Team:Copenhagen/Notebook

From 2012.igem.org

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<head>
<head>
<a name="June"></a><h2>June</h2>
<a name="June"></a><h2>June</h2>
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<a name="Week 1a">
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<br>
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<h2>Week 1: 4th-8th</h2>
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<a name="Week 1a"></a><h2>Week 1: 4th-8th</h2>
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Exam period starts :(
Exam period starts :(
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<br>
 
</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 2a"></a><h2>Week 2: 11th-15th</h2>
<a name="Week 2a"></a><h2>Week 2: 11th-15th</h2>
Exams for a lot of our team members but we start designing our primers.  
Exams for a lot of our team members but we start designing our primers.  
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<br>
 
</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 3a"></a><h2>Week 3: 18th-22nd</h2>
<a name="Week 3a"></a><h2>Week 3: 18th-22nd</h2>
Primers are designed and ordered so we'll have them next week.
Primers are designed and ordered so we'll have them next week.
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<br>
 
</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 3a"></a><h2>Week 4: 25th-29th</h2>
<a name="Week 3a"></a><h2>Week 4: 25th-29th</h2>
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All our templates, kindly provided by Uppsala, are sent to sequencing in Holland.
All our templates, kindly provided by Uppsala, are sent to sequencing in Holland.
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</a>
</a>
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<br>
 
<br>
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<a name="July"></a><h2>July</h2>
<a name="July"></a><h2>July</h2>
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<br>
 
<a name="Week 1b"></a><h2><h2>Week 1: 2nd-6th</h2>
<a name="Week 1b"></a><h2><h2>Week 1: 2nd-6th</h2>
The sequencing results have come back, and everything was as we hoped.  
The sequencing results have come back, and everything was as we hoped.  
It took more time than expected to get the new primers so the first days has been spend applying for sponsors, remaking our website, and deciding how to do the next experiments.
It took more time than expected to get the new primers so the first days has been spend applying for sponsors, remaking our website, and deciding how to do the next experiments.
-
  PCR on the backbone (pSB1C3), and our constitutive promoter has been unsuccessful while we have been able to amplify and cut out a fine band of YF1.
+
  PCR on the backbone (pSB1C3), and our constitutive promoter (ProC) has been unsuccessful while we have been able to amplify and cut out a fine band of the gene encoding the histidine kinase YF1.
   
   
-
<br>
 
</a>
</a>
-
<br>
 
<br>
<br>
<a name="Week 2b"></a><h2>Week 2: 9th-13th</h2>
<a name="Week 2b"></a><h2>Week 2: 9th-13th</h2>
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</table>
</table>
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We're still having trouble with both pSB1C3 and ProC. We're currently running a self-annealing programme for ProC because it is to small to do PCR. pSB1C3, on the other hand, seems too big so therefore we've lowered the annealing temperature and chosen a longer extension time. So far it has had no effect but we will keep optimizing.
+
This week, we managed to amplify most of the genes needed in our control construct!
 +
We succesfully amplified the promoter FixK2 and the gene encoding its regulator FixJ.
 +
We found out that the backbone, pSB1C3, was supplied as linear DNA and we discovered its conversion into circular DNA after transformation into E. coli. We confirmed the insertion of the backbone DNA by another discovery - red fluorescence when looking at the bacteria with fluorescence microscopy because the pSB1C3 biobrick contains a red flourescence protein gene - wow! We purified DNA from these bacteria and finally got our DNA product.
 +
We also managed to amplify the terminator sequence.  
 +
We are having problems with PCR on the large luxCDABE cassette but we found out that the template we are using might be contaminated. We are also still having trouble with the very small constitutive promoter proC - we forund out that it is too small for PCR because it is about the same size as the primers.. So we have tried to amplify it using the gene in two single strands - which we have tried to anneal to each other - but this has been unsuccesful so far.
-
<br>
 
</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 3b"></a><h2>Week 3: dato</h2>
<a name="Week 3b"></a><h2>Week 3: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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<br>
+
</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 4b"></a><h2>Week 4: dato</h2>
<a name="Week 4b"></a><h2>Week 4: dato</h2>
-
JahDah JahDah ... Text ...
+
To be added.  
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<br>
+
</a>
</a>
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<br>
 
<br>
<br>
<a name="August"></a><h2>August</h2>
<a name="August"></a><h2>August</h2>
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<br>
 
