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26/9/2014

CRG: A new study on how to engineer synthetic gene networks, recreates the stripe patterns found in animals, using bacteria

CRG: A new study on how to engineer synthetic gene networks, recreates the stripe patterns found in animals, using bacteria


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Pattern formation is essential in the development of animals and plants. The central problem in pattern formation is how can genetic information be translated in a reliable manner to give specific spatial patterns of cellular differentiation.

In previous studies, gene circuits with predefined behaviors have been successfully built and modeled, but mostly on a case-by-case basis. In this study published in Nature Communications, researchers from the EMBL/CRG Systems Biology Research Unit at the CRG, went beyond individual networks and explored both computational and synthetic mechanisms for a complete set of 3-node stripe-forming networks in Escherichia coli. The approach combined experimental synthetic biology led by Mark Isalan, now Reader in Gene Network Engineering at the Department of Life Sciences of Imperial College London with computational modelling led by James Sharpe, ICREA Research Professor and head of the Multicellular Systems Biology lab at the CRG.

"We have performed a very innovative and ambitious study: we applied a three-step approach for the effective exploration and creation of successful synthetic gene circuits. We created a theoretical framework to study the GRNs exhaustively” - 100,000 versions of over 2800 networks were simulated on the computer. We then successfully developed a synthetic network engineering system and, finally, we confirmed all the new experimental data by fitting it to a single mathematical model" explains the corresponding author James Sharpe.

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Reference:
Schaerli, Y., et al. A unified design space of synthetic stripe-forming networks. Nature Communications, 5:4905. DOI: 10.1038/ncomms5905