Team:Edinburgh/Notebook

Wednesday 28th

The team assembled in the Waddington building, ready to pit our five ideas against each other. Some had not survived the research process (the glowsticks), some did not seem to constitute a full project (the switch), and the others were not without their problems either. No clear consensus emerged, and team stuck around until late at night, trying to make them work.

Thursday 29th

Both L-glucose and dye manufacture were more or less ruled out on this day, which left us with no actual project to speak of. This was widely considered an undesirable state of affairs, and great efforts were gone to in the search for something new. Another late night, another intensive search through the track lists – still no success.

Friday 30th

Two fresh ideas came out of this day’s efforts. One – synthetic honey – went pretty much nowhere since bacteria would just be killed by honey, but the other seemed to have more life to it. This was metabolic wiring, and arose from a recent paper on the subject. This occupied most of the day.

Saturday 31st

Work continued into metabolic wiring, and a second project idea arose – could simple biological logic gates enable bacteria to play a game of Iterated Prisoner’s Dilemma against each other? The two ideas were developed in parallel, and it seemed we were getting somewhere at last.

Sunday 1st

The two project ideas continued their development, with diagrams and schematics being produced. Population control was looked at as a possible use for the metabolic wiring.

Monday 2nd

We presented the two ideas to one of the supervisors, Jon Marles-Wright, and it was agreed to combine the two into one project – develop metabolic wiring and BioBrick it, and use IPD as a showcase for how it can be used. More detailed research also began.

Tuesday 3rd – Friday 6th

Much more intensive research could now be done, now that the idea was ‘official.’ Actual genes and pathways were found which could be implemented, and circuit diagrams for different IPD strategies were devised.

Saturday 7th – 8th

It was time to get ready for the SULSA conference next week, where we would be presenting our idea for the first time, and making our first poster. This redefined what we had previously considered a ‘late night’ for iGEM.

Monday 9th – Tuesday 10th

SULSA! The week kicked off with the two day SULSA conference held here in Edinburgh. This was a really great experience. We got to meet the other three Scottish iGEM teams [LINKS], Kim de Mora from iGEM HQ, and lots of professionals in the field of Synthetic Biology who presented their work on the second day. We also got to present our idea to the world for the first time.

Wednesday 11th

Today we focused mainly on filling out the kind of overdue safety form, and also started handing out official roles within the group. The wiki was begun today, though nothing was uploaded yet, and we got to see our lab for the very first time.

Thursday 12th

Our first meeting of any real organisation was today, thanks to Chiara. The main outcome of this meeting was the role allocation. Philip is the ‘Trello man,’ Sam and Rikki are responsible for the wiki, Carrie and Charlotte are safety officers, Sam and Charlotte are the tweetsters, Chiara is the secretary, Philip and Elize are in charge of organising collaborations, Yuma is the Google Drive organiser.

We also started looking at organising the scientific aspects of the project. The Biologists broke into three teams to look at finding metabolic wires, creating IPD circuits, and looking at the population control aspect.

Finally, Philip also worked on trying to get funding for the iGEM meetup in Oxford later this month – we may be able to get SULSA funding (is there anything they can’t do?).

Friday 13th

We were given a tour of our lab by Jon today, who wisely advised us not to injure ourselves whilst in the lab. We also continued with experiment plans and started looking into wiki design.

We had two excellent pieces of input from actual professionals today also. First of all, Maryia Trubitsyna came to explain how her now paperclip method of parts assembly works and left us really excellent notes. And secondly, Yuma and Cesar attended an Informatics forum and gave a surprise presentation of the project. The feedback we got from some of the guys over there was to think about using metabolic wiring as a digilog signal as well as a digitial signal (so as to provide information on the metabolic load of the sender strain) and, again, to look at introducing elements of selection pressure to the IPD system. We decided to think about these suggestions but take them with a grain of salt from people who might be less familiar with iGEM than other advisers we have had.

Weekend 14th-15th

After a long sunny week where we were trapped inside for all of it, the weekend was mostly cloudy with occasional rain. Welcome to Scotland.

The team mostly relaxed over the weekend, but Philip and Yuma’s dedication recognises no weekend. Philip read some reviews on aromatics degradation, among other things, and Yuma looked some more into an idea brought up by advisors Chris French and Jon – sugar signalling. He and Philip decided it was promising but would require more research.

Monday 16th

Today we got to do actual lab work for the first time. We might have done little more than plate out some bacterial cells to make them competent, but it felt very encouraging. We learned some of the practical stuff you never learn about in the course, like how to prepare agar plates, and who to ask for various pieces of equipment.

We met with Dr. Garry Blakely to discuss a mechanism for slowing growth in our proposed population control demonstration of metabolic wiring, and he suggested a ribosome bases approach, such as targeting rpsL. We also further discussed the sugar logic idea as a way of getting started, though it was agreed a better metabolic pathway should be sought out. The main problem we are having at the moment is that all goof pathways produce toxic chemicals that cause horrific nerve diseases or cancer – not ideal.

Presentation skills were also worked on – rather fun – and looked into multicellular IPD, and alternative aromatic pathways.

Tuesday 17th

In the lab we just plated the cells from yesterday onto LB media – apparently the streaking went well. Small victories are heroic victories this early on.

Today was pretty research-heavy, with more metabolic pathways being sought out with limited success. We have a database of possible molecules we can use but they’re all so toxic, presumably because they are membrane-diffusible which is what we need. The sugar logic system would provide an alternative but it is not without its own problems.

Some of the groundwork was laid for the modelling too – mainly skill learning today – and primers were designed.

Many people seem stressed about the amount of time left - probably more because we have only a vague idea of how long things will take rather than any actual shortage of time. Time will tell.

Wednesday 18th

We finished making our cells competent today, and learnt how to make up the TSS buffer necessary to do so. Transformations should begin tomorrow. We also really need to source more materials and pieces of equipment for our lab – it has a real ‘abandoned’ feel.

Meanwhile a number of problems with the theoretical aspects were worked on. Four of us met with Dr. French to see if he had a workaround for a problem with our sugar logic system – the problem that each strain is too sensitive to false positives because it doesn’t rely on the prior strain for precursor. He didn’t have a solution, but did offer a possible solution to the secondary problem of signal quenching – make the enzymes unstable rather than use a degradation tag (which wouldn’t work outside the cell). We also looked for a way to source E. coli cells with the tetR gene as the strain we are working with is missing it, and we sort of need it for all our IPD circuits.

In addition, more organised circuit diagrams were made alongside matching plasmid diagrams, which will hopefully make the transition to multi-cell IPD easier, and a more in depth investigation of the Hbp operon (required for the metabolic wiring) was done. Philip and Cesar left us today to go and attend the Oxford iGEM meetup as our representatives. Good luck guys!

Finally, it was far too hot today. We almost denatured.

Thursday 19th

The first transformations were done today, which was exciting. They’re being incubated overnight, ready for a miniprep tomorrow. We were also very kindly given some TetR+ cells by Dr. Garry Blakely (once we’d prepared the tetracycline plate for him).

Meanwhile there was a discussion about what our ultimate aims should be, and some questions from the dry team about the specifics of metabolic wiring were answered. It was felt we need to make sure we are all on the same page, so to speak, lest we drift apart into different, unrelated subprojects.

Elize is looking into a Synthetic Biology Film Festival which previous iGEM teams have entered into with some success. The deadline for entries is in 11 days however, so this might not be feasible. Looks fun though.

Philip and Cesar attended the Oxford iGEM meetup but since they didn’t write up their logs they have been lost to history.

Friday 20th

The famous transformation efficiency kit was a complete failure – our first failed experiment! The first biobrick transformations seemed to have transformed quite well however, so the cells are at least competent.

Not a lot else happened today. Elize continued with the film, some more wiki research was done, and otherwise the day generally consisted of reading and research. The first minipreps will be done on Monday.

Weekend 21st-22nd

Recovery, mostly. First day of Summer, and the approach of July, all starting to get a bit stressful.

Monday 23rd

Lab work is now a major component of every day – as it should be. Today we performed our first minipreps of the three biobrick plasmids, ran them on a gel, and prepared for our first PCR. With then weeks to go until the end of August, it’s good that . We also have our first lab book!

The sugar project lumbered onward. We had a meeting with a resident expert on the subject who gave us a list of potential sugars we might use. The ongoing quest for potential metabolic pathways seems to be making some headway too, with some good potential operons found. Getting them on the other hand...

The film submission idea seems to be looking more doable – we churned out the first draft of a script and we have a vague idea of what we might do. The deadline is in seven days though...