Source 1primary paper2018
Toolkit/closed loop optogenetic compensation
closed loop optogenetic compensation
Also known as: CLOC
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Closed loop optogenetic compensation (CLOC) is an engineering methodology that monitors pathway output in real time and computes an optogenetically driven transcriptional input to compensate for deletion of a feedback regulator. It was applied to the Saccharomyces cerevisiae pheromone response pathway to define the dynamic requirements of feedback control.
Usefulness & Problems
Why this is useful
CLOC is useful for experimentally determining the dynamic function of biological feedback regulators rather than only their static contribution. The reported study presents it as a broadly applicable framework for linking real-time pathway measurements to light-controlled transcriptional compensation.
Source:
Using a custom-built hardware and software infrastructure, CLOC monitors in real time the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver—on the fly—an optogenetically-enabled transcriptional input designed to compensate for the effects of the feedback deletion.
Problem solved
CLOC addresses the problem of defining how feedback regulators must act over time to maintain normal pathway behavior after genetic deletion. In the cited work, it solved this by restoring regulator function operationally through computed optogenetic transcriptional input in the yeast pheromone response pathway.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete method used to build, optimize, or evolve an engineered system.
Techniques
Computational DesignTarget processes
transcriptionInput: Light
Implementation Constraints
Implementation requires real-time measurement of pathway output, a minimal computational model, and an optogenetic system capable of driving transcriptional input with light. The available evidence supports use in yeast and in the context of compensating feedback regulator deletion, but does not specify wavelengths, construct architecture, or cofactors.
The supplied evidence documents application in the yeast pheromone response pathway, but does not provide broader cross-system validation details. The evidence also does not specify quantitative performance metrics, hardware requirements, or the exact optogenetic actuator used.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Application of closed loop optogenetic compensation to the yeast pheromone response pathway revealed distinct dynamic requirements for three well-studied feedback regulators.
Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators.
Application of closed loop optogenetic compensation to the yeast pheromone response pathway revealed distinct dynamic requirements for three well-studied feedback regulators.
Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators.
Application of closed loop optogenetic compensation to the yeast pheromone response pathway revealed distinct dynamic requirements for three well-studied feedback regulators.
Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators.
Application of closed loop optogenetic compensation to the yeast pheromone response pathway revealed distinct dynamic requirements for three well-studied feedback regulators.
Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators.
Application of closed loop optogenetic compensation to the yeast pheromone response pathway revealed distinct dynamic requirements for three well-studied feedback regulators.
Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators.
Application of closed loop optogenetic compensation to the yeast pheromone response pathway revealed distinct dynamic requirements for three well-studied feedback regulators.
Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators.
Application of closed loop optogenetic compensation to the yeast pheromone response pathway revealed distinct dynamic requirements for three well-studied feedback regulators.
Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators.
Closed loop optogenetic compensation is presented as a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
Closed loop optogenetic compensation is presented as a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
Closed loop optogenetic compensation is presented as a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
Closed loop optogenetic compensation is presented as a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
Closed loop optogenetic compensation is presented as a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
Closed loop optogenetic compensation is presented as a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
Closed loop optogenetic compensation is presented as a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
Closed loop optogenetic compensation monitors pathway output in real time and uses a minimal model to calculate and deliver an optogenetically enabled transcriptional input that compensates for feedback regulator deletion.
Using a custom-built hardware and software infrastructure, CLOC monitors in real time the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver—on the fly—an optogenetically-enabled transcriptional input designed to compensate for the effects of the feedback deletion.
Closed loop optogenetic compensation monitors pathway output in real time and uses a minimal model to calculate and deliver an optogenetically enabled transcriptional input that compensates for feedback regulator deletion.
Using a custom-built hardware and software infrastructure, CLOC monitors in real time the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver—on the fly—an optogenetically-enabled transcriptional input designed to compensate for the effects of the feedback deletion.
Closed loop optogenetic compensation monitors pathway output in real time and uses a minimal model to calculate and deliver an optogenetically enabled transcriptional input that compensates for feedback regulator deletion.
Using a custom-built hardware and software infrastructure, CLOC monitors in real time the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver—on the fly—an optogenetically-enabled transcriptional input designed to compensate for the effects of the feedback deletion.
Closed loop optogenetic compensation monitors pathway output in real time and uses a minimal model to calculate and deliver an optogenetically enabled transcriptional input that compensates for feedback regulator deletion.
Using a custom-built hardware and software infrastructure, CLOC monitors in real time the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver—on the fly—an optogenetically-enabled transcriptional input designed to compensate for the effects of the feedback deletion.
Closed loop optogenetic compensation monitors pathway output in real time and uses a minimal model to calculate and deliver an optogenetically enabled transcriptional input that compensates for feedback regulator deletion.
Using a custom-built hardware and software infrastructure, CLOC monitors in real time the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver—on the fly—an optogenetically-enabled transcriptional input designed to compensate for the effects of the feedback deletion.
Closed loop optogenetic compensation monitors pathway output in real time and uses a minimal model to calculate and deliver an optogenetically enabled transcriptional input that compensates for feedback regulator deletion.
Using a custom-built hardware and software infrastructure, CLOC monitors in real time the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver—on the fly—an optogenetically-enabled transcriptional input designed to compensate for the effects of the feedback deletion.
Closed loop optogenetic compensation monitors pathway output in real time and uses a minimal model to calculate and deliver an optogenetically enabled transcriptional input that compensates for feedback regulator deletion.
Using a custom-built hardware and software infrastructure, CLOC monitors in real time the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver—on the fly—an optogenetically-enabled transcriptional input designed to compensate for the effects of the feedback deletion.
Approval Evidence
1 source3 linked approval claimsfirst-pass slug closed-loop-optogenetic-compensation
Here, we implement a new strategy, closed loop optogenetic compensation (CLOC), to address this problem.
Source:
biological findingsupports
Application of closed loop optogenetic compensation to the yeast pheromone response pathway revealed distinct dynamic requirements for three well-studied feedback regulators.
Application of CLOC to the yeast pheromone response pathway revealed surprisingly distinct dynamic requirements for three well-studied feedback regulators.
Source:
general applicabilitysupports
Closed loop optogenetic compensation is presented as a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
CLOC, a marriage of control theory and traditional genetics, presents a broadly applicable methodology for defining the dynamic function of biological feedback regulators.
Source:
method capabilitysupports
Closed loop optogenetic compensation monitors pathway output in real time and uses a minimal model to calculate and deliver an optogenetically enabled transcriptional input that compensates for feedback regulator deletion.
Using a custom-built hardware and software infrastructure, CLOC monitors in real time the output of a pathway deleted for a feedback regulator. A minimal model uses these measurements to calculate and deliver—on the fly—an optogenetically-enabled transcriptional input designed to compensate for the effects of the feedback deletion.
Source:
Comparisons
Source-backed strengths
The method combines real-time monitoring with a minimal model to calculate compensatory transcriptional input during an ongoing experiment. Its application revealed distinct dynamic requirements for three well-studied feedback regulators in the yeast pheromone response pathway, supporting its ability to resolve regulator-specific temporal control demands.
Ranked Citations
- 1.