A unified design space of synthetic stripe-forming networks

Mostra el registre complet Registre parcial de l'ítem

• dc.contributor.author Schaerli, Yolanda
• dc.contributor.author Munteanu, Andreea
• dc.contributor.author Gili, Magüi
• dc.contributor.author Cotterell, James
• dc.contributor.author Sharpe, James
• dc.contributor.author Isalan, Mark
• dc.date.accessioned 2025-01-14T08:12:14Z
• dc.date.available 2025-01-14T08:12:14Z
• dc.date.issued 2014
• dc.description.abstract Synthetic biology is a promising tool to study the function and properties of gene regulatory networks. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case-by-case basis. Here we go beyond individual networks and explore both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally test every possible 3-node network for stripe formation in a morphogen gradient. We discover four different dynamical mechanisms to form a stripe and identify the minimal network of each group. Next, with the help of newly established engineering criteria we build these four networks synthetically and show that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allows us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.en
• dc.description.sponsorship We thank Jordi Garcia-Ojalvo, Luis Serrano, Andreas Wagner and Nicolas Buchler for critical reading. We thank Marco Musy, Julien Renggli, Alba Jiménez and Pau Fernández for technical help. Y.S. was funded by a Swiss National Science Foundation Fellowship (PBSKP3_134331/1) and by the Marie Curie Action (FP7 PIEF-GA-2011-298348). A.M. was funded by Plan Nacional à BFU2010-16428 (Ministerio de Economia y Contabilidad) and TV3 Maratón à 082030 (FUNDACIÓ LA MARATÓ DE TV3). J.C. was funded by the CRG and J.S. by the CRG and ICREA (Institut Catalan de Recerca i Estudis Avancats). M.I. is funded by the European Research Council (FP7-ERC-201249-ZINC-HUBS), the MEC-EMBL agreement and Ministerio de Ciencia e Innovación Grant MICINN BFU2010-17953. We acknowledge support from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208. We acknowledge Manjunatha Kogenaru and Sander J. Tans for providing strain MK01.en
• dc.format.mimetype application/pdf
• dc.identifier.citation Schaerli Y, Munteanu A, Gili M, Cotterell J, Sharpe J, Isalan M. A unified design space of synthetic stripe-forming networks. Nat Commun. 2014 Sep 23;5(1):4905. DOI: 10.1038/ncomms5905
• dc.identifier.doi http://dx.doi.org/10.1038/ncomms5905
• dc.identifier.issn 2041-1723
• dc.identifier.uri http://hdl.handle.net/10230/69093
• dc.language.iso eng
• dc.publisher Nature Research
• dc.relation.ispartof Nature Communications. 2014 Sep 23;5(1):4905
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/298348
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2010-16428
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/201249
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2010-17953
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV2012-0208
• dc.rights This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc-sa/4.0/
• dc.subject.other Biologia sintèticaca
• dc.subject.other Morfogènesica
• dc.subject.other Anàlisi de xarxes (Planificació)ca
• dc.title A unified design space of synthetic stripe-forming networksen
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion