Spatial biology of Ising-like synthetic genetic networks

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dc.article.number185
dc.catalogadorgjm
dc.contributor.authorSimpson, Kevin
dc.contributor.authorL'Homme Iriarte, Alfredo Juan
dc.contributor.authorKeymer, Juan E.
dc.contributor.authorFederici, Fernán
dc.date.accessioned2023-09-22T14:06:23Z
dc.date.available2023-09-22T14:06:23Z
dc.date.issued2023
dc.date.updated2023-09-12T16:04:29Z
dc.description.abstractBackground: Understanding how spatial patterns of gene expression emerge from the interaction of individual gene networks is a fundamental challenge in biology. Developing a synthetic experimental system with a common theoretical framework that captures the emergence of short- and long-range spatial correlations (and anti-correlations) from interacting gene networks could serve to uncover generic scaling properties of these ubiquitous phenomena. Results: Here, we combine synthetic biology, statistical mechanics models, and computational simulations to study the spatial behavior of synthetic gene networks (SGNs) in Escherichia coli quasi-2D colonies growing on hard agar surfaces. Guided by the combined mechanisms of the contact process lattice simulation and two-dimensional Ising model (CPIM), we describe the spatial behavior of bi-stable and chemically coupled SGNs that self-organize into patterns of long-range correlations with power-law scaling or short-range anti-correlations. These patterns, resembling ferromagnetic and anti-ferromagnetic configurations of the Ising model near critical points, maintain their scaling properties upon changes in growth rate and cell shape. Conclusions: Our findings shed light on the spatial biology of coupled and bistable gene networks in growing cell populations. This emergent spatial behavior could provide insights into the study and engineering of self-organizing gene patterns in eukaryotic tissues and bacterial consortia.
dc.fechaingreso.objetodigital2023-09-22
dc.format.extent16 páginas
dc.fuente.origenBiomed Central
dc.identifier.citationBMC Biology. 2023 Sep 04;21(1):185
dc.identifier.doi10.1186/s12915-023-01681-4
dc.identifier.urihttps://doi.org/10.1186/s12915-023-01681-4
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/74649
dc.information.autorucInstituto de Ingeniería Biológica y Médica; L'Homme Iriarte, Alfredo Juan; S/I; 215460
dc.information.autorucFacultad de Ciencias Biológicas; Keymer, Juan E.; 0000-0001-6566-3778; 93580
dc.information.autorucInstituto de Ingeniería Biológica y Médica; Federici, Fernán; 0000-0001-9200-5383; 123357
dc.language.isoen
dc.nota.accesoContenido completo
dc.revistaBMC Biology
dc.rightsacceso abierto
dc.rights.holderBioMed Central Ltd., part of Springer Nature
dc.subjectIsing model
dc.subjectSynthetic gene networks
dc.subjectSpatial correlation
dc.subjectCriticality
dc.subject.ddc570
dc.subject.deweyBiologíaes_ES
dc.titleSpatial biology of Ising-like synthetic genetic networks
dc.typeartículo
dc.volumen21
sipa.codpersvinculados215460
sipa.codpersvinculados93580
sipa.codpersvinculados123357
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