Is the Coupling of Circadian Rhythms and Metabolism/Redox Regulating Morphogenesis

Self Organisation Far from Equilibrium

New states can arise from far from equilibrium, possessing an extraordinary degree of order, whereby trillions of molecules coordinate their actions in space and time. Under certain circumstances, entropy producing processes are able to organise themselves in the presence of noise, in a way that so called dissipative structures are formed (Prigogine and Lefever 1975, and Nicolis and Prigogine 1977).  Also see J England 2015 on ‘dissipative adaptation in driven self-assembly’.

Dissipative processes are present in biology.  It is asked whether these could be contributing to morphogenesis.

Stochastic reaction-diffusion simulations have been successfully used in a number of biological applications. Formation of skin patterns and the biochemical processes in living cells (like gene regulatory networks), the cell cycle, circadian rhythms, signal transduction in E Coli chemotaxis, MAPK pathway, oscillations of Min proteins in cell division, and intracellular calcium dynamics are examples of processes mathematically modelled by reaction and reaction-diffusion systems. T Vejchodsky 2013, J Eliaš – ‎2014A Zakharov 2014T Hinze 2011.

Bio-Rhythms Influencing the Whole Organism

Circadian Rhythms operate far-from- equilibrium and generate order spontaneously by exchanging energy with their external environment, and can be described as dissipative systems A Goldbeter 2007.

Evidence suggests that circadian clocks control a number of biological processes through an organism. Exhaustive research over the past few decades has begun to elucidate the full range of human physiology that is regulated in synchrony with the solar day. With regard to neuronal function, this includes not only the control of sleep and wakefulness, but also modulation of mood, cognition, sensory acuity, breathing rate and body temperature. Nearly all aspects of digestion and detoxication – from gastric emptying time to fat processing and xenobiotic degradation by the liver – are under circadian control. Many aspects of the circulatory and immune systems, including heartbeat and blood pressure, vascular leakage and even plasma composition, are also regulated daily. Underlying this panorama of circadian physiology are circadian clocks that regulate cellular and molecular processes at all levels: in each tissue examined, the expression of one in ten genes is regulated in a circadian fashion, either through circadian initiation of transcription or through circadian control of post-transcriptional processes, such as elongation and message stability Mitochondrial activity is also regulated by the circadian clock, along with a variety of intracellular signalling cascades . Supporting this widespread control, the circadian clock mechanism itself is cell-autonomous; most cells of the human body possess the same molecular clockwork. These clocks are then synchronized to one another via redundant systemic cues to ensure optimum correspondence with the environment. For the most part, these cues originate from the suprachiasmatic nuclei (SCN) of the hypothalamus: the ‘master clock’ tissue in mammals. S A Brown 2014. Recent advances demonstrate that interactions occur between the circadian clocks of cells of individual tissues, different tissues, and different organs. AN Dodd – ‎2015.

In plants the molecular oscillator sets a prevalent transcriptional landscape that potentiates homeostasis from the cellular to the whole-plant level. In this a coordination of rhythmic metabolism overlays plant nutrition and stress resistance to biotic and abiotic cues. Frontiers,  A N. Dodd 2014, AN Dodd – ‎2015 and Maria L. Guerriero et al 2014.

Biological Clocks, Redox and Morphogenesis

Biological clocks (of various types) have been found across many species, and may ultimately be found to be fundamental to all life. Increasingly it is also being found that they have a strong association with cellular redox oscillations.

Circadian rhythms are present in all living organisms. They organise processes such as gene transcription, mitosis, feeding, and rest at different times of day and night. These rhythms are orchestrated by a network of core ‘clock genes’ that are organised into transcription–translation feedback loops (TTFLs), producing oscillations with a period of approximately 24 h. The modern understanding of circadian timekeeping has revolved around the TTFL paradigm. Recently, however, this has been challenged by new findings that redox reactions persist in the absence of gene transcription, and that cycles of oxidation and reduction are conserved across all domain of life. These results suggest that non-transcriptional processes such as metabolic state may interact and work in parallel with the canonical genetic mechanisms of keeping circadian time….Mechanistic links between the redox state and the TTFL framework of circadian rhythms have begun to appear in a variety of organisms – from bacteria to flies to mammals. Although a single model has yet to emerge, studies strongly suggest that redox state may be an oscillation that feeds back upon the TTFL, whereby a cell’s redox state may alter clock gene expression and the clock genes, in turn, regulate redox state.

