Difference between revisions of "Team:Munich/Collaborations"

Line 75: Line 75:
  
  
−
<tr><td colspan=4 align=center valign=center>
+
<tr class="lastRow"><td colspan=4 align=center valign=center>
 
<h3><a class="myLink" href="/Team:TUDelft">iGEM TU Delft</a></h3>
 
<h3><a class="myLink" href="/Team:TUDelft">iGEM TU Delft</a></h3>
 
<p>   
 
<p>   
−
Their iGEM project is called CASE13A. Both our projects are similar in terms of the use of Cas13a and paper microfluidics. Our collaboration started with our meeting in Delft. We were excited to see that TU Delft were also working with Cas13a as their major protein. We both are trying to work on different ways of tackling the problem of the antibiotic resistance using Cas13a. Therefore we decided to collaborate since it gave us the opportunity to discuss the challenges and also to try out new stuffs together. We started a collaboration for our <a class="myLink" href="/Team:Munich/Software">software</a> since we both were working on optimizing the crRNA for the different targets. In our team, we designed a software that could give us the best design and structure of the crRNA for different targets. For this we created a database of different possible sequences using NUPACK and other platforms. Team Delft had a similar project where they predict the part of the target that can best serve as a crRNA. We provided them with a list of possible targets and best crRNAs structures for their software. </p>
+
Their iGEM project is called CASE13A. Both our projects are similar in terms of the use of Cas13a and paper microfluidics. Our collaboration started with our meeting in Delft. We were excited to see that TU Delft were also working with Cas13a as their major protein. We both are trying to work on different ways of tackling the problem of the antibiotic resistance using Cas13a. Therefore we decided to collaborate since it gave us the opportunity to discuss the challenges and also to try out new stuffs together. We started a collaboration for our <a class="myLink" href="/Team:Munich/Software">software</a> since we both were working on optimizing the crRNA for the different targets. In our team, we designed a software that could give us the best design and structure of the crRNA for different targets. For this we created a database of different possible sequences using NUPACK and other platforms. The team Delft had a similar project where they predict the part of the target that can best serve as a crRNA. We provided them with a list of possible targets and best crRNAs structures for their software. Also, the team Delft sent us the Tardigrade proteins(TDPs) to experiment them with the Cas13a and to check the activity and stability of the Cas13a when used together with TDPs. We did some cleavage assay of the Cas13a along with the TDPs, to see if it can create some difference in the reactivity.</p>
 
</td>
 
</td>
 
<td colspan=2 align=center valign=center>
 
<td colspan=2 align=center valign=center>
−
<a href="/Team:TUDelft"><img src="https://static.igem.org/mediawiki/2017/e/e7/T--Munich--Collaborations_TUDelft_Logo.png"></a>
+
<a href="/Team:TUDelft"><img src="https://pbs.twimg.com/profile_images/869900215146487808/51JLvK2L_400x400.jpg" alt="Diagram for Cas13a's function"></a>
−
</td>
+
−
</tr>
+
−
 
+
−
<tr class="lastRow"><td colspan=6 align=center valign=center>
+
−
<div class="captionPicture">
+
−
<img width=600 src="https://static.igem.org/mediawiki/2017/0/05/T--Munich--Collaborations_TUDelft_Skype.jpg" alt="Skype session with team Delft">
+
−
<p>One of the skype sessions with TU Delft</p>
+
−
</div>
+
−
<p>
+
−
Also, team Delft sent us the Tardigrade intrinsically Disordered Proteins(TDPs) to experiment them with our Cas13a and to check the activity and stability of the Cas13a when used together with TDPs. From our team, Dawa did the characterization of the TDPs that were sent by the team TU Delft.  Both our teams are using Cas13a but from different strains. Our team mostly used Leptrotricia buccalis and Leptrotricia wadei Cas13a for our experiments. We did also tried the Leptrotricia shahi but we couldn't purify it that well for our experiments. Team TU Delft were using the Leptroticia shahi Cas13a for their experiments.
+
−
</p>
+
−
<p>
+
−
During the characterization of the TDPs, Team TU Delft found that whenever their Cas13a was dried in combination with a TDP of the type CAHS, the resuspended Cas13a would start cleaving RNA even in absence of the target RNA, hence losing its specificity.  We therefore did the characterization of the TDPs they provided with our Cas13a (Lbu) and repeated the exact same drying experiment with the CAHS protein, in order to corroborate our results and to find the cause of such an unexpected result. As observed in figure 1 below, we also got the same unexpected results when Cas13a was tried with CAHS TDP.
+
−
</p>
+
−
</td>
+
−
</tr>
+
−
 
+
−
<tr>
+
−
<td colspan=2 align=center valing=center>
+
−
<div class="captionPicture">
+
−
<img width=300 src="https://static.igem.org/mediawiki/2017/4/4f/T--Munich--Collaborations_TuDelft_Package.jpg" alt="Skype session with team Delft">
+
−
<p>TDP package from TU Delft</p>
+
−
</div>
+
−
</td>
+
−
<td colspan=4 align=center valing=center>
+
−
<div class="captionPicture">
+
−
<img width=600 src="https://static.igem.org/mediawiki/2017/f/f1/T--Munich--Collaborations_TUDelft_Results.png" alt="Skype session with team Delft">
+
−
<p>Figure 1: RNAseAlert fluorescence assay with our Cas13a (Lbu) and TDP from TU Delft</p>
+
−
</div>
+
 
