Topology-dependent interference of synthetic gene circuit function by growth feedback

R Zhang, J Li, J Melendez-Alvarez, X Chen… - Nature chemical …, 2020 - nature.com
Growth-mediated feedback between synthetic gene circuits and host organisms leads to
diverse emerged behaviors, including growth bistability and enhanced ultrasensitivity …

Winner-takes-all resource competition redirects cascading cell fate transitions

R Zhang, H Goetz, J Melendez-Alvarez, J Li… - Nature …, 2021 - nature.com
Failure of modularity remains a significant challenge for assembling synthetic gene circuits
with tested modules as they often do not function as expected. Competition over shared …

Revealing the host-dependent nature of an engineered genetic inverter in concordance with physiology

DTC Chan, GS Baldwin, HC Bernstein - Biodesign Research, 2023 - spj.science.org
Broad-host-range synthetic biology is an emerging frontier that aims to expand our current
engineerable domain of microbial hosts for biodesign applications. As more novel species …

Exploiting noise to engineer adaptability in synthetic multicellular systems

MS Aronson, C Ricci-Tam, X Zhu, AE Sgro - Current Opinion in Biomedical …, 2020 - Elsevier
Multicellular systems feature a stunning array of complex emergent behaviors that are
compelling engineering targets. These behaviors often arise from cells taking on different …

Emergent damped oscillation induced by nutrient-modulating growth feedback

J Melendez-Alvarez, C He, R Zhang… - ACS synthetic …, 2021 - ACS Publications
Growth feedback, the inherent coupling between the synthetic gene circuit and the host cell
growth, could significantly change the circuit behaviors. Previously, a diverse array of …

Potential landscapes, bifurcations, and robustness of tristable networks

A Dey, D Barik - ACS Synthetic Biology, 2021 - ACS Publications
Bistable switches that produce all-or-none responses have been found to regulate a number
of natural cellular decision making processes, and subsequently synthetic switches were …

Trajectory-based energy landscapes of gene regulatory networks

H Venkatachalapathy, SM Azarin, CA Sarkar - Biophysical journal, 2021 - cell.com
Multistability and natural biological variability can result in significant heterogeneity within a
cell population, leading to challenges in understanding and modulating cell behavior …

Pulsatile signaling of bistable switches reveal the distinct nature of pulse processing by mutual activation and mutual inhibition loop

S Das, D Barik - Journal of Theoretical Biology, 2022 - Elsevier
Cells often encounter various external and internal signals in a non-sustained pulsatile
manner with varying amplitude, duration and residual value. However, the effect of signal …

Multifaceted Effects of Resource Competition on Gene Expression and Noise

HE Goetz - 2022 - search.proquest.com
A notable challenge when assembling synthetic gene circuits is that modularity often fails to
function as intended. A crucial underlying reason for this modularity failure is the existence …

Emergent Dynamics Arising from the Feedback Between Synthetic Gene Circuit and Host Cell Growth

JR Meléndez-Álvarez - 2022 - search.proquest.com
The mutual inhibition between synthetic gene circuits and cell growth produces growth
feedback in the host-circuit system. Previous studies have demonstrated that the growth …