Perturbation of the transcription–translation feedback loop clockwork or the redox system results in a perturbation of the other, indicating that they have a reciprocal relationship. Lisa Wulund 2015,  A Stangherlin – ‎2013. K Nishio 2015N B Milev 2015.  M Purker 2016.  

Redox balance is key for molecules utilised in the context of anti-oxidation protection. A critical event of oxidative stress resets the circadian clock in other mammalian cell lines, resulting in a concurrent activation of a network of circadian genes that then continued onward to modulate an antioxidant, cell survival response. These results strongly suggest that the circadian clockwork is involved in complex cellular programmes that regulate endogenous ROS and also defend the organism against exogenous oxidative challenge. Current evidence seems to support the conclusion that the responses to ROS are mediated both through the regular function of the molecular clockwork and the involvement of the TTFL genes in extra-circadian pathways. Lisa Wulund 2015

Increasingly evident is that metabolic homeostasis at the systems level relies on accurate and collaborative circadian timing within individual cells and tissues of the body. K Eckel-Mahan 2013. J S O’Neill 2014. JD Johnston – ‎2016. In animals, the current understanding of cellular circadian rhythms throughout an organism is that while the core clock genes are oscillating in most tissues and in the midst of enormous environmental pressures, metabolic circadian oscillations are strongly shaped by the environment…feeding is a critical modulator of the internal clock and, in addition to affecting synchronicity between the central pacemaker and metabolically active peripheral tissues, it likely controls the extent to which peripheral tissues are in phase with one another.  A Ribas-Latre 2016

There is a circadian regulation of the redox state of cell which in turn regulates the cell cycle (and possible apoptotic cell death). Data suggests that the relationship between cell cycle and cell death are both likely to undergo circadian rhythms. The redox state of the cell and hormones such as glucocorticoid shows rhythms that seem to regulate the circadian fluctuation of the overall cell cycle. However both factors are regulated by the hormone melatonin which is ultimately a transmitter of the light rhythms in the organism. T Vanden Driessche et al 2000.

There is a growing realisation in biology that transcription based clocks do not operate in isolation, but rather are mutually dependent upon intrinsically rhythmic cytosolic signals (cAMP, Ca2+, kinases) such as that the cell as a whole has a resonant structure tuned to 24 hour operations (Hastings et al 2008 in C Colwell 2015). Circadian rhythms are linked to a wider system of biological rhythms.  And evidence has emerged of  redox coupling to transcription based clocks, with the link between circadian rhythms and the metabolism likely to be key to growth.

Clocks, Cell Division and Morphogenesis

Frequently stochastic effects simply add noise to an essentially deterministic output, but in others, such as asymmetric cell division, their role is essential. Radek Erban 2014.   Lev S. Tsimring 2014.  Circadian regulation has been proposed to modify developmental programs in eukaryotes, such as the changes from vegetative to reproductive organs in plants and the initiation of differentiation from embryonic stem cells in mammals. Circadian rhythms are found in single cells or neurons and show sub-cellular molecular feedback loops.

S A Brown (2014) has provided an overview of the molecular mechanisms involved in circadian clocks and then discuss how such mechanisms can influence stem cell biology and hence tissue development, homeostasis and regeneration.

Cellular metabolism is under circadian control. As mitochondrial metabolism is the major source of cellular ROS in most cell types, rhythmic oxidative phosphorylation potentially contributes to cellular redox oscillations (excepting erythrocytes).  Oxygen consumption of rat liver cells exhibit circadian oscillations, suggesting some underlying circadian regulation of metabolic activity. Circadian oscillations in mitochondrial respiration have been found in mouse liver,  skin , and a myotube model . These oscillations coincide with diurnal BMAL1-dependent oscillations in mitochondrial biogenesis, protein expression and morphology…..In summary a strong and growing body of evidence suggests that circadian rhythms in redox balance occur cell-autonomously as well as in vivo, and moreover that circadian disruption can be associated with deregulation of redox homeostasis.  Marrit Putker 2016. Synchronized cells exhibit an autonomous ultradian mitochondrial respiratory activity which is abrogated by silencing the master clock geneARNTL/BMAL1. Findings provide a novel level of complexity in the interlocked feedback loop controlling the interplay between cellular bioenergetics and the molecular clockwork.   R Scrime 2016.

