Team:Imperial College London/Notebook/week7



This is our diary page which records the daily activities of the team. Click on the links below to see a summary of events and activities happening each week.

Week 7: 15th August to 21st August

Monday, 15th August

Si is demonstating the kill switch and working out the ratio of Holin and antiholin which appears to be 4000. 400 is another preferable ratio Nina is working on the density map of the auxin. Yaunwei is helping on the modelling of auxin uptake and chemotaxis. Nick is checking plates for results, and write the new protocol for solid agar assay. Frank is also writing the containment device protocol, make a gel, and transfect the DNA no. 25. Rebekka carries out Kiran experiment and write down the implementation part. Nikki is doing Gibson of chemoreceptor PA2652 and Chris is working on the kill swithch. Ming is carrying on the research for seed coating material. He also conntinues the root splitting experiment. For the review, Si reviews on the kill switch, Nick on the human practise overview, Rebekka on auxin result, Nikki on chemotaxis and Ming on auxin overview

Tuesday, 16th August

The day started off great! All the transformations from the previous day worked great and the gibson reaction seems to have worked (we have colonies of bacteria on the plate). The rest of the day was really productive. The primers for the containment module assembly (name pending) have been made and ordered. Mini-preps were performed on the newly transformed cells followed by restriction digests, M9 media plates were poured for chemotaxis experiments that have been set off, the implementation of our system was worked on extensively, animations were made, more bacteria were transformed, the modelers made awesome models of Arabidopsis root growth and finally we had a Skype date with the team of University of the Witwatersrand on chemotaxis assays yielded valuable fruits for both of our teams as we exchanged knowledge on chemotaxis assays. This list only scratches the surface of all that was done today.

Wednesday, 17th August

Today was a bad day to be a modeller. After days of frustration they finally concluded that their model for the effects of auxin concentration would not work. They are currently working on some new ideas for the modelling, including an extrapolation of Ming's root growth data and a program that takes 8 days to run on a supercomputer! Chris and Frank entertained themselves (and nobody else) with Radio iGEM, an online podcast that, this week, featured a brief introduction to our project, an interview with Ming the plant specialist and some questionable songs. This was in addition to mini-prepping and a restriction digest. Nick spent his day setting up his chemotaxis assays and learning how to use the FACs machine, it doesn't sound like much, but poor Nick didn't have a chance to sit down today. Nikki was also rushed off her feet, loading gels, doing gel extractions, a transformation and the next gibson. Rebekka ploughed on with Kiran's experiments and set up the materials for when we start using B. subtilis. Also, Rebekka has worms, and she'll start the experiments soon. CJ from the RCA was here too, she helped us write stuff on the wiki and is going to find us some cool people to interview for Radio iGEM. The plan is to have a podcast based debate on the practicality of our project and GM technology in general. She and Chris are also putting together a short narrative to accompany the project that we will record with a team of voice actors and put on Radio iGEM.

Thursday, 18th August

Our worms laid eggs! We plan to name the survivors.

We finally can say that the modeling of chemotaxis and kill switch(Bactrap) are done. The new ratio of promoter strength(400) given by Si seens correct. Nina came up with the plan for the modeling team in the next three weeks, which is mostly about data fitting. Yuanwei started looking at flash animation for our game and the intro to the wiki. Ming designed the experiment of soil erosion. It a simulation of rainfall towards a slope surface covered by arabidopsis. Nikki did gel extraction and the assay of auxin fragment, also she ran the Gibson assembly. Frack and Chris spent the day mainly on cloning strategy and the primers. Rebekka did a lot about human practice platform and set up the meeting with two people in September, in addition, the plates of E.coli and B.subtilis are done. Nick is so busy playing with worms (- -#).
Everyone prepares the slide for the presentation on Friday

Friday, 19th August

Today was marked by missing Si, who was too ill to come and work. I think that is acceptable to miss a day in iGEM. The rest of us had a progress report ahead for our supervisors and therefore most of the day was just a day of making presentation slides, while running other lab and modelling stuff alongside. Chris has been making presentation slides much like all other people in the team, but he also had to change cloning strategy for the BacTrap, and gota promoter he required from James Chappell. To top it all up and show that he is indeed a busy man, he recieved a phone call from Ming during presentation. Funnily enough Ming was sitting right in front of him and to our surprise he did not even touch his phone, well the joys of MingĀ“s phone. Frank was making gels and was helping Chris with the cloning strategy, also he was figuring out more stuff for RadioIGEM. Rebekka had a busy day too, she was imaging roots of YFP plants responding to auxin, some pretty images were obtained, but still need to be worked on. Nikki was trying auxin genes assembly using Gibson, she also transformed some cells. Nick was doing presentation slides far too long, I wonder why. However he also learnt how to use FACS machine and took some of our first quantitative readings for chemotaxis. On the modelling front, Nina was trying to do a 3D animation of roots growth, and had a long modelling talk at the presentation to our supervisors. Yuanwei is going for Yuanwin as always. He was working on the animations and introduction video for our wiki. At the end of the day, a subgroup of us all ended up in the union. Good week.