Team:Bielefeld-Germany/Labjournal/July

From 2013.igem.org

(Difference between revisions)
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<div class="cyt_primer">
<div class="cyt_primer">
-
*The mtrCAB fragment has two illegal PstI restriction sites at x xbp and yy bp, so we had to design new primers to remove them. We replaced one base in each restriction site, without affecting the coding triplett, by respective primer overlaps . We ended up with three different fragments, which will be ligated back together via Gibson Assembly.
+
**The mtrCAB fragment has two illegal PstI restriction sites at x xbp and yy bp, so we had to design new primers to remove them. We replaced one base in each restriction site, without affecting the coding triplett, by respective primer overlaps . We ended up with three different fragments, which will be ligated back together via Gibson Assembly.
-
*mtrCAB_Frag1_rev:
+
**mtrCAB_Frag1_rev:
-
*mtrCAB_Frag2_fwd:     
+
**mtrCAB_Frag2_fwd:     
-
*mtrCAB_Frag2_rev:     
+
**mtrCAB_Frag2_rev:     
-
*mtrCAB_Frag3_fwd:     
+
**mtrCAB_Frag3_fwd:     
</div>
</div>
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<br><br><br><br>
 +
<br><br><br><br>
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<h3><a name=2.Week>2.Week</a></h3>
 
-
<h4><a href="https://2013.igem.org/Team:Bielefeld-Germany/Project/#">Organization</a></h4>
+
 
-
<ul>
+
 
-
<li>We can present new sponsors of iGEM-Team Bielefeld: Stockmeier, Baxter, Promega, BIO.NRW and Applichem will support our team.</li>
+
<div id="2.Week">
-
</ul>
+
===2.Week===
 +
</div>
 +
 
 +
====Organization====
 +
*We can present new sponsors of iGEM-Team Bielefeld: Stockmeier, Baxter, Promega, BIO.NRW and Applichem will support our team.</li>
====MFC====
====MFC====
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<h3><a name=3.Week>3.Week</a></h3>
+
<div id="3.Week">
-
 
+
===3.Week===
-
<h4><a href="https://2013.igem.org/Team:Bielefeld-Germany/Project/#">Organization</a></h4>
+
</div>
-
<ul>
+
====Organization====
-
<li>We’ve presented us at the congress “BioNRW pHD Student Convention” in Düsseldorf at 13. July 2013 with a short presentation about iGEM and our project. </li>
+
*We’ve presented us at the congress “BioNRW pHD Student Convention” in Düsseldorf at 13. July 2013 with a short presentation about iGEM and our project.
-
<li>We are proudly to present our <a href="http://ekvv.uni-bielefeld.de/blog/uniaktuell/entry/mit_bakterien_batterie_strom_erzeugen">  first press release</a> it was amazing to see how often our press release was picked of.</li>
+
*We are proudly to present our <a href="http://ekvv.uni-bielefeld.de/blog/uniaktuell/entry/mit_bakterien_batterie_strom_erzeugen">  first press release</a> it was amazing to see how often our press release was picked up.
-
</ul>
+
====MFC====
====MFC====
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 +
<div id="4.Week">
 +
===4.Week===
 +
</div>
-
<h3><a name=4.Week>4.Week</a></h3>
+
====Organization====
-
 
+
*Dr. Falk Harnisch will have a presentation at CeBiTec colloquium as an expert for our team.
-
<h4><a href="https://2013.igem.org/Team:Bielefeld-Germany/Project/#">Organization</a></h4>
+
*Preparing experiments for the ‘Day of Synthetic Biology’. Our ideas are to have different experiments like DNA isolation from fruit and vegetables, pipetting of bright colors, chromatography with markers, a potato battery or microscopy.
-
<ul>
+
*The TV station WDR would like to contribute with us on our topic
-
<li>Dr. Falk Harnisch will have a presentation at CeBiTec colloquium as an expert for our team.</li>
+
-
<li>Preparing experiments for the ‘Day of Synthetic Biology’. Our ideas are to have different experiments like DNA isolation from fruit and vegetables, pipetting of bright colors, chromatography with markers, a potato battery or microscopy. </li>
+
-
<li>The TV station WDR would like to contribute with us on our topic</li>
+
-
</ul>
+
====MFC====
====MFC====
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====Mediators====
====Mediators====
 +
====Cytochromes====
-
<h4><a href="https://2013.igem.org/Team:Bielefeld-Germany/Project/Cytochromes">Cytochromes</a></h4>
+
<div class="cyt_frag1_hl">
-
 
