Team:Vilnius-Lithuania

Project Description

Optogenetic tools offer unprecedented ways to control cellular behavior in a precise and spatiotemporal manner. The integration of light-regulated systems into synthetic biology would drastically increase the level of control and open up a way for creative and innovative applications. However, current light modular systems have a variety of serious drawbacks, such as low dynamic range, slow response time, lack of portability, and a lack of parts. What is more, it is possible to modulate bacteria dynamics only at the transcriptional level. To address these shortcomings and open new avenues in bacteria regulation, we decided to develop our project “Colight” - a multi-level collection of optogenetic tools for modular bacteria control. Our newly developed systems fulfill the gaps in optogenetic bacteria control in transcription regulation and open up a possibility of light control expression dynamics in plasmid copy number and post-translational levels.


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Software.
Metagenomic mining

While searching for proteins with light-inducible domains, we managed to build software that enables the user to quickly and effortlessly discover proteins of interest by scanning through terabytes of metagenomic sequences. Our software takes advantage of MG-RAST database API and allows users to search & download hundreds of thousands of metagenomic samples to our server with just one click in their web-browser. Then it automatically standardizes and cleans the selected sequences to prepare them for further analysis. The user can choose from a variety of pre-made protein profiles obtained from the Pfam database; the primary tool used for similarity search is HMMER. This way, our software eliminates the previously required workload & knowledge and opens up the true potential of metagenomic research.


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Modeling

For the past decade, the interest to adapt control theory tools for the use in synthetic biology has been growing. While control theory is seeping its way into synthetic biology, it has not yet been explored in iGEM. Since control plays a central role in our project, Colight, we have decided to bring this sort of mathematical analysis. The models analyze the dynamics of control systems with light as an input. We check if it is possible to create potential in-silico feedback controllers. A design for an in-silico adaptive feedback controller for post-translational protein control has been constructed and tested by simulation. Most emphasis is put on the post-translational control model in which we describe our modeling approach in detail. For brevity, the same considerations are not repeated in the transcriptional regulation, and more emphasis is given to the results.


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Public engagement
AND human practices

The beginning of 2019 was marked by a WHO statement exposing a health crisis caused by the movement of anti-vaccination. In February we witnessed the pinnacle of this movement in Lithuania, where it manifested through the outbreak of measles. It came to light that many people are having doubts about the validity of scientific findings, and, therefore, turn to other sources for information, for example, famous people in the media, who have little to no scientific knowledge. People do not take science seriously and these views are both manifested and fueled through the media. Naturally, we raised a question – what is the cause of the miscommunication and disagreement? What is the main culprit of science skepticism?


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