Team:UCL/Notebook
- Origin Story
- Week 1 (15th June – 21st June)
- Week 2 (22nd June – 28th June)
- Week 3 (29th June – 5th July)
Origin Story
Week 1 (15th June – 21st June)
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 15th
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 16th
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 17th
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 18th
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 19th
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.
Saturday 20th
Sunday 21st
Week 2 (22nd June – 28th June)
Monday 22nd
Tuesday 23rd
Wednesday 24th
Hackathon part 1
The beginning of our actual project. Before today we knew that our project would be about the mind gut axis which means trying to tackle mental health problems with engineered probiotics. Today we made an actual list of effectors and promoters that we want to use in our biobricks. It was brainstorming mayhem, but we cut down our list to about ten candidates from each category for which we are going to collect more information for tomorrow.
Thursday 25th
Hackathon part 2
We finished our list today and had a lengthy vote on the g Blocks to order for our biobricks. Our main criterium for now is the likeliness for the gene products to yield useful data. Here is our list for the genes and promoters that we are starting to work on next week:
- Effectors
- TPH1 gene with an adrenaline-sensitive promoter, BBa_K554001. TPH1 converts tryptophan to a precursor of serotonin.
- TPH1 gene with nitric oxide sensitive promoter, BBa_K381001
- naked sequence for GAD, which codes for the enzyme glutamate decarboxylase which produces GABA.
- naked sequence for KAT (kynurenine aminotransferase), an important enzyme in serotonin metabolism
- naked sequence for Cholin Acetyltransferase, which makes Acetylcholin, an important neurotransmiter
- Promoters
- biobrick of the adrenaline sensitive promoter BBa_K554001
- biobrick of an osmotic stress sensitive promoter BBa_R0082
- biobrick of the nitric oxide sensitive promoter BBa_K381001
- biobrick of a pH sensitive promoter BBa_K318512
- Constructs
- An estrogen induced construct that is not yet fully characterized. We are going to transfect HeLa cells to model a pathway in mammalian cells which is central to our project as it involves bacteria interfering with humans
- An anti-sense Tryptophanase construct. We want to use this to control the tryptophanase expression which would allow us (or a cell) to regulate serotonin expression.
Friday 26th
Saturday 27th
Sunday 28th
Week 3 (29th June – 5th July)
Monday 29nd
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: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 :)
