Solution

ID: past-exam-of-the-biological-physics-course-of-the-university-of-oxford/2019/3/e/solution

A fluorescent reporter associated with one phase of the repressilator should show repeated rises and falls in a tracked cell, with the same underlying oscillatory period but generally delayed and smoothed relative to instantaneous promoter activity. If mature GFP is fused to a repressor and is sufficiently fast to mature, fluorescence approximately tracks that protein's abundance. If GFP is a separately expressed reporter, its own production, maturation, degradation and dilution introduce an additional filter.
For example, converts a periodic gate into a periodic, phase-lagged concentration. Very stable GFP can accumulate a large baseline and obscure oscillations rather than reproducing the regulator trace exactly; maturation delay and bleaching also matter. Biological noise and cell-to-cell phase differences can make individual cycles irregular and wash out oscillations in a population average. The appropriate sketch is therefore a delayed, rounded oscillatory fluorescence trace, with amplitude and baseline depending on reporter turnover, rather than an unqualified copy of a Boolean gate.

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