Source 1primary paper2013Nucleic Acids Research
Toolkit/quantitative model
quantitative model
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
This quantitative model is a computational analysis component used in a 2013 study of multi-chromatic optogenetic control of mammalian gene expression and signaling. It was applied to determine critical system parameters for the reported light-responsive expression platform.
Usefulness & Problems
Why this is useful
The model is useful for system characterization because it supports identification of critical parameters in an engineered multi-wavelength gene control system. In the cited study, this analytical role accompanied a platform that enabled differential induction of up to three genes in mammalian cells with different light wavelengths.
Source:
The quantitative model was used to determine critical parameters of the reported system. The abstract presents it as an analytical component supporting system characterization.
Source:
determining critical system parameters
Problem solved
It helps solve the parameter-identification problem for a complex light-responsive mammalian gene expression system. The available evidence indicates that it was used to determine critical system parameters, but does not specify the exact model structure or parameter classes.
Source:
It helps identify critical system parameters for the engineered light-responsive expression system.
Source:
supports parameterization of the optogenetic expression system
Published Workflows
Objective: Develop and combine wavelength-specific optogenetic gene control systems to achieve predictable multi-chromatic control of mammalian gene expression and signaling.
Why it works: The workflow combines orthogonal light-responsive control channels so that different wavelengths can independently regulate different gene outputs in the same mammalian cell culture.
light-responsive split transcription factor activationdifferential gene induction by distinct wavelengthssynthetic system designquantitative modelingsystem combination
Stages
- 1.UVB-responsive system design(library_design)
To create a new UVB-inducible control channel for mammalian gene expression.
Selection: Design of a UVB-responsive split transcription factor based on UVR8 and the WD40 domain of COP1
- 2.Mammalian cell characterization of UVB induction(functional_characterization)
To establish that the engineered UVB system functions strongly in mammalian cells.
Selection: Magnitude of UVB-induced gene expression across mammalian cells
- 3.Quantitative parameter determination(secondary_characterization)
To identify critical parameters that govern system behavior.
Selection: Determination of critical system parameters using a quantitative model
- 4.Combination into multi-chromatic control(confirmatory_validation)
To show that the UVB module can be integrated with blue and red systems for multi-chromatic control.
Selection: Ability to differentially express three genes in one mammalian cell culture using different wavelengths
- 5.Angiogenic signaling application(confirmatory_validation)
To demonstrate that the multi-chromatic control system can regulate a biologically relevant signaling process.
Selection: Application of the multi-chromatic system to control angiogenic signaling processes
Steps
- 1.Design UVB-responsive split transcription factorengineered expression system
Create a UVB-inducible gene expression module for mammalian cells.
A UVB-responsive control channel had to be engineered before it could be characterized or combined with other light-responsive systems.
- 2.Measure UVB-induced gene expression across mammalian cellssystem being characterized
Establish inducibility and host-range performance of the UVB-responsive system.
The newly designed system needed functional characterization before broader integration into a multi-color platform.
- 3.Determine critical system parameters using a quantitative modelanalysis method applied to engineered system
Identify critical parameters governing system behavior.
After establishing that the system functions, modeling supports quantitative understanding needed for predictable use and integration.
- 4.Combine UVB, blue, and red light-inducible systems for multi-gene controlcombined control platform
Build a multi-chromatic system capable of differential control of multiple genes in one culture.
The UVB module was combined with existing blue and red systems only after it had been developed and characterized.
- 5.Apply the multi-chromatic system to angiogenic signaling controlsystem being applied
Demonstrate functional control of a biologically relevant signaling process.
After showing multi-gene control, the authors tested whether the platform could control angiogenic signaling processes.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
quantitative parameter inferenceTechniques
Computational DesignTarget processes
No target processes tagged yet.
Implementation Constraints
Practical implementation details are not provided in the available evidence. The source does not specify required datasets, computational framework, parameter-estimation workflow, or how the model interfaces with the UVB-, blue-, and red-light-responsive gene control components.