</td>
 
</td>
 
</tr>
 
</tr>
Line 116: Line 87:
 
<tr class="lastRow">
 
<tr class="lastRow">
 
<td colspan=2 align=center valign=center>
 
<td colspan=2 align=center valign=center>
−
<a href="/Team:BOKU-Vienna"><img src="https://static.igem.org/mediawiki/2017/1/11/T--Munich--Collaborations_Vienna_Logo.png" alt="Diagram for Cas13a's function" width=360></a>
+
<a href="/Team:BOKU-Vienna"><img src="https://scontent-frt3-2.xx.fbcdn.net/v/t1.0-9/19225725_348727538877849_3047761210741052842_n.png?oh=e6ed107d0086bfe169e3911be7c558a4&oe=5A735810" alt="Diagram for Cas13a's function" width=360></a>
 
</td>
 
</td>
 
<td colspan=4 align=center valign=center>
 
<td colspan=4 align=center valign=center>
Line 131: Line 102:
 
</td>
 
</td>
 
<td colspan=2 align=center valign=center>
 
<td colspan=2 align=center valign=center>
−
<a href="/Team:Bristol"><img src="https://static.igem.org/mediawiki/2017/5/5d/T--Bristol--TeamLogo.svg" width=400 alt="Diagram for Cas13a's function"></a>
+
<a href="/Team:Bristol"><img src="https://static.igem.org/mediawiki/2017/5/5d/T--Bristol--TeamLogo.svg" width=360 alt="Diagram for Cas13a's function"></a>
 
</td>
 
</td>
 
</tr>
 
</tr>
−
 
  
  

Revision as of 12:54, 29 October 2017

Description

Design

Demonstrate

Measurement

Applied Design

Final Results

Achievements

Protocols

Notebook

Safety

Parts

Improved Part

Part Collection

InterLab

Model

Software

Collaboration

Detector

Quake Valve

Paperstrips

Sample Processing

Silver

Gold

Engagement

Collaborations

Team members

Sponsors

Attributions

Gallery

Collaborations

Collaborations play a very important role in terms of the development of project. Collaborations with other teams helps us to learn about better ways to handle a problem, to learn new ways of working, to perceive different ideologies and to develop the project in general. It provides us a better chance to get to know other teams and to learn to cooperate. In scientific fields, cooperation and collaborations play a major role for growth and discovery. We are highly encouraged to work with other teams since it increases our horizon of knowledge and we are happy that iGEM promotes the idea of sharing knowledge and scientific materials. The following are the teams whom we can proudly call the collaborators this year.

iGEM TU Delft

Their iGEM project is called CASE13A. Both our projects are similar in terms of the use of Cas13a and paper microfluidics. Our collaboration started with our meeting in Delft. We were excited to see that TU Delft were also working with Cas13a as their major protein. We both are trying to work on different ways of tackling the problem of the antibiotic resistance using Cas13a. Therefore we decided to collaborate since it gave us the opportunity to discuss the challenges and also to try out new stuffs together. We started a collaboration for our software since we both were working on optimizing the crRNA for the different targets. In our team, we designed a software that could give us the best design and structure of the crRNA for different targets. For this we created a database of different possible sequences using NUPACK and other platforms. The team Delft had a similar project where they predict the part of the target that can best serve as a crRNA. We provided them with a list of possible targets and best crRNAs structures for their software. Also, the team Delft sent us the Tardigrade proteins(TDPs) to experiment them with the Cas13a and to check the activity and stability of the Cas13a when used together with TDPs. We did some cleavage assay of the Cas13a along with the TDPs, to see if it can create some difference in the reactivity.

 Diagram for Cas13a's function
Diagram for Cas13a's function

iGEM BOKU Vienna

Michael and Julian from the iGEM BOKU Vienna came to do some experiments in our lab on 4th and 5th of October. Their iGEM project is called D.I.V.E.R.T. (Directed in vivo evolution via reverse transcription) and they are trying out new strategies for in vivo evolution which shows potential advantages over classical in vitro methods. For this they use yeast and E.coli to demonstrate their concept. They used the flow cytometer in our lab in Garching to better characterize their constructs from E.coli and S. cerevisiae. For the use one of our lab member explained them how to use the flow cytometer in the lab and also provided them the necessary help. It was a long day work for them but they got convincing results by the end. We also had a small gathering in the evening before they left together with the old igemers who came to meet us. We were very happy to have them in our lab and to get to know each other's team.

iGEM Bristol

Team Bristol have a project called BREATHE, in which they modify E.coli cells to metabolise NOx compounds from the atmosphere into ammonia. With help from a bioreactor, the ammonia can be oxidized to molecular nitrogen, producing electricity. This way, BREATHE not only reduces air pollution, but provides energy, too. As a side project, team Bristol developed the iGEM Development Environment (IDE) to help other teams edit their wiki faster and efficiently. When we found out about this tool, we wanted to try it out and reached team Bristol, who happily explained us how to use it. The IDE helped us speed up our wiki editing, specially in the initial steps, and make working on the wiki all around more convienient and easy. In turn, we provided them feedback about the software, so they can further develop this useful tool for future iGEM teams.

 Diagram for Cas13a's function