Foundational Advance Track
Synthetic Biology has the potential to achieve great things in the 21st century, which has already been described as the century of biology. While DNA sequencing and synthesis are advancing in capacity at a rate about five times faster than Moore's law, they are not the only technologies necessary to bring about this revolution. Reading and writing DNA will become ever more crucial tools as the field of synthetic biology advances but knowing how to program using DNA will be the key to the field.
iGEM relies on a number of foundational technologies to function. We use BioBricks, standardization (RFCs), high-throughput quality control and many other processes to run the competition. We are continually expanding our capacities and a number of the projects listed below are examples of teams who have contributed parts, kits or work that advances iGEM. Unlike most other tracks, teams are not competing to solve a practical problem. The Foundational Advance track allows teams to come up with novel solution to technical problems surrounding core synbio technologies.
You will find images and abstracts of the winning Foundational Advance teams from 2013 to 2015 in the page below. Also, follow the links below to see projects from all the Foundational Advance track teams.
Ecolibrium - developing a framework for engineering co-cultures
In nature, microorganisms live together and cooperate to accomplish complex tasks. As synthetic biology advances, we transition from unicellular systems to engineering at the multicellular level. A major obstacle, however, is ensuring stable coexistence of different cell types in co-culture. This year we are developing a Genetically Engineered Artificial Ratio (GEAR) system to control population ratios in microbial consortia. GEAR will employ a bi-directional communication system and novel RNA control that can be implemented across different bacterial strains. We are also developing a software to facilitate the design and optimisation of co-cultures. In the future, we envision our GEAR system being used for distributed multicellular biocomputing and bioprocessing, as well as for microbiome engineering.
Synthetic biology opens exciting perspectives to design and apply regulatory circuits to control cellular response. Transcriptional regulation may be too slow for therapeutic or diagnostic applications. Several medical doctors and researchers that we consulted stressed the wish for a faster response. Therefore we decided to select as the challenge to design faster responsive cellular circuits. The system we aim to design is composed of the sensing module, which may be triggered by selected molecules, light or other signals; a processing module, which combines different inputs based on protein modifications and interactions and an output module, to provide rapid release of the selected proteins from cells, with a target specification to achieve a response within minutes rather than within hours and days, characteristic for current mammalian cell circuits. We expect that the proof of principle of the designed system and newly designed components may provide important foundational advances for synthetic biology.
Developing conditionally dimerizable split protein systems for genetic logic and genome editing applications
The field of synthetic biology seeks to engineer desirable cellular functionalities by developing molecular technologies that enable precise genetic manipulation. A promising solution is to reliably control proteins that naturally execute genetic modifications. Current strategies to regulate activity of such proteins primarily rely on modulating protein expression level through transcriptional control; however, these methods are susceptible to slow response and leaky expression. In contrast, strategies that exploit post-translational regulation of activity, such as conditional dimerization of split protein halves, have been demonstrated to bypass these limitations. Here, we compare the relative efficiency of previously characterized dimerization domains in regulating activities of three important genetic manipulation proteins - integrases and recombination directionality factors for genetic logic applications, and saCas9 for in vivo genome editing applications. We also establish guidelines to rationally identify promising protein split sites. Our characterization of these systems in mammalian cells ultimately paves way for important biomedical applications.
Catch it if you can
Like Proteins, RNA folds into a unique, functionally relevant 3D structure – as a catalytic ribozyme or an aptamer detecting and selectively binding a ligand. To obtain these functional RNAs, simple transcription of a DNA sequence is sufficient. Yet finding the few functional sequences has so far been challenging and has impeded its widespread use in synthetic biology. As a part of our project, we develop a software that drastically reduces both required resources and effort of directed evolution, as it creates aptamers for virtually any molecule through computational simulation. With the goal to provide the iGEM community with the power of RNA, we develop a toolbox consisting of easy to use standards for in vitro RNA usage, practical readouts and means for mRNA editing. To reach the end user with our work, we create straightforward tests for the detection of numerous noxious substances.