Source 1primary paper2020PLoS ONE
Toolkit/switched differential equations
switched differential equations
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Switched differential equations were developed as a computational framework to model oscillatory behavior of circadian clock cells in the Madeira cockroach. The model was used to interpret RNAi perturbation phenotypes and to support a hypothesis of coupled morning and evening oscillators linked by mutual inhibition.
Usefulness & Problems
Why this is useful
This method is useful for formalizing circadian clock dynamics when gene knockdown data indicate persistent rhythmicity despite perturbation of individual clock genes. In the cited study, it provided a systems-level interpretation connecting behavioral phenotypes and mRNA knockdown results to a two-oscillator network architecture.
Problem solved
It addresses the problem of explaining how cockroach circadian rhythms remain rhythmic after single knockdown of per, tim1, or cry2, despite altered rhythm strength or period. The framework was applied to infer how coupled oscillator populations could account for these non-lethal perturbation phenotypes.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete computational method used to design, rank, or analyze an engineered system.
Mechanisms
mutual inhibitionmutual inhibitionnegative feedbacknegative feedbackoscillatory dynamical systems modelingoscillatory dynamical systems modelingstate switchingstate switchingTechniques
Computational DesignTarget processes
No target processes tagged yet.
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: builder
The method was implemented as a basic network of switched differential equations for circadian clock cells. Its application in the cited work was tied to dsRNA-mediated single-gene knockdown experiments in the Madeira cockroach, where target mRNA levels were permanently reduced within about two weeks.
The available evidence describes consistency with one cockroach circadian dataset but does not provide quantitative performance metrics, parameter identifiability, or benchmarking against alternative modeling frameworks. Independent replication and broader validation across organisms or clock architectures are not documented in the supplied evidence.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Most cockroaches remained rhythmically active after each clock gene knockdown, with weakened rhythms after per RNAi and shorter periods after tim1 RNAi and cry2 RNAi.
Unexpectedly, circadian locomotor activity of most cockroaches remained rhythmic for each clock gene knockdown employed. It expressed weakened rhythms and unchanged periods for Rm´perRNAi and shorter periods for Rm´tim1RNAi and Rm´cry2RNAi.
Section: abstract
Most cockroaches remained rhythmically active after each clock gene knockdown, with weakened rhythms after per RNAi and shorter periods after tim1 RNAi and cry2 RNAi.
Unexpectedly, circadian locomotor activity of most cockroaches remained rhythmic for each clock gene knockdown employed. It expressed weakened rhythms and unchanged periods for Rm´perRNAi and shorter periods for Rm´tim1RNAi and Rm´cry2RNAi.
Section: abstract
Most cockroaches remained rhythmically active after each clock gene knockdown, with weakened rhythms after per RNAi and shorter periods after tim1 RNAi and cry2 RNAi.
Unexpectedly, circadian locomotor activity of most cockroaches remained rhythmic for each clock gene knockdown employed. It expressed weakened rhythms and unchanged periods for Rm´perRNAi and shorter periods for Rm´tim1RNAi and Rm´cry2RNAi.
Section: abstract
Most cockroaches remained rhythmically active after each clock gene knockdown, with weakened rhythms after per RNAi and shorter periods after tim1 RNAi and cry2 RNAi.
Unexpectedly, circadian locomotor activity of most cockroaches remained rhythmic for each clock gene knockdown employed. It expressed weakened rhythms and unchanged periods for Rm´perRNAi and shorter periods for Rm´tim1RNAi and Rm´cry2RNAi.
Section: abstract
Most cockroaches remained rhythmically active after each clock gene knockdown, with weakened rhythms after per RNAi and shorter periods after tim1 RNAi and cry2 RNAi.
Unexpectedly, circadian locomotor activity of most cockroaches remained rhythmic for each clock gene knockdown employed. It expressed weakened rhythms and unchanged periods for Rm´perRNAi and shorter periods for Rm´tim1RNAi and Rm´cry2RNAi.
