Difference between revisions of "Team:IIT-Madras/Collaborations"

 
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<h1 style="font-family: 'title', sans-serif; font-size: 12mm; padding-left: 20%; color: #00b355;">Collaborations</h1>
 
<h1 style="font-family: 'title', sans-serif; font-size: 12mm; padding-left: 20%; color: #00b355;">Collaborations</h1>
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<center>
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<div class="box" style="display: block;">
 
<div class="box" style="display: block;">
 
<h2 style="font-size: 9mm;">Language Project Collaborations</h2>
 
<h2 style="font-size: 9mm;">Language Project Collaborations</h2>
  
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<div class="grid">
 
  
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<p style="font-family: title; font-size: 5.5mm;">
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The collaboration involves sending the English script to the collaborator, who translate it into another language record the translated script and send us the audio file(s). We stitch together the audio clips and the presentation slides to make the video. <br>We have had 13 different iGEM teams collaborate with us, resulting in language project videos in 17 different languages for a total of 25 videos. Through these collaborations, we were able to interact and share with all these teams, and it formed a big part of our iGEM experience to talk with such a diverse group of people working for the same goal. <br>
 +
 +
<ol type="1" style="font-family: title; font-size: 5.5mm;" ALIGN LEFT>
 +
 +
<li><strong>Pasteur Paris</strong>:<ul><li> French - Introduction to Synthetic Biology</li></ul>
 
<div>
 
<div>
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<img src="https://static.igem.org/mediawiki/2018/e/ec/T--IIT-Madras--Pasteur.png" alt="" style="max-width=100%;">
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<img src="https://static.igem.org/mediawiki/2018/e/ec/T--IIT-Madras--Pasteur.png" alt="" style="width: 50%;height : 10%;">
 
</div>
 
</div>
 +
</li>
  
 +
<li><strong>NYU Abu Dhabi</strong><ul>
 +
<li>Mandarin - Introduction to Synthetic Biology</li>
 +
<li>Bosnian - Introduction to Synthetic Biology</li>
 +
<li>Korean - Introduction to Synthetic Biology</li>
 +
<li>Arabic - DNA & RNA</li></ul>
 
<div>
 
<div>
−
<p style="font-size:5.5mm; font-family: 'title', sans-serif;" ALIGN=LEFT>
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<img src="https://static.igem.org/mediawiki/2018/d/d5/T--IIT-Madras--NYUAbuDhabi.png " alt="" style="width:50%;height:50%;">
−
The collaboration involves sending the English script to the collaborator, who translate it into another language record the translated script and send us the audio file(s). We stitch together the audio clips and the presentation slides to make the video.
+
−
</p>
+
 
</div>
 
</div>
 +
</li>
 +
 +
<li><strong>Warwick </strong><ul> <li>Malay - Introduction to Synthetic Biology</li>
 +
<li>Catalan - Introduction to Synthetic Biology</li>
 +
</ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/4/4c/T--IIT-Madras--Warwick.png " style=" width:30%;height:30%;">
 +
</div>
 +
</li>
 +
<li><strong>Tec de Monterrey Campus Guadalajara</strong><ul><li>Spanish - Introduction to Synthetic Biology</li></ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/f/fb/T--IIT-Madras--TecdeMonterrey.png " alt="" style="width: 30%;height:30%;">
 +
</div>
 +
</li>
 +
<li><strong>Anhui University of Technology</strong><ul><li>Chinese - Introduction to Synthetic Biology</li></ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/3/37/T--IIT-Madras--AHUTChina.png " style="width:  30%;height:30%;">
 +
</div>
 +
</li>
 +
<li><strong>ECUST</strong><ul><li>Mandarin - DNA & RNA</li></ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/0/0f/T--IIT-Madras--ECUST.png" style="width:50%;height:50%;">
 
</div>
 
</div>
 +
</li>
  
 +
<li><strong>Ruia Mumbai</strong><ul><li>Assamese - Introduction to Synthetic Biology</li>
 +
<li>Sanskrit - Introduction to Synthetic Biology</li>
 +
<li>Tulu - Introduction to Synthetic Biology</li>
 +
<li>Bhojpuri - Introduction to Synthetic Biology</li>
 +
</ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/7/71/T--IIT-Madras--Ruia.png" style="width: 50%;height:50%;">
 +
</div>
 +
</li>
  
−
<p style="font-size:5.5mm; font-family: 'title', sans-serif;" ALIGN=LEFT>
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<li><strong>ICT Mumbai</strong><ul><li>Urdu - Introduction to Synthetic Biology</li>
 +
<li>Marathi - Central Dogma and Translation</li>
 +
</ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/a/a3/T--IIT-Madras--ICT.png" style="width: 30%;height:30%;">
 +
</div>
 +
</li>
  
  
 +
<li><strong>Paris 2018</strong>
 +
<ul>
 +
<li>Italian - DNA & RNA</li>
 +
<li>French - DNA & RNA</li>
 +
<li>Persian - Introduction to Synthetic Biology</li>
 +
</ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/9/93/T--IIT-Madras--Paris.png" style="width:30%;height:30%;">
 +
</div>
 +
</li>
  
−
<div class="p12">
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<li><strong>NUS Singapore Science</strong><ul><li>Korean - DNA & RNA</li></ul>
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<ol type="I" style="font-size: 5.5mm; text-align: justify; " ALIGN=LEFT>
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<div>
 +
<img src="https://static.igem.org/mediawiki/2018/f/f6/T--IIT-Madras--NUS.png" style="width:30%;height:30%;">
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</div>
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</li>
  
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<li>The original idea was to study the degradation of lignin to produce vanillin which has higher economic value.
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<li><strong>Hamburg</strong>
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We conducted a literature survey regarding the degradation of the aromatic rings of lignin and organisms capable of degrading such aromatics.</li>
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<ul>
−
<li>For popular organisms like <em>E. coli</em> and <em>L. lactis.</em> competent cells are required for transformation. From a brief literature survey we found several ‘naturally competent’ microorganisms. However, most of them were pathogenic and are known to harm humans. Hence, we cannot work with them in a biosafety level 1 laboratory.
+
<li>German - Introduction to Synthetic Biology</li>
−
</ol>
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<li>Polish - Introduction to Synthetic Biology</li>
 +
</ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/b/b5/T--IIT-Madras--Hamburg.png" style="width: 30%;height:30%;">
 
</div>
 
</div>
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</p>
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</li>
  
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<span style="padding-right: 77%;"><strong>Solution:</strong></span>
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<li><strong>Nanjing China</strong>
 +
<ul>
 +
<li>Mandarin - Proteins</li></ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/b/bc/T--IIT-Madras--ANJING.png" style="width: 50%;height : 20%;">
 +
</div>
 +
</li>
  
−
<p style="font-size:5.5mm; font-family: 'title', sans-serif;" class="p12 p16" ALIGN=LEFT >
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<li><strong>Biomarvel</strong><ul><li>Korean - Intro to Synthetic Biology</li></ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/2/28/T--IIT-Madras--Biomarvel.png" style="width: 40%;height:20%;">
 +
</div>
 +
</li>
  
  
−
An organism that best fits both these requirements is <em>Acinetobacter baylyi</em>. The ADP1 strain of this organism is naturally competent, non-pathogenic, and has the property of degrading aromatics. This strain can be purchased from DSMZ.
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</ol>
  
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</p>
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<ol type="1" style="font-family: title; font-size: 5.5mm;" ALIGN LEFT>
 +
<h2 style="font-size: 9mm;">ChassiDex Collaborations</h2>
  
  
 +
<p style="font-family: title; font-size: 5.5mm;">
  
−
<span style="padding-right: 75%;"><strong>Motivation:</strong></span>
+
ChassiDex is a database of host organisms containing all the information needed to work with the organism listed.
 +
The following two teams helped us out by by providing data on different chassis which was further curated and put up on our database. <br>
 +
<li><strong>Marburg</strong><ul><li>Data on Vibrio natriegens</li>
 +
</ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/c/c6/T--IIT-Madras--IBRIGENS.png" style="width: 30%;height:30%;">
 +
</div>
 +
</li>
 +
<li><strong>SKLMT China</strong><ul><li>Data on Pseudomonas fluorescens</li>
 +
</ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/4/4c/T--IIT-Madras--KLXMCHINA.png" style="width: 30%;height:10%;">
 +
</div>
 +
</li>
  
