Difference between revisions of "Team:Goettingen/Attributions"

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    <h1>Attributions</h1>
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  </div>
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  <h2>Outside of the team roster</h2>
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  <div class="article_picture article_picture-right">
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    <img src="https://static.igem.org/mediawiki/2018/c/cb/T--Goettingen--attributions-seqlab.png">
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  </div>
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  <h3>DNA sequencing</h3>
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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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  </p>
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<div class="article_picture article_picture-right">
  
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    <img src="https://static.igem.org/mediawiki/2018/1/13/T--Goettingen--attributions-genomics.png">
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  </div>
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  <h3>RNA sequencing</h3>
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  <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.
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  </p>
  
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  <h3>Analyses of DNA and genome sequences</h3>
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<h3>★  ALERT! </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.
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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  </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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</div>
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<h3>Bacterial strains</h3>
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  <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>
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  <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.
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  </p>
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<h3 class="article_clear-right">
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    Detection of glyphosate </h3>
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  <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.
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  </p>
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<h3 class="article_clear-right">
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    Filtration system</h3>
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  <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.
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  </p>
  
  
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  <h3>Contributions from other lab members</h3>
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  <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 />
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<h1>Attributions</h1>
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    <strong>Anika Klewing</strong> supported us with buffers, kits and chemicals that we needed for our work in the wetlab.<br/>
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<p>This page is your opportunity to explain what parts of your project you did and what was done by technicians, advisers, etc. This requirement is not about literature references - these can and should be displayed throughout your wiki.
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<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.
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  </p>
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<h3>Miscellaneous</h3>
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<h3> Bronze Medal Criterion #3</h3>
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  <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!).
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<p> All of the work done in your project must be attributed correctly on this page. You must clearly state the work that was done by the students on your team and note any work that was done by people outside of your team, including the host labs, advisors, instructors, and individuals not on the team roster.  
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  </p>
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  <h2>Work from team roster</h2>
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Please see the <a href="https://2018.igem.org/Judging/Medals">Medals requirements page</a> for more details.</p>
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  <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.
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  </p>
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  <h3>Supervisors</h3>
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  <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>
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  <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>
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  <h3>Construction of strains</h3>
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  <p>We are grateful to Sabine Lentes and PD. Dr. Fabian M. Commichau for the construction of <i>B. subtilis</i> mutants.
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  </p>
 
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<h3> What should this page contain?</h3>
 
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<li>Clearly state what the team accomplished</li>
 
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<li>General Support</li>
 
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<li>Project support and advice</li>
 
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<li>Fundraising help and advice</li>
 
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<li>Lab support</li>
 
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<li>Difficult technique support</li>
 
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<li> Thanks and acknowledgements for all other people involved in helping make a successful iGEM team</li>
 
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<p>Tell us if your institution teaches an iGEM or synthetic biology class and when you started your project:</p>
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<li>Does your institution teach an iGEM or synthetic biology course?</li>
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<li>When did you start this course?</li>
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<li>Are the syllabus and course materials freely available online?</li>
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<li>When did you start your brainstorming?</li>
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<li>When did you start in the lab?</li>
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<h3>Inspiration</h3>
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<p>Take a look at what other teams have done:</p>
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<li><a href="https://2011.igem.org/Team:Imperial_College_London/Team">2011 Imperial College London</a> (scroll to the bottom)</li>
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<li><a href="https://2014.igem.org/Team:Exeter/Attributions">2014 Exeter </a></li>
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<li><a href="https://2014.igem.org/Team:Melbourne/Attributions">2014 Melbourne </a></li>
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<li><a href="https://2014.igem.org/Team:Valencia_Biocampus/Attributions">2014 Valencia Biocampus</a></li>
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<h3> Why is this page needed? </h3>
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<p>The Attribution requirement helps the judges know what you did yourselves and what you had help with. We don't mind if you get help with difficult or complex techniques, but you must report what work your team did and what work was done by others.</p>
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For example, you might choose to work with an animal model during your project. Working with animals requires getting a license and applying far in advance to conduct certain experiments in many countries. This is difficult to achieve during the course of a summer, but much easier if you can work with a postdoc or PI who has the right licenses.</p>
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<h3> Can we base our project on a previous one? </h3>
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<p>Yes! You can have a project based on a previous team, or based on someone else's idea, <b>as long as you state this fact very clearly and give credit for the original project.</b> </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.