Team:Gothenburg-Sweden/Lab Note

From 2010.igem.org

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<td>&nbsp;</td>
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<td width="301" height="203"><ul class="list1">
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<td width="301"><ul class="list1">
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                   <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project">Project</a></li>
                   <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Project">Project</a></li>
                   <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Lab_Note">Lab Note </a></li>
                   <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Lab_Note">Lab Note </a></li>
                   <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Results">Results</a></li>
                   <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Results">Results</a></li>
  <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us">About Us</a></li>
  <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/About_us">About Us</a></li>
 +
  <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Sponsors">Sponsors</a></li>
                   <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Contact">Contact Us</a></li>
                   <li><a href="http://2010.igem.org/Team:Gothenburg-Sweden/Contact">Contact Us</a></li>
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</ul></td>
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  </ul></td>
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    </ul>
    </ul>
    <p class="STYLE6">&nbsp;</p>
    <p class="STYLE6">&nbsp;</p>
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    <p class="STYLE6">Plasmid:</p> pSP-GM
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    <p class="STYLE6">Plasmid:</p>
    <p>&nbsp;</p>
    <p>&nbsp;</p>
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    <p class="STYLE6">SNF1 (modified subunits):</p> Snf1 (alfa) and Snf4 (gamma)
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    <p class="STYLE6">Snf1  (subunits):</p>
    <p>&nbsp;</p>
    <p>&nbsp;</p>
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    <p class="STYLE6">FP  positions:</p> N-terminal alfa and N-terminal gamma, N-terminal gamma and C-terminal gamma
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    <p class="STYLE6">FP  positions:</p>
    <p>&nbsp;</p>
    <p>&nbsp;</p>
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    <p class="STYLE6">Primers  design:</p> Fusion primers with restriction enzyme ends included at end parts. Each annealing section has a melting temperature around 60 C
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    <p class="STYLE6">Primers  design:</p>
    <p>&nbsp;</p></td>
    <p>&nbsp;</p></td>
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      Malin, Katarina and Peidi<br>
      Malin, Katarina and Peidi<br>
      Colony 1 and 2 were picked to do a miniprep.  The plasmids were extracted and a plasmid integrity check was performed. By  cutting with BamHI, one cut were made to get the size of the plasmid. Then we  cut with ClaI which is a two-cutter that gives a fragment that is 600 bp and  one that is 6800. The gel which should confirm this was not satisfactory since  the 600 band was missing.<br>
      Colony 1 and 2 were picked to do a miniprep.  The plasmids were extracted and a plasmid integrity check was performed. By  cutting with BamHI, one cut were made to get the size of the plasmid. Then we  cut with ClaI which is a two-cutter that gives a fragment that is 600 bp and  one that is 6800. The gel which should confirm this was not satisfactory since  the 600 band was missing.<br>
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      </p>
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        </p>
    <p><span class="STYLE8">2010-07-07 </span><br>
    <p><span class="STYLE8">2010-07-07 </span><br>
      Adnan,  Katarina and Julia<br>
      Adnan,  Katarina and Julia<br>
      As the gels  from Tuesday showed ambigous results we decided to redo the miniprep of the  plamids. We used the overnight preparations of the two unused colonies (3 &amp;  4). The miniprep went smoothly except for major difficulties regarding  untrustworthy pipettes. The pipettes marked with green tape are the ones to use  from now on together with the tips with the same markings! A gel was molded and  this time we decided to use a full gel to get a better resolution.  The results on the gel where very good.  The plasmids had clearly been cut in one or  two places and the fragment sizes seem to correspond to the expected sizes.<br>
      As the gels  from Tuesday showed ambigous results we decided to redo the miniprep of the  plamids. We used the overnight preparations of the two unused colonies (3 &amp;  4). The miniprep went smoothly except for major difficulties regarding  untrustworthy pipettes. The pipettes marked with green tape are the ones to use  from now on together with the tips with the same markings! A gel was molded and  this time we decided to use a full gel to get a better resolution.  The results on the gel where very good.  The plasmids had clearly been cut in one or  two places and the fragment sizes seem to correspond to the expected sizes.<br>
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      </p>
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        </p>
    <p><span class="STYLE8">2010-07-08</span><br>
    <p><span class="STYLE8">2010-07-08</span><br>
      Malin,  Julia and Peidi<br>
      Malin,  Julia and Peidi<br>
      The two  BioBricks EYFP and ECFP were extracted from the kit plates and stored in the  freezer. A SOC-medium was prepared.<br>
      The two  BioBricks EYFP and ECFP were extracted from the kit plates and stored in the  freezer. A SOC-medium was prepared.<br>
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      </p>
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        </p>
    <p><span class="STYLE8">2010-07-09</span><br>
    <p><span class="STYLE8">2010-07-09</span><br>
      Malin and  Julia<br>
      Malin and  Julia<br>
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      Adnan and  Katarina<br>
      Adnan and  Katarina<br>
      Picked up  primers at Chalmers and checked if they were ok. The concentration of the  genomic DNA (SNF1 gene) were measured. Prepared a master mix so that the  PCR-reactions could be started Monday morning.<br>
      Picked up  primers at Chalmers and checked if they were ok. The concentration of the  genomic DNA (SNF1 gene) were measured. Prepared a master mix so that the  PCR-reactions could be started Monday morning.<br>
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      </p>
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        </p>
    <p><span class="STYLE8">2010-07-13</span><br>
    <p><span class="STYLE8">2010-07-13</span><br>
      Karl and  Adnan<br>
      Karl and  Adnan<br>
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      We made  duplicates of the haploid Snf4∆ and wildtype strains on new plates in case the  original plate would be contaminated. Prepared a sporulation medium that was  autoclaved and poured into empty growth plates to stay in room temperature over  night.</p>
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      We made  duplicates of the haploid Snf4∆ and wildtype strains on new plates in case the  original plate would be contaminated. Prepared a sporulation medium that was  autoclaved and poured into empty growth plates to stay in room temperature over  night.</p></td>
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                                                            <p><span class="STYLE8">2010-07-14</span><br>
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      Karl and  Malin<br>
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      Dioploid Snf1 deletion mutatants was transfered to two sporulation plates, incubated at 30 C.</p></td>
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                                     <td>PIC 1: Gel of plasmid (cut) </td>
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                                     <td>PIC 1: Gel of plasmid (cutted) </td>
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                                 </table></td>
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Revision as of 12:58, 14 July 2010

Chalmers University of Technology

preliminary work & lab notes
 
 
 
preliminary
 
 

Fluorescent Proteins:

Bioluminescence is used as a defense, offense and communication mechanism by various organisms in nature including insects, fish, squid, sea cacti, sea pansies, clam, shrimps and jellyfish(1). After the discovery of the Green Fluorescent Protein (GFP) by Shimomura et al. from Aequorea jellyfish(2),  an unprecedented tool for visualizing living organisms was also being introduced to molecular biology, leading to a Nobel Prize in 2008(3). The Aequorea GFP is a 238 aa, 30 kDa monomer that emits green fluorescence  maximum at 509 nm wavelength(4).  It has a unique structure with an 11 stranded β - barrel like shape involving α- helixes running through the center of the can; to which the chromophore is attached(5). Autocatalytic formation of the chromophore of the GFP without the neccessity of any substrates or cofactors is a rather useful property of the GFPs allowing them to express in fusion with different proteins. Remarkably, the fusion of GFP to a protein does not have any vital effect on the activity or mobility of the protein in addition to its nontoxic nature(1).   

GFP

Figure 1: Structure of the GFP taken from the PDB, code 1EMA

 

References:

  • (1) Zimmer, M. (2002) “Green Fluorescent Protein (GFP): Applications, Structure and Related Photophysical Behavior.” Chemical Reviews. v. 102 (3) pp. 759-781.
  • (2) Shimomura, O., Johnson, F.H. & Saiga, Y. (1962) “Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan.”  Aequorea. J. Cell. Comp. Physiol. v. 59, pp. 223–239.
  • (3) Shimomura, O., Chalfie, M. & Tsien, R. Y. (2008) “The discovery and development of the green fluorescent protein, GFP.”  The Nobel Prize in Chemistry. Retrieved from the website http://nobelprize.org/nobel_prizes/chemistry/laureates/2008/
  • (4) Prasher, D., C.,  Eckenrode, V., K., Ward,W.,W., Prendergast, F., G. & Cormier, M., J. (1992) “Primary structure of the Aequorea victoria green-fluorescent protein” Gene., v. 111, pp. 229-233.
  • (5) Tsien, R., Y. (1998) “The Green Fluorescent Protein”  Annual Review of Biochemistry.  v. 67, pp. 509–544

 

Plasmid:

 

Snf1 (subunits):

 

FP positions:

 

Primers design:

 

 
 
lab work by date
 
 

2010-07-05
Malin och Katarina
An overnight culture were made from 4 different colonies of E.coli containing the plasmid pSB-GM1.

2010-07-06
Malin, Katarina and Peidi
Colony 1 and 2 were picked to do a miniprep. The plasmids were extracted and a plasmid integrity check was performed. By cutting with BamHI, one cut were made to get the size of the plasmid. Then we cut with ClaI which is a two-cutter that gives a fragment that is 600 bp and one that is 6800. The gel which should confirm this was not satisfactory since the 600 band was missing.

2010-07-07
Adnan, Katarina and Julia
As the gels from Tuesday showed ambigous results we decided to redo the miniprep of the plamids. We used the overnight preparations of the two unused colonies (3 & 4). The miniprep went smoothly except for major difficulties regarding untrustworthy pipettes. The pipettes marked with green tape are the ones to use from now on together with the tips with the same markings! A gel was molded and this time we decided to use a full gel to get a better resolution.  The results on the gel where very good.  The plasmids had clearly been cut in one or two places and the fragment sizes seem to correspond to the expected sizes.

2010-07-08
Malin, Julia and Peidi
The two BioBricks EYFP and ECFP were extracted from the kit plates and stored in the freezer. A SOC-medium was prepared.

2010-07-09
Malin and Julia
The SOC medium was autoclaved. Competent E.coli cells were transformed with our FPs through heat shock and plated on petri dishes. 20 new LB-amp plates were made.
Adnan and Katarina
Picked up primers at Chalmers and checked if they were ok. The concentration of the genomic DNA (SNF1 gene) were measured. Prepared a master mix so that the PCR-reactions could be started Monday morning.

2010-07-13
Karl and Adnan
We made duplicates of the haploid Snf4∆ and wildtype strains on new plates in case the original plate would be contaminated. Prepared a sporulation medium that was autoclaved and poured into empty growth plates to stay in room temperature over night.

 
pictures
 
 

gel_plasmid

PIC 1: Gel of plasmid (cutted)
 
 
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