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Team:Imperial College London/Notebook/week8
From 2011.igem.org
Diary
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 8: 22nd August to 28th August
Monday, 22nd August
Today was a VERY long Monday but we got some good stuff done! Yuan Wei was glued to his laptop all day working on a Flash animation which is looking AWESOME. Chris did new minipreps of DNA we're running low on and also picked up the Krim plasmid and B. sub from the SBL lab. Nick and Rebekka had a full on day of chemotaxis assay - they used a growth curve modelled by Yuan Wei to get their cultures at mid exponential phase for the capillary assay and FACS analysis. Frank made some funky DNA ladder, serious art work, performed the BacTrap ligation and gel extracted some PCR product. Ming prepared media for the auxin experiment as well as auxin stocks. Nikki tried auxin assembly by CPEC with vector 8A and transformed cells overnight. To verify CPEC results she also kicked off a PCR with the sequencing primers.
Tuesday, 23rd August
We had another full day. Frank made gels, ran a couple of gels, gel extracted, did PCR and ordered Chinese food. Nick made stocks, autoclaved them, did minipreps and worked on a chemotaxis diagram. He is also updated the wiki. He and Rebekka talked to Chris Hirst about the robot and how to improve the capillary assay. Si modelled the auxin production and will be able to tell Chris a number tomorrow because the model will probably need to run overnight. Nina helped Si with the parameters in the modelling and made a graph with equations from literature to compare ideal conditions (root length against auxin conditions) to what we can later compare our data to it. Ming planted seeds for the auxin uptake experiment. He is searching for boxes and is taking pictures of roots. Rebekka processed imaging data and organised the human practices panel. Nikki assembled the auxin! She transformed bacteria last night and did a colony PCR. The results look good so she is inoculating culture to do minipreps tomorrow and send the DNA off for sequencing.
Wednesday, 24th August
Today is another frustrating day for modeler. We tried to model the auxin production, which will heavily inform our design, but we failed in finding out all the parameters :( However, all others did a lot of work. Frank run a gel of antiholin PCR, and then run the whole kill switch on a gel and get it purified with Chris. He also re-draft the radio show to make to more fancy. Yuanwei made an amazing introduction flash, which will be on the wiki homepage soon. Chris and Nikki mini-prepared auxin assay for tomorrow, so we will be able to know whether the sequencing is right or not. Chris also tested the supernatant of cpec culture from yesterday. Rebekka was preparing for tomorrow panel for human practices. Finally, the end of today, we all made the slides for tomorrow’s practice panel.
Thursday, 25th August
Today, Nick set up the chemotaxis assays with the help of Frank with 36 samples running. Nick also corrected yesterday's errors. Frank wrote up the BacTrap overview for the wiki and threw up some ideas for the engineering cycle. However, Chris had a bad day as his auxin assays failed. Nikki managed to assemble the PA2652 construct and transform more cells. Rebecca wrote more stuff on the wiki about chemotaxis and made phytogel, panels, plates. Ming filled his day by planning the soil erosion experiments for the next 5 weeks. He also came with the good news that he had secured the equipment (soil, shower, tray, etc) for the soil erosion experiment. Si continued to search for the parameters for modeling. She also started to clean up previous codes, commenting and properly documenting them. She and Nina also began to write up on the BacTrap modeling. Nina included the data fitting design on the wiki and consulted Dr Guy-Bart Stan about diffusion modelling.
Friday, 26th August
This friday it seems like a lot of people disappear. The rest of us have to work twice as hard but seems we are a bit tired from the whole week. Nikki grows PA2652 colony overnight along with picking up the colony, PCR, and analysing PCR of the assemble where the results are looking good!!!. Chris digests GFP construct no.17 which turns out to miss the spacing site and therefore needs to be reengineered with PCR. He also transform the dendra2 and use the nanodrop machine to transfer antiholin into 1C3 vector. After a long day yesterday, Nick write up his wiki and make some more LB plates. Si and Nina have atalk with expert in chemotaxis which turns out to be very useful. They also summarize on the whole auxin pathway, its secretion and the related calculation. Rebekka continues her phytogel experiment. And finally Ming has start the real action on the soil erosion experiment after all the stuffs ; shower, soil, containers, slopes, and plants are ready (taking like a whole week Phew ><) He starts preparing the soil by incubating the soils in antifungal solution and also making the stock solution of auxin for watering arabidopsis. The soil is incubated for 1 day and ready to be planted in the next day.
