Team:SDU-Denmark/labwork/Notebook/week5

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<h2>Laboratory Notebook</h2>
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<h1>Laboratory Notebook</h1>
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Here you find the log book for the procedures carried out in the laboratory, starting from week 27. 
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     <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week4"><b>4th week</b>     </a></span>    </regulartext></td>
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     <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week4">4th week    </a></span>    </regulartext></td>
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     <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week5">5th week      </a></span>    </regulartext></td>
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     <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week5"><b>5th week</b>     </a></span>    </regulartext></td>
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     <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week8">8th week      </a></span>    </regulartext></td>
     <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week8">8th week      </a></span>    </regulartext></td>
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    <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week9">9th week</a></span>    </regulartext></td>
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                                            <!----------5th WEEK---------->
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    <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week10">10th week</a></span>    </regulartext></td>
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    <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week11">11th week</a></span>    </regulartext></td>
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<p> <b>07-08-2012:</b> </p>
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<h2>SST send for sequencing </h2> <br/>  
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    <span class="classred"><a href="https://2012.igem.org/Team:SDU-Denmark/labwork/Notebook/week12">12th week</a></span>     </regulartext></td>
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Today our primes arrived. We did a mutagenesis on SST and FFT to correct some genetic errors which our sequencing results showed us.
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-primers arrived
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                                            <!----------5th WEEK---------->
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→ run mutagenesis → transform and grow new mutated colonies
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mutagenesis kit: agilent technologies stratagene quickchange lightning multi site-directed mutagenesis kit
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8/8-12 Lars, Ida, Victor, Malou
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The SST plates that had been grown over night showed some colonies that were selected and put into liquid LB. for overnight culture. The FFT plates showed no colonies.
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we tried again to run a mutagenesis on the FFT genes, this time following the protocol that was delivered with the mutagenesis kit. next we transformed XL10-GOLD e.coli with the mutated genes and plated them out on agar plates with ampicilin, and left ON. in the incubator. 
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9/8-12 Lars, Victor, Gabi
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FFT plates from the day before showed colonies and were transferred to liquid medium and incubated overnight. Plasmid SST DNA from liquid cultures from the day before were purified, digested with EcoRI, SpeI, XbaI and PstI, then run on a gel(picture not included). Results were awesome.
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EcoRI+PstI: 1-8
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Ladders: 9-10
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XbaI+SpeI: 11-18
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Colony 1 and 2 were most awesome. Will be shipped for sequencing later on.
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10/8-12 Lars
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The plasmid DNA from the liquid cultures of FFT from the day before were purified, digested with EcoRI, SpeI, XbaI and PstI, then run on a gel. While the gel was running, appropriate values of expected lengths were calculated:
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EcoRI+SpeI: 2000bp+3000bp  WRONG:200bp+1800bp+3000bp  or  1length
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XbaI+PstI: 2000bp+400+2600bp WRONG: 1200bp+800bp+400bp+2600bp  or  1length  or 
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800bp+400bp+3800bp
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On the gel, the XbaI+PstI is seen on the left, EcoRI+SpeI is seen on the right
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The results from the gel:
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The conclusion from the gel is that the illegal XbaI site is removed, the desired XbaI site is present, and.... unfortunately almost all the plasmids still contain the illegal EcoRI site... except either of colony 3 and 4, which were mixed by accident the day before, and can be found at position 3 from the left on the gel. Beforehand, we expected trouble with the Primer designed to remove the EcoRI site, because it had a lot of problematic alignments(see sequence).
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Following, another two batches of liquid colony was prepared (from the remains of colony 3 and 4) and incubated overnight, also another two plates were prepared as a safety backup with the mixed liquid medium of the two colonies.
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11/8-12 Lars
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The backup plates showed immense growth. They will be kept at 4C and saved for later use, if the liquid cultures fail.
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The liquid cultures of FFT colonies 3 and 4 from the day before were purified, digested with EcoRI+SpeI and XbaI+PstI, then run on a gel.
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The results:
 
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In conclusion: though faint, colony 4 shows signs of the illegal EcoRI restriction site. It is easier to see on a picture taken on the gel from earlier, which can be found in the Lab. No digital copy was made from the early gel photo.
 
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Meanwhile, colony 3 is awesome. It will be prepared and sent for sequencing monday.
 
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<p> <b>30-07-2012 to 05-08-2012</b> </p>
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<h2>No lab work this week</h2>
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<p>Our genes were sent to sequencing so we had no lab work this week. Instead we have been working on our Wiki, and trying to improve some of our protocols.</p>
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Latest revision as of 13:48, 26 September 2012

iGEM TEAM ::: SDU-DENMARK

Laboratory Notebook

1st week 2nd week 3th week 4th week
5th week 6th week 7th week 8th week
9th week 10th week 11th week 12th week

30-07-2012 to 05-08-2012

No lab work this week

Our genes were sent to sequencing so we had no lab work this week. Instead we have been working on our Wiki, and trying to improve some of our protocols.

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