Cut the noise or couple up: Coordinating circadian and synthetic clocks

The seasons within: a theoretical perspective on photoperiodic entrainment and encoding

Circadian clocks are internal timing devices that have evolved as an adaption to the omnipresent natural 24 h rhythmicity of daylight intensity. Properties of the circadian system are photoperiod dependent. The phase of entrainment varies systematically with season. Plastic photoperiod-dependent re-arrangements in the mammalian circadian core pacemaker yield an internal representation of season. Output pathways of the circadian clock regulate photoperiodic responses such as flowering time in plants or hibernation in mammals. Here, we review the concepts of seasonal entrainment and photoperiodic encoding. We introduce conceptual phase oscillator models as their high level of abstraction, but, yet, intuitive interpretation of underlying parameters allows for a straightforward analysis of principles that determine entrainment characteristics. Results from this class of models are related and discussed in the context of more complex conceptual amplitude-phase oscillators as well as contextual molecular models that take into account organism, tissue, and cell-type-specific details.

Cell-type specific circadian transcription factor BMAL1 roles in excitotoxic hippocampal lesions to enhance neurogenesis

Circadian clocks, generating daily rhythms in biological processes, maintain homeostasis in physiology, so clock alterations are considered detrimental. Studies in brain pathology support this by reporting abnormal circadian phenotypes in patients, but restoring the abnormalities by light therapy shows no dramatic effects. Recent studies on glial clocks report the complex effects of altered clocks by showing their beneficial effects on brain repairs. However, how neuronal clocks respond to brain pathology is elusive. This study shows that neuronal BMAL1, a core of circadian clocks, reduces its expression levels in neurodegenerative excitotoxicity. In the dentate gyrus of excitotoxic hippocampal lesions, reduced BMAL1 in granule cells precedes apoptosis. This subsequently reduces BMAL1 levels in neighbor neural stem cells and progenitors in the subgranular zone, enhancing proliferation. This shows the various BMAL1 roles depending on cell types, and its alterations can benefit brain repair. Thus, cell-type-specific BMAL1 targeting is necessary to treat brain pathology.

Enhanced precision of circadian rhythm by output system

Circadian rhythms are biological rhythms with a period of approximately 24 h that persist even under constant conditions without daily environmental cues. The molecular circadian clock machinery generates physiological rhythms, which can be transmitted into the downstream output system. Owing to the stochastic nature of the biochemical reactions and the extracellular environment, the oscillation period of circadian rhythms exhibited by individual organisms or cells is not constant on a daily basis with variations as high as 10%, as reflected by the coefficient of variation. Although the fluctuations in the circadian rhythm are measured through a reporter system such as bioluminescence or fluorescence, which is an example of output systems, experimentally confirming whether the fluctuations found in the reporter system are the same as those in the circadian clock is challenging. This study investigated a coupled system of a circadian clock and its output system numerically and analytically, and then compared the fluctuations in the oscillation period of the two systems. We found that the amount of fluctuations in the output system is smaller than that in the circadian clock, assuming the degradation rate of the molecules responsible for the output system is a typical value for protein degradation. The results indicate that the output system can improve the accuracy of the circadian rhythm without the need for any denoising processes.

A synthetic population-level oscillator in non-microfluidic environments

Synthetic oscillators have become a research hotspot because of their complexity and importance. The construction and stable operation of oscillators in large-scale environments are important and challenging. Here, we introduce a synthetic population-level oscillator in Escherichia coli that operates stably during continuous culture in non-microfluidic environments without the addition of inducers or frequent dilution. Specifically, quorum-sensing components and protease regulating elements are employed, which form delayed negative feedback to trigger oscillation and accomplish the reset of signals through transcriptional and post-translational regulation. We test the circuit in devices with 1 mL, 50 mL, 400 mL of medium, and demonstrate that the circuit could maintain stable population-level oscillations. Finally, we explore potential applications of the circuit in regulating cellular morphology and metabolism. Our work contributes to the design and testing of synthetic biological clocks that function in large populations.

A new player in circadian networks: Role of electrical synapses in regulating functions of the circadian clock

Several studies have indicated that coherent circadian rhythms in behaviour can be manifested only when the underlying circadian oscillators function as a well-coupled network. The current literature suggests that circadian pacemaker neuronal networks rely heavily on communication mediated by chemical synapses comprising neuropeptides and neurotransmitters to regulate several behaviours and physiological processes. It has become increasingly clear that chemical synapses closely interact with electrical synapses and function together in the neuronal networks of most organisms. However, there are only a few studies which have examined the role of electrical synapses in circadian networks and here, we review our current understanding of gap junction proteins in circadian networks of various model systems. We describe the general mechanisms by which electrical synapses function in neural networks, their interactions with chemical neuromodulators and their contributions to the regulation of circadian rhythms. We also discuss the various methods available to characterize functional electrical synapses in these networks and the potential directions that remain to be explored to understand the roles of this relatively understudied mechanism of communication in modulating circadian behaviour.

Spatially specific mechanisms and functions of the plant circadian clock

Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.

Coupled and Synchronization Models of Rhythmic Arm Movement in Planar Plane

Nonlinear dynamics have become a new perspective on model human movement variability; however, it is still a debate whether chaotic behavior is indeed possible to present during a rhythmic movement. This paper reports on the nonlinear dynamical behavior of coupled and synchronization models of a planar rhythmic arm movement. Two coupling schemes between a planar arm and an extended Duffing-Van der Pol (DVP) oscillator are investigated. Chaos tools, namely phase space, Poincare section, Lyapunov Exponent (LE), and heuristic approach are applied to observe the dynamical behavior of orbit solutions. For the synchronization, an orientation angle is modeled as a single well DVP oscillator implementing a Proportional Derivative (PD)-scheme. The extended DVP oscillator is used as a drive system, while the orientation angle of the planar arm is a response system. The results show that the coupled system exhibits very rich dynamical behavior where a variety of solutions from periodic, quasi-periodic, to chaotic orbits exist. An advanced coupling scheme is necessary to yield the route to chaos. By modeling the orientation angle as the single well DVP oscillator, which can synchronize with other dynamical systems, the synchronization can be achieved through the PD-scheme approach.