Boston calling back – German students return with a gold medal!

In this follow-up article to our previous blog post about the iGEM team from Tübingen, we congratulate the Team Tübingen to its victory at the iGEM Giant Jamboree in Boston this year. We spoke to Katharina, a Biochemistry student at the University of Tübingen and team member, to find out more…

What is the iGEM, and for how long have you participated?

iGEM (international Genetically Engineered Machine) is an annual competition for synthetic biology, first organised in 2003. The event has been held in Boston for the last 2 years, with the Giant Jamboree allowing each team to present their project and showcase what they have achieved over the summer. Our team, initially founded by biology and biochemistry students, visited iGEM for the fourth time this year.

Can you explain your project?

This year’s project was the development of a sensor memory module in yeast. A number of sensors have been built over the last few years to be used in various projects, including one from Team Tübingen in 2013. However, all of these sensors produce an instant readout, like for example, a change in colour or fluorescence or the emission of light. As it might not always be convenient or possible to measure the output signal immediately, we developed a versatile memory model for all sensors already present in the registry. For this memory module, we combined two different molecular systems: The Cre recombinase and Dronpa. Cre recombinase is an enzyme which allows the site-specific excision of DNA from the genome of an organism if special DNA sequences, the so-called loxP sites, are present. Dronpa, on the other hand, is a fluorescent protein in which fluorescence can be switched on and off by illuminating it with light at different wavelengths. Upon activating fluorescence by illuminating Dronpa with 488 nm light, Dronpa loses its ability to bind to copies of itself, and Dronpa dimers dissociate. This property was exploited by ‘caging’ Cre recombinase with two fluorescent Dronpa proteins which were fused to the start and the end of the Cre recombinase. In the dark, these two Dronpa proteins bind to each other and prevent activation of Cre recombinase. Once illuminated, the dimers dissociate and Cre recombinase becomes active. After the sensor is activated, the Dronpa-Cre fusion protein is expressed in its caged and inactive state. By illuminating the fusion protein with 488nm light, the Dronpa proteins around the Cre recombinase dissociate and thereby activate it. The Cre recombinase can excise parts from the DNA flanked by the loxP sites. We used this system to create a reporter cassette, in which the genetic information for red fluorescent protein (RFP) is inserted between the promoter for luciferase and the luciferase coding site. The RFP gene is flanked by loxP site. Upon expression and light-activation of the Dronpa-Cre recombinase, the RFP gene is cut out and the luciferase gene becomes active. Because the excision from the DNA is permanent, it can be passed on to subsequent yeast generations and therefore allows readouts at a later time.

That sounds really complex – Why did you decide to do what you do?

We gathered ideas from all team members and began looking for promising candidates to assist us. For some of the ideas, applications came to mind pretty fast. Unfortunately, because we could only do one project, we had to make a decision on what exactly we wanted to do, but also be realistic about financing and equipment. This unfortunately ruled out some of our proposed projects, so in the end we decided on this year’s sensor memory project.

What is your team’s motivation?

We’re all passionate scientists. As a result, we like a challenge where we can work on something we’ve always wanted to try and compete with people who have the same enthusiasm. It’s a great way of meeting people, each of whom come from very different backgrounds.

Different backgrounds but all studying Biological sciences? What is your team’s background?

We are a mix of Bachelor and Masters students from the Science Faculty, studying Biochemistry, Biology or Bioinformatics.

How big is the team then? How did you manage the workflow?

Our team consists of 20 students. Because we’re self-organised, we allocated the workload ourselves and formed several teams. Apart from general organisation, we had a fundraising team to find sponsors as we depended on financial support for our project. We had teams responsible for our wiki page and our website as well as for the design of the websites, for co-operation with other iGEM teams, human practices and modelling. Last but not least, we had a team which organised the lab work itself. Everybody worked as hard as they could, working on the project in our free time and fitting it around our studies. As the lab work had to be done consecutively, we had to make time available over the summer to spend whole weeks at a time in the lab. The majority of the rest of the work was done in the evenings and on weekends, and of course, whenever one of us had any free time!

 

Sounds like a lot of work! How did you organise yourselves, and how did labfolder help?

In the lab, it’s very important to record information in a way that is accessible to everyone who needs it, and can give an accurate overview of the methods and results. Over the last few years we have tried several approaches – unfortunately they always ended in chaos! This year, we used labfolder as our Electronic Lab Notebook. It allowed everyone in the group to access the data and meant we could link our results directly to the experiments, allowing us to find them again easily and to also verify who had the data. This was important because it meant we could write the wiki easily after the experiment, when writing the wiki is usually very stressful as everyone has different pieces of information.

What is your team’s vision for the future?

We’re looking to attract more students outside of our own studies like chemistry, physics and medicine. This would help us broaden our expertise and also offer new possibilities for different approaches to the topic of synthetic biology.

And what does your team want to achieve?

Because we won our first gold medal this year, we aim to continue our success and win again next year, and hopefully win a couple of other prizes along the way.

 

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