Chapter 5 - Positive feedback, bistability and memory. Flashcards
What is the crucial changes in developmental transcriptional networks?
There is memory making irreversibel changes.
Name Network motifs in developmental transcription networks not normally found in sensory transcriptional networks.
1) Positive autoregulation networks (PAR)
2) Transcriptional cascades
How can PARs create memory?
PARs possess separate steady state because the production rate crosses the degredation rate at multiple occasions.
What is bistability?
Two stable fixed points.
What are basins of attraction?
Intervals of X concentrations that lead to different stable steady state points.
Name two two-node feedback loops:
1) Double positive feedback loop
2) Double negative feedback loop
Steady states for the double positive feedback loop:
1) Both low
2) Both high
Transition into high by production of either.
Steady states for the double negative feedback loop:
1) 1 high 2 low
2) 1 low 2 high
Toggle switch:
Other name for double negative
Lock on:
Other name for double positive.
Null-cline analysis:
like rate plot but with 2 concentrations.
What is Regulating feedback loop?
When the two nodes in the two node feedback loop both regulate a third not - Z.
What is regulated feedback?
When two nodes in a two node feedback loop is both regulated by a third node - Z.
What is the purpose of regulated feedback?
Can “toggle a switch” by inducing the steady state levels and thereby inducing memory.
How does a transcriptional cascade work?
X regulates Y that regulates Z and so on. Too slow for sensory but works in development.
Often cascade of repressors because they are more robvust timing wise in regards to protein fluctuations.
What does PPI stand for?
Protein-protein-interaction networks
What can be the purpose of having Proteins regulate transcriptional networks?
The faster time scale of the proteins are faster at adapting so they will cause the TF much faster than a feedback loop of TF-TF (transcriptional). Think the heater-radioator anlogy.
What is a hybrid FFL?
A loop where one of the components is a protein with a fast interaction.
Name diffferent types of hybrid network motifs:
1) Negative feedback (X activates Y, Y inhibits X)
2) FFLs.
How can Hybrid FFLs cause memory?
Imagine X transcribing Y and Z and protein Y phosphorylating Z. Y and Z can take long for the cell to break down, so even if X is not active the proteins can still interact. This is called transient memory.
What does coherent FFLs and positive feedback loops have in common?
They can both generate delays and memory.
What does incoherent FFLs and negative feedback loops have in common?
They can both generate pulses and and speed responses.