The evidence is sparse and only states that a quantitative model was used to determine critical system parameters. There is no information on equations, inputs, software implementation, training or fitting procedures, or whether the model was validated independently of the reported study.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Combining the UVB-responsive system with blue and red light-inducible gene control technology enabled multi-chromatic multi-gene control and was applied to angiogenic signaling processes.
By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes.
Combining the UVB-responsive system with blue and red light-inducible gene control technology enabled multi-chromatic multi-gene control and was applied to angiogenic signaling processes.
By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes.
Combining the UVB-responsive system with blue and red light-inducible gene control technology enabled multi-chromatic multi-gene control and was applied to angiogenic signaling processes.
By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes.
Combining the UVB-responsive system with blue and red light-inducible gene control technology enabled multi-chromatic multi-gene control and was applied to angiogenic signaling processes.
By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes.
Combining the UVB-responsive system with blue and red light-inducible gene control technology enabled multi-chromatic multi-gene control and was applied to angiogenic signaling processes.
By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes.
Combining the UVB-responsive system with blue and red light-inducible gene control technology enabled multi-chromatic multi-gene control and was applied to angiogenic signaling processes.
By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes.
Combining the UVB-responsive system with blue and red light-inducible gene control technology enabled multi-chromatic multi-gene control and was applied to angiogenic signaling processes.
By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes.
Combining the UVB-responsive system with blue and red light-inducible gene control technology enabled multi-chromatic multi-gene control and was applied to angiogenic signaling processes.
By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes.
Combining the UVB-responsive system with blue and red light-inducible gene control technology enabled multi-chromatic multi-gene control and was applied to angiogenic signaling processes.
By combining this UVB-responsive system with blue and red light-inducible gene control technology, we demonstrate multi-chromatic multi-gene control by differentially expressing three genes in a single cell culture in mammalian cells, and we apply this system for the multi-chromatic control of angiogenic signaling processes.
The study demonstrates multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to different wavelengths of light.
we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths
genes differentially induced 3
The study demonstrates multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to different wavelengths of light.
we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths
genes differentially induced 3
The study demonstrates multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to different wavelengths of light.
we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths
genes differentially induced 3
The study demonstrates multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to different wavelengths of light.
we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths
genes differentially induced 3
The study demonstrates multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to different wavelengths of light.
we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths
genes differentially induced 3
The study demonstrates multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to different wavelengths of light.
we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths
genes differentially induced 3
The study demonstrates multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to different wavelengths of light.
we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths
genes differentially induced 3
The study demonstrates multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to different wavelengths of light.
we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths
genes differentially induced 3
The study demonstrates multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to different wavelengths of light.
we demonstrate for the first time multi-chromatic expression control in mammalian cells by differentially inducing up to three genes in a single cell culture in response to light of different wavelengths
genes differentially induced 3
The authors developed a UVB-inducible expression system by designing a UVB-responsive split transcription factor based on UVR8 and the WD40 domain of COP1.
we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1
The authors developed a UVB-inducible expression system by designing a UVB-responsive split transcription factor based on UVR8 and the WD40 domain of COP1.
we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1
The authors developed a UVB-inducible expression system by designing a UVB-responsive split transcription factor based on UVR8 and the WD40 domain of COP1.
we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1
The authors developed a UVB-inducible expression system by designing a UVB-responsive split transcription factor based on UVR8 and the WD40 domain of COP1.
we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1
The authors developed a UVB-inducible expression system by designing a UVB-responsive split transcription factor based on UVR8 and the WD40 domain of COP1.
we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1
The authors developed a UVB-inducible expression system by designing a UVB-responsive split transcription factor based on UVR8 and the WD40 domain of COP1.
we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1
The authors developed a UVB-inducible expression system by designing a UVB-responsive split transcription factor based on UVR8 and the WD40 domain of COP1.
we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1
The authors developed a UVB-inducible expression system by designing a UVB-responsive split transcription factor based on UVR8 and the WD40 domain of COP1.
we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1
The authors developed a UVB-inducible expression system by designing a UVB-responsive split transcription factor based on UVR8 and the WD40 domain of COP1.
we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks with unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks with unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks with unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks with unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks with unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks with unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks with unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks with unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks with unmatched spatiotemporal precision for future research and biomedical applications.
This portfolio of optogenetic tools enables the design and implementation of synthetic biological networks showing unmatched spatiotemporal precision for future research and biomedical applications.
A quantitative model was used to determine critical system parameters.
Based on a quantitative model, we determined critical system parameters.
A quantitative model was used to determine critical system parameters.
Based on a quantitative model, we determined critical system parameters.
A quantitative model was used to determine critical system parameters.
Based on a quantitative model, we determined critical system parameters.
A quantitative model was used to determine critical system parameters.
Based on a quantitative model, we determined critical system parameters.
A quantitative model was used to determine critical system parameters.
Based on a quantitative model, we determined critical system parameters.
A quantitative model was used to determine critical system parameters.
Based on a quantitative model, we determined critical system parameters.
A quantitative model was used to determine critical system parameters.
Based on a quantitative model, we determined critical system parameters.
A quantitative model was used to determine critical system parameters.
Based on a quantitative model, we determined critical system parameters.
A quantitative model was used to determine critical system parameters.
Based on a quantitative model, we determined critical system parameters.
The UVB-inducible expression system enabled up to 800-fold UVB-induced gene expression in human, monkey, hamster, and mouse cells.
The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells.
UVB-induced gene expression fold induction 800 fold
The UVB-inducible expression system enabled up to 800-fold UVB-induced gene expression in human, monkey, hamster, and mouse cells.
The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells.
UVB-induced gene expression fold induction 800 fold
The UVB-inducible expression system enabled up to 800-fold UVB-induced gene expression in human, monkey, hamster, and mouse cells.
The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells.
UVB-induced gene expression fold induction 800 fold
The UVB-inducible expression system enabled up to 800-fold UVB-induced gene expression in human, monkey, hamster, and mouse cells.
The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells.
UVB-induced gene expression fold induction 800 fold
The UVB-inducible expression system enabled up to 800-fold UVB-induced gene expression in human, monkey, hamster, and mouse cells.
The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells.
UVB-induced gene expression fold induction 800 fold
The UVB-inducible expression system enabled up to 800-fold UVB-induced gene expression in human, monkey, hamster, and mouse cells.
The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells.
UVB-induced gene expression fold induction 800 fold
The UVB-inducible expression system enabled up to 800-fold UVB-induced gene expression in human, monkey, hamster, and mouse cells.
The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells.
UVB-induced gene expression fold induction 800 fold
The UVB-inducible expression system enabled up to 800-fold UVB-induced gene expression in human, monkey, hamster, and mouse cells.
The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells.
UVB-induced gene expression fold induction 800 fold
The UVB-inducible expression system enabled up to 800-fold UVB-induced gene expression in human, monkey, hamster, and mouse cells.
The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells.
UVB-induced gene expression fold induction 800 fold
Approval Evidence
1 source1 linked approval claimfirst-pass slug quantitative-model
Based on a quantitative model, we determined critical system parameters.
Source:
modeling resultsupports
A quantitative model was used to determine critical system parameters.
Based on a quantitative model, we determined critical system parameters.
Source:
Comparisons
Source-backed strengths
A clear strength is that the model was directly used in the context of an experimentally demonstrated multi-chromatic mammalian expression system. The evidence supports its utility for extracting critical system parameters, but does not report predictive accuracy, generalizability, or benchmarking.
Source:
we developed an ultraviolet B (UVB)-inducible expression system by designing a UVB-responsive split transcription factor based on the Arabidopsis thaliana UVB receptor UVR8 and the WD40 domain of COP1
Source:
The system allowed high (up to 800-fold) UVB-induced gene expression in human, monkey, hamster and mouse cells.
Ranked Citations
- 1.