We aim at advancing synthetic biology by proposing general methodologies and technologies for engineering and characterising completely synthetic circuits (de novo design) in living cells. The generality of our approaches will allow using them in high-throughput, which could generate a disruptive impact in basic science and technology. A high-throughput design and characterisation methodology together with the corresponding modelling will allow scaling up the complexity of the cellular circuitry that could be engineered in living cells through the assembly of synthetic parts. In our EVOPROG consortium we will program phage and bacteria to compute our combinatorial optimisation algorithms by constructing and using a high-throughput droplet device for the directed evolution of biomolecules de novo, integrating for the first time in silico and in vivo evolution. For this, we will develop a general-purpose 3D biochip utilizing computational and fluidics automation which could also be applied to perform in vivo molecular biology operations in high-throughput (including time-dependent characterisations of gene expression levels using fluorescent proteins).
In our research we focus in the de novo engineering of synthetic RNA parts (sometimes including proteins as cofactors) and circuits working robustly as targeted in a given cellular context. We construct devices able to respond in a complex way after processing a suitable time-dependent signal, which would open the way towards the engineering of signal processing in living cells. We use a novel characterisation of regulatory parts that will include measuring gene expression dynamics at the single-cell level. In particular, the RNAs require fewer model assumptions than proteins. Such characterization of our de novo designed biomolecules and their networks will provide more quantitative predictions in biology.
- EVOPROG consortium (FP7-ICT), coordinated by Alfonso Jaramillo, gets funded.
- We participate as partner in the PROMYS (FP7-KBBE) consortium that recently also got funded.
- 4 new articles got published in 2013
- The CNRS press highlights our two PNAS papers in Vers une automatisation de la biologie de synthèse
- We published in ACS Synth Bio the first Full Biodesign Automation methodology able to design unsupervised the nucleotide sequence of genetic circuits with targeted dynamics: AutoBioCAD software. http://dx.doi.org/10.1021/sb300084h
- We got 3rd price in the Synthetic Biology Gen9 contest!
- Teaching a computer to design by itself fully synthetic riboregulators working in bacteria? Synth-Bio full design automation! Rodrigo et al. PNAS 2012
- Another PNAS: the first automated methodology for the computational design of genomes. Refactoring E. coli global regulation. Synth-Bio full design automation! Carrera et al. PNAS 2012
- 1st report of a computer designing by itself the nucleotide sequence (or even a degenerate sequence library) of a gene circuit. Synth-Bio full design automation! Rodrigo et al. NAR 2011