Difference between revisions of "Team:IIT Delhi/berlin"

Latest revision as of 23:29, 1 November 2017

iGEM IIT Delhi

Collaboration with Berlin diagnostX

Overview

The IIT Delhi iGEM team whole-heartedly collaborated with Berlin diagnostX team. Berlin team was working on affordable, practical and effective diagnostics of the widespread third world parasitic disease -Tapeworm Infection. Since India is one of the countries where millions of people are infected by this parasite, IIT Delhi directed Berlin team to a suitable site. It was a hospital in Varanasi, Uttar Pradesh where many cases of tapeworm were reported. After the successful extraction and lysis of the Tapeworm eggs, Berlin team obtained RNA molecules of the T. Solium species of the Tapeworm. IIT Delhi further assisted them by providing our own lab as -20 and -80 degrees centigrade refrigerators and other required lab apparatus were not available in the above-mentioned hospital. Sequencing of the RNA was also done and all the samples were shipped to them. This was not only constricted to iGEM collaboration as we further plan to adopt this technology for affordable diagnostic of tapeworm infection which is otherwise done using fecal inspection using a microscope. This would help in timely detection of infection and thus would save lives of many people. Following this, Berlin team provided us the protease stains without Degradation Tags required by us to generate oscillations in the form of a square. Here is the link to the iGEM Berlin Team:
https://2017.igem.org/Team:Berlin_diagnostX/Collaborations

We would like to thank and congratulate the iGEM Berlin diagnostX team on this successful collaboration and look forward to doing more work together in the future.

It all began when we got in touch with the Berlin diagnostX through facebook initially followed by a skype call. We started out by increasing each other’s outreach and impact on social media platforms like facebook.

This very small collaboration worked, and we promoted each other on social media. Although this beginning seems unimportant and small, we guess it was the critical factor, that initiated our larger collaboration – because, without this pre-existing contact, we may not have talked to them through skype call.In our Skype call, we discussed at length about each other’s projects.It was then that we got to know about them researching on a disease caused by Tapeworms found in India.

Later in 2017 Henrik and Dimi from Berlin team came to India to build new research cooperations. They contacted iGEM IIT Delhi to ask whether they could visit their lab and exchange research ideas. Throughout our first skype call with the IGEM Berlin-Team, we got along that well, that we formed the idea to jointly built a pipeline, that allows PCR and RNA isolation on lysed, non-infectious S1-security level samples, that Berlin diagnostX was planning to acquire from India. For this reason, Berlin diagnostX tried to order some RNA isolation kits and PCR reagents to the lab of iGEM IIT Delhi, but it turned out that multinational companies like NEB, ThermoFisher, and QIAGEN are unable to send a bill to Germany and to deliver the products to India. At this point, iGEM IIT Delhi helped and bought the kits for Berlin diagnostX from a local reseller.

After visiting physicians and villages with people affected by T. solium, Dimi and Henrik went to IIT Delhi to establish RNA isolation in the lab of iGEM IIT Delhi. Having this option to do RNA isolation was crucial for diagnostX because laboratories in Varanasi did not have the equipment to isolate RNA and there was a realistic chance that isolation of RNA was necessary for export. The team from Delhi found a student dorm for Henrik and Dimi to stay in and thus we could work day and night to optimize an RNA isolation protocol that ultimately yielded high-quality RNA.

Once Dr. Mishra from Heritage Institute for Medical Sciences received a tapeworm sample containing eggs from Taenia Solium and processed them, the Berlin Team had to transport the RNA-sample from India to Germany. The only problem was, that the Indian government changed their trade policy in June 2015. Since then, no company, hospital or physician can send a sample abroad without obtaining an “Import Export Code”. Obtaining this code is bureaucratic and makes taxation more complex. For this reason, despite having the sample and a carrier with expertise in the field (World Courier, an AmerisourceBergen company), diagnostX was unable to get the sample to Germany. At this point, iGEM IIT Delhi supported the Berlin team again by shipping the sample to IIT and subsequently exporting it with permission of the IIT. This process described in one sentence took over two months and the joint effort of the Berlin and Delhi iGEM team to manage this challenge was the key to the transcriptome and the sensor described by iGEM Berlin diagnostX.

