Difference between revisions of "Team:Goettingen/Attributions"

 
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   <h2>Outside of the team roster</h2>
 
   <h2>Outside of the team roster</h2>
 
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     <img src="https://static.igem.org/mediawiki/2018/1/13/T--Goettingen--attributions-genomics.png"
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     <img src="https://static.igem.org/mediawiki/2018/c/cb/T--Goettingen--attributions-seqlab.png">
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        alt="Göttingen Genomics Laboratory">
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    <p>Göttingen Genomics Laboratory</p>
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   </div>
 
   </div>
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   <h3>RNA sequencing</h3>
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   <h3>DNA sequencing</h3>
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   <p>For acquiring RNA sequencing data, we asked <strong>Professor Rolf Daniel</strong> from Göttingen Genomics Laboratory (G2L) to support our project. He provided us a lot of RNA sequencing data that enabled us to overthink our detection method with reporter genes.</p>
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   <p>The best thing that can happen to a DNA: to acquire DNA sequences, we sent our samples to the <a href="https://www.microsynth.seqlab.de/home-de.html" target="_blank">Microsynth Seqlab sequencing laboratories</a> Microsynth Seqlab sequencing laboratories in Göttingen.
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  <h3 class="article_clear-right">
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    ITC measurements</h3>
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  <p>For isothermal titration calorimetry (ITC) measurements and structure elucidation of our purified proteins AroA from <em>Escherichia&nbsp;coli</em> and AroE from <em>Bacillus&nbsp;subtilis</em> we sent our samples to the Bange lab in Marburg. <strong>Gert Bange</strong> is also supervising an iGEM team this year and will hopefully provide us with data? TO DO
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     <img src="https://static.igem.org/mediawiki/2018/c/cb/T--Goettingen--attributions-seqlab.png"
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        alt="Seqlab Göttingen">
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     <img src="https://static.igem.org/mediawiki/2018/1/13/T--Goettingen--attributions-genomics.png">
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    <p>Seqlab Göttingen</p>
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   </div>
 
   </div>
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   <h3>DNA sequencing</h3>
+
   <h3>RNA sequencing</h3>
−
   <p>To acquire DNA sequences, we sent our samples as described in the notebook section to <em>Microsynth Seqlab</em>, based in Göttingen.
+
   <p>RNA sequencing analyses were done by <strong>Dr. Anja Poehlein</strong> and <strong>Prof. Dr. Rolf Daniel</strong> from the <a href="http://appmibio.uni-goettingen.de/index.php?sec=g2l" target="_blank">Göttingen Genomics Laboratory</a>. The comprehensive RNA sequencing data set helped us to develop a glyphosate reporter system.</p>
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 +
<h3>Genes</h3>
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  <p>We ordered some genes, called g-Blocks, from <a href="https://eu.idtdna.com/pages" target="_blank">Integrated DNA Technologies</a>, which was free of charge because the company supports the iGEM competition.
 
   </p>
 
   </p>
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   <h3 class="article_clear-right">
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  <h3>Analyses of DNA and genome sequences</h3>
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   <p>DNA sequences and genome sequences were analyzed using the <a href="https://www.geneious.com" target="_blank">Geneious</a> software package. We are grateful to <strong>Mrs. Claire Westwood</strong> who provided us with four Geneious license keys.
 +
  </p>
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 +
<h3>Bacterial strains</h3>
 +
  <p>We are grateful to <strong>Dr. Daniel R. Zeigler</strong> and <strong>Prof. Dr. John Helmann</strong> from the <a href="http://www.bgsc.org" target="_blank">Bacillus Genetic Stock Center</a> at The Ohio State University and the <a href="https://micro.cornell.edu/research/helmann-lab/" target="_blank">Helman lab</a> at the Cornell University, respectively, for providing <i>B. subtilis</i> strains.
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  </p>
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<h3 class="article_clear-right">
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    Biochemical and structural characterization of EPSP synthases</h3>
 +
  <p>For isothermal titration calorimetry (ITC) measurements and structure determination of the purified EPSP synthases from <em>E. coli</em> and <em>B. subtilis</em>, we sent our proteins to the members of the <a href="https://2018.igem.org/Team:Marburg" target="_blank">iGEM team of Marburg</a> that is hosted by the <a href="https://www.bangelab.org" target="_blank">Bange lab</a> in Marburg. <strong>Prof. Dr. Gert Bange</strong> is again supervising an iGEM team, which is acknowledged for collaborating.
 +
  </p>
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 +
 
