Difference between revisions of "Team:UCL/Notebook"

Bootcamp

This is how it begins. The iGEM bootcamp at UCL is intended to prepare us for the roles we are going to play this summer. We get to talk to some of the founding members of iGEM and meet two other iGEM teams from London, from the Biohackspace in Hackney and Birkbeck College.

Monday 15^th

We met at 09:30 in the lab. It is the first time we could all meet each other after our exams. The team members from the Biohackspace and Birkbeck were there as well. After the briefing on lab safety and other things we started with a SpeI and PstI digestion using the backbones from the InterlabStudy 2015: J23101, J23106, J23117 . As an insert we used an RFP containing vector from the iGEM 2014 distribution. We confirmed the digestions through an agarose gel electrophoresis and went for a break in the sun. Afterwards we performed the ligation of the insert and the backbone.

In the afternoon we had a skype meeting with Randy Rettberg from the iGEM foundation and learned something about the spirit and history of iGEM.

Tuesday 16^th

We split up into two groups to transform bacteria with the ligation reaction from yesterday. One group was using electroporation and the other chemical transformation. We incubated the bacteria overnight.

For the afternoon we split up into different groups preparing us for the individual roles that we will take in the team.

DIYbio

We discussed about the principles of DIY biology and the barriers preventing people from participating in biology. We were inroduced to the concept of the microcontroller Arduino.

Software & Automation

We talked to Synthace founding member Rob Stanley. Automating lab work cannot start early enough! We later talked to computational biologists about software methods for modelling biological systems.

Extralab

Wednesday 17^th

This morning we discovered that the RFP insert did not really fluoresce. At least not in red. We picked colonies to grow overnight in order to check whether something went wrong in the ligation or if the biobrick was not working. This could be done on Thursday through an agarose gel of the recombinant DNA.

In the afternoon we went back into our groups from yesterday.

DIYbio

We headed for the Biohackspace in Hackney and started doing manual. We 3D printed the parts and soldered everything together to make a spectrophotometer. Unfortunately, it didn't quite work. But being in the Hackspace was definitely worthwhile.

Software & Automation

We explored how the iGem wiki works which was more than this one sentence indicates.

Extra Lab

Thursday 18^th

We made a mini prep of our bacterial cultures and digested the final plasmid again, this time with SpeI and XbaI to check the insert. We then did the anticipated gel-electrophoresis. The result was that the ligation worked as we got the expected bands on the gel. Our conclusion to why the fluorescence did not work is that something was wrong with the biobrick...

DIY bio

We went to the Hackspace again and finished the sensor for the photometer and measured

Interlab study meeting

We had a skype meeting with the head of InterLab Study, Jacob Beal, and had a chat about this year's interlab study.

Friday 19^th

Mini Jamboree!

We have organised a mini jamboree in collaboration with Birkbeck iGEM and Biohackspace iGEM teams. We have invited people from the London synthetic biology community as well as the UCL Academy iGEM team to attend the jamboree. Each team presented what they did during the bootcamp.

Friday 26^th

Monday 29^th

This week we finally managed to start the proper lab work! In the morning prepared agar plates with ampicillin/chloramphenicol. Then we carried out transformations of four promoters from the 2014 distribution that we plan to use for characterization of our parts:

BBa_K554001 FlhDC promoter)

BBa_R0082 (OmpR promoter)

BBa_K144300 (blue light activated system) we got from our friends from Aalto-Helsinki team

BBa_K864400 (PTac promoter)

+ DH5 alpha competent cells control

In the meantime some of us were cleaning and organizing our new lab to make it ours and pretty! We will post a picture once it's ready :)
We also tried to autoclave our tipette pits but they didn't quite like the autoclave!

Tuesday 30^th

In the morning, we have checked the plates and obtained some pretty colonies!

We have inoculated 4 colonies per plate to be incubated overnight at 37C

In the afternoon, we planned the assembly of our BBa_J23100-BBa_B0034-TPH1-BBa_B0015. We have digested the gBlock1 with EcoRI and gBlock2 with PstI. Then we have performed the Gibson assembly of digested gBlock 1, gBlock 2, and linearized pSB1C plasmid, followed by the transformation.

July 1^st

There was only one colony on our plates from the Gibson assembly! We suspect that this is because the overlap between the linearized pSB1C backbone and our synthetic constructs was not long enough. We plan to try the Gibson assembly of two gBlocks alone tomorrow, followed by ligation to the plasmid backbone. We will see if this works better!

We have also purified the DNA from the transformants of four promoters from Monday. Some parts from the kit were missing, so we spent 4 hours on making a miniprep! This is bad!

In the afternoon, we have transformed the BBa_I13504 part from the 2014 distribution which we plan to use for our InterLab study.