Cargando…
Automated design of gene circuits with optimal mushroom-bifurcation behavior
Recent advances in synthetic biology are enabling exciting technologies, including the next generation of biosensors, the rational design of cell memory, modulated synthetic cell differentiation, and generic multifunctional biocircuits. These novel applications require the design of gene circuits le...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225937/ https://www.ncbi.nlm.nih.gov/pubmed/37255663 http://dx.doi.org/10.1016/j.isci.2023.106836 |
_version_ | 1785050480874881024 |
---|---|
author | Otero-Muras, Irene Perez-Carrasco, Ruben Banga, Julio R. Barnes, Chris P. |
author_facet | Otero-Muras, Irene Perez-Carrasco, Ruben Banga, Julio R. Barnes, Chris P. |
author_sort | Otero-Muras, Irene |
collection | PubMed |
description | Recent advances in synthetic biology are enabling exciting technologies, including the next generation of biosensors, the rational design of cell memory, modulated synthetic cell differentiation, and generic multifunctional biocircuits. These novel applications require the design of gene circuits leading to sophisticated behaviors and functionalities. At the same time, designs need to be kept minimal to avoid compromising cell viability. Bifurcation theory addresses such challenges by associating circuit dynamical properties with molecular details of its design. Nevertheless, incorporating bifurcation analysis into automated design processes has not been accomplished yet. This work presents an optimization-based method for the automated design of synthetic gene circuits with specified bifurcation diagrams that employ minimal network topologies. Using this approach, we designed circuits exhibiting the mushroom bifurcation, distilled the most robust topologies, and explored its multifunctional behavior. We then outline potential applications in biosensors, memory devices, and synthetic cell differentiation. |
format | Online Article Text |
id | pubmed-10225937 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-102259372023-05-30 Automated design of gene circuits with optimal mushroom-bifurcation behavior Otero-Muras, Irene Perez-Carrasco, Ruben Banga, Julio R. Barnes, Chris P. iScience Article Recent advances in synthetic biology are enabling exciting technologies, including the next generation of biosensors, the rational design of cell memory, modulated synthetic cell differentiation, and generic multifunctional biocircuits. These novel applications require the design of gene circuits leading to sophisticated behaviors and functionalities. At the same time, designs need to be kept minimal to avoid compromising cell viability. Bifurcation theory addresses such challenges by associating circuit dynamical properties with molecular details of its design. Nevertheless, incorporating bifurcation analysis into automated design processes has not been accomplished yet. This work presents an optimization-based method for the automated design of synthetic gene circuits with specified bifurcation diagrams that employ minimal network topologies. Using this approach, we designed circuits exhibiting the mushroom bifurcation, distilled the most robust topologies, and explored its multifunctional behavior. We then outline potential applications in biosensors, memory devices, and synthetic cell differentiation. Elsevier 2023-05-09 /pmc/articles/PMC10225937/ /pubmed/37255663 http://dx.doi.org/10.1016/j.isci.2023.106836 Text en © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Otero-Muras, Irene Perez-Carrasco, Ruben Banga, Julio R. Barnes, Chris P. Automated design of gene circuits with optimal mushroom-bifurcation behavior |
title | Automated design of gene circuits with optimal mushroom-bifurcation behavior |
title_full | Automated design of gene circuits with optimal mushroom-bifurcation behavior |
title_fullStr | Automated design of gene circuits with optimal mushroom-bifurcation behavior |
title_full_unstemmed | Automated design of gene circuits with optimal mushroom-bifurcation behavior |
title_short | Automated design of gene circuits with optimal mushroom-bifurcation behavior |
title_sort | automated design of gene circuits with optimal mushroom-bifurcation behavior |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10225937/ https://www.ncbi.nlm.nih.gov/pubmed/37255663 http://dx.doi.org/10.1016/j.isci.2023.106836 |
work_keys_str_mv | AT oteromurasirene automateddesignofgenecircuitswithoptimalmushroombifurcationbehavior AT perezcarrascoruben automateddesignofgenecircuitswithoptimalmushroombifurcationbehavior AT bangajulior automateddesignofgenecircuitswithoptimalmushroombifurcationbehavior AT barneschrisp automateddesignofgenecircuitswithoptimalmushroombifurcationbehavior |