Simulations of temperature sensitivity of the peroxidase-oxidase oscillator

Development of FRET biosensors for mammalian and plant systems

Genetically encoded biosensors are increasingly used in visualising signalling processes in different organisms. Sensors based on green fluorescent protein technology are providing a great opportunity for using Förster resonance energy transfer (FRET) as a tool that allows for monitoring dynamic processes in living cells. The development of these FRET biosensors requires careful selection of fluorophores, substrates and recognition domains. In this review, we will discuss recent developments, strategies to create and optimise FRET biosensors and applications of FRET-based biosensors for use in the two major eukaryotic kingdoms and elaborate on different methods for FRET detection.

Simulating dark expressions and interactions of frq and wc-1 in the Neurospora circadian clock

Circadian rhythms are considered to play an essential part in the adaptation of organisms to their environments. The occurrence of circadian oscillations appears to be based on the presence of transcriptional-translational negative feedback loops. In Neurospora crassa, the protein FREQUENCY (FRQ) is part of such a negative feedback loop apparently by a direct interaction with its transcription factor WHITE COLLAR-1 (WC-1). Based on the observation that nuclear FRQ levels are significantly lower than nuclear WC-1 levels, it was suggested that FRQ would act more like a catalyst in inhibiting WC-1 rather than binding to WC-1 and making an inactive FRQ:WC-1 complex. Intrigued by this hypothesis, we constructed a model for the Neurospora circadian clock, which includes expression of the frq and the wc-1 genes and their possible interactions. The model suggests that even small amounts of nuclear FRQ-protein are capable of inhibiting frq transcription in a rhythmic manner by binding to WC-1 and promoting its degradation. Our model predicts the importance of a FRQ dependent degradation of WC-1 in closing the negative feedback loop. The model shows good agreement with experimental levels in nuclear and cytosolic FRQ and WC-1, their phase relationships, and several clock mutant phenotypes.

Semi-algebraic optimization of temperature compensation in a general switch-type negative feedback model of circadian clocks

Temperature compensation is an essential property of circadian oscillators which enables them to act as physiological clocks. We have analyzed the temperature compensating behavior of a generalized transcriptional-translational negative feedback oscillator with a hard hysteretic switch and rate constants with an Arrhenius-type temperature dependence. These oscillations can be considered as the result of a lowpass filtering operator acting on a train of rectangular pulses. Such a signal-processing viewpoint makes it possible to express, in a semi-algebraic manner, the period length, the oscillator's control (sensitivity) coefficients, and the first and second-order derivatives of the period-temperature relationship. We have used the semi-algebraic approach to investigate a 3-dimensional Goodwin-type representation of the oscillator, where local optimization for temperature compensation has been considered. In the local optimization, activation energies are found, which lead to a zero first order derivative and to a closest-to-zero second order derivative at a given reference temperature. We find that the major contribution to temperature compensation over an extended temperature range is given by the (local) zero first order derivative, while only minor contributions to temperature compensation are given by an optimized second order derivative. In biological terms this could be interpreted to relate to a circadian clock mechanism which during evolution is being optimized for a certain but relative narrow (habitat) temperature range.

Temperature compensation in the oscillatory bray reaction

The influence of temperature on the oscillatory frequency of the hydrogen peroxide-iodate ion reaction is found to be two-sided: (i) the period length decreases with increasing temperature in most of the instances studied, (ii) or in some cases an opposite change is observed. A temperature-independent period length (temperature compensation) is also discovered experimentally in a rather wide temperature interval at a narrow concentration range of reactants both in a batch configuration and under flow conditions. A simple model was considered to simulate this behavior. Opposing effects of the composite reactions of the model on the calculated period length with changing temperature are shown to be responsible for temperature compensation or overcompensation.

Temperature compensation in circadian clock models

Circadian clock of organisms has a free-running period that does not change much with ambient temperature. This property "temperature compensation" is studied when the rate of all reaction steps increase with temperature in the biochemical network generating the rhythm. The period becomes shorter when all the rate parameters are enhanced by the same factor. However, the period becomes longer as degradation rate of proteins and/or transcription rate of the clock gene increase (their elasticity is positive). This holds for a wide range of models, including N-variable model, and PER-TIM double oscillator model, provided that (1) branch reactions (e.g. degradation of proteins or mRNAs) are strongly saturated, and that (2) the cooperativity of transcription inhibition by nuclear proteins is not very large. A strong temperature sensitivity of degradation of PER proteins and/or temperature-sensitive alternative splicing of per gene, known for Drosophila, can be mechanisms for the temperature compensation of circadian clock.

Temperature dependency and temperature compensation in a model of yeast glycolytic oscillations

Temperature sensitivities and conditions for temperature compensation have been investigated in a model for yeast glycolytic oscillations. The model can quantitatively simulate the experimental observation that the period length of glycolytic oscillations decreases with increasing temperature. Temperature compensation is studied by using control coefficients describing the effect of rate constants on oscillatory frequencies. Temperature compensation of the oscillatory period is observed when the positive contributions to the sum of products between control coefficients and activation energies balance the corresponding sum of the negative contributions. The calculations suggest that by changing the activation energies for one or several of the processes, i.e. by mutations, it could be possible to obtain temperature compensation in the yeast glycolytic oscillator.