−
<p style="font-size:5.5mm; font-family: 'title', sans-serif;" class="p12 p16" ALIGN=LEFT >
+
</ol>
 +
<ol type="1" style="font-family: title; font-size: 5.5mm;" ALIGN LEFT>
 +
<h2 style="font-size: 9mm;">Other Collaborations</h2>
  
−
While perusing literature for <em>Acinetobacter baylyi</em> ADP1 we couldn't find substantial material, as information was sparse and not many tools were available to undertake synthetic biology experiments with this organism. This motivated us to build a toolbox for <em>Acinetobacter baylyi</em> that was generic and hence could effectively be used by research groups working with other organisms as well.
 
−
</p>
 
  
 +
<p style="font-family: title; font-size: 5.5mm;">
  
−
<span style="padding-right: 80%;"><strong>Project:</strong></span>
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We collaborated with other teams to contribute to one of their social initiatives. <br>
 +
<li><strong>IISER Mohali, India</strong>
 +
<ul><li>We had a great time mentoring the Mohali team regarding their modelling which helped them in evolving their algorithm. We got to share our knowlegde and learn from them in the process.</li></ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/b/b9/T--IIT-Madras--IISERMOHALI.png" alt="" style="width: 50%;height :50%;">
 +
</div>
 +
</li>
 +
<li><strong>Vit Vellore</strong>
 +
<ul><li>We participated in a beach clean-up organised by VIT at Marina Beach, Chennai. </li></ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/d/de/T--IIT-Madras--VIT.png" alt="" style="width: 50%;height :50%;">
 +
</div>
 +
</li>
  
−
<p style="font-size:5.5mm; font-family: 'title', sans-serif;" class="p12 p16" ALIGN=LEFT >
 
−
 
−
A primary requirement for experimentation in synthetic biology is a fluorescent reporter protein. Hence we planned to codon-optimize two reporter proteins, GFP and mCherry, for <em>A. baylyi</em>. </p>
 
−
 
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<p style="font-size:5.5mm; font-family: 'title', sans-serif;" class="p12 p16" ALIGN=LEFT >
 
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When we approached companies for codon-optimized reporter proteins they did not have a codon bias table available for <em>A. baylyi</em>.Thus we made a freely available online tool called CUTE (Codon Usage Table Enumerator) that can generate a codon usage table by taking the protein coding annotation into consideration. This tool can be used for all organisms whose genome has been sequenced and whose protein coding regions are annotated. CUTE can be found on the <a href="https://cute.chassidex.org" target="_blank">CUTE ChassiDex website.</a> <br>
 
−
 
−
</br>We generated the codon usage table from the protein annotation of <em>A. baylyi</em> available on the  <a href="https://ncbi.nlm.nih.gov" target="_blank">NCBI</a>website. Using this codon table, we codon optimized reporter proteins and the characterization can be found here. <br>
 
−
</p>
 
−
 
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<p style="font-size:5.5mm; font-family: 'title', sans-serif;" class="p12 p16" ALIGN=LEFT >
 
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Following this we conceptualised our next tool - a synthetic promoter library for <em>Acinetobacter baylyi</em> ADP1. We designed a T5 promoter-based library which can exhibit varying expression strengths. Our aim was to make this library as generic as possible so as it maximise its use in synthetic biology.
 
