Vl 9 - Phenotypic Heterogeneity in Microbes Flashcards
(random) stochastic gene expression in a single cell
transcriptional noise can be measured as fluctuations in reporter protein expression (noise=fluctuation)
What are the difficulties in understanding the gene circuits? What is the biggest challenge?
Gene circuits are dynamic. The concentration changes constantly.
Gene circuits are ‘Noisy’: they are subject to stochastic fluctuations.
-The behaviour could be hereditary, non-deterministic*. Determinism is the view that all - especially future - events are clearly determined by preconditions.
Gene circuits are complex: some of the interactions may be known, but they are not always the most relevant.
Biggest challenge: Try to figure out the core circuit.
Stochastic = non-deterministic.
What are the approaches that are being taken in research to understand such gene circuits?
Use of synthetic biology to build simple gene circuits that program cellular behavior.
Investigation and biochemistry
Analysis of many ‘same cells’ ⇒ observe and compare gene circuits of the individual cells.
How can one find out whether the behaviour of a genetic system is stochastic (noisy) or deterministic (quiet)?
Add 2 copies of the same gene (with a point mutation so that they fluoresce, for example, in different colors red and yellow) to sister cells and investigate gene expression. If cells green the same gene expression of both genes ⇒ deterministic gene expression. If cells yellow or red stochastic gene expression.
What is important is not the resulting final color of the cells, but whether both cells have the same (deterministic) or different (noisy) color.
Gene expression is non-deterministic = noisy.
How can transcriptional noise be measured? What do intrinsic and extrinsic noise depend on?
Measured as fluctuations in reporter protein expression.
Intrinsic and extrinsic noise depend on the strength of gene expression. Noise is lowest in strong expression. Noise is strongest in an intermediate state.
What does ‘Excitability’ mean? + Example for excitables system.
- system in constant, stable steady state
- one parameters is changed strongly enough (over a threshold)
- produces a stronger response in proportion to push
- response strength is the same, no matter how strong the push was (as long as threshold is reached)
- system returns to its initial steady state
- strong, constant push will not result in stronger response, but multiple responses
Excitable System: Neurons.
How can noise be dammed up in a biological system?
- increases the volume of the cells, but leaves the concentrations of the molecules equal (only the number of molecules increases). (By point mutation cells replicate, but do not divide).
Large cells are less variable.
ZSM 1:
Cellular events involving interactions with a small number of molecules are stochastic, at least beyond physical boundaries of regulation (intrinsic noise) or external factors (extrinsic noise).
Noise-driven excitation systems naturally have the two main characteristics: probabilistic and (transient).
Stochastics is biologically functional (e.g. subtilis competence).
The phenotypic heterogeneity of infectious agents can impair the effectiveness of antimicrobial treatments (salmonella).
What can be the origins of phenotypic heterogeneity?
epigenetic regulation, transcription, translation, post-translational modifications, asymmetric cell division, etc.
Do stochastic events play a role in microbial infections?
Yes
- e.g.: Salmonella: phenotypic variation/heterogeneity of this cell in host tissue delays extinction by antimicrobial chemotherapy
What are the two main characteristics of noise driven excitation systems?
They are probabilistic and transient
What can be investigated by measuring noise?
- regulatory relationships active in genetic circuits
- can help answering: “Which genes effectively regulate each other?” in any particular cellular context
What is intrinsic noise?
Intrinsic: variation in hypothetically identic cells. (same C, stage etc). -> random microscopic events.
Intrinsic noise: Binding of TF to promoter and many other mechanisms of molecular machinery are stochastic events -> 2 genes with the same sequence never have the same sequence
Intrinsic noise: expression of two genes with the same promoter in one cell.
What is extrinsic noise?
Extrinsic: Abundance activity of TFs in isogenic strains.
Extrinsic noise -cells in different types of microscopic events. cell stages -diff. many molecules of transcription / translation -activity of these differently sized -cells of different size, etc.
Extrinsic noise: Expression of a gene varies between cells of a population.
