Team:Tongji China/tags/v0.2/json/design.json

{

"header": "

DESIGN

", "content": "

With SJTU-BioX-Shanghai<img src=\"\" alt=\"Raised circle image\" class=\"img-fluid rounded-circle shadow-lg\" style=\"width: 130px;margin-left: 50px;margin-bottom: 20px;\">

This year, we kept our close contact with our friends from Shanghai Jiao Tong University: SJTU-BioX-Shanghai. We were both facing some problems with gene knock-out of E. coli, and surprisingly we found that our gene knock-out (gene KO) systems are the same. We met SJTU-BioX-Shanghai at their campus, introduced our projects with each other, and shared our protocols on gene KO.

• We also talked about our Human Practices work. They had done many exciting works and shared the results on how philosophers think of modern biology. We also suggested to them that they could try to find some enterprises that may be interested in their project or their competitor for the future development of their project.

• When we were performing electroporation, we didn’t get an expected result using our protocol at first. SJTU-BioX-Shanghai then provided their parameter consideration. With their help, we optimized our parameter and finally succeeded. Thanks for their help!

<img src=\"\" class=\"img img-fluid\">

See their <a href=\"https://2019.igem.org/Team:SJTU-BioX-Shanghai/Collaborations\">Collaboration Page</a>

With Tongji_Software<img src=\"\" alt=\"Raised circle image\" class=\"img-fluid rounded-circle shadow-lg\" style=\"width: 130px;margin-left: 50px;margin-bottom: 20px;padding-top: 30px;padding-bottom: 30px;\">

Tongji_Software had made a software for pathway design last year, and this year they are trying to make further improvements. Our teams had an integrated collaboration from the beginning to help both of us make our projects better.

Our project this year was about indigo producing. We wanted to know what help and inspiration we could get from Tongji_Software’s software, so we used their software and made some pathway searching.

• First, we tried to use their algorithm to search a pathway on indole producing, because it was the substrate of indoxyl (which would naturally be oxidized by oxygen and form indigo). We were trying to find a source of indole which was cheaper than tryptophan. However, we found some interesting high-score results which put indole into some compounds and then breaking them apart. Obviously, nobody would like to try a pathway like this. We noticed this and suggested them to add some codes checking whether all the substrates were not our final product. They fixed this bug in the follow-up version of their software.

• At the end of this summer, after they optimized their algorithm, they invited us to compare the pathway we use based on our literature research with the results provided by their software. This time, we found some instructive results which inspired us for our future work. We re-searched the pathway of indole synthesis, and we found that the pathway we were using did't get a high score. The first thing occurred to us is that maybe we could find another better pathway to perform our indigo/indican synthesis. However, their software didn’t give any suggestion on which enzymes we could try to overexpress. A numerous of work were needed to design end test, so we decided to leave this to our future work. We thought Tongji_Software could try adding enzyme overexpression suggestions to their software, which was very helpful when designing pathways. Tongji_Software also agreed with us and put that into their future work plan. We hopefully expected to have more collaboration in the next iGEM season.

<img src=\"\" class=\"img img-fluid\">

See their <a href=\"https://2019.igem.org/Team:Tongji_Software/Project#Collaboration\">Collaboration Page</a>

With GreatBay_SZ<img src=\"\" alt=\"Raised circle image\" class=\"img-fluid rounded-circle shadow-lg\" style=\"width: 130px;margin-left: 50px;margin-bottom: 20px;\">

This year, GreatBay_SZ also designed a part to produce indigo. They tried to use indigo to dye their. Since we were experienced in characterizing this kind of parts, we helped them characterize their part. The characterization concerned the indigo production under different conditions. Our characterization helped them to understand how to improve their dyeing process.

See their <a href=\"https://2019.igem.org/Team:GreatBay_SZ/Collaborations\">Collaboration Page</a>

"

}