Team:Groningen/international cooperation

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<z1>Collaboration</z1>
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<br>
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<br>
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<p>
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<z2> iGEM Cambridge</z2>
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<br>
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<br>
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At the European Jamboree we got in contact with the Cambridge team. Since they work on <i>Bacillus subtilis</i> too, we have quite a few things in common. Cambridge uses the magnificient ability of our favourite bacterium to form spores to store their sensor system. <br><br>
 +
Since the Cambridge team had trouble with their sporulation protocol, we provided the Cambridge team with our protocols and some tips & tricks for sporulation. Luckily this gave them higher yielding spores in the last weeks! We also were really happy to discuss the topic of germination with them.
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<br>
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<br>
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</p>
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<p>
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<z2>Characterization of <i>B.subtilis</i> plasmid backbone created by iGEM LMU Munich 2012</z2>
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<br>
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<br>
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The iGEM team LMU Munich 2012 has developed a plasmid backbone that is suitable for gene expression in <i>B. subtilis</i> <b>(BBa_K823023)</b>.
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This plasmid backbone contains an integration locus in amyE, which means that after being transformed into <i>B. subtilis</i>,
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the cloned insert will be integrated with the <i>B. subtilis</i> genome at the amyE locus. <i>B. subtilis</i> is known for its
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starch degrading ability and amyE is a gene responsible for the starch degradation phenotype in <i>B.subtilis</i> by regulating a-amylase production.
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<img src="https://static.igem.org/mediawiki/2012/5/5b/Groningen2012_ID_20120923_backbone_K823023.jpg" width="auto" height="300">
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<p>
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We characterized this plasmid backbone by doing a growth experiment on a starch agar plate. <i>B. subtilis</i>
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strains (168 wildtype, pSac-Cm, and K823023, clockwise respectively) were inoculated in LB agar+0.4% starch and incubated overnight
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in 37<sup>o</sup>C (left picture). After the addition of 0.1% iodine, a clear zone was formed around <i>B. subtilis</i>
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wildtype and <i>B. subtilis</i> strain containing pSac-Cm. There was no clear zone observed around
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<i>B. subtilis</i> strain containing backbone K823023 (right picture).
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<br>
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<br>
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The inability of the <i>B. subtilis</i> strain containing BBa_K823023 to degrade starch has demonstrated that the amyE locus in
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the <i>B. subtilis</i> genome had been replaced. Apart from this characterization experiment, our team has been using BBa_K823023
 +
as a plasmid backbone for our volatile detection device in <i>B. subtilis</i>
 +
<a class="inlink" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K818500">sboA-lycopene</a>.
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<br>
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<br>
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<z4>References</z4>
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<ol class="ref">
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<li>
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Nicholson, W.L, Park, Y.K, Henkin, T.M, Won, M., Weickert, M.J, Gaskell, J.A, Chambliss, G.H. 2006.
 +
Catabolite repression-resistant mutations of the Bacillus subtilis alpha-amylase promoter affect
 +
transcription levels and are in an operator-like sequence. J Mol Biol. 1987 Dec 20;198(4):609-18.
 +
</li>
 +
<li>
 +
Zeigler, Daniel R. 2002. Bacillus Genetic Stock Center Catalog of Strains, Seventh Edition, Volume 4:
 +
Integration Vectors for Gram-Positive Organisms. The Bacillus Genetic Stock Center. Department of Biochemistry,
 +
The Ohio State University. 484 West Twelfth Avenue,Columbus, Ohio 43210.
 +
</li>
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</ol>
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<br>
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</p>
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<p>
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<z2>TU Munich iGEM 2012 </z2>
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<br>
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<br>
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We participated in the survey of the iGEM TU Munich and are very proud that we got their original Bavarian Collaboration-Medal.
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<br>
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</p>
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<img id="TUM12_badge" width="200px" src="https://static.igem.org/mediawiki/2012/c/c6/TUM12_Collaboration_medal1.png" alt="This team completed TU Munich's survey on Standardization of BioBrick part descriptions"/>
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<z2>iGEM Uppsala</z2>
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<br>
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<br>
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At the beginning of August we received the chromoproteins amilCP (blue), amilGFP (yellow) from
 +
<a class="inlink" href="https://2011.igem.org/Team:Uppsala-Sweden">iGEM Uppsala 2011</a>.
 +
We were able to transform their BBa_K592009 and BBa_K592010 behind our identified promoters into <i>E.coli</i>
 +
and managed to turn <i>B.subtilis</i> into blue and yellow, which has never been done before!
 +
For the latest results, check our <a class="inlink" href="https://2012.igem.org/Team:Groningen/pigmentproduction">Pigment page</a>.
 +
<br><br> After the European Jamboree, the Uppsala team sent us the red chromoprotein eforRed (BBa_K592012). Although we could prove succesful cloning into our plasmid psac-cm connected to our promoter P<i>sboaA</i>, into <i>E. coli</i> and <i>Bacillus subtilis</i> by restriction analysis, there was no visible expression of the protein.
 +
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<br>
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<p>
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<z2>Dutch iGEM teams (iGEM Wageningen, Amsterdam, Delft, Eindhoven)</z2>
 +
<br>
 +
<br>
 +
All of the Dutch iGEM teams collaborated to create an iGEM presence at the
 +
<a class="inlink" href="http://www.discoveryfestival.nl/" >Discovery Festival</a> on Friday 28 September
 +
in Amsterdam, Rotterdam and Eindhoven. We will aim to get the public in touch with Synthetic Biology in a playful way.
 +
<br>
 +
<br>
 +
Besides these Dutch iGEM meetings and the Discovery Festival, we also collaborated with Wageningen and Amsterdam on a molecular level.
 +
Many times our transformation of <i>E.coli</i> failed, so we ran out of the backbone biobricks for <i>B. subtilis</i>. Luckily Wageningen
 +
and Amsterdam were so kind to provide us with some of their bricks. Thank you guys!
 +
</p>
 +
<br>
 +
 +
<p>
 +
<z2>iGEM Calgary 2012</z2>
 +
<br>
 +
<br>
 +
Emily Hicks from the winning Calgary iGEM team in 2011, and now member of iGEM Calgary 2012, has studied in Groningen during her exchange period.
 +
She was very interested in her iGEM Groningen colleagues; therefore we asked her to give a lecture about her previous iGEM experience.
 +
We were really motivated by Emily's suggestions concerning medal requirements, information about wiki etc. Thank you Emily!
 +
</p>
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<z2> iGEM Virginia</z2>
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Prof. Papin, supervisor to the iGEM Virginia team and supervising author to the idFBA article, graciously shared his knowledge and scripts relating to  
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<p class="margin"><FONT COLOR=#ff6700><b>iGEM Calgary 2012 </b></FONT><br><br>Emily Hicks from the winning iGEM team in 2011 and now member of iGEM Calgary 2012, has studied in Groningen during her (short) exchange period. And she was very interested in her iGEM Groningen colleagues; therefore we asked her to give a lecture about her previous iGEM experience. We we're really motivated by Emily's tips concerning medal requirements, information about wiki etc. Thanks Emily!</p>
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<p class="margin"><FONT COLOR=#ff6700><b>Dutch iGEM teams (iGEM Wageningen, Amsterdam, Delft, Eindhoven)</b></FONT><br><br>
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On the 10th of July all Dutch iGEM met in Wageningen for the first mini-symposium (Greek for meeting and having a drink together). We could share our ideas, get in touch with other team colleagues and present our team subject. See video <A HREF="http://wurtv.wur.nl/P2GTV/cataloguepage.aspx" TARGET="_blank"><FONT COLOR=#ff6700>Symposium iGEM Netherlands 2</FONT></A> (posted on July 9 2012). The iGEM Groningen presentation starts at time point 1:42. After these serious talks, a great dinner was served: we had a BBQ inside an old school building. The lab space as very suitable as dinner space. 
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And there are more interesting symposia to come. On the 6th of September we are invited for the next iGEM- The Netherlands symposium in Eindhoven. And also Amsterdam invited us for a next one.
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After the wiki freeze, all Dutch iGEM teams work together on a nice activity: during the Discovery Festival on Friday 28 September located in Amsterdam, Rotterdam and Eindhoven, the teams aim to get the public in touch with Synthetic Biology in a playful way. We want to let them guess about the ideas of previous iGEM teams and humbug. Or in other words, Synthetic Biology: Science or Science Fiction?
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Besides these Dutch iGEM meetings and the Discovery Festival, we also collaborated with Wageningen and Amsterdam on a molecular level. Many times our transformation of E.coli failed, so we ran out of the backbone biobricks for Bacillus subtilis. Luckily Wageningen and Amsterdam we’re so kind to provide us with their bricks. Thank you guys!</p>
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<p class="margin"><FONT COLOR=#ff6700><b>iGEM Uppsala</b></FONT><br><br>
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At the beginning of August we received the chromo proteins amilCP (blue), amilGFP (yellow) from iGEM Uppsala <A HREF="https://2011.igem.org/Team:Uppsala-Sweden" TARGET="_blank"><FONT COLOR=#ff6700>iGEM Uppsala 2011</FONT></A>. We hope we can use BBa_K592009 and BBa_K592010 for the coloring system we want to use in B. subtilis.</p>
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<p class="margin"><FONT COLOR=#ff6700><b>iGEM Cambridge</b></FONT><br><br>
 
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Together with iGEM Cambridge we want to develop a sporulation and germination protocol for Bacillus subtilis. The whole idea of Bacillus spores that can be stored and used only at a desired time point is the same goal iGEM Groningen and iGEM Cambridge want to achieve, therefore a collaboration would be very advantageous. </p>
 
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<p class="margin"><FONT COLOR=#ff6700><b>iGEM LMU Munich</b></FONT><br><br>
 
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This iGEM team is also working on B. subtilis and therefore an ideal partner for testing each other’s constructs. They sent us 6 plasmids and 4 promoters and we are using them for testing. Hopefully we are able to return our constructs to them soon!</p>
 
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<p class="margin"><FONT COLOR=#ff6700><b> iGEM Virginia</b></FONT><br><br>
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Latest revision as of 02:42, 27 October 2012





Collaboration


iGEM Cambridge

At the European Jamboree we got in contact with the Cambridge team. Since they work on Bacillus subtilis too, we have quite a few things in common. Cambridge uses the magnificient ability of our favourite bacterium to form spores to store their sensor system.

Since the Cambridge team had trouble with their sporulation protocol, we provided the Cambridge team with our protocols and some tips & tricks for sporulation. Luckily this gave them higher yielding spores in the last weeks! We also were really happy to discuss the topic of germination with them.

Characterization of B.subtilis plasmid backbone created by iGEM LMU Munich 2012

The iGEM team LMU Munich 2012 has developed a plasmid backbone that is suitable for gene expression in B. subtilis (BBa_K823023). This plasmid backbone contains an integration locus in amyE, which means that after being transformed into B. subtilis, the cloned insert will be integrated with the B. subtilis genome at the amyE locus. B. subtilis is known for its starch degrading ability and amyE is a gene responsible for the starch degradation phenotype in B.subtilis by regulating a-amylase production.

We characterized this plasmid backbone by doing a growth experiment on a starch agar plate. B. subtilis strains (168 wildtype, pSac-Cm, and K823023, clockwise respectively) were inoculated in LB agar+0.4% starch and incubated overnight in 37oC (left picture). After the addition of 0.1% iodine, a clear zone was formed around B. subtilis wildtype and B. subtilis strain containing pSac-Cm. There was no clear zone observed around B. subtilis strain containing backbone K823023 (right picture).

The inability of the B. subtilis strain containing BBa_K823023 to degrade starch has demonstrated that the amyE locus in the B. subtilis genome had been replaced. Apart from this characterization experiment, our team has been using BBa_K823023 as a plasmid backbone for our volatile detection device in B. subtilis sboA-lycopene.

References

  1. Nicholson, W.L, Park, Y.K, Henkin, T.M, Won, M., Weickert, M.J, Gaskell, J.A, Chambliss, G.H. 2006. Catabolite repression-resistant mutations of the Bacillus subtilis alpha-amylase promoter affect transcription levels and are in an operator-like sequence. J Mol Biol. 1987 Dec 20;198(4):609-18.
  2. Zeigler, Daniel R. 2002. Bacillus Genetic Stock Center Catalog of Strains, Seventh Edition, Volume 4: Integration Vectors for Gram-Positive Organisms. The Bacillus Genetic Stock Center. Department of Biochemistry, The Ohio State University. 484 West Twelfth Avenue,Columbus, Ohio 43210.

TU Munich iGEM 2012

We participated in the survey of the iGEM TU Munich and are very proud that we got their original Bavarian Collaboration-Medal.

This team completed TU Munich's survey on Standardization of BioBrick part descriptions

iGEM Uppsala

At the beginning of August we received the chromoproteins amilCP (blue), amilGFP (yellow) from iGEM Uppsala 2011. We were able to transform their BBa_K592009 and BBa_K592010 behind our identified promoters into E.coli and managed to turn B.subtilis into blue and yellow, which has never been done before! For the latest results, check our Pigment page.

After the European Jamboree, the Uppsala team sent us the red chromoprotein eforRed (BBa_K592012). Although we could prove succesful cloning into our plasmid psac-cm connected to our promoter PsboaA, into E. coli and Bacillus subtilis by restriction analysis, there was no visible expression of the protein.


Dutch iGEM teams (iGEM Wageningen, Amsterdam, Delft, Eindhoven)

All of the Dutch iGEM teams collaborated to create an iGEM presence at the Discovery Festival on Friday 28 September in Amsterdam, Rotterdam and Eindhoven. We will aim to get the public in touch with Synthetic Biology in a playful way.

Besides these Dutch iGEM meetings and the Discovery Festival, we also collaborated with Wageningen and Amsterdam on a molecular level. Many times our transformation of E.coli failed, so we ran out of the backbone biobricks for B. subtilis. Luckily Wageningen and Amsterdam were so kind to provide us with some of their bricks. Thank you guys!


iGEM Calgary 2012

Emily Hicks from the winning Calgary iGEM team in 2011, and now member of iGEM Calgary 2012, has studied in Groningen during her exchange period. She was very interested in her iGEM Groningen colleagues; therefore we asked her to give a lecture about her previous iGEM experience. We were really motivated by Emily's suggestions concerning medal requirements, information about wiki etc. Thank you Emily!


iGEM Virginia

Prof. Papin, supervisor to the iGEM Virginia team and supervising author to the idFBA article, graciously shared his knowledge and scripts relating to idFBA.




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