Source 1primary paper2016Nucleic Acids Research
Toolkit/mathematical model
mathematical model
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
This mathematical model is a computational method used to quantitatively analyze the kinetics of blue light-inducible and blue light-repressible gene expression in an EL222-based bidirectional promoter system in Escherichia coli. It describes expression dynamics under optical input in the context of a rapidly reversible bacterial optogenetic transcription system.
Usefulness & Problems
Why this is useful
The model is useful for quantitatively characterizing how blue-light input shapes transcriptional output in an EL222-based bidirectional promoter system. The associated study also showed that gene expression levels in this system can be precisely controlled by modulating blue-light pulse dosage or intensity, indicating the model supports analysis of tunable optical control.
Source:
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
Problem solved
It addresses the problem of quantitatively describing the kinetics of both light-induced and light-repressed gene expression in a single bacterial optogenetic system. This is relevant to systems where blue light is used as a timing signal, including synchronization of receiver cells performing different logic behaviors over time.
Source:
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
Problem links
Need precise spatiotemporal control with light input
DerivedThis mathematical model was used to quantitatively analyze the kinetics of blue light-inducible and blue light-repressible gene expression in an EL222-based bidirectional promoter system in Escherichia coli. It serves as a computational method for describing expression dynamics under optical input.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Techniques
Computational DesignTarget processes
No target processes tagged yet.
Input: Light
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementoperating role: builder
The model was used in the context of an EL222-based bidirectional promoter system engineered in Escherichia coli and driven by blue-light input. The supplied evidence does not specify software, parameterization strategy, training data requirements, or how the model should be implemented computationally.
The available evidence only states that the model was used for quantitative kinetic analysis, without providing its equations, parameters, predictive accuracy, or scope beyond the reported EL222 system in E. coli. No independent replication or validation across other organisms, optogenetic modules, or experimental contexts is described in the supplied evidence.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
The system was applied to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal.
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
The system was applied to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal.
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
The system was applied to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal.
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
The system was applied to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal.
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
The system was applied to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal.
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
The system was applied to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal.
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
The system was applied to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal.
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
The system was applied to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal.
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
The system was applied to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal.
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
The system was applied to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal.
We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal
Gene expression level in the system can be precisely controlled by modulating blue-light pulse dosage or intensity.
by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely
Gene expression level in the system can be precisely controlled by modulating blue-light pulse dosage or intensity.
by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely
Gene expression level in the system can be precisely controlled by modulating blue-light pulse dosage or intensity.
by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely
Gene expression level in the system can be precisely controlled by modulating blue-light pulse dosage or intensity.
by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely
Gene expression level in the system can be precisely controlled by modulating blue-light pulse dosage or intensity.
by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely
Gene expression level in the system can be precisely controlled by modulating blue-light pulse dosage or intensity.
by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely
Gene expression level in the system can be precisely controlled by modulating blue-light pulse dosage or intensity.
by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely
Gene expression level in the system can be precisely controlled by modulating blue-light pulse dosage or intensity.
by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely
Gene expression level in the system can be precisely controlled by modulating blue-light pulse dosage or intensity.
by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely
Gene expression level in the system can be precisely controlled by modulating blue-light pulse dosage or intensity.
by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely
The authors engineered a novel EL222-based bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly by blue light.
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
The authors engineered a novel EL222-based bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly by blue light.
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
The authors engineered a novel EL222-based bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly by blue light.
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
The authors engineered a novel EL222-based bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly by blue light.
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
The authors engineered a novel EL222-based bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly by blue light.
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
The authors engineered a novel EL222-based bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly by blue light.
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
The authors engineered a novel EL222-based bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly by blue light.
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
The authors engineered a novel EL222-based bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly by blue light.
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
The authors engineered a novel EL222-based bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly by blue light.
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
The authors engineered a novel EL222-based bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly by blue light.
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
The light-inducible and light-repressible systems can function in parallel with high spatial precision in a single cell and can be switched stably between ON and OFF states by repetitive blue-light pulses.
both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light
The light-inducible and light-repressible systems can function in parallel with high spatial precision in a single cell and can be switched stably between ON and OFF states by repetitive blue-light pulses.
both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light
The light-inducible and light-repressible systems can function in parallel with high spatial precision in a single cell and can be switched stably between ON and OFF states by repetitive blue-light pulses.
both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light
The light-inducible and light-repressible systems can function in parallel with high spatial precision in a single cell and can be switched stably between ON and OFF states by repetitive blue-light pulses.
both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light
The light-inducible and light-repressible systems can function in parallel with high spatial precision in a single cell and can be switched stably between ON and OFF states by repetitive blue-light pulses.
both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light
The light-inducible and light-repressible systems can function in parallel with high spatial precision in a single cell and can be switched stably between ON and OFF states by repetitive blue-light pulses.
both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light
The light-inducible and light-repressible systems can function in parallel with high spatial precision in a single cell and can be switched stably between ON and OFF states by repetitive blue-light pulses.
both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light
The light-inducible and light-repressible systems can function in parallel with high spatial precision in a single cell and can be switched stably between ON and OFF states by repetitive blue-light pulses.
both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light
The light-inducible and light-repressible systems can function in parallel with high spatial precision in a single cell and can be switched stably between ON and OFF states by repetitive blue-light pulses.
both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light
The light-inducible and light-repressible systems can function in parallel with high spatial precision in a single cell and can be switched stably between ON and OFF states by repetitive blue-light pulses.
both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light
Approval Evidence
1 source1 linked approval claimfirst-pass slug mathematical-model
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
Source:
modeling analysissupports
The kinetics of light-inducible and repressible expression were quantitatively analyzed using a mathematical model.
the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model
Source:
Comparisons
Source-backed strengths
A key strength is that it was applied to quantitatively analyze both inducible and repressible expression kinetics in the same EL222-based bidirectional promoter framework. The underlying biological system was reported to respond rapidly and reversibly to blue light, and its expression level could be precisely controlled by pulse dosage or intensity.
Source:
we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222
Compared with mathematical model of light-induced expression kinetics
mathematical model and mathematical model of light-induced expression kinetics address a similar problem space.
Shared frame: same top-level item type; shared mechanisms: kinetic modeling; same primary input modality: light
Compared with model bioinformatics analysis
mathematical model and model bioinformatics analysis address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Compared with molecular dynamics simulations
mathematical model and molecular dynamics simulations address a similar problem space.
Shared frame: same top-level item type; same primary input modality: light
Relative tradeoffs: appears more independently replicated; looks easier to implement in practice.
Ranked Citations
- 1.