There have been observations that the circadian clock regulates cell division in cultured mammalian cells and in adult animal tissues. Circadian cell division has been documented in adult hippocampal neurogenesis  in intestinal and skin epithelial cell division , and in multiple immune cell populations  – essentially anywhere that cell division occurs in adult animals. S A Brown 2014,  Phillip Karpowicz 2013.

Clock development is a gradual process that enables anticipation to the in utero environment and might prepare the fetus for life after delivery. First, expression of clock genes increases, then clock genes start oscillating, and finally period, amplitude, and phase are optimized for the outside world.

In stem cells in the adult body, circadian rhythms appear to be closely linked to proliferation. The potential role of circadian rhythms in stem cell maturation was recently discovered. C Du Pre Bastiaan 2014.

Circadian clocks have been suggested to underlie heterogeneity in stem cell populations, to optimize cycles of cell division during wound healing, and to alter immune progenitor differentiation and migrationS A Brown 2014.

In the mammal cell, there are two intertwined cycles: the cell division cycle (CDC) – a clock, and the daily (circadian) biological clock. The circadian clock keeps track of solar time and programs biological processes to occur at environmentally appropriate times.

The circadian clock is a cell‐autonomous and self‐sustained oscillator with a period of about 24 h and thought to function as a cellular metronome that temporally controls key aspects of cell physiology, including metabolism, redox balance, chromatin landscapes and transcriptional states, and cell signalling. In growth conditions, successive divisions and progression through the cell cycle can also be considered as a periodic process…Studies in cyanobacteria, fungi, zebrafish, and mammalian cells reported that cell cycle states fluctuate with circadian time…Less is known about the reverse interaction, or how the cell cycle influences the circadian cycle. However, a signature thereof is the dependency of circadian period on the time of mitosis…and NIH3T3 cells grown under standard conditions, the cell cycle has a dominant influence on the circadian cycle. Jonathan Bieler 2014.  Researchers have also key molecular components linking circadian rhythms and cell division cycles in Neurospora crassa. Also see J Eliaš – ‎2014,and  Goldbeter 2007.

It has also been found that the human Timeless protein interacts with both the circadian clock protein cryptochrome 2 and with the cell cycle checkpoint proteins ChK1 and the ATR-ATRIP complex and plays an important role in the DNA damage checkpoint response.  Evidence has been presented that the mammalian Timeless (Tim) protein which is required for circadian rhythms is also a core component of the cycle cycle checkpoint system, suggesting a possibly more intimate and direct connection between the circadian cycle and cell cycle checkpoints in mammals.  K Ünsal-Kaçmaz 2005

Temperature, genetic, and pharmacological perturbations showed that the two interacting cellular oscillators adopt a synchronized state that is highly robust over a wide range of parameters.  J Bieler 2014 

Oscillations can experience a significant phase shift under typical growth conditions, so that a population of cells with simultaneous oscillations will quickly lose synchronisation after a few cell divisions. An organism must somehow cope with asynchrony if the regular phase is to be restored to cells, which becomes particularly important in the case of tissue-wide circadian rhythms where loss of synchronisation can lead to disease. Circadian rhythms are thought to play a role in regulating the timing and efficiency of the cell cycle, and in many tissues there is a strong correlation relating the expression of clock genes and events of cell division. It therefore seems likely that cross-talk with the cell cycle is one way in which mammals prevent geometric phase shifts from destabilising the circadian clock. In addition to the circadian clock, countless other processes taking place inside growing cells display all sorts of oscillatory behaviour. These occur with periods ranging from hours to milliseconds, and so a large variety are susceptible to the geometric phase shift. D S. Tourigny 2014.

Cell Differentiation May also be Under Circadian Control

Cell differentiation, e.g. that of stem cell populations, might be also under circadian influence. Studies have shown that clock genes can indeed directly influence stem and progenitor cell fate.  S Brown 2014,  Y Inada 2014, X Yu 201. Circadian clock genes have recently been found to modulate human bone marrow mesenchymal stem cell differentiation, migration, and cell cycle.  H Boucher 2016.

