Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering
Metabolic pathways can be engineered to maximize the synthesis of various products of
interest. With the advent of computational systems biology, this endeavour is usually carried …
interest. With the advent of computational systems biology, this endeavour is usually carried …
Crosstalk between transcription and metabolism: how much enzyme is enough for a cell?
Cells employ various mechanisms for dynamic control of enzyme expression. An important
mechanism is mutual feedback—or crosstalk—between transcription and metabolism. As …
mechanism is mutual feedback—or crosstalk—between transcription and metabolism. As …
Design of a synthetic integral feedback circuit: dynamic analysis and DNA implementation
The design and implementation of regulation motifs ensuring robust perfect adaptation are
challenging problems in synthetic biology. Indeed, the design of high-yield robust metabolic …
challenging problems in synthetic biology. Indeed, the design of high-yield robust metabolic …
Macromolecular networks and intelligence in microorganisms
Living organisms persist by virtue of complex interactions among many components
organized into dynamic, environment-responsive networks that span multiple scales and …
organized into dynamic, environment-responsive networks that span multiple scales and …
Trade-offs in biosensor optimization for dynamic pathway engineering
Recent progress in synthetic biology allows the construction of dynamic control circuits for
metabolic engineering. This technology promises to overcome many challenges …
metabolic engineering. This technology promises to overcome many challenges …
Pareto optimality between growth-rate and lag-time couples metabolic noise to phenotypic heterogeneity in Escherichia coli
DAF Fuentes, P Manfredi, U Jenal… - Nature communications, 2021 - nature.com
Despite mounting evidence that in clonal bacterial populations, phenotypic variability
originates from stochasticity in gene expression, little is known about noise-shaping …
originates from stochasticity in gene expression, little is known about noise-shaping …
Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic …
Multidrug-resistant (MDR) Acinetobacter baumannii has emerged as a very problematic
pathogen over the past decades, with a high incidence in nosocomial infections. Discovered …
pathogen over the past decades, with a high incidence in nosocomial infections. Discovered …
Law of localization in chemical reaction networks
T Okada, A Mochizuki - Physical review letters, 2016 - APS
In living cells, chemical reactions are connected by sharing their products and substrates,
and form complex networks, eg, metabolic pathways. Here we developed a theory to predict …
and form complex networks, eg, metabolic pathways. Here we developed a theory to predict …
[HTML][HTML] On paradoxes between optimal growth, metabolic control analysis, and flux balance analysis
HV Westerhoff - Biosystems, 2023 - Elsevier
In Microbiology it is often assumed that growth rate is maximal. This may be taken to suggest
that the dependence of the growth rate on every enzyme activity is at the top of an inverse …
that the dependence of the growth rate on every enzyme activity is at the top of an inverse …
A biomolecular proportional integral controller based on feedback regulations of protein level and activity
F Mairet - Royal Society open science, 2018 - royalsocietypublishing.org
Homeostasis is the capacity of living organisms to keep internal conditions regulated at a
constant level, despite environmental fluctuations. Integral feedback control is known to play …
constant level, despite environmental fluctuations. Integral feedback control is known to play …