 +
 
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<h3 class="article_clear-right">
 
     Detection of glyphosate </h3>
 
     Detection of glyphosate </h3>
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   <p>For the detection of glyphosate, we sent our samples to the <strong>Ischebeck lab</strong> in Göttingen, which provided us with the possibility to use their gas chromatography and mass spectrometry devices for determining the concentration of glyphosate in samples. TO DO
+
   <p>For the detection of glyphosate, we sent our samples to the lab from <strong> Dr. Till Ischebeck</strong> in the <a href="https://www.uni-goettingen.de/de/533683.html" target="_blank">Department of Plant Biochemistry</a> at the University of Göttingen. The samples were analyzed by GC/MS.
 
   </p>
 
   </p>
−
   <h3>Genes</h3>
+
    
−
   <p>We ordered some genes, called g-Blocks, from <em>Integrated DNA Technologies</em>, which was free, since they sponsor the iGEM competition.
+
<h3 class="article_clear-right">
 +
    Filtration system</h3>
 +
   <p>We are grateful to <strong>Dr. Karl Pflanz</strong> from the <a href="https://www.sartorius.co.uk/sartoriusUK/en/GBP/Products/Laboratory/Microbiology-Products/Claristep®-Station-17C--M8/p/17C--M8?setCountry=GB-en" target="_blank">Sartorius AG</a> who provided us with a Claristep® Filtration System for sample preparation to determine the glyphosate concentration.</p>
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<h3 class="article_clear-right">
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    Modeling </h3>
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  <p>We thank <strong> Prof. Dr. Stefan Klumpp</strong>, the head of the <a href="http://www.uni-goettingen.de/en/527801.html" target="_blank">Theoretical Biophysics Group</a> at the University of Göttingen, for his support to develop a model for our glyphosate detection system.
 
   </p>
 
   </p>
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   <h3>Contributions from the lab members</h3>
+
 
−
   <p>We want to thank <strong>Sabine Lentes</strong> for enduring eight people in the lab with many questions. She helped us in every situation and was a great aid.<br /> Furthermore, we want to thank <strong>Johannes Gibhardt</strong> for his help with any technical devices that we used. Especially he is an expert for the platereader.<br /> <strong>Christina Herzberg</strong> supported us with strains and plasmids, knowledge about technical methods, and answered many questions.<br /> <strong>Cedric Blötz</strong> helped us with his experience of being a former iGEM participant and for helpful discussions regarding our project.<br />
+
 
