Designing biological circuits: synthetic biology within the operon model and beyond

MA English, RV Gayet, JJ Collins - Annual Review of …, 2021 - annualreviews.org
In 1961, Jacob and Monod proposed the operon model of gene regulation. At the model's
core was the modular assembly of regulators, operators, and structural genes. To illustrate …

Control theory for synthetic biology: recent advances in system characterization, control design, and controller implementation for synthetic biology

V Hsiao, A Swaminathan… - IEEE Control Systems …, 2018 - ieeexplore.ieee.org
Living organisms are differentiated by their genetic material-millions to billions of DNA bases
encoding thousands of genes. These genes are translated into a vast array of proteins …

Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies

CJ Bashor, N Patel, S Choubey, A Beyzavi, J Kondev… - Science, 2019 - science.org
Eukaryotic genes are regulated by multivalent transcription factor complexes. Through
cooperative self-assembly, these complexes perform nonlinear regulatory operations …

[HTML][HTML] Tracing information flow from Erk to target gene induction reveals mechanisms of dynamic and combinatorial control

MZ Wilson, PT Ravindran, WA Lim, JE Toettcher - Molecular cell, 2017 - cell.com
Cell signaling networks coordinate specific patterns of protein expression in response to
external cues, yet the logic by which signaling pathway activity determines the eventual …

What is stress? A systems perspective

M Del Giudice, CL Buck, LE Chaby… - Integrative and …, 2018 - academic.oup.com
The term “stress” is used to describe important phenomena at multiple levels of biological
organization, but finding a general and rigorous definition of the concept has proven …

T cells selectively filter oscillatory signals on the minutes timescale

GP O'Donoghue, LJ Bugaj… - Proceedings of the …, 2021 - National Acad Sciences
T cells experience complex temporal patterns of stimulus via receptor–ligand-binding
interactions with surrounding cells. From these temporal patterns, T cells are able to pick out …

Spatial and temporal signal processing and decision making by MAPK pathways

O Atay, JM Skotheim - Journal of Cell Biology, 2017 - rupress.org
Mitogen-activated protein kinase (MAPK) pathways are conserved from yeast to man and
regulate a variety of cellular processes, including proliferation and differentiation. Recent …

Biological feedback control—Respect the loops

H El-Samad - Cell Systems, 2021 - cell.com
We, and all organisms, are an evolutionary masterpiece of multiscale feedback control.
Feedback loops enable our cells to grow and then stop at the right size, to divide and self …

Distributed and dynamic intracellular organization of extracellular information

AA Granados, JMJ Pietsch… - Proceedings of the …, 2018 - National Acad Sciences
Although cells respond specifically to environments, how environmental identity is encoded
intracellularly is not understood. Here, we study this organization of information in budding …

Bacterial virulence mediated by orthogonal post-translational modification

KA Chambers, RA Scheck - Nature Chemical Biology, 2020 - nature.com
Many bacterial pathogens secrete virulence factors, also known as effector proteins, directly
into host cells. These effectors suppress pro-inflammatory host signaling while promoting …