Source 1primary paper2018arXiv (Cornell University)
Toolkit/Cph8
Cph8
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Cph8 is a photo-reversible phytochrome-based optogenetic switch used to control gene expression in Escherichia coli. The cited work applies stimulated depletion quenching to improve control over its photoswitching behavior.
Usefulness & Problems
Why this is useful
This tool is useful for light-based regulation of bacterial gene expression. The cited study indicates that stimulated depletion quenching can enhance control of Cph8 when conventional linear photoswitching is limited by spectral cross-talk.
Source:
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Source:
Stimulated Depletion Quenching (SDQ), is used to overcome spectral cross-talk by exploiting the molecules' unique dynamic response to ultrashort laser pulses
Problem solved
Cph8 helps address the problem of externally controlling gene expression in E. coli with light. In the cited work, the specific problem is incomplete conversion to the biologically inactive PFR state during linear photoswitching because reverse photoswitching drives the system back to the active PR state.
Source:
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Source:
the technique is hampered by spectral cross-talk: the broad absorption spectra of compatible biochemical chromophores limits the number of switches that can be independently controlled and restricts the dynamic range of each switch
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A composed arrangement of multiple parts that instantiates one or more mechanisms.
Techniques
Computational DesignTarget processes
No target processes tagged yet.
Input: Light
Implementation Constraints
The available evidence places Cph8 in Escherichia coli and identifies it as a phytochrome-based, light-controlled gene-expression switch. The supplied material does not specify construct architecture, chromophore requirements, illumination wavelengths, or delivery and expression details.
The supplied evidence states that linear photoswitching cannot fully convert Cph8 to the biologically inactive PFR state because spectral cross-talk promotes reverse photoswitching to the active PR state. The provided evidence does not report quantitative performance, dynamic range, response times, or validation beyond the cited study.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Stimulated Depletion Quenching is employed to enhance control of the Cph8 optogenetic switch.
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Stimulated Depletion Quenching is employed to enhance control of the Cph8 optogenetic switch.
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Stimulated Depletion Quenching is employed to enhance control of the Cph8 optogenetic switch.
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Stimulated Depletion Quenching is employed to enhance control of the Cph8 optogenetic switch.
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Stimulated Depletion Quenching is employed to enhance control of the Cph8 optogenetic switch.
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Stimulated Depletion Quenching is employed to enhance control of the Cph8 optogenetic switch.
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Stimulated Depletion Quenching is employed to enhance control of the Cph8 optogenetic switch.
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Linear photoswitching cannot fully convert Cph8 to the biologically inactive PFR state because spectral cross-talk drives reverse photoswitching back to the active PR state.
The Cph8 switch can not be fully converted to it's biologically inactive state ($P_{FR}$) by linear photos-witching, as spectral cross-talk causes a reverse photoswitching reaction to revert to it back to the active state ($P_{R}$).
Linear photoswitching cannot fully convert Cph8 to the biologically inactive PFR state because spectral cross-talk drives reverse photoswitching back to the active PR state.
The Cph8 switch can not be fully converted to it's biologically inactive state ($P_{FR}$) by linear photos-witching, as spectral cross-talk causes a reverse photoswitching reaction to revert to it back to the active state ($P_{R}$).
Linear photoswitching cannot fully convert Cph8 to the biologically inactive PFR state because spectral cross-talk drives reverse photoswitching back to the active PR state.
The Cph8 switch can not be fully converted to it's biologically inactive state ($P_{FR}$) by linear photos-witching, as spectral cross-talk causes a reverse photoswitching reaction to revert to it back to the active state ($P_{R}$).
Linear photoswitching cannot fully convert Cph8 to the biologically inactive PFR state because spectral cross-talk drives reverse photoswitching back to the active PR state.
The Cph8 switch can not be fully converted to it's biologically inactive state ($P_{FR}$) by linear photos-witching, as spectral cross-talk causes a reverse photoswitching reaction to revert to it back to the active state ($P_{R}$).