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     <strong>Anika Klewing</strong>helped us with buffers, kits and chemicals that we needed every day.<br /> Last but not least we want to thank all members from the Stülke lab for their support and endorsement in the time we used their lab and blocked technical devices with our experiments.
+
   <h3>Contributions from other lab members</h3>
 +
   <p>We thank <strong>Sabine Lentes</strong> for enduring eight people in the lab with many questions. She helped us in every situation and was a great aid.<br /> Furthermore, we thank <strong>Johannes Gibhardt</strong> for introducing us to technical devices. He is an expert for the multi well plate readers!<br /> <strong>Christina Herzberg</strong> supported us with strains and plasmids, knowledge about technical methods, and answered >1000 questions.<br /> <strong>Cedric Blötz</strong> helped us with his experience of being a former iGEM participant.<br />
 +
     <strong>Anika Klewing</strong> supported us with buffers, kits and chemicals that we needed for our work in the wetlab.<br/>
 +
<strong>Dr. Cornelia Herrfurth</strong> and <strong>Prof. Dr. Ivo Feußner</strong> helped out with HPLC glas vials for our glyphosate detection system.<br/>Last but not least, we thank all members from the <a href="http://www.uni-goettingen.de/en/577601.html" target="_blank">Stülke lab</a> for their support and endorsement during the time we used the lab and blocked technical devices with our experiments.
 +
  </p>
 +
<h3>Miscellaneous</h3>
 +
  <p><a href="https://www.biozym.com/site/Lang__de-DE/0/default.aspx" target="_blank">Biozym</a> is acknowledged for providing us with > 100 ball pens, 50 writing pads, 50 carrying bags (that are quite useful to transport used coffee cups from the lab to the <a href="https://www.studentenwerk-goettingen.de/index.php?id=206&L=1" target="_blank">Nordmensa</a> (students restaurant selling delicious food)) and 100 <a href="https://www.youtube.com/watch?v=astISOttCQ0" target="_blank">gummy bear</a> bags (old!).
 
   </p>
 
   </p>
 
   <h2>Work from team roster</h2>
 
   <h2>Work from team roster</h2>
−
   <p>We did all of the lab work by ourselfs as described in the notebook section. The experiments were developed in teamwork with our supervisors.</p>
+
   <p>We did all of the lab work by ourselfs as described in the notebook section. The experiments were developed in teamwork with our supervisors. The over all design was drafted by ourselves. Moreover, the wiki site and website were constructed on our own.
−
  <p>The over all design was drafted by ourselves. Also, the wiki and website were constructed by us.
+
 
   </p>
 
   </p>
 
   <h3>Supervisors</h3>
 
   <h3>Supervisors</h3>
−
   <p>The whole project is based on the ideas from <strong>Dr. Fabian Commichau</strong> that came up to his mind on a train ride to Brussels. We want to thank him for his infectious enthusiasm towards microbiology and great help with each question!</p>
+
   <p>The whole project was stimulated by the ideas from <strong>PD Dr. Fabian M. Commichau</strong> that came up in his mind during a train ride to <a href="http://www.bruxelles.be" target="_blank">Brussels</a> (that took not place: <a href="https://www.youtube.com/watch?v=D9K0uCbkm8U" target="_blank">Senk ju vor träwelling</a> with <a href="https://www.bahn.de/p/view/index.shtml?dbkanal_032=1&dbkanal_001=L01_S01_D001_KSE0001_Brand-AdWords-ADG-Brand_LZ01&gclid=Cj0KCQjwuafdBRDmARIsAPpBmVWjc4MHTWPS6GAy5ExezaBwdoMXOsomZZvQe0amH_Yyk_DWTX7NmhEaAty5EALw_wcB" target="_blank">DEUTSCHE BAHN</a>). We want to thank him for his infectious enthusiasm for microbiology and his help to solve experimental problems!</p>
−
   <p>We want to thank also <strong>Prof. Dr. Jörg Stülke</strong> for kindly providing us with a laboratory, which is obviously necessary for such a project. Furthermore, he greatly supported us with the funding and his experience in leading former iGEM teams.</p>
+
   <p>We thank <strong>Prof. Dr. Jörg Stülke</strong> for kindly providing us with lab space, which is essential for a research project. Furthermore, he greatly supported us with funding and his experience as a leader of the iGEM team of the University Göttingen in 2013.</p>
 
   <h3>Construction of strains</h3>
 
   <h3>Construction of strains</h3>
−
   <p>We want to thank Dr. Fabian Commichau and Sabine Lentes for help with the construction of the deletion strains that were needed for our work.
+
   <p>We are grateful to Sabine Lentes and PD. Dr. Fabian M. Commichau for the construction of <i>B. subtilis</i> mutants.
 