+
*Amplification of Fragment 1
-
<div class="cyt_frag1_hl"><p><a>Amplification of Fragment 1</a></p></div>
+
</div>
<div class="cyt_frag1">
<div class="cyt_frag1">
-
<blockquote>
+
**Size: 1800 bp
-
Size: 1800 bp
+
**Program: <a href="https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/ProtocolsPrograms#cyt_frag1">PhusionPCR</a>
-
<br>Program: <a href="https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/ProtocolsPrograms#cyt_frag1">PhusionPCR</a>
+
**Gradient: 54°C - 71°C over 8 steps
-
<br>Gradient: 54°C - 71°C over 8 steps
+
**Primer: mtrC_fwd & mtr_Frag1_rev
-
<br>Primer: mtrC_fwd & mtr_Frag1_rev
+
<br>Template: S. oneidensis PCR Template from genomic DNA
<br>Template: S. oneidensis PCR Template from genomic DNA
<br>Notes: Annealing temperature has no significant impact on the PCR
<br>Notes: Annealing temperature has no significant impact on the PCR
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</div>
</div>
-
<div class="cyt_frag2_hl"><p><a>Amplification of Fragment 2</a></p></div>
+
<div class="cyt_frag2_hl">
 +
*Amplification of Fragment 2
 +
</div>
<div class="cyt_frag2">
<div class="cyt_frag2">
-
<blockquote>
+
**Size: 330 bp
-
Size: 330 bp
+
**Program: <a href="https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/ProtocolsPrograms#cyt_frag2">PhusionPCR</a>
-
<br>Program: <a href="https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/ProtocolsPrograms#cyt_frag2">PhusionPCR</a>
+
**Primer: mtr_Frag2_fwd & mtr_Frag2_rev
-
<br>Primer: mtr_Frag2_fwd & mtr_Frag2_rev
+
**Template: S. oneidensis PCR Template from genomic DNA
-
<br>Template: S. oneidensis PCR Template from genomic DNA
+
**Notes:  
-
<br>Notes:  
+
-
</blockquote>
+
</div>
</div>
-
<div class="cyt_frag3_hl"><p><a>Amplification of Fragment 3</a></p></div>
+
<div class="cyt_frag3_hl">
 +
*Amplification of Fragment 3
 +
</div>
<div class="cyt_frag3">
<div class="cyt_frag3">
-
<blockquote>
+
**Size: 3000 bp
-
Size: 3000 bp
+
**Program: <a href="https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/ProtocolsPrograms#cyt_frag3">PhusionPCR</a>
-
<br>Program: <a href="https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/ProtocolsPrograms#cyt_frag3">PhusionPCR</a>
+
**Gradient: 54°C - 71°C over 8 steps
-
<<br>Gradient: 54°C - 71°C over 8 steps
+
**Primer: mtr_Frag3_fwd & mtrB_rev
-
<br>Primer: mtr_Frag3_fwd & mtrB_rev
+
**Template: S. oneidensis PCR Template from genomic DNA
-
<br>Template: S. oneidensis PCR Template from genomic DNA
+
**Notes: Annealing temperature has no significant impact on the PCR
-
<br>Notes: Annealing temperature has no significant impact on the PCR