<a name="Week 1c"></a><h2><h2>Week 1: dato</h2>
<a name="Week 1c"></a><h2><h2>Week 1: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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<br>
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</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 2c"></a><h2>Week 2: dato</h2>
<a name="Week 2c"></a><h2>Week 2: dato</h2>
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JahDah JahDah ... Text ...
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To be added.
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<br>
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</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 3c"></a><h2>Week 3: dato</h2>
<a name="Week 3c"></a><h2>Week 3: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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<br>
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</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 4c"></a><h2>Week 4: dato</h2>
<a name="Week 4c"></a><h2>Week 4: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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<br>
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</a>
</a>
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<br>
<br>
<a name="September"></a><h2>September</h2>
<a name="September"></a><h2>September</h2>
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<a name="Week 1d"></a><h2><h2>Week 1: dato</h2>
<a name="Week 1d"></a><h2><h2>Week 1: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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</a>
</a>
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<br>
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<a name="Week 2d"></a><h2>Week 2: dato</h2>
<a name="Week 2d"></a><h2>Week 2: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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<br>
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</a>
</a>
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<br>
<br>
<a name="Week 3d"></a><h2><h2>Week 3: dato</h2>
<a name="Week 3d"></a><h2><h2>Week 3: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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<br>
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</a>
</a>
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<br>
<br>
<a name="Week 4d"></a><h2>Week 4: dato</h2>
<a name="Week 4d"></a><h2>Week 4: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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<br>
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</a>
</a>
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<br>
 
<br>
<br>
<a name="October"></a><h2>October</h2>
<a name="October"></a><h2>October</h2>
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<br>
 
<a name="Week 1e"></a><h2><h2>Week 1: dato</h2>
<a name="Week 1e"></a><h2><h2>Week 1: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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<br>
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</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 2e"></a><h2><h2>Week 2: dato</h2>
<a name="Week 2e"></a><h2><h2>Week 2: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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<br>
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</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 3e"></a><h2>Week 3: dato</h2>
<a name="Week 3e"></a><h2>Week 3: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
-
<br>
+
</a>
</a>
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<br>
 
<br>
<br>
<a name="Week 4e"></a><h2>Week 4: dato</h2>
<a name="Week 4e"></a><h2>Week 4: dato</h2>
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JahDah JahDah ... Text ...
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To be added.  
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<br>
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</a>
</a>
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<br>
<br>

Latest revision as of 09:09, 19 July 2012

Notebook

Follow our work here in the notebook. We will post the most important of our findings from the lab-work. We will also post pictures from our great summer!!! The light at the department of Plant Biology will probably shine brighter than the Danish summer sun anyway ;)


June

Week 1: 4th-8th

Exam period starts :(

Week 2: 11th-15th

Exams for a lot of our team members but we start designing our primers.

Week 3: 18th-22nd

Primers are designed and ordered so we'll have them next week.

Week 4: 25th-29th

Exams are finally over and we can start some of the lab work! Yay!!! :D We've divided our construct into two halfs and will in this week be doing PCR on the first half of our construct. We've designed primers for the second half of our construct and ordered them. All our templates, kindly provided by Uppsala, are sent to sequencing in Holland.

July

Week 1: 2nd-6th

The sequencing results have come back, and everything was as we hoped. It took more time than expected to get the new primers so the first days has been spend applying for sponsors, remaking our website, and deciding how to do the next experiments. PCR on the backbone (pSB1C3), and our constitutive promoter (ProC) has been unsuccessful while we have been able to amplify and cut out a fine band of the gene encoding the histidine kinase YF1.

Week 2: 9th-13th

Info

This week, we managed to amplify most of the genes needed in our control construct! We succesfully amplified the promoter FixK2 and the gene encoding its regulator FixJ. We found out that the backbone, pSB1C3, was supplied as linear DNA and we discovered its conversion into circular DNA after transformation into E. coli. We confirmed the insertion of the backbone DNA by another discovery - red fluorescence when looking at the bacteria with fluorescence microscopy because the pSB1C3 biobrick contains a red flourescence protein gene - wow! We purified DNA from these bacteria and finally got our DNA product. We also managed to amplify the terminator sequence. We are having problems with PCR on the large luxCDABE cassette but we found out that the template we are using might be contaminated. We are also still having trouble with the very small constitutive promoter proC - we forund out that it is too small for PCR because it is about the same size as the primers.. So we have tried to amplify it using the gene in two single strands - which we have tried to anneal to each other - but this has been unsuccesful so far.

Week 3: dato

To be added.

Week 4: dato

To be added.

August

Week 1: dato

To be added.

Week 2: dato

To be added.

Week 3: dato

To be added.

Week 4: dato

To be added.

September


Week 1: dato

To be added.

Week 2: dato

To be added.

Week 3: dato

To be added.

Week 4: dato

To be added.

October

Week 1: dato

To be added.

Week 2: dato

To be added.

Week 3: dato

To be added.

Week 4: dato

To be added.

This is our notebook, displaying how our work has progressed throughout the summer.

Retrieved from "http://2012.igem.org/Team:Copenhagen/Notebook"