Difference between revisions of "Team:Munich/HP/Gold Integrated"

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<font size=7 color=#51a7f9><b style="color: #51a7f9">Collaborations</b></font>
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<font size=7 color=#51a7f9><b style="color: #51a7f9">Human Practices (Gold)</b></font>
 
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<h3><a class="myLink" href="/Team:TUDelft">iGEM TU Delft</a></h3>
 
<h3><a class="myLink" href="/Team:TUDelft">iGEM TU Delft</a></h3>
 
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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>
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We had the chance to interview and talk with Dr. Keith Pardee on September 21th via Skype. He
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was impressed with our project and gave us very useful feedback. One of his suggestions was
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that we tried to make our device as easy as possible in the beginning and then get to the next
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level of complexity. For that reason, he suggested us to use first purified RNA that mimicked our
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target and at high concentrations, instead of considering using human samples. We followed his
 +
recommendations and could detect the 16S ribosomal subunit from Escherichia coli, from
 +
purified total RNA and in vitro RNA. When we asked him about our readout ideas (fluorescence
 +
and colorimetric), he told us that the fluorescent readout would be enough to prove that our
 +
device worked. Also, he recommended us to implement trehalose as a cryoprotectant in our
 +
method to lyophilize Cas13a into our paperstrip.</p>
 
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<a href="/Team:TUDelft"><img src="https://pbs.twimg.com/profile_images/869900215146487808/51JLvK2L_400x400.jpg" alt="Diagram for Cas13a's function"></a>
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<img src="https://i1.rgstatic.net/ii/profile.image/AS%3A411862849081350%401475207163702_xl/Keith_Pardee.png" alt="Keith Pardee">
 
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Revision as of 17:49, 17 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

Human Practices (Gold)

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

We had the chance to interview and talk with Dr. Keith Pardee on September 21th via Skype. He was impressed with our project and gave us very useful feedback. One of his suggestions was that we tried to make our device as easy as possible in the beginning and then get to the next level of complexity. For that reason, he suggested us to use first purified RNA that mimicked our target and at high concentrations, instead of considering using human samples. We followed his recommendations and could detect the 16S ribosomal subunit from Escherichia coli, from purified total RNA and in vitro RNA. When we asked him about our readout ideas (fluorescence and colorimetric), he told us that the fluorescent readout would be enough to prove that our device worked. Also, he recommended us to implement trehalose as a cryoprotectant in our method to lyophilize Cas13a into our paperstrip.

 Keith Pardee
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.