While we were working on our square wave generator project, one of the essential things was to remove the Degradation tags in order to reduce noise. But the parts we got from the kit plates had Degradation Tags attached to them already. So, in order to remove them, we decided to use knockout strains. CLPP Protease is a strain which recognizes the degradation tags and degrades them, but it wasn’t available to us in our lab. This is when iGEM Berlin Team helped us out and they sent us the strains as they were available in the Berlin diagnostX lab. We would like to thank and congratulate the iGEM Berlin diagnostX team on this successful collaboration and look forward to doing more work together in the future.

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        							<a href="/Team:IIT_Delhi/Circuit_Design">Circuit design and construction</a>
-       							<a href="/Team:IIT_Delhi/Microfluidics">Microfluidics and Fluroscence</a>
+       							<a href="/Team:IIT_Delhi/Microfluidics">Microfluidics and Fluorescence</a>
        							<a href="/Team:IIT_Delhi/Photobleaching">Photobleaching</a>
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-             <h2 class="h2font">BERLIN</h2>
+             <h2 class="h2font" style="line-height: 1em;">Collaboration with Berlin diagnostX</h2><br>
+<h6 class="h2font"> Overview </h6>
              <p> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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   </p>
-<h2 id="pfont">The credits for accomplishment of this project goes to the dedication, commitment and enthusiasm shown by a large number of people and parties from multiple disciplines. It gives us immense pleasure and gratification to acknowledge their support and assistance towards the execution of the project.
+<h2 id="pfont">The IIT Delhi iGEM team whole-heartedly collaborated with Berlin diagnostX team. Berlin team was working on affordable, practical and effective diagnostics of the widespread third world parasitic disease -Tapeworm Infection. Since India is one of the countries where millions of people are infected by this parasite, IIT Delhi directed Berlin team to a suitable site. It was a hospital in Varanasi, Uttar Pradesh where many cases of tapeworm were reported. After the successful extraction and lysis of the Tapeworm eggs, Berlin team obtained RNA molecules of the T. Solium species of the Tapeworm. IIT Delhi further assisted them by providing our own lab as -20 and -80 degrees centigrade refrigerators and other required lab apparatus were not available in the above-mentioned hospital. Sequencing of the RNA was also done and all the samples were shipped to them.
-</h2>
+This was not only constricted to iGEM collaboration as we further plan to adopt this technology for affordable diagnostic of tapeworm infection which is otherwise done using fecal inspection using a microscope. This would help in timely detection of infection and thus would save lives of many people. Following this, Berlin team provided us the protease stains without Degradation Tags required by us to generate oscillations in the form of a square. Here is the link to the iGEM Berlin Team:
+<br>
+<a href = "https://2017.igem.org/Team:Berlin_diagnostX/Collaborations">https://2017.igem.org/Team:Berlin_diagnostX/Collaborations<br></a>
+<br>
+We would like to thank and congratulate the iGEM Berlin diagnostX team on this successful collaboration and look forward to doing more work together in the future.</h2>
            </header>
-           <button class="accordion back1" style="font-weight: bold;"></button>
+           <button class="accordion back1" style="font-weight: bold;">How it all started?</button>
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 <left>
-							<h2 id="pfont1"><span class="image left"><img src="https://static.igem.org/mediawiki/2017/a/a3/T--IIT_Delhi--Berlin.jpg" alt="" /></span><br> The IIT Delhi iGEM team whole-heartedly collaborated with Berlin team. Berlin team was working on the affordable, practical and effective diagnostic of the widespread third world parasitic disease -Tapeworm Infection. Since India is one of the countries where millions of people are infected by this parasite, IIT Delhi directed Berlin team to a suitable site. It was a hospital in Varanasi, Uttar Pradesh where many cases of tapeworm were reported. After the successful extraction and lysis of the Tapeworm eggs, Berlin team obtained RNA molecules of the T. Solium species of the Tapeworm. IIT Delhi further assisted them by providing our own lab as -20 and -80 degrees centigrade refrigerators and other required lab apparatus were not available in the above-mentioned hospital. Sequencing of the RNA was also done and all the samples were shipped to them.<br>
