Synthetic Biology builds upon the knowledge generated through systems approaches to understand interactions among components in biological networks, namely those in microbes that are the basis of biocatalytic processes for innovative BioBased products. This project pursues capitalizing the systems information available on the extant, natural strain Pseudomonas putida KT2440 with the goal of setting a computational framework to assist producing a simplified genomic chassis (platform) for optimized biocatalysis `a la carte (“cell factory”). The specific objectives are a) to identify engineering principles of orthogonality and hierarchy of abstraction to assemble novel biological systems for the design of novel processes, and b) the model-driven generation of a (re-) programmable Pseudomonas putida.
chassis aimed a the design of “cell factories” a la carte. The project will be carried out along three main poles of activity and will intertwine experimental-driven model development (here) and modeldriven experimentation (matching projects). This entails the description of the system by defining cellular block diagrams of P. putida, the recreation of key pathways as clusters of logical operators and as autonomous catalytic blocks and the system reconstruction/reprogramming towards superior biocatalysts. The integrated approach envisaged here combines optimally the “ethos” of Systems with that of Synthetic Biology following an engineering agenda. It is anticipated that this project will open new avenues in the way biocatalysis and cell re-programming is dealt with.
Design and analysis of a tunable synchronized oscillatorJournal of Biological Engineering 7 (2013). - ISSN 1754-1611 - 10 p.
Green genes: bioinformatics and systems-biology innovations drive algal biotechnologyTrends in Biotechnology 32 (2014)12. - ISSN 0167-7799 - p. 617 - 626.
Toolkit for Visualization of the Cellular Structure and Organelles in Aspergillus nigerACS synthetic biology 3 (2014)12. - ISSN 2161-5063 - p. 995 - 998.