There is regulation of alternative splicing by the circadian clock (NJ Mcglincy 2012 and E Petrillo 2011) and this likely to be important to tissue identity and function.

Here it is proposed that circadian cycles interact with cell cycles (as part of an overall biological clock system) to produce biomass clusters and cell layers, therefore shaping tissues and organs, and dictating multicellular morphogenesis.

As A Winfree (1980) has stated “consider a sheet of cells, all of which are regularly carrying out some rhythmic function such as cell division.  Given a sufficiently clear snapshot of such a sheet of cells, one could write labels all over it, indicating at each point in the plane, which stage of the cycle the cells have reached..Glass (1977) called such maps “phase maps” and uses them to interpret the symmetries of regeneration and reduplication….  These can also be used to discuss circadian rhythms“.

Examples of how Circadian Rhythm Are Influencing the Self Organisation of Biomass 


A functioning circadian clock enhances survival and biomass accumulation. Intriguingly, altered clock function contributes to the increased growth. Intuitively, given the plethora of processes regulated by the clock, one might expect that the mechanisms by which the circadian clock confers a growth advantage may be both many and complex.   C. Robertson McClung 2010. C. Robertson McClung 2006Maria L. Guerriero et al 2014.

It has been found that oscillating gene expression determines competence for periodic Arabidopsis root branching.  Genetic studies show that some oscillating transcriptional regulators are required for periodicity in one or both developmental processes. This molecular mechanism has characteristics that resemble molecular clock-driven activities in animal species. Moreno-Risueno 2010.  Nora Bujdoso 2013.  

The shoot apical meritstem of the Arabidopsis thaliana exhibits self organisation, and a mechanism for pattern formation during organogenesis that seems to included mechanical and biochemical inputs… Mathematical models have recent been proposed to explain the observed patterns by combining these different inputs and also introducing feedback loops. The Arabidopsis clock combines timing information from the central rhythm generator and light-signalling pathways to control output rhythms such as cytosolic calcium oscillations. Maria L. Guerriero et al 2014. Also See MG Heisler – ‎2010, O Hamant – ‎2008 . 

Recently been suggested that circadian rhythms synchronise intracellular calcium dynamics and ATP production for facilitating Arabidopsis pollen tube growth. X Yue – ‎2015.  Starch regulation maintains the plant’s optimum growth rate in a 24-hour rhythm.  TiMet 2014.

Cryptochromes receptors cause plants to respond to blue light via photomorphogenesis. Cryptochromes help control seed and seedling development, as well as the switch from the vegetative to the flowering stage of development.  U V Pedmale 2016.


The phenomenon of synchronous oscillations in assembly of  microtubules can serve as a model for the self-organization of biomolecules in time and in space, i.e., microtubules can generate “clocks” and “patterns”.  Eva-Maria Mandelkow 1992

Evidence is presented that microtubule solutions in vitro self-organise through reaction diffusion and that similar processes may occur in vivo during embryogenesis.  J Tabony 1999.   N Glade – ‎2004

Intermediate behaviors also exist, showing concentration waves of microtubules forming and propagating periodically throughout the solution (Mandelkow et al 1989). This self-organized spatial behavior looks similar to those observed in some excitable media such as the Belousov-Zhabotinskii reaction Glade 2012

Brush Border Architecture

Recent research has shown that the microbiota affects the biology of associated host epithelial tissues, including their circadian rhythms, although few data are available on how such influences shape the microarchitecture of the brush border. The squid-vibrio system exhibits two modifications of the brush border that supports the symbionts: effacement and repolarization. Together these occur on a daily rhythm in adult animals, at the dawn expulsion of symbionts into the environment; and, symbiont colonization of the juvenile host induces an increase in microvillar density… Data demonstrates that a partnering of environmental and symbiont cues shape the brush border and that MAMPs play a role in the regulation of brush-border microarchitecture.  E A C Heath-Heckman 2016.

Dendritic Spines

Synaptic plasticity can be defined as changes in the strength of existing synapses, changes in synapse number of size, or changes in morphological structures that contain or form synapses e.g dendritic spines and synaptic boutons.