   </p>
 
   </p>
 
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Latest revision as of 15:08, 17 October 2018

Attributions

Outside of the team roster

DNA sequencing

The best thing that can happen to a DNA: to acquire DNA sequences, we sent our samples to the Microsynth Seqlab sequencing laboratories Microsynth Seqlab sequencing laboratories in Göttingen.

RNA sequencing

RNA sequencing analyses were done by Dr. Anja Poehlein and Prof. Dr. Rolf Daniel from the Göttingen Genomics Laboratory. The comprehensive RNA sequencing data set helped us to develop a glyphosate reporter system.

Genes

We ordered some genes, called g-Blocks, from Integrated DNA Technologies, which was free of charge because the company supports the iGEM competition.

Analyses of DNA and genome sequences

DNA sequences and genome sequences were analyzed using the Geneious software package. We are grateful to Mrs. Claire Westwood who provided us with four Geneious license keys.

Bacterial strains

We are grateful to Dr. Daniel R. Zeigler and Prof. Dr. John Helmann from the Bacillus Genetic Stock Center at The Ohio State University and the Helman lab at the Cornell University, respectively, for providing B. subtilis strains.

Biochemical and structural characterization of EPSP synthases

For isothermal titration calorimetry (ITC) measurements and structure determination of the purified EPSP synthases from E. coli and B. subtilis, we sent our proteins to the members of the iGEM team of Marburg that is hosted by the Bange lab in Marburg. Prof. Dr. Gert Bange is again supervising an iGEM team, which is acknowledged for collaborating.

Detection of glyphosate

For the detection of glyphosate, we sent our samples to the lab from Dr. Till Ischebeck in the Department of Plant Biochemistry at the University of Göttingen. The samples were analyzed by GC/MS.

Filtration system

We are grateful to Dr. Karl Pflanz from the Sartorius AG who provided us with a Claristep® Filtration System for sample preparation to determine the glyphosate concentration.

Modeling

We thank Prof. Dr. Stefan Klumpp, the head of the Theoretical Biophysics Group at the University of Göttingen, for his support to develop a model for our glyphosate detection system.

Contributions from other lab members

We thank Sabine Lentes for enduring eight people in the lab with many questions. She helped us in every situation and was a great aid.
Furthermore, we thank Johannes Gibhardt for introducing us to technical devices. He is an expert for the multi well plate readers!
Christina Herzberg supported us with strains and plasmids, knowledge about technical methods, and answered >1000 questions.
Cedric Blötz helped us with his experience of being a former iGEM participant.
Anika Klewing supported us with buffers, kits and chemicals that we needed for our work in the wetlab.
Dr. Cornelia Herrfurth and Prof. Dr. Ivo Feußner helped out with HPLC glas vials for our glyphosate detection system.
Last but not least, we thank all members from the Stülke lab for their support and endorsement during the time we used the lab and blocked technical devices with our experiments.

Miscellaneous

Biozym is acknowledged for providing us with > 100 ball pens, 50 writing pads, 50 carrying bags (that are quite useful to transport used coffee cups from the lab to the Nordmensa (students restaurant selling delicious food)) and 100 gummy bear bags (old!).

Work from team roster

We did all of the lab work by ourselfs as described in the notebook section. The experiments were developed in teamwork with our supervisors. The over all design was drafted by ourselves. Moreover, the wiki site and website were constructed on our own.

Supervisors

The whole project was stimulated by the ideas from PD Dr. Fabian M. Commichau that came up in his mind during a train ride to Brussels (that took not place: Senk ju vor träwelling with DEUTSCHE BAHN). We want to thank him for his infectious enthusiasm for microbiology and his help to solve experimental problems!

We thank Prof. Dr. Jörg Stülke for kindly providing us with lab space, which is essential for a research project. Furthermore, he greatly supported us with funding and his experience as a leader of the iGEM team of the University Göttingen in 2013.

Construction of strains

We are grateful to Sabine Lentes and PD. Dr. Fabian M. Commichau for the construction of B. subtilis mutants.