Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Dynamical Modeling of Optogenetic Circuits in Yeast for Metabolic Engineering Applications

Journal Article · · ACS Synthetic Biology
 [1];  [2];  [2];  [3];  [4];  [5]
  1. Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States; OSTI
  2. Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
  3. Department of Molecular Biology, Princeton, New Jersey 08544, United States
  4. Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
  5. Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States; The Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
Not provided.
Research Organization:
Princeton Univ., NJ (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
DOE Contract Number:
SC0019363
OSTI ID:
1853117
Journal Information:
ACS Synthetic Biology, Journal Name: ACS Synthetic Biology Journal Issue: 2 Vol. 10; ISSN 2161-5063
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English

References (45)

Some common features of periodically forced reacting systems journal January 1986
Dynamic pathway regulation: recent advances and methods of construction journal December 2017
Long-term model predictive control of gene expression at the population and single-cell levels journal August 2012
Integrative Analysis of Cell Cycle Control in Budding Yeast journal August 2004
An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation journal May 2018
In Vivo Real-Time Control of Gene Expression: A Comparative Analysis of Feedback Control Strategies in Yeast journal December 2015
Proteasomes Begin Ornithine Decarboxylase Digestion at the C Terminus journal May 2004
Model predictive control: Theory and practice—A survey journal May 1989
Redirection of flux through the FPP branch-point in Saccharomyces cerevisiae by down-regulating squalene synthase journal June 2008
Modelling and analysis of gene regulatory networks journal September 2008
Balancing a genetic toggle switch by real-time feedback control and periodic forcing journal November 2017
An optogenetic gene expression system with rapid activation and deactivation kinetics journal January 2014
Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities journal June 2015
Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response journal November 2012
In silico feedback for in vivo regulation of a gene expression circuit journal November 2011
Optogenetics and biosensors set the stage for metabolic cybergenetics journal October 2020
Controlling Central Carbon Metabolism for Improved Pathway Yields in Saccharomyces cerevisiae journal November 2015
The promise of optogenetics in cell biology: interrogating molecular circuits in space and time journal December 2010
Method for targeting protein destruction by using a ubiquitin-independent, proteasome-mediated degradation pathway journal October 2005
Sequential control of biosynthetic pathways for balanced utilization of metabolic intermediates in Saccharomyces cerevisiae journal March 2015
Blue Light-Induced Dimerization of a Bacterial LOV–HTH DNA-Binding Protein journal September 2013
Current and future modalities of dynamic control in metabolic engineering journal August 2018
Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth journal August 2016
Constrained model predictive control: Stability and optimality journal June 2000
Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control journal October 2018
Partial Observations and Conservation Laws: Gray-Box Modeling in Biotechnology and Optogenetics journal November 2019
Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering journal November 2020
A survey of industrial model predictive control technology journal July 2003
Dynamic control of endogenous metabolism with combinatorial logic circuits journal November 2018
Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization journal December 1997
Ubiquitin-independent Mechanisms of Mouse Ornithine Decarboxylase Degradation Are Conserved between Mammalian and Fungal Cells journal April 2003
Systems metabolic engineering of Escherichia coli for gram scale production of the antitumor drug deoxyviolacein from glycerol: Deoxyviolacein production in engineered E. coli journal August 2014
Adaptive Model Predictive Control of an optogenetic system conference December 2015
Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals journal March 2014
Review: Optimizing inducer and culture conditions for expression of foreign proteins under the control of thelac promoter journal March 1996
Optogenetic control of the lac operon for bacterial chemical and protein production journal September 2020
A photoconversion model for full spectral programming and multiplexing of optogenetic systems journal April 2017
VODE: A Variable-Coefficient ODE Solver
  • Brown, Peter N.; Byrne, George D.; Hindmarsh, Alan C.
  • SIAM Journal on Scientific and Statistical Computing, Vol. 10, Issue 5 https://doi.org/10.1137/0910062
journal September 1989
Optogenetic regulation of engineered cellular metabolism for microbial chemical production journal March 2018
A LOV2 Domain-Based Optogenetic Tool to Control Protein Degradation and Cellular Function journal April 2013
Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints journal August 2017
Real-time optogenetic control of intracellular protein concentration in microbial cell cultures journal January 2014
Efficient protein depletion by genetically controlled deprotection of a dormant N‐degron journal January 2009
Interlinked Fast and Slow Positive Feedback Loops Drive Reliable Cell Decisions journal October 2005
The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system journal May 1998

Similar Records

Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering
Journal Article · Mon Nov 23 23:00:00 EST 2020 · ACS Synthetic Biology · OSTI ID:1853116

Optogenetic Amplification Circuits for Light-Induced Metabolic Control
Journal Article · Fri Apr 09 00:00:00 EDT 2021 · ACS Synthetic Biology · OSTI ID:1853118

Optogenetics Illuminates Applications in Microbial Engineering
Journal Article · Tue Mar 22 20:00:00 EDT 2022 · Annual Review of Chemical and Biomolecular Engineering · OSTI ID:1900143