- This was not only constricted to iGEM collaboration as we further plan to adopt this technology for affordable diagnostic of tapeworm infection which is otherwise done using fecal inspection using a microscope. This would help in timely detection of infection and thus would save lives of many people. Following this, Berlin team provided us the protease stains without Degradation Tags required by us to generate oscillations in the form of a square. Here is the link to the iGEM Berlin Team.
+							<h2 id="pfont1"><span class="image left"><img src="https://static.igem.org/mediawiki/2017/f/f2/T--IIT_Delhi--berlin01.jpg" alt="" /><img src="https://static.igem.org/mediawiki/2017/c/c9/T--IIT_Delhi--berlin02.jpg" alt="" /></span><br>It all began when we got in touch with the Berlin diagnostX through facebook initially followed by a skype call. We started out by increasing each other’s outreach and impact on social media platforms like facebook.
-<a href="https://2017.igem.org/Team:Berlin_diagnostX/Collaborations"> https://2017.igem.org/Team:Berlin_diagnostX/Collaborations </a>
+<br><br>
+This very small collaboration worked, and we promoted each other on social media. Although this beginning seems unimportant and small, we guess it was the critical factor, that initiated our larger collaboration – because, without this pre-existing contact, we may not have talked to them through skype call.In our Skype call, we discussed at length about each other’s projects.It was then that we got to know about them researching on a disease caused by Tapeworms found in India.
 </h2>
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            </div>
-           <button class="accordion back2" style="font-weight: bold;">Skype Call</button>
+           <button class="accordion back2" style="font-weight: bold;">The first Gasp of transcontinental research</button>
            <div class="panel">
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 <left>
-							<h2 id="pfont1"><span class="image left"><img src="https://static.igem.org/mediawiki/2017/b/bb/T--IIT_Delhi--Glassgow.jpg" alt="" /></span><br> iGEM IIT Delhi assisted team Glasgow in 2016 for filling up survey forms designed for the people of India. This year iGEM Glasgow helped us by providing the biological parts ( pPhlF, RBS+PhlF + T, pSrpR, RBS + SrpR + T) which turned to be of immense use in forming the Oscillator.
+							<h2 id="pfont1"><span class="image left"><img src="https://static.igem.org/mediawiki/2017/a/a3/T--IIT_Delhi--berlin03.jpg" alt="" /></span><br>Later in 2017 Henrik and Dimi from Berlin team came to India to build new research cooperations. They contacted iGEM IIT Delhi to ask whether they could visit their lab and exchange research ideas. Throughout our first skype call with the IGEM Berlin-Team, we got along that well, that we formed the idea to jointly built a pipeline, that allows PCR and RNA isolation on lysed, non-infectious S1-security level samples, that Berlin diagnostX was planning to acquire from India.
+For this reason, Berlin diagnostX tried to order some RNA isolation kits and PCR reagents to the lab of iGEM IIT Delhi, but it turned out that multinational companies like NEB, ThermoFisher, and QIAGEN are unable to send a bill to Germany and to deliver the products to India. At this point, iGEM IIT Delhi helped and bought the kits for Berlin diagnostX from a local reseller.
 </h2>
@@ Line 1,753: / Line 1,762: @@
            </div>
-<button class="accordion back3" style="font-weight: bold;">iGEM Berlin visits India</button>
+<button class="accordion back3" style="font-weight: bold;">Jointly established RNA isolation pipeline at IIT Delhi
+</button>
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 <left>
-							<h2 id="pfont1"><span class="image left"><img src="https://static.igem.org/mediawiki/2017/2/23/T--IIT_Delhi--iGEM_mohali.jpg" alt="" /></span>A PhD student, Mr. Mahendra Sahare, doing a humanities project under a Supreme Court lawyer, Dr. Naveen Thayyil, has been in collaboration with iGEM IIT Delhi for the past two years. Together, we have worked on the aspect of ‘Ethical Scientific Practices’. Also, on his recent visit to IISER Mohali, he came back with a collaborative offer for iGEM IIT Delhi to mentor IISER Mohali and help in the establishment of iGEM club there. On our return from the Giant Jamboree 2016, our team members gave a presentation scheduled there, and thereafter our