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<br>
 
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</p>
 
  
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<li><strong>Tec de Monterrey Campus Guadalajara</strong>
 +
<ul><li>We clicked a picture of us at a landmark in Chennai, with a placard and the distance of Chennai to Boston written on it.</li></ul>
 +
<div>
 +
<img src=" https://static.igem.org/mediawiki/2018/f/fb/T--IIT-Madras--TecdeMonterrey.png " style="width: 30%;height:30%;">
 +
</div>
 +
</li>
  
 +
<li><strong>US AFRL CarrollHS </strong>
 +
<ul><li> Mike the Microbe came to our lab here at IIT Madras, Chennai and we got to click pictures with him.</li></ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/c/c5/T--IIT-Madras--mike.jpg" style="width: 30%;height:30%;">
 +
</div>
 +
</li>
  
 +
<li><strong>HAFS South Korea</strong>
 +
<ul><li>We contributed an Indian recipe that is easy to cook, healthy and diabetes-friendly. This will be used for Diabetic people to learn to manage cooking food. </li></ul>
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2018/b/be/T--IIT-Madras--HAFS.png" alt="" style="width: 30%;height:30%;">
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</div>
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</li>
  
  
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Latest revision as of 03:05, 18 October 2018

iGEM Collaborations Page

☰

Team: IIT-Madras/ADaPtat1on

Collaborations

Language Project Collaborations

The collaboration involves sending the English script to the collaborator, who translate it into another language record the translated script and send us the audio file(s). We stitch together the audio clips and the presentation slides to make the video.
We have had 13 different iGEM teams collaborate with us, resulting in language project videos in 17 different languages for a total of 25 videos. Through these collaborations, we were able to interact and share with all these teams, and it formed a big part of our iGEM experience to talk with such a diverse group of people working for the same goal.

  1. Pasteur Paris:
    • French - Introduction to Synthetic Biology
  2. NYU Abu Dhabi
    • Mandarin - Introduction to Synthetic Biology
    • Bosnian - Introduction to Synthetic Biology
    • Korean - Introduction to Synthetic Biology
    • Arabic - DNA & RNA
  3. Warwick
    • Malay - Introduction to Synthetic Biology
    • Catalan - Introduction to Synthetic Biology
  4. Tec de Monterrey Campus Guadalajara
    • Spanish - Introduction to Synthetic Biology
  5. Anhui University of Technology
    • Chinese - Introduction to Synthetic Biology
  6. ECUST
    • Mandarin - DNA & RNA
  7. Ruia Mumbai
    • Assamese - Introduction to Synthetic Biology
    • Sanskrit - Introduction to Synthetic Biology
    • Tulu - Introduction to Synthetic Biology
    • Bhojpuri - Introduction to Synthetic Biology
  8. ICT Mumbai
    • Urdu - Introduction to Synthetic Biology
    • Marathi - Central Dogma and Translation
  9. Paris 2018
    • Italian - DNA & RNA
    • French - DNA & RNA
    • Persian - Introduction to Synthetic Biology
  10. NUS Singapore Science
    • Korean - DNA & RNA
  11. Hamburg
    • German - Introduction to Synthetic Biology
    • Polish - Introduction to Synthetic Biology
  12. Nanjing China
    • Mandarin - Proteins
  13. Biomarvel
    • Korean - Intro to Synthetic Biology

    ChassiDex Collaborations

    ChassiDex is a database of host organisms containing all the information needed to work with the organism listed. The following two teams helped us out by by providing data on different chassis which was further curated and put up on our database.

  1. Marburg
    • Data on Vibrio natriegens
  2. SKLMT China
    • Data on Pseudomonas fluorescens

    Other Collaborations

    We collaborated with other teams to contribute to one of their social initiatives.

  1. IISER Mohali, India
    • We had a great time mentoring the Mohali team regarding their modelling which helped them in evolving their algorithm. We got to share our knowlegde and learn from them in the process.
  2. Vit Vellore
    • We participated in a beach clean-up organised by VIT at Marina Beach, Chennai.
  3. Tec de Monterrey Campus Guadalajara
    • We clicked a picture of us at a landmark in Chennai, with a placard and the distance of Chennai to Boston written on it.
  4. US AFRL CarrollHS
    • Mike the Microbe came to our lab here at IIT Madras, Chennai and we got to click pictures with him.
  5. HAFS South Korea
    • We contributed an Indian recipe that is easy to cook, healthy and diabetes-friendly. This will be used for Diabetic people to learn to manage cooking food.