Team:Imperial College London/Notebook/week6



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 6: 8th August to 14th August

Monday, 8th August

Today started pretty chilled as some people were a bit late, however soon the igem massive workload, particularly tranformation mania took over. Chris have transformed the newly arrived auxin fragments, which have arrived. However it was not all of them and therefore he will still have opportunity to further improve his street rep as transformation master. Also he has analysed and completed results for the Salkowski reagent assay and poured some agar plates. There is never enough plates. Nikki, Frank and Nick have joined the transformation craze with transformations of PA2652 fragments and transformation of RFP gene obtained from registry. In addition to this Nikki have ran gel electrophoresis of gel extracted purified backbone vector to make sure her efforts were not fruitless. They were not. Frank was also figuring out the kill switch situation by finding the suitable promoter for the whole system and tried to set new trend of minipreping with miniprep of the lysis casette gene. Maybe the rest of us will switch from transformation mode to miniprep mode. Nick have also set up chemotaxis agar plug in assay again. Meanwhile Rebekka have figured out protocol for what is later to be known as ┬┤the worm experiment┬┤ (with some help from Nick), then was largely working with Ming on the design of the auxin uptake experiment. However she did not forget to send an email to an ecology expert and also did more research into the problems of desertification. Ming was largely working on experimental design involving auxin, working on uptake and effects of auxin with increasing distance from the roots. He also helped modelling team and started thinking about new experiment involving water retention by the roots in the soil. Si have picked up her boyfriend from the airport in the morning and then went straight back to modelling. Large portion of the day she was working on modelling of the auxin uptake experiment and then have planned workload for the rest of the week. Nina continued to model root branching and have managed to include 1st order branching in her models. Apparently they all look just like hairs. She will look more into modelling the speed of the root growth, which affects branching. Yuanwei was mastering wiki as always, started to look into the different ideas of backround, colors and general pleasant outlook of the wiki. Overall a good day.

Tuesday, 9th August

This morning we checked the plates we cultured last night. All of the cells transformed with the newly arrived gene parts grew nicely. The plates with the DpnI digested backbone vectores didn't grow as expected, except one of the plates had one or two colonies, to be on the safe side we re-digested with DpnI and did a PCR purification. Nick had inconclusive results again, darnnn. Rebekka and Ming started the auxin uptake experiment which will take about three days. Frank inoculated the RFP transformants for the containment circuit which is on its way now. We had a brainstorming sesh on human practice and our Syngenta meeting for thursday. On the modeling front, Nina made a SICK video of root growth.

Wednesday, 10th August

Today, Frank ran his digest. He and Rebekka also organised some compost and food for the worms. Chris did mini preps and worked on the wiki. He is also in the process of writing a literature review on auxin, which he is hoping to have done by Tuesday or Wednesday. Nick's experiment results were inconclusive so he added attractant but the experiment was still wrong. He also did a midi prep and organised a collaboration with the CSIR Wits team in South Africa. He and Frank will have a skype conference with that team next week. Kiran also midi prep'd. His experiment is still running and he is in the process of writing it up. Nina modelled the density of the roots with and without auxin. Yuanwei helped Si with modelling the containment device but the values they are getting are still much larger than we would expect. He also used comsol to model auxin distribution. This will be used to model the auxin distribution in 3D. Ming planned how to do the experiment of putting auxin at different distances from seeds on phytogel. Rebekka helped set up the plates for this. Nikki midi prep'd and made Gibson buffer. She also made the handout for Syngenta.

Thursday, 11th August

Today we had a trip to Syngenta, which is a leader company in crop protection. We arrived about 10:30am; a warm welcome introduction talk was firstly given by Dr. Stuart John Dunbar. Then we had a science trip around their company, we visited green house and different types of machinery. The one, which can punch holes on leaves, was very interesting. Finally, we had a meeting with two auxin expertise about our project in the perspective of human practices and implementation.

Friday, 12th August

Today, Chris did more mini-preps, digest and gel. There seems to be some problems with the digest and restriction enzymes but it shouldn't be a big problem. Chris also did more research and read more reviews on auxin and had an interview with Kieran who has been here with us for over a week to get a feel of iGEM. Nikki looked into the implementation of the project and did some research on the manufacturing of the seed coat. She and Rebecca also read up more on desertification and now we have gained new insights into the desertification problem. Ming and Rebecca continued with the preparation of cultures, medium and autoclave works. They have also planned and carried out their split root experiments. Frank and Si managed to get the kill switch model to work finally. Frank is planning to do the transform next Monday. Nick was still working hard on his chemotaxis assays, plating and growing cells despite the fact that some of his bacteria died. Si and Yuanwei also meet up with Dr. Siggers to resolve some problems regarding the modelling of chemoattractant diffusion. They also got some new ideas and methods for modelling the auxin transport within the roots. Nina continues to work on the root growth model and has written much content for the modelling part on the wiki. Everyone also worked extremely hard to build the content of the wiki. Everyone has started to write the work that they did onto the wiki.