyTeam:UNITN-Trento/Notebook/Labposts/08/37 - Revision history2024-03-29T08:22:46ZRevision history for this page on the wikiMediaWiki 1.16.5http://2013.igem.org/wiki/index.php?title=Team:UNITN-Trento/Notebook/Labposts/08/37&diff=273570&oldid=prevGgirelli at 09:12, 3 October 20132013-10-03T09:12:58Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 09:12, 3 October 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</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> "date" : "2013-08-<del class="diffchange diffchange-inline">14</del>",</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> "date" : "2013-08-<ins class="diffchange diffchange-inline">15</ins>",</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> "author" : "fabio-thomas",</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> "author" : "fabio-thomas",</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> "title" : " blue light induction, <del class="diffchange diffchange-inline">NO WAY!</del>!",</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> "title" : " blue light induction, <ins class="diffchange diffchange-inline">festivity time</ins>!",</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> "content" : " <html> <del class="diffchange diffchange-inline"> this morning I saw the results of the experiment and… horror</del>: the <del class="diffchange diffchange-inline">induced bacteria pellet was lighter </del>then the <del class="diffchange diffchange-inline">other two pellets </del>(<del class="diffchange diffchange-inline">by </del>the <del class="diffchange diffchange-inline">way</del>, <del class="diffchange diffchange-inline">they weren’t blue, just a little bit bluish </del>) <del class="diffchange diffchange-inline">THAT SHOULDN’T HAVE HAPPENED!dang it</del>.<del class="diffchange diffchange-inline">Maybe the blue LED was too intense</del>, <del class="diffchange diffchange-inline">maybe there’s something wrong with our device</del>, <del class="diffchange diffchange-inline">don’t know. We only need to take a crack at some other solution at </del>the <del class="diffchange diffchange-inline">same time in order to solve this problem</del>: <del class="diffchange diffchange-inline">first I will repeat </del>the <del class="diffchange diffchange-inline">experiment with less intense blue light</del>, <del class="diffchange diffchange-inline">then </del>we <del class="diffchange diffchange-inline">are thinking about cotransforming bacteria with two plasmids</del>, <del class="diffchange diffchange-inline">one with j23100-YF1-Fixj</del>, <del class="diffchange diffchange-inline">the other with -FixK2-CI-Plambda-amilCPbecause </del>we <del class="diffchange diffchange-inline">noticed that the device used yesterday lacks a terminator after fixJ </del>and <del class="diffchange diffchange-inline">that could be the reason of the disfunction. Thomas made the cotransformation plates even though the plasmids actually aren’t compatible</del>. Meanwhile <del class="diffchange diffchange-inline">we discussed about using a new backbone for </del>the <del class="diffchange diffchange-inline">separate parts so that cotransformation could be achievable: so we made PCR amplification of </del>the <del class="diffchange diffchange-inline">new vector pSB4K5</del>, the <del class="diffchange diffchange-inline">first part </del>(<del class="diffchange diffchange-inline">j23100-YF1-FixJ</del>) and <del class="diffchange diffchange-inline">K592020 (FixK2-CI-Plambda-amilCP)</del>. <del class="diffchange diffchange-inline">As we can see from </del>the <del class="diffchange diffchange-inline">gel</del>, the <del class="diffchange diffchange-inline">screening of (j23100_YF1_FixJ) didn’t succeed</del>, <del class="diffchange diffchange-inline">probably because the backbone’s structure is quite unusual</del>.Furthermore I <del class="diffchange diffchange-inline">tried also to plate the entire device on 3 plates in order to make </del>some <del class="diffchange diffchange-inline">mask experiment (induce </del>colonies <del class="diffchange diffchange-inline">on </del>the <del class="diffchange diffchange-inline">plate)</del>.