Section: abstract
Most cockroaches remained rhythmically active after each clock gene knockdown, with weakened rhythms after per RNAi and shorter periods after tim1 RNAi and cry2 RNAi.
Unexpectedly, circadian locomotor activity of most cockroaches remained rhythmic for each clock gene knockdown employed. It expressed weakened rhythms and unchanged periods for Rm´perRNAi and shorter periods for Rm´tim1RNAi and Rm´cry2RNAi.
Section: abstract
Most cockroaches remained rhythmically active after each clock gene knockdown, with weakened rhythms after per RNAi and shorter periods after tim1 RNAi and cry2 RNAi.
Unexpectedly, circadian locomotor activity of most cockroaches remained rhythmic for each clock gene knockdown employed. It expressed weakened rhythms and unchanged periods for Rm´perRNAi and shorter periods for Rm´tim1RNAi and Rm´cry2RNAi.
Section: abstract
Most cockroaches remained rhythmically active after each clock gene knockdown, with weakened rhythms after per RNAi and shorter periods after tim1 RNAi and cry2 RNAi.
Unexpectedly, circadian locomotor activity of most cockroaches remained rhythmic for each clock gene knockdown employed. It expressed weakened rhythms and unchanged periods for Rm´perRNAi and shorter periods for Rm´tim1RNAi and Rm´cry2RNAi.
Section: abstract
Most cockroaches remained rhythmically active after each clock gene knockdown, with weakened rhythms after per RNAi and shorter periods after tim1 RNAi and cry2 RNAi.
Unexpectedly, circadian locomotor activity of most cockroaches remained rhythmic for each clock gene knockdown employed. It expressed weakened rhythms and unchanged periods for Rm´perRNAi and shorter periods for Rm´tim1RNAi and Rm´cry2RNAi.
Section: abstract
Most cockroaches remained rhythmically active after each clock gene knockdown, with weakened rhythms after per RNAi and shorter periods after tim1 RNAi and cry2 RNAi.
Unexpectedly, circadian locomotor activity of most cockroaches remained rhythmic for each clock gene knockdown employed. It expressed weakened rhythms and unchanged periods for Rm´perRNAi and shorter periods for Rm´tim1RNAi and Rm´cry2RNAi.
Section: abstract
Single dsRNA injections against each clock gene successfully and permanently knocked down the respective mRNA levels within about two weeks.
Single injections of dsRNA of each clock gene into adult cockroaches successfully and permanently knocked down respective mRNA levels within ~two weeks
Section: abstract
time to knockdown ~two weeks
Single dsRNA injections against each clock gene successfully and permanently knocked down the respective mRNA levels within about two weeks.
Single injections of dsRNA of each clock gene into adult cockroaches successfully and permanently knocked down respective mRNA levels within ~two weeks
Section: abstract
time to knockdown ~two weeks
Single dsRNA injections against each clock gene successfully and permanently knocked down the respective mRNA levels within about two weeks.
Single injections of dsRNA of each clock gene into adult cockroaches successfully and permanently knocked down respective mRNA levels within ~two weeks
Section: abstract
time to knockdown ~two weeks
Single dsRNA injections against each clock gene successfully and permanently knocked down the respective mRNA levels within about two weeks.
Single injections of dsRNA of each clock gene into adult cockroaches successfully and permanently knocked down respective mRNA levels within ~two weeks
Section: abstract
time to knockdown ~two weeks
Single dsRNA injections against each clock gene successfully and permanently knocked down the respective mRNA levels within about two weeks.
Single injections of dsRNA of each clock gene into adult cockroaches successfully and permanently knocked down respective mRNA levels within ~two weeks
Section: abstract
time to knockdown ~two weeks
Single dsRNA injections against each clock gene successfully and permanently knocked down the respective mRNA levels within about two weeks.
Single injections of dsRNA of each clock gene into adult cockroaches successfully and permanently knocked down respective mRNA levels within ~two weeks
Section: abstract
time to knockdown ~two weeks
Single dsRNA injections against each clock gene successfully and permanently knocked down the respective mRNA levels within about two weeks.
