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Collaborations
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Collaborations play a very important role in terms of project development. Collaborations with other teams help 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 our collaborators this year.
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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 different approaches together. We started a collaboration for our software since we both were working on optimizing the crRNA for our 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 reason, we created a database of different possible sequences using NUPACK and other platforms. Team TU Delft has 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.
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One of the skype sessions with TU Delft
Moreover, team TU Delft sent us the Tardigrade intrinsically Disordered Proteins(TDPs) to test them with our purified Cas13a, to check its activity and stability 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 were 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 could not purify it properly for our experiments. Team TU Delft used the Leptroticia shahi Cas13a for their experiments.
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 outcome. As observed in figure 1, we also got the same unexpected results when Cas13a was dried with CAHS TDP.
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TDP package from TU Delft
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Figure 1: RNAseAlert fluorescence assay with our Cas13a (Lbu) and TDP from TU Delft
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Michael and Julian from the iGEM BOKU Vienna Team came to our lab to run some experiments 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 used yeast and E.coli to demonstrate their concept. They used the flow cytometer in our lab to better characterize their constructs from E.coli and S. cerevisiae. One of our lab members explained them how to use the flow cytometer and also provided them the necessary help. It was a long day work for them but at the end they collected positive results. We also had a small gathering in the evening before they left together with the last year´s 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.
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Team Bristol have a project called BREATHE, in which they modify E.coli cells to metabolize 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 them, who happily explained us how to use it. The IDE helped us speed up our wiki editing, specially in the initial steps, and made working on the wiki more convenient and easy. In turn, we provided them feedback about the software, so they can further develop this useful tool for future iGEM teams.
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Their iGEM project is called Wormspotter, where they want to use a toehold switch to diagnose tape worm infections. Tape worm infections are very common in many countries in Asia and Africa, and Team Berlin wants to help make the detection of such infections rapid and affordable. We have some similarities in the project regarding the use of RNA and paper strips. They are also working a lot on RNA extraction and on amplification of the RNA product. They also want to have a visible readout on the paper to detect the presence of tapeworm RNA as we do. Therefore we decided to help each other by addressing each other's problems and by helping to solve them. We had Skype meeting sessions and exchanged emails to keep each other updated. We also talked on how the challenges of RNA amplification could be optimized and how we can make good use of each other's detection system.
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Their project is called LIT (Light Induced Technologies)and they work with light-activated gene networks in mammalian cells and aim to create a novel transmembrane protein. For that reason, they were looking for a signal peptide to deliver their protein of interest to the ER as well as a transmembrane domain to ensure its embedding inside the plasma membrane. We sent them two BioBricks from last year's team that were not released yet by the iGEM Registry: BM-40 (BBa_K2170214) and TMD-EGFR (BBa_K2170214). They were able to integrate them into their designs and characterized them.
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