22.12.17 - The EPFL team competing in the 2017 iGEM competition in Synthetic Biology has won a Gold medal, an award in the Best Education & Public Engagement category, and nominated in four others.

The International Genetically Engineered Machine (iGEM) competition takes place every year, pitting international teams of students from high schools and universities on synthetic biology projects.

The annual competition is organized by the iGEM foundation, an independent non-profit “dedicated to education, competition, the advancement of synthetic biology, and the development of an open community and collaboration.” The work for the competition occupies the teams for the better part of a year, and culminates at the iGEM Giant Jamboree in Boston, where projects are presented and judged by expert in bioengineering. This year's Jamboree took place from 9-13 November.

Every year, EPFL participates in the iGEM competition with a team of undergraduates supervised by two senior scientists. This year, Professor Sebastian Maerkl (School of Engineering and Interfaculty Institute of Bioengineering) and Dr Barbara Grisoni (School of Life Sciences) led a team of nine undergraduates: Felix Faltings, Jonathan Melis, Lena Bruhin, Elia Fernandez, Timothée Ferrari, Matteo Pirson, Lisa Dratva, Malek Kabani, and Natalija Gucevska. It is noteworthy that this year’s team was interdisciplinary, including students from Chemistry (Matteo Pirson) and Computer Science (Natalija Gucevska).

The team also enjoyed the additional support of five instructors: Ivan Istomin, Barbora Lavickova, Gregoire Michielin, Ekaterina Petrova, and Zoe Swank. Most of the work took place in the infrastructure of EPFL's Discovery Learning Labs, as well as Professor Maerkl’s lab.

This year, the team won a gold medal for their project and an award in the category Best Education & Public Engagement, as their work holds much educational potential. They were also nominated in four other categories:

  • Best Diagnostics Project
  • Best Integrated Human Practices
  • Best New Basic Part
  • Best Software

(See all competition results)

The project

Titled "Aptasense" (from aptamer, a sequence on the toehold structure that can bind a target molecule), the EPFL project for iGEM 2017 focused on developing open-source software for the design and evaluation of RNA-based devices called "toehold switches". These are mRNA fragments that can be used to activate or repress the translation of a particular gene. As such, they can be used to control the expression of a given protein, which gives toehold switches enormous potential as biological detectors.

Toehold switches are prominent in the emerging field of cell-free synthetic biology, which aims to develop tools for molecular diagnostics. Such systems promise fast testing cycles, ready-to-use detection devices, better biosafety, as well as cheap and easy transport and storage, making them ideal for field diagnostics.

The EPFL team built on a 2016 paper demonstrating that toehold switches can be used to detect Zika virus in cell-free paper-based expression systems. The idea is that the viral RNA would trigger the toehold to activate the expression of a reporter gene — namely, the lacZ gene, which is part of the cluster of genes required for the transport and metabolism of lactose in E. coli bacteria. The effect on the cell due to the disruption or non-disruption of its metabolism act as the diagnostic signal of the virus's presence in a low-cost, easy-to-use, and portable diagnostic testing kit.

Aiming to improve on this, the EPFL students developed a novel way for detecting proteins with an aptamer-based biosensor. Their innovation was to employ an ELISA test to detect expressed proteins in a sample, but replacing the two antibodies used in ELISA with two DNA aptamers (they call this the "aptamer Sandwich Assay"). The change means that the biosensor can now be retooled to detect virtually any protein, as it is considerably easier to design a new nucleotide sequence than develop a new antibody against a protein.

Then came the matter of the read-out. Normally, antibodies in ELISAs give out a fluorescent light when they detect the protein of interest. But most areas of the world that would be using this new biosensor would not have access to such biotechnology. So instead of attaching a fluorophore to our second aptamer, the students attached a trigger sequence, which is a nucleotide sequence that turns the toehold switch on to allow gene expression.

When the system detects the protein of interest, instead of measuring a fluorescent signal, the trigger sequence switches on the transcription and translation of the lacZ gene, producing the enzyme beta-galactosidase. The enzyme then processes its substrate into a colored product, causing the sample to visibly change color.

As there is no convenient software available to design toehold switches, Computer Science student Natalija Gucevska wrote open-source software for designing aptamers. With it, work that previously would require days now takes only a few minutes.

The overall system can be rapidly engineered and deployed, and all parts can be modified to recognize different protein or RNA molecules. This makes it a highly modular and novel diagnostic.