Single injections of dsRNA of each clock gene into adult cockroaches successfully and permanently knocked down respective mRNA levels within ~two weeks
Section: abstract
time to knockdown ~two weeks
Single dsRNA injections against each clock gene successfully and permanently knocked down the respective mRNA levels within about two weeks.
Single injections of dsRNA of each clock gene into adult cockroaches successfully and permanently knocked down respective mRNA levels within ~two weeks
Section: abstract
time to knockdown ~two weeks
Single dsRNA injections against each clock gene successfully and permanently knocked down the respective mRNA levels within about two weeks.
Single injections of dsRNA of each clock gene into adult cockroaches successfully and permanently knocked down respective mRNA levels within ~two weeks
Section: abstract
time to knockdown ~two weeks
Single dsRNA injections against each clock gene successfully and permanently knocked down the respective mRNA levels within about two weeks.
Single injections of dsRNA of each clock gene into adult cockroaches successfully and permanently knocked down respective mRNA levels within ~two weeks
Section: abstract
time to knockdown ~two weeks
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Section: abstract
Neither per, tim1, nor cry2 alone is an essential component of the molecular circadian clockwork in the Madeira cockroach.
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Section: title_abstract
Neither per, tim1, nor cry2 alone is an essential component of the molecular circadian clockwork in the Madeira cockroach.
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Section: title_abstract
Neither per, tim1, nor cry2 alone is an essential component of the molecular circadian clockwork in the Madeira cockroach.
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Section: title_abstract
Neither per, tim1, nor cry2 alone is an essential component of the molecular circadian clockwork in the Madeira cockroach.
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Section: title_abstract
Neither per, tim1, nor cry2 alone is an essential component of the molecular circadian clockwork in the Madeira cockroach.
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Section: title_abstract
Neither per, tim1, nor cry2 alone is an essential component of the molecular circadian clockwork in the Madeira cockroach.
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Section: title_abstract
Neither per, tim1, nor cry2 alone is an essential component of the molecular circadian clockwork in the Madeira cockroach.
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Section: title_abstract
Neither per, tim1, nor cry2 alone is an essential component of the molecular circadian clockwork in the Madeira cockroach.
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Section: title_abstract
Neither per, tim1, nor cry2 alone is an essential component of the molecular circadian clockwork in the Madeira cockroach.
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Section: title_abstract
Neither per, tim1, nor cry2 alone is an essential component of the molecular circadian clockwork in the Madeira cockroach.
Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Section: title_abstract
Approval Evidence
1 source2 linked approval claimsfirst-pass slug switched-differential-equations
a basic network of switched differential equations was developed to model the oscillatory behavior of clock cells
Source:
model consistencysupports
The data were consistent with two synchronized groups of coupled oscillator cells, a leading morning oscillator and a lagging evening oscillator, coupled via mutual inhibition.
Data were consistent with two synchronized main groups of coupled oscillator cells, a leading (morning) oscillator, or a lagging (evening) oscillator that couple via mutual inhibition.
Source:
model hypothesissupports
Modelling suggests an additional negative feedback exists next to Rm-PER in cockroach morning oscillator cells.
Modelling suggests that there is an additional negative feedback next to Rm´PER in cockroach morning oscillator cells.
Source:
Comparisons
Source-backed strengths
The model was explicitly developed to represent oscillatory clock-cell behavior and was reported to be consistent with experimental data from gene knockdown studies in the Madeira cockroach. It supported a biologically specific interpretation involving a leading morning oscillator, a lagging evening oscillator, and coupling via mutual inhibition.
Compared with free-energy calculations
switched differential equations and free-energy calculations address a similar problem space.
Shared frame: same top-level item type
Compared with mathematical model
switched differential equations and mathematical model address a similar problem space.
Shared frame: same top-level item type
Strengths here: looks easier to implement in practice.
Compared with SwiftLib
switched differential equations and SwiftLib address a similar problem space.
Shared frame: same top-level item type
Ranked Citations
- 1.