+							<h2 id="pfont1">After visiting physicians and villages with people affected by T. solium, Dimi and Henrik went to IIT Delhi to establish RNA isolation in the lab of iGEM IIT Delhi. Having this option to do RNA isolation was crucial for diagnostX because laboratories in Varanasi did not have the equipment to isolate RNA and there was a realistic chance that isolation of RNA was necessary for export. The team from Delhi found a student dorm for Henrik and Dimi to stay in and thus we could work day and night to optimize an RNA isolation protocol that ultimately yielded high-quality RNA.
-team mentored the iGEM Mohali team.
-Here is the link for Mohali iGEM Team: <a href="https://2017.igem.org/Team:IISER-Mohali-INDIA"> https://2017.igem.org/Team:IISER-Mohali-INDIA </a>
 </h2>
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-<button class="accordion back4" style="font-weight: bold;">Strain by IIT Delhi</button>
+<button class="accordion back4" style="font-weight: bold;">Championing international trade and safety regulations
+</button>
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 <left>
-							<h2 id="pfont1"><span class="image left"><img src="https://static.igem.org/mediawiki/2017/3/3e/T--IIT_Delhi--iGEM_Manchester.jpg" alt="" /></span>Have a look at the fruits of the 3 months-long interactions, discussions and meet-ups at <a href="https://2017.igem.org/Team:IIT_Delhi/GMM_legislation"> https://2017.igem.org/Team:IIT_Delhi/GMM_legislation </a>.
+							<h2 id="pfont1"><span class="image left"><img src="https://static.igem.org/mediawiki/2017/2/28/T--IIT_Delhi--Berlin_03.jpg" alt="" /></span>Once Dr. Mishra from Heritage Institute for Medical Sciences received a tapeworm sample containing eggs from Taenia Solium and processed them, the Berlin Team had to transport the RNA-sample from India to Germany. The only problem was, that the Indian government changed their trade policy in June 2015. Since then, no company, hospital or physician can send a sample abroad without obtaining an “Import Export Code”. Obtaining this code is bureaucratic and makes taxation more complex. For this reason, despite having the sample and a carrier with expertise in the field (World Courier, an AmerisourceBergen company), diagnostX was unable to get the sample to Germany. At this point, iGEM IIT Delhi supported the Berlin team again by shipping the sample to IIT and subsequently exporting it with permission of the IIT. This process described in one sentence took over two months and the joint effort of the Berlin and Delhi iGEM team to manage this challenge was the key to the transcriptome and the sensor described by iGEM Berlin diagnostX.
 </h2>
@@ Line 1,800: / Line 1,811: @@
            </div>
+<button class="accordion back1" style="font-weight: bold;">How iGEM Berlin team assisted us?
-<button class="accordion back4" style="font-weight: bold;">Further Discussion</button>
+</button>
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-            <p>Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.</p>
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+<div align="left" style="font-size: 84%;" class="padding1">
+<left>
+<h2 id="pfont1">While we were working on our square wave generator project, one of the essential things was to remove the Degradation tags in order to reduce noise. But the parts we got from the kit plates had Degradation Tags attached to them already. So, in order to remove them, we decided to use knockout strains. CLPP Protease is a strain which recognizes the degradation tags and degrades them, but it wasn’t available to us in our lab. This is when iGEM Berlin Team helped us out and they sent us the strains as they were available in the Berlin diagnostX lab.
+We would like to thank and congratulate the iGEM Berlin diagnostX team on this successful collaboration and look forward to doing more work together in the future.
+</h2>
+</left>
+</div>
+<br>
+<div align="left" style="font-size: 84%;">
+</div>
+            </p>
+          </div>
      <br>
      <br>

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	E-mail: iitd.igem@gmail.com Undergraduate Laboratory Department of Biotechnology and Biochemical Engineering, IIT Delhi