Journal Article

Spatial biology of Ising-like synthetic genetic networks

L’Homme, Alfredo, Simpson, Kevin, Federici, Fernán, Keymer, Juan

2023

Overview

Background 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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Bi-stable / Biology / Biomedical and Life Sciences / Cell size / Correlation / Critical phenomena / Critical point / Criticality / E coli / Escherichia coli / Ferromagnetism / Fractals / Gene expression / Genes / Genetic aspects / Genetic research / Geospatial data / Ising model / Life Sciences / Mathematical models / Microbiota (Symbiotic organisms) / Networks / Phase transitions / Research Article / Scaling / Simulation / Spatial correlation / Statistical analysis / Statistical mechanics / Synthetic gene networks / Two dimensional models