There is evidence or circadian rhythms in synaptic plasticity, in some cases driven by the central clock and in others by peripheral clocks. Circadian rhythms in brain temperature, hormone/neuromodulator concentrations and GABAergic signalling may adjust the gain of different forms of plasticity as a function of circadian time.  These central influences likely work in concert with peripheral clocks that modulate the response to the central influence and also control cellular processes that impact on plasticity. M G Frank 2016.

Synapses and interNeurons

In Drosophila, numerous circadian rhythms have also been detected in non-clock neurons, especially in the first optic neuropil (lamina) of the fly’s visual system. Such rhythms have been observed in the number of synapses and in the structure of interneurons, which exhibit changes in size and shape in a circadian manner….Although circadian neuroplasticity in D. melanogaster L2 cells has been intensively studied, the molecular mechanism of those changes is still unknown. It has been observed that swelling and shrinking of L1 and L2 monopolar cells are not a result of osmotic shifts. It is also known that the circadian plasticity of neurons requires a functional cytoskeleton and involves microtubules remodeling and actin microfilament organization.  Ewelina Kijak 2017.  Signalling pathways such as TOR which influence this process, also evidence circadian rhythms.


Cultured mouse fibroblasts show a complex clock gating pattern that suggests multiple control points. Other subsequent studies have highlighted potential control via the CHK1/2 (CHEK1/2 – Mouse Genome Informatics) proteins binding to the clock-associated TIM protein or via transcriptional control of the p16-Ink4A (Cdkn2a – Mouse Genome Informatics) locus by the clock protein NONO, which acts as a partner for PER proteins. Such regulations imply circadian G2/M checkpoint control and, consistent with the importance of these regulations, elimination of NONO has been shown to be sufficient to eliminate circadian cell cycle gating in fibroblasts.  S Brown 2014


Skin has emerged as a model for studying circadian clock regulation of cell proliferation, stem cell functions, tissue regeneration, aging, and carcinogenesis. Morphologically, skin is complex, containing multiple cell types and structures, and there is evidence for a functional circadian clock in most, if not all, of its cell types. Despite the complexity, skin stem cell populations are well defined, experimentally tractable, and exhibit prominent daily cell proliferation cycles.


Embryonic deletion of a core circadian clock gene Bmal1, leads to problems associated with accelerated aging in adult mice, including neurodegeneration, poor hair growth, eye and bone pathologies, and a decreased lifespan. Yet mice in which the gene is knocked out after birth don’t exhibit many of these aging-related phenotypes.  The results suggest that the circadian clock gene plays different roles during embryogenesis and after birth.  G. Yang et al 2016.

In addition to circadian fluctuation, CLOCK–regulated genes are also modulated in phase with the mouse hair growth cycle. Kevin Lin.  2009.   MV Plikus 2015.   The circadian clock genes play a role in regulation of the hair growth cycle during synchronized hair follicle cycling, uncovering an unexpected connection between these two timing systems within skin.  Mikhail Geyfman  Y Watabe 2013.

Hair tissues proceed through alternate stages of hair production (anagen) and inactivity (telogen), in which spatially distinct niches harbor populations of dormant stem cells, dividing stem cells or mixtures of the two at different times. Different roles for the circadian clock have been proposed in each of these phases and their transitions. During anagen, proliferating stem cells of the hair follicle show marked circadian oscillations in cell division similar to those outlined above for other tissues. S Brown 2014.

In the transition to anagen, a circadian pattern of cell division was seen in dividing cells, but this time gating progression to anagen (Lin et al., 2009). S Brown 2014.


A circadian clock is also present in tooth ameloblasts, where it controls antiphase rhythms of enamel matrix endocytosis and secretion, as well as ameloblast maturation (Lacruz et al., 2012Zheng et al., 2013)  S Brown 2014)


Pervasive, large-amplitude, and phase-locked oscillations of gene expression in developing C. elegans larvae, is caused by periodic transcription…..Ribosome profiling reveals that periodic mRNA accumulation causes rhythmic translation, potentially facilitating transient protein accumulation as well as coordinated production of stable, complex structures such as the cuticle. Finally, large-amplitude oscillations in RNA sampled from whole worms indicate robust synchronization of gene expression programs across cells and tissues, suggesting that these oscillations are a powerful model to study coordinated gene expression in an animal.  GJ Hendriks – ‎2014 .