+
-
</blockquote>
+
</div>
</div>
-
<div class="cyt_ccm_hl"><p><a>Amplification of ccmAH cluster</a></p></div>
+
<div class="cyt_ccm_hl">
 +
*Amplification of ccmAH cluster
 +
</div>
<div class="cyt_ccm">
<div class="cyt_ccm">
-
<blockquote>
+
**Size:6311 bp
-
Size:6311 bp
+
*Program: <a href="https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/ProtocolsPrograms#cyt_ccmAH">PhusionPCR</a>
-
<br>Program: <a href="https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/ProtocolsPrograms#cyt_ccmAH">PhusionPCR</a>
+
*Gradient: 51.5°C - 68°C over 8 steps
-
<<br>Gradient: 51.5°C - 68°C over 8 steps
+
*Primer: ccmAH_fwd & ccmAH_rev
-
<br>Primer: ccmAH_fwd & ccmAH_rev
+
*Template: E. coli PCR Template from genomic DNA
-
<br>Template: E. coli PCR Template from genomic DNA
+
*Notes: A high annealing temperature of 68°C or more increases yield as well as reduces unspecific bands and is therefore recommended.
-
<br>Notes: A high annealing temperature of 68°C or more increases yield as well as reduces unspecific bands and is therefore recommended.
+
-
</blockquote>
+
</div>
</div>
-
<div class="cyt_cleanup1_hl"><p><a>Gelextraction and cleanup of Fragment 1, 2, 3 and ccmAH</a></p></div>
+
<div class="cyt_cleanup1_hl">
 +
*Gelextraction and cleanup of Fragment 1, 2, 3 and ccmAH
 +
</div>
<div class="cyt_cleanup1">
<div class="cyt_cleanup1">
-
<blockquote>
+
**Gelextraction and clean up with the AnalytikJena GelExtraction-Kit
-
<u>Gelextraction and clean up with the AnalytikJena GelExtraction-Kit</u>
+
**Elution buffer was preheated to 50°C
-
<p>-Elution buffer was preheated to 50°C </p>
+
**We eluted each column twice, with 20 ul each and combined it afterwards
-
<p>-We eluted each column twice, with 20 ul each and combined it afterwards</p>
+
**Measurement of nucleid acid concentration via NanoDrop
-
<br><u>Measurement of nucleid acid concentration via NanoDrop </u>
+
***Fragment1: 4-2607-304: 10.5 ng/ul</p>
-
<p>-Fragment1: 4-2607-304: 10.5 ng/ul</p>
+
***Fragment2: 4-2707-003: 44.6 ng/ul</p>
-
<p>-Fragment2: 4-2707-003: 44.6 ng/ul</p>
+
***Fragment2: 4-2707-004: 13.5 ng/ul</p>
-
<p>-Fragment2: 4-2707-004: 13.5 ng/ul</p>
+
***Fragment3: 4-2607-301: 11.1 ng/ul</p>
-
<p>-Fragment3: 4-2607-301: 11.1 ng/ul</p>
+
***Fragment3: 4-2607-302: 8.9 ng/ul</p>
-
<p>-Fragment3: 4-2607-302: 8.9 ng/ul</p>
+
***Fragment3: 4-2607-303: 9.2 ng/ul</p>
-
<p>-Fragment3: 4-2607-303: 9.2 ng/ul</p>
+
***ccmAH: 4-2807-302: 11.0 ng/ul</p>
-
<p>-ccmAH: 4-2807-302: 11.0 ng/ul</p>
+
***ccmAH: 4-2807-303: 11.5 ng/ul</p>
-
<p>-ccmAH: 4-2807-303: 11.5 ng/ul</p>
+
-
 
+
-
</blockquote>
+
</div>
</div>
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-
<h3><a name=5.Week>5.Week</a></h3>
+
<div id="5.Week">
 +
===5.Week===
 +
</div>
 +
 
 +
====Organization====
 +
*Spontaneous visit of Radio Bielefeld in our laboratory. In addition to a radio interview a
 +
[[http://www.radiobielefeld.de/programm/bei-uns-im-programm/studenten-entwickeln-biobatterie.html"|short video clip]] was filmed.
-
<h4><a href="https://2013.igem.org/Team:Bielefeld-Germany/Project/#">Organization</a></h4>
 
-
<ul>
 
-
<li>Spontaneous visit of Radio Bielefeld in our laboratory. In addition to a radio interview a
 
-
<a href="http://www.radiobielefeld.de/programm/bei-uns-im-programm/studenten-entwickeln-biobatterie.html">short video clip </a>was filmed</li>
 
-
</ul>
 
====MFC====
====MFC====

Revision as of 09:16, 25 September 2013










July



Milesstones




1.Week

Organization

  • We’ve presented us at the congress ‘Next generation of biotechnological processes 2020+’ in Berlin at 27. June 2013. There we have met an expert (Dr. Falk Harnisch) on the topic of MFC and we have decided to participate the German Synthetic Biology Day.


MFC

Mediators

Cytochromes

  • Design and order of new Primers
    • The mtrCAB fragment has two illegal PstI restriction sites at x xbp and yy bp, so we had to design new primers to remove them. We replaced one base in each restriction site, without affecting the coding triplett, by respective primer overlaps . We ended up with three different fragments, which will be ligated back together via Gibson Assembly.
    • mtrCAB_Frag1_rev:
    • mtrCAB_Frag2_fwd:
    • mtrCAB_Frag2_rev:
    • mtrCAB_Frag3_fwd:


Biosafety

Porines













2.Week

Organization

  • We can present new sponsors of iGEM-Team Bielefeld: Stockmeier, Baxter, Promega, BIO.NRW and Applichem will support our team.</li>

MFC

Mediators

Cytochromes

Biosafety

Porines

















3.Week

Organization

  • We’ve presented us at the congress “BioNRW pHD Student Convention” in Düsseldorf at 13. July 2013 with a short presentation about iGEM and our project.
  • We are proudly to present our <a href="http://ekvv.uni-bielefeld.de/blog/uniaktuell/entry/mit_bakterien_batterie_strom_erzeugen"> first press release</a> it was amazing to see how often our press release was picked up.

MFC

Mediators

Cytochromes

Biosafety

Porines















4.Week

Organization

  • Dr. Falk Harnisch will have a presentation at CeBiTec colloquium as an expert for our team.
  • Preparing experiments for the ‘Day of Synthetic Biology’. Our ideas are to have different experiments like DNA isolation from fruit and vegetables, pipetting of bright colors, chromatography with markers, a potato battery or microscopy.
  • The TV station WDR would like to contribute with us on our topic

MFC

Mediators

Cytochromes

  • Amplification of Fragment 1


Template: S. oneidensis PCR Template from genomic DNA
Notes: Annealing temperature has no significant impact on the PCR </blockquote>

  • Amplification of Fragment 2
  • Amplification of Fragment 3
  • Amplification of ccmAH cluster
  • Gelextraction and cleanup of Fragment 1, 2, 3 and ccmAH
    • Gelextraction and clean up with the AnalytikJena GelExtraction-Kit
    • Elution buffer was preheated to 50°C
    • We eluted each column twice, with 20 ul each and combined it afterwards
    • Measurement of nucleid acid concentration via NanoDrop
      • Fragment1: 4-2607-304: 10.5 ng/ul</p>
      • Fragment2: 4-2707-003: 44.6 ng/ul</p>
      • Fragment2: 4-2707-004: 13.5 ng/ul</p>
      • Fragment3: 4-2607-301: 11.1 ng/ul</p>
      • Fragment3: 4-2607-302: 8.9 ng/ul</p>
      • Fragment3: 4-2607-303: 9.2 ng/ul</p>
      • ccmAH: 4-2807-302: 11.0 ng/ul</p>
      • ccmAH: 4-2807-303: 11.5 ng/ul</p>


Cytochromes

Biosafety

Porines
















5.Week

Organization

  • Spontaneous visit of Radio Bielefeld in our laboratory. In addition to a radio interview a

short video clip was filmed.


MFC

Mediators

Cytochromes

Biosafety

Porines

Retrieved from "http://2013.igem.org/Team:Bielefeld-Germany/Labjournal/July"