</html>",</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> "content" : "<html> <ins class="diffchange diffchange-inline">after yesterday disastrous PCR, we decided to take another direction</ins>: <ins class="diffchange diffchange-inline">put </ins>the <ins class="diffchange diffchange-inline">terminator B0015 downstream of j23100_YF1_FixJ, </ins>then <ins class="diffchange diffchange-inline">rebuild </ins>the <ins class="diffchange diffchange-inline">complete device.We started from digestion </ins>(<ins class="diffchange diffchange-inline">biobrick cloning protocol) of 500 ng in 25 ul of both </ins>the <ins class="diffchange diffchange-inline">parts (j23100_YF1_FixJ part starting concentration= 234 ng/ul and B0015 starting concentration = 309</ins>,<ins class="diffchange diffchange-inline">9 ng/ul</ins>). <ins class="diffchange diffchange-inline">We deactivated enzymes</ins>, <ins class="diffchange diffchange-inline">added SAP</ins>, <ins class="diffchange diffchange-inline">deactivated it, then started </ins>the <ins class="diffchange diffchange-inline">ligation</ins>: <ins class="diffchange diffchange-inline">following </ins>the <ins class="diffchange diffchange-inline">protocol</ins>, we <ins class="diffchange diffchange-inline">used concentration values for both parts= 20 ng/ul. We made the control sample and three ligation samples (1:1</ins>, <ins class="diffchange diffchange-inline">1:2</ins>, <ins class="diffchange diffchange-inline">1:3); </ins>we <ins class="diffchange diffchange-inline">transformed </ins>and <ins class="diffchange diffchange-inline">plated them</ins>.Meanwhile <ins class="diffchange diffchange-inline">I took back </ins>the <ins class="diffchange diffchange-inline">experiments with </ins>the <ins class="diffchange diffchange-inline">complete device</ins>, <ins class="diffchange diffchange-inline">so I repeated </ins>the <ins class="diffchange diffchange-inline">dilution cultures </ins>(<ins class="diffchange diffchange-inline">5 ml this time</ins>) and <ins class="diffchange diffchange-inline">tried it again, with a Blue lamp and a less intense LED induction</ins>. <ins class="diffchange diffchange-inline">Moreover I induced with blue light </ins>the <ins class="diffchange diffchange-inline">“mask plates” </ins>,<ins class="diffchange diffchange-inline">with </ins>the <ins class="diffchange diffchange-inline">entire device</ins>, <ins class="diffchange diffchange-inline">to see if colonies produce blue color if induced</ins>.Furthermore I <ins class="diffchange diffchange-inline">inoculate </ins>some colonies <ins class="diffchange diffchange-inline">from Viola’s plate containing </ins>the <ins class="diffchange diffchange-inline">part S04617+EFE</ins>.</html>",</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> "tags" : " BlueLight_amilCP"</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> "tags" : " BlueLight_amilCP<ins class="diffchange diffchange-inline">-B0015- S04617+EFE </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>
</table>Ggirellihttp://2013.igem.org/wiki/index.php?title=Team:UNITN-Trento/Notebook/Labposts/08/37&diff=110300&oldid=prevGgirelli: moved Team:UNITN-Trento/Notebook/Labposts/174 to Team:UNITN-Trento/Notebook/Labposts/08/372013-09-09T07:38:21Z<p>moved <a href="/Team:UNITN-Trento/Notebook/Labposts/174" class="mw-redirect" title="Team:UNITN-Trento/Notebook/Labposts/174">Team:UNITN-Trento/Notebook/Labposts/174</a> to <a href="/Team:UNITN-Trento/Notebook/Labposts/08/37" title="Team:UNITN-Trento/Notebook/Labposts/08/37">Team:UNITN-Trento/Notebook/Labposts/08/37</a></p>
<table style="background-color: white; color:black;">
<tr valign='top'>
<td colspan='1' style="background-color: white; color:black;">← Older revision</td>
<td colspan='1' style="background-color: white; color:black;">Revision as of 07:38, 9 September 2013</td>
</tr></table>Ggirellihttp://2013.igem.org/wiki/index.php?title=Team:UNITN-Trento/Notebook/Labposts/08/37&diff=94470&oldid=prevGgirelli at 08:18, 30 August 20132013-08-30T08:18:42Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 08:18, 30 August 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 4:</td>
<td colspan="2" class="diff-lineno">Line 4:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> "title" : " blue light induction, NO WAY!!",</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> "title" : " blue light induction, NO WAY!!",</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> "content" : " <html> this morning I saw the results of the experiment and… horror: the induced bacteria pellet was lighter then the other two pellets (by the way, they weren’t blue, just a little bit bluish ) THAT SHOULDN’T HAVE HAPPENED!dang it.Maybe the blue LED was too intense, maybe there’s something wrong with our device, don’t know. We only need to take a crack at some other solution at the same time in order to solve this problem: first I will repeat the experiment with less intense blue light, then we are thinking about cotransforming bacteria with two plasmids, one with j23100-YF1-Fixj, the other with -FixK2-CI-Plambda-amilCPbecause we noticed that the device used yesterday lacks a terminator after fixJ and that could be the reason of the disfunction. Thomas made the cotransformation plates even though the plasmids actually aren’t compatible. Meanwhile we discussed about using a new backbone for the separate parts so that cotransformation could be achievable: so we made PCR amplification of the new vector pSB4K5, the first part (j23100-YF1-FixJ) and K592020 (FixK2-CI-Plambda-amilCP). As we can see from the gel, the screening of (j23100_YF1_FixJ) didn’t succeed, probably because the backbone’s structure is quite unusual.Furthermore I tried also to plate the entire device on 3 plates in order to make some mask experiment (induce colonies on the plate).</html>",</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> "content" : " <html> this morning I saw the results of the experiment and… horror: the induced bacteria pellet was lighter then the other two pellets (by the way, they weren’t blue, just a little bit bluish ) THAT SHOULDN’T HAVE HAPPENED!dang it.Maybe the blue LED was too intense, maybe there’s something wrong with our device, don’t know. We only need to take a crack at some other solution at the same time in order to solve this problem: first I will repeat the experiment with less intense blue light, then we are thinking about cotransforming bacteria with two plasmids, one with j23100-YF1-Fixj, the other with -FixK2-CI-Plambda-amilCPbecause we noticed that the device used yesterday lacks a terminator after fixJ and that could be the reason of the disfunction. Thomas made the cotransformation plates even though the plasmids actually aren’t compatible. Meanwhile we discussed about using a new backbone for the separate parts so that cotransformation could be achievable: so we made PCR amplification of the new vector pSB4K5, the first part (j23100-YF1-FixJ) and K592020 (FixK2-CI-Plambda-amilCP). As we can see from the gel, the screening of (j23100_YF1_FixJ) didn’t succeed, probably because the backbone’s structure is quite unusual.Furthermore I tried also to plate the entire device on 3 plates in order to make some mask experiment (induce colonies on the plate).</html>",</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> "tags" : " <del class="diffchange diffchange-inline">j23100_YF1_FixJ_FixK2_CI_Plambda_amilCP</del>"</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> "tags" : " <ins class="diffchange diffchange-inline">BlueLight_amilCP</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>
</table>Ggirellihttp://2013.igem.org/wiki/index.php?title=Team:UNITN-Trento/Notebook/Labposts/08/37&diff=78704&oldid=prevGgirelli: Created page with "{ "date" : "2013-08-14", "author" : "fabio-thomas", "title" : " blue light induction, NO WAY!!", "content" : " <html> this morning I saw the results of the experiment and…..."2013-08-19T13:58:27Z<p>Created page with "{ "date" : "2013-08-14", "author" : "fabio-thomas", "title" : " blue light induction, NO WAY!!", "content" : " <html> this morning I saw the results of the experiment and…..."</p>
<p><b>New page</b></p><div>{<br />
"date" : "2013-08-14",<br />
"author" : "fabio-thomas",<br />
"title" : " blue light induction, NO WAY!!",<br />
"content" : " <html> this morning I saw the results of the experiment and… horror: the induced bacteria pellet was lighter then the other two pellets (by the way, they weren’t blue, just a little bit bluish ) THAT SHOULDN’T HAVE HAPPENED!dang it.Maybe the blue LED was too intense, maybe there’s something wrong with our device, don’t know. We only need to take a crack at some other solution at the same time in order to solve this problem: first I will repeat the experiment with less intense blue light, then we are thinking about cotransforming bacteria with two plasmids, one with j23100-YF1-Fixj, the other with -FixK2-CI-Plambda-amilCPbecause we noticed that the device used yesterday lacks a terminator after fixJ and that could be the reason of the disfunction. Thomas made the cotransformation plates even though the plasmids actually aren’t compatible. Meanwhile we discussed about using a new backbone for the separate parts so that cotransformation could be achievable: so we made PCR amplification of the new vector pSB4K5, the first part (j23100-YF1-FixJ) and K592020 (FixK2-CI-Plambda-amilCP). As we can see from the gel, the screening of (j23100_YF1_FixJ) didn’t succeed, probably because the backbone’s structure is quite unusual.Furthermore I tried also to plate the entire device on 3 plates in order to make some mask experiment (induce colonies on the plate).</html>",<br />
"tags" : " j23100_YF1_FixJ_FixK2_CI_Plambda_amilCP"<br />
}</div>Ggirelli