James Brown, Alan Walbridge, Vivian Mullen
Chris - Every year since 2003, teams of university students around the world - including from Cambridge University - have been taking part in a synthetic biology competition called iGEM. That stands for the International Genetically Engineered Machine. The teams who take part are actually given a kit of biological bits and pieces which include DNA and some gene sequences, and they have to use those to solve a bigger biological problem and then make their solution work in real living cells. In previous years, the teams have made bugs smell like bananas or even wintergreen, which smells nice, and they've even built a bacterial arsenic sensor. Meera Senthilingam has been along to talk to last year’s Cambridge E. chromi team. They built colour changing E. coli and actually won the competition and she’s been finding out how they got into it and what they got out of it. Graduate student James Brown was one of the supervisors involved.
James - iGEM is an educational initiative that started about five years ago out of MIT, and it really is about bringing together students of different disciplines, typically biological science students and engineering students to think about some of the new challenges we’re facing in the 21st century. The teams vary in size from 6 to 12 undergraduates typically. They're given a set of biological parts. That’s pieces of DNA that they’re shipped at the beginning of the summer and that’s made up of a series of switches and fluorescent proteins from coral and jellyfish. All of the basic components that have been designed and built by previous teams over the summers gone by and then their challenged to not only create their own ones, but use those basic components to piece together and build modular biological systems.
Meera - Thank you, James. The E. chromi team consisted of four biologists, two engineers, and one physicist. And with me is one of the biologists, Vivian Mullen. Now Vivian, tell me about E. chromi then. So what is it and what does it do exactly?
Vivian - So E. chromi was our project that we developed over the summer. Basically, it’s a bacterial biosensor. We built a bacteria to be able to sense the presence of a pollutant for example, heavy metal and then change colour depending on the concentration of that chemical.
Meera - What is this biosensor made up of?
Vivian - So it consists of three parts which are DNA parts. The first part is the heavy metal sensor and which basically involves a protein that binds to the DNA when the chemical is present. Then when it does, as it causes an output, so in a simple system, it would directly cause the output of colour. But on our system, we also had a thing called a sensitivity tuner. We had the heavy metal sensor then cause the expression of a protein which then bound to another piece of DNA and then made the colour output. So basically, using different combinations of this protein and the other piece of DNA, we were able to change the thresholds of the output from the original heavy metal sensor.
Meera - So essentially, you'd be able to test for different concentrations of certain chemicals.
Vivian - Yes and then you would actually have a visible output and multiple different colours depending on how you design the system.
Meera - And what bacteria was this all inserted into?
Vivian - So this was an E. coli which is a standard host that we used.
Meera - The main aim of iGEM is to bring together biologists, engineers, so people of different scientific areas. So also here is Alan Walbridge who was one of the engineers on the team. Alan, what was your contribution to this project? So what would you say your key role was to look at when this E. chromi was being developed?
Alan - So we brought numerical analysis to this project. So we’re looking at gene expression and an easy way to measure this is using a fluorescent protein and because we know that that doesn’t decay very quickly, if we look at the rates of change of fluorescence, we can be fairly sure that corresponds to the rate of production of fluorescence and that then is the gene activity at that particular point. And so, by doing large scale analysis, over different concentrations we’re able to work out this gene activity.
Meera - Essentially, you were kind of looking at the data and the actual kind of numbers involved with the project in order to see how effective it was.
Alan - Yes, that’s right.
Meera - And how Vivian, would you summarise the biological contributions to the project?
Vivian - So we were able to do the lab work and then bring some biological incites to interpret the data set the engineers had put forward.
Meera - What would the aims then of this type of design be? What would be some hopeful or potential applications of this?
Vivian - A member of our team is actually – she’s graduating this year and is staying on to move some of these parts into a different host so we were working in E. coli, but possibly, other hosts would be more useful for applications of this design, and then other members of the lab are working on moving it into plants.
Meera - What would be some potential real world applications if this was developed even further?
Vivian - So the point of our project was to solve a problem of water contamination. We wanted to develop a really accessible user friendly technology that anyone could use to test whether or not the water is contaminated and safe to drink.
Meera - And just lastly, I guess a key part of the project is just to mix the disciplines up as well. So, what would you say you both learned about each other’s disciplines?
Vivian - So I learned how to think like an engineer which is not to think of what this does in its natural environment, but how could we use this in a system with other parts and how can we piece them together. That was really interesting.
Meera - And Alan?
Alan - Like I said, I entered this with very little biological experience, but I learned an awful lot about how the bacteria work and through some intensive lab work over the summer, I feel I've become a little bit of a biologist now.
Chris - I’d like to take part myself. It sounds like fantastic, fun. That was Alan Walbridge and before him, Vivian Mullen. They're both students at Cambridge University and the winners of last year’s iGEM competition. You also heard the team supervisor and a graduate student, James Brown. He was talking at the beginning and they were all chatting with Meera Senthilingam. And looking at the iGEM website, it looks like they're expecting 180 teams around the world to take part this year, so it’s certainly flourishing.