Linear photoswitching cannot fully convert Cph8 to the biologically inactive PFR state because spectral cross-talk drives reverse photoswitching back to the active PR state.
The Cph8 switch can not be fully converted to it's biologically inactive state ($P_{FR}$) by linear photos-witching, as spectral cross-talk causes a reverse photoswitching reaction to revert to it back to the active state ($P_{R}$).
Linear photoswitching cannot fully convert Cph8 to the biologically inactive PFR state because spectral cross-talk drives reverse photoswitching back to the active PR state.
The Cph8 switch can not be fully converted to it's biologically inactive state ($P_{FR}$) by linear photos-witching, as spectral cross-talk causes a reverse photoswitching reaction to revert to it back to the active state ($P_{R}$).
Linear photoswitching cannot fully convert Cph8 to the biologically inactive PFR state because spectral cross-talk drives reverse photoswitching back to the active PR state.
The Cph8 switch can not be fully converted to it's biologically inactive state ($P_{FR}$) by linear photos-witching, as spectral cross-talk causes a reverse photoswitching reaction to revert to it back to the active state ($P_{R}$).
Stimulated Depletion Quenching selectively halts the reverse photoswitching reaction of Cph8 while allowing the forward reaction to proceed.
SDQ selectively halts this reverse reaction while allowing the forward reaction to proceed.
Stimulated Depletion Quenching selectively halts the reverse photoswitching reaction of Cph8 while allowing the forward reaction to proceed.
SDQ selectively halts this reverse reaction while allowing the forward reaction to proceed.
Stimulated Depletion Quenching selectively halts the reverse photoswitching reaction of Cph8 while allowing the forward reaction to proceed.
SDQ selectively halts this reverse reaction while allowing the forward reaction to proceed.
Stimulated Depletion Quenching selectively halts the reverse photoswitching reaction of Cph8 while allowing the forward reaction to proceed.
SDQ selectively halts this reverse reaction while allowing the forward reaction to proceed.
Stimulated Depletion Quenching selectively halts the reverse photoswitching reaction of Cph8 while allowing the forward reaction to proceed.
SDQ selectively halts this reverse reaction while allowing the forward reaction to proceed.
Stimulated Depletion Quenching selectively halts the reverse photoswitching reaction of Cph8 while allowing the forward reaction to proceed.
SDQ selectively halts this reverse reaction while allowing the forward reaction to proceed.
Stimulated Depletion Quenching selectively halts the reverse photoswitching reaction of Cph8 while allowing the forward reaction to proceed.
SDQ selectively halts this reverse reaction while allowing the forward reaction to proceed.
Stimulated Depletion Quenching is used to overcome spectral cross-talk in optogenetic photoswitching.
Stimulated Depletion Quenching (SDQ), is used to overcome spectral cross-talk by exploiting the molecules' unique dynamic response to ultrashort laser pulses
Stimulated Depletion Quenching is used to overcome spectral cross-talk in optogenetic photoswitching.
Stimulated Depletion Quenching (SDQ), is used to overcome spectral cross-talk by exploiting the molecules' unique dynamic response to ultrashort laser pulses
Stimulated Depletion Quenching is used to overcome spectral cross-talk in optogenetic photoswitching.
Stimulated Depletion Quenching (SDQ), is used to overcome spectral cross-talk by exploiting the molecules' unique dynamic response to ultrashort laser pulses
Stimulated Depletion Quenching is used to overcome spectral cross-talk in optogenetic photoswitching.
Stimulated Depletion Quenching (SDQ), is used to overcome spectral cross-talk by exploiting the molecules' unique dynamic response to ultrashort laser pulses
Stimulated Depletion Quenching is used to overcome spectral cross-talk in optogenetic photoswitching.
Stimulated Depletion Quenching (SDQ), is used to overcome spectral cross-talk by exploiting the molecules' unique dynamic response to ultrashort laser pulses
Stimulated Depletion Quenching is used to overcome spectral cross-talk in optogenetic photoswitching.
Stimulated Depletion Quenching (SDQ), is used to overcome spectral cross-talk by exploiting the molecules' unique dynamic response to ultrashort laser pulses
Stimulated Depletion Quenching is used to overcome spectral cross-talk in optogenetic photoswitching.
Stimulated Depletion Quenching (SDQ), is used to overcome spectral cross-talk by exploiting the molecules' unique dynamic response to ultrashort laser pulses
Spectral cross-talk hampers optogenetic switches by limiting independent control and restricting dynamic range.
the technique is hampered by spectral cross-talk: the broad absorption spectra of compatible biochemical chromophores limits the number of switches that can be independently controlled and restricts the dynamic range of each switch
Spectral cross-talk hampers optogenetic switches by limiting independent control and restricting dynamic range.
the technique is hampered by spectral cross-talk: the broad absorption spectra of compatible biochemical chromophores limits the number of switches that can be independently controlled and restricts the dynamic range of each switch
Spectral cross-talk hampers optogenetic switches by limiting independent control and restricting dynamic range.
the technique is hampered by spectral cross-talk: the broad absorption spectra of compatible biochemical chromophores limits the number of switches that can be independently controlled and restricts the dynamic range of each switch
Spectral cross-talk hampers optogenetic switches by limiting independent control and restricting dynamic range.
the technique is hampered by spectral cross-talk: the broad absorption spectra of compatible biochemical chromophores limits the number of switches that can be independently controlled and restricts the dynamic range of each switch
Spectral cross-talk hampers optogenetic switches by limiting independent control and restricting dynamic range.
the technique is hampered by spectral cross-talk: the broad absorption spectra of compatible biochemical chromophores limits the number of switches that can be independently controlled and restricts the dynamic range of each switch
Spectral cross-talk hampers optogenetic switches by limiting independent control and restricting dynamic range.
the technique is hampered by spectral cross-talk: the broad absorption spectra of compatible biochemical chromophores limits the number of switches that can be independently controlled and restricts the dynamic range of each switch
Spectral cross-talk hampers optogenetic switches by limiting independent control and restricting dynamic range.
the technique is hampered by spectral cross-talk: the broad absorption spectra of compatible biochemical chromophores limits the number of switches that can be independently controlled and restricts the dynamic range of each switch
Approval Evidence
1 source4 linked approval claimsfirst-pass slug cph8
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Source:
applicationsupports
Stimulated Depletion Quenching is employed to enhance control of the Cph8 optogenetic switch.
SDQ is employed to enhance the control of Cph8, a photo-reversible phytochrome based optogenetic switch designed to control gene expression in E. Coli bacteria.
Source:
limitationsupports
Linear photoswitching cannot fully convert Cph8 to the biologically inactive PFR state because spectral cross-talk drives reverse photoswitching back to the active PR state.
The Cph8 switch can not be fully converted to it's biologically inactive state ($P_{FR}$) by linear photos-witching, as spectral cross-talk causes a reverse photoswitching reaction to revert to it back to the active state ($P_{R}$).
Source:
mechanismsupports
Stimulated Depletion Quenching selectively halts the reverse photoswitching reaction of Cph8 while allowing the forward reaction to proceed.
SDQ selectively halts this reverse reaction while allowing the forward reaction to proceed.
Source:
problem statementsupports
Spectral cross-talk hampers optogenetic switches by limiting independent control and restricting dynamic range.
the technique is hampered by spectral cross-talk: the broad absorption spectra of compatible biochemical chromophores limits the number of switches that can be independently controlled and restricts the dynamic range of each switch
Source:
Comparisons
Source-backed strengths
Cph8 is explicitly described as photo-reversible, enabling optical switching between states relevant to gene-expression control. The cited study further reports that stimulated depletion quenching selectively halts the reverse photoswitching reaction while allowing the forward reaction to proceed, improving switching control.
Ranked Citations
- 1.