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iGEM 2018: Two synbio teams from Greece are here to leave their mark

iGEM workshop in Athens. I can be seen presenting in the blue shirt

 

iGEM competition has attracted participants from all around the world, and Greece couldn’t be the exception. The first Greek team, iGEM Greece, had a quite successful participation last year. This picked the interest of more students, and in 2018 teams from Greece’s two largest metropolitan centres, Athens and Thessaloniki signed up. I met the students in a synbio workshop in Athens—always good to be back home—and was impressed by their enthusiasm and dedication.

 

iGEM Thessaloniki 2018: Stable and constant protein production decoupled from gene and plasmid copy number

iGEM Thessaloniki 2018 team

Mankind was always interested in how life works, how life adapts, how life evolves, how life flourishes, and how life ends. Scientific and technological breakthroughs allowed organism manipulations and genetic material modification, creating “biological factories” and enabling the production of valuable biological products. Still, challenges are present, such as the sheer complexity of every living organism and the constantly changing cellular environment.

Biological systems are unpredictable, noisy, and difficult to stabilize, even under standardized conditions. Combined with the fickleness and stochasticity of gene expression, even on single cell level, the production rate of a desired protein inevitably fluctuates.

iGEM Thessaloniki aims to design a tunable synthetic biology circuit which guarantees a constant protein expression pattern. We apply control theory to design promoters which maintain constant levels of expression at any copy number. Furthermore, we introduce an element that makes our system tunable to make our system a dynamic and versatile tool with broader manufacturing and therapeutic application capabilities. Finally, we aim to apply machine learning to enable automatic tuning of gene expression depending on a case-by-case basis.

Multiple levels of dynamic copy number control, as envisioned by iGEM Thessaloniki

This system will function as a foundational advance tool for both research and industry uses. Genetic engineers/synthetic biologists will have a wider choice of suitable  cloning vectors, while the conducted experiment’s accuracy will increase  significantly and inter-laboratory variations concerning experimental results will be eliminated. On industrial level, protein production will become more efficient, improving the product to cost ratio, thus maximizing profit and product quality.

Our team combines from different scientific backgrounds, such as Biology, Pharmacy, Engineering and Computer Science, our interdisciplinary team. As part of the iGEM 2018 Competition, we organize activities and workshops to communicate our project’s goals, while receiving valuable feedback from the public. Furthermore, we acknowledge the significance of bioethics and public engagement, so we recruited people specialized in fields such as anthropology and law. While we interacted with entrepreneurs, seeking funding and sponsorships, we came up with ways to integrate our project in business. We will tiresly continue our activities, talks, and other social events over the summer until late October and the Giant Jamboree. Till then, keep in touch with our team and ask us questions about the project on our social media pages!

iGEM Athens 2018: Tackling a future epidemic

iGEM Athens 2018 team. From left to right: Elena, Nelly, Maria, Natalia, Stelios, Yannis, Leda, Panos and Vasilis.

MERS-CoV (Middle East Respiratory Syndrome Coronavirus) is a Coronavirus, endemic to the Middle East. The virus attacks the human respiratory system and is highly pathogenic, causing a series of non-specific symptoms which complicate the diagnosis. The World Health Organization has declared MERS-CoV as one of the most likely to cause a future epidemic and urges for further research. The mortality rate of humans infected by MERS-CoV is approximately 35%, making on-time diagnosis critical for treatment and epidemic prevention.

iGEM Athens 2018 team aims to develop a molecular diagnostics kit for the detection of MERS-CoV. To meet the existing societal needs, we aim for an easy-to-use, rapid test that is reliable, safe, and usable on the field – even by the untrained.

MERS-CoV detection kit, as envisioned by iGEM Athens

Our detection mechanism is based on the Toehold-Switch technology. Toehold switches are hairpin-shaped riboregulators that precede a protein coding sequence in a synthetic mRNA molecule. The conformation of the switch regulates the expression of the protein; in the absence of a trigger complementary RNA sequence, the switch region folds, inhibiting the binding of the ribosome to the RNA and subsequently the expression of the coding sequence. If the target sequence is present, it binds to the switch region causing its unfolding, allowing the protein production.

Incorporating this mechanism as a DNA construct in a cell-free transcription and translation system creates a robust, genetically engineered circuit that can be used as a biosensor. DNA or RNA segments of viral or pathogenic origin can provoke the unfolding of a specific toehold switch-gene complex and lead to the expression of a reporter protein, indicating the existence of the target segments. It is preferable that the reporter protein produce an easy-to-read signal, such as a change in colour.

We attempt to refine the existing technology further by testing alternative peptides as strong reporters, improving the rapidness and the sensitivity of our diagnostic test. The reporter protein has to be of a relatively small size, alleviating the transcriptional and translational load as much as possible. We will design toeholds activated by MERS-CoV sequences and regulate the expression of an engineered enzyme

The toehold switch design is assisted by bioinformatics tools suggesting the best candidate target sequences, taking into consideration the viral genome, the sample origin and the natural microbiota of the sample. On this scope, we are designing Pre.Di.C.T. (Predictive Diagnostic Custom Toehold-Switch), a user-friendly generalized workflow that will facilitate the design of molecular-diagnostics systems for future research on other viruses.

For more information about our project’s progress you can visit our official website or follow us on social media: Facebook, Twitter, Instagram.

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