Week 2 (02/07/12)

From 2012.igem.org



We did the final jobs with our sample colonies today, subjecting them to a restriction digest to check that the GFP gene had been integrated in the correct way. To aid in this, we were introduced to the plasmid analysis tool ApE, which helped us to choose which restriction enzymes could be used diagnostically. Another crucial ability for the successful integration of artificial plasmids into the bacteria we will be using.

The restriction fragments were then characterized with DNA gel electrophoresis.

In between these steps, we continued our brainstorming sessions. We are aiming to have a basic project description complete by Wednesday, so we are really trying to pull together lots of different ideas to create a cohesive project with a well defined end goal. Input from our Human Practices specialist (Charlie) helps with this.


More brainstorming today. Although the ideas that were pitched in the morning were not particularly promising, we finally hit on a good idea just after coffee. It has the potential to integrate many of the ideas that we already had into a single project, and everyone seems keen to get started on it. A description can be found here. We still need to thrash out the details of the project, but as a general goal it looks highly promising.

On top of this, we started the wiki properly. Paul, Andreas and Emmy are looking into the ways we can make it look flash with html.


Today we had a presentation from one of the guys at Microsoft Research, who demonstrated their (very useful) visual GEC tool for constructing and modeling genetic circuits. We had a go at designing a few different systems, learning the syntax and structure of the software. Of particular note was the XOR gate we constructed, which despite being a fairly complex device could quickly and realistically be constructed and modeled without having to spend days building genetic constructs. This could come in very handy, given our ambitions to standardize these many different biosensors - we really want a high throughput system for constructing them, something which is only really feasible if we have a good idea that our constructs will eventually work.

Later there was a workshop from one of the PhD students in Jim H's lab. He discussed the possibility of using computer programs to model bacterial populations. For example, he demonstrated a program in python that was capable of making simulated bacterial colonies with many of the same emergent properties as those seen in real bacteria.

The day was capped off with, what else, brainstorming. Aptamers seem to be beginning to gain some interest.


Our focus today was on the electronic side of the project. Jim H. talked to us about the Arduino open source integrated chip, and what things it could be used for. In the afternoon we were set loose with several Arduino kits, learning how to use the programming environment.

Unfortunately, a single afternoon was not enough time to recapitulate the successes of the Tyrell corporation, but we were still able to come up with a few cool devices. Given that our biosensor idea would ideally be both open source and cheap, using design principles similar to the Arduino could be a lucrative avenue. Additionally, the use of open source electronics such as the Arduino or the Raspberry Pi could directly make our product cheaper and more easily accessible for modification and improvement.


The last of the seminars today. This one was about the genetic systems that we will be hijacking with our project (in particular fleshing out the central dogma). A big emphasis on the challenges faced by synthetic biology due to the vast complexity of the chemical systems we are trying to insert new constructs into. However, this just goes further to demonstrate the potential value of our project - managing to put any biosensor into a system and be confident that the genetic system will not simply break could have an incredible impact upon synthetic biology.

At two o'clock, everyone pitched their own ideas for potential modules. Aptamers, yeast GPCRs and the different techniques for tuning the response curves were presented, along with potential circuits for the instrumentation portion of the project. The ensuing discussion took... some time, but at the end we had a general idea of what to do in the ensuing weeks, on both the biological and technological fronts.

We still lack any real direction on finding some sort of novel biological system to apply however. Something for us to think about over the weekend.