In somitogenesis.In vertebrates, somites give rise to skeletal muscle, cartilage, tendons, endothelial cells, and dermis.

It is thought likely that oscillator networks constitute the core of the segmentation clock- which involves cyclic gene expression. R Kageyama – ‎2012.  L Zhang 2008.  Expression of  the “clock genes” must oscillate with a periodicity equal to the time necessary for one somite to form.  (Something similar maybe taking place in chrondogenesis, and involve ATP oscillations depending on glycolysis and mitochondrial respiration and driven by Ca2+ HJ Kwon – ‎2012).

The Heart

There is evidence that the circadian clock gene, dCry, plays an essential role in heart morphogenesiand function – in Drosophila. A Alex – ‎2015.

In mice, heart specific ablation of the circadian clock gene Bmal 1 results in cardiac mitochondrial defects that include morphological changes and functional abnormalities.  A Kohsaka 2014.

The Liver

An initial report of cell division in the regenerating mouse liver documented circadian transcription of the Wee1 checkpoint gene, suggesting control at the G2/M checkpoint. Consistent with this idea, CDC2, the target of the WEE1 kinase, shows circadian phosphorylation in the liver (Matsuo et al., 2003).

Circadian variations of glucocorticoids have been found to be responsible for both circadian rhythms in proliferation and the differentiation in rat liver cells under physiological conditions…inducing in the evening the synthesis of proteins in GO cells and inhibiting DNA synthesis in cycling cells.  Corticoids were already known to be involved in the regulation of mitotic activity and its circadian rhythms….It has also been found that its concentration in serum regulates a circadian variation of cell proliferation in epidermal tissue as well as liver cells, and diurnal variation of bone marrow cell proliferation… It has also been suggested that just as there is a circadian regulation of the redox state of the cell which regulates the cell cycle, there is a relationship between circadian rhythms and apoptotic cell death. C Rodiguez et al  (Edited by T Vanden Driessche 2000).

Mammary Gland

Data suggests that circadian clock genes may play a role in mouse mammary gland development. Xiaoyu Qu 

Cancer and Biological Clocks

It has been suggested that abnormal metabolism in cancer could also be a consequence of a disrupted circadian clock. S Sahar 2009.

Clock-deficient mouse strains (notably Per2-deficient mice) have been documented to have increased spontaneous cancer rates in some, but not all studies (Antoch et al., 2013Fu et al., 2002). This reflects possible increases in DNA damage and supports a role for clock genes as tumor suppressors (Cao et al., 2009Yang et al., 2009). However, these observations are a simplification: other clock-deficient mice do not show increased cancer rates (Antoch et al., 2008Gauger and Sancar, 2005.  S Brown 2014. There has been a considerable amount of indirect evidence that mitosis (division) in cancer cells is not under 24-hour control. For example, experiments have found that cells turn cancerous when certain circadian clock genes have been knocked out.  The results of other experiments that have periodically sampled cancer cell division rates also support this possibility.   In addition the intermeshing of cell cycles is thought to be responsible for the observation that disruption of the circadian system can influence cancer. C H Johnson CH 2010. Also see F Levi et al 2007. Also see XM Tan – ‎2015  and S A Brown 2014.   Some studies suggest that disruption the circadian clock could disrupt the spread of cancer. R V Puram 2016. 

In rodent studies exploring how cancer in one organ spreads to others, it was found that lung adenocarcinoma sends signals to the liver through an inflammatory response, which rewires the circadian mechanisms that manage metabolic pathways. As a result of this inflammation, the insulin signalling pathway is inhibited in the liver, leading to decreased glucose tolerance and reorganization of lipid metabolism.  Lung tumors take control of circadian metabolic function in the liver, potentially to support the heightened metabolic demands of cancer cells.  It is believed that this distal rewiring of metabolic tissues does not occur only in the liver, suggesting a systemic shake-up of metabolism.” Sassone-Corsi  2016.

Cell growth and death in A. flosaquae (a cyanobacterium) appear to be under the control of circadian clocks, and thus it seