Highlights of the International Synthetic and Systems Biology Summer School 2014

Last week I joined the International Synthetic and Systems Biology Summer School in Taormina, Italy and as the title describes it was all about Synthetic and Systems biology with some pretty cool speakers.  Weiss talked about the general principles of genetic circuits and the current limitations (record is currently 12 different synthetic promoters in 1 designed network). Sarpeshkar focused on the stochastic nature and the associated noise of cells, he showed how they can be simulated or mirrored using analog circuits. Paul Freemont took Ron Weiss’ design principles and showed how to apply them on different examples, he also elaborated on an efficient way of characterizing new circuits and parts. Tanja Kortemme, a former postdoc from the Baker lab, gave an introduction to the capabilities of computational protein design and using some neat examples showed the power (and limitations) of computational design. Below some highlights and the relevant links of the literature that was discussed.

Ron Weiss, MIT

About the noise propagation and general rules for building genetic circuits:

Hooshangi, S., Thiberge, S. & Weiss, R. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl. Acad. Sci. U. S. A. 102, 3581–3586 (2005). [$]

A software tool to program genetic networks called BioCompiler:

Beal, J., Lu, T. & Weiss, R. Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS One 6, e22490 (2011). [OA]

Rahul  Sarpeshkar, MIT

About analog vs. digital

Daniel, R., Rubens, J. R., Sarpeshkar, R. & Lu, T. K. Synthetic analog computation in living cells. Nature 497, 619–23 (2013) [$]

On the deep connections and entanglement between electronics  and biochemistry

Sarpeshkar, R. Analog synthetic biology Analog synthetic biology. Philos Trans A Math Phys Eng Sci. 372, (2014). [OA]

An almost 1000 page book Sarpeshkar wrote on “bioelectronics” couple of chapters are freely downloadable:

Ultra Low Power Bioelectronics: Fundamentals, Biomedical Applications, and Bio-inspired Systems

Farren Isaacs, Yale

Review on the current genome editing tools:

Esvelt, K. M. & Wang, H. H. Genome-scale engineering for systems and synthetic biology. Mol. Syst. Biol. 9, 641 (2013). [OA]

Paul Freemont, Imperial College London

On the standardisation of DNA elements (RBS, promotor, etc):

Chappell, J., Jensen, K. & Freemont, P. S. Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology. Nucleic Acids Res. 41, 3471–81 (2013). [OA]

Very nice “How to build a biosensor review/guide/tutorial”:

Goers, L. et al. Engineering Microbial Biosensors. Microb. Synth. Biol. 40, 119–156 [$]

Tanja Kortemme, UCSF

Loop closure in protein design based on robot algorithms:

Mandell, D. J., Coutsias, E. a & Kortemme, T. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat. Methods 6, 551–2 (2009). [OA]

Rewiring cellular signal pathways using computational protein design:

Kapp, G. T. et al. Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc. Natl. Acad. Sci. U. S. A. 109, 5277–82 (2012). [$]

The seminal article of the Bakerlab on the basic design rules of proteins:

 Koga, N. et al. Principles for designing ideal protein structures. Nature 491, 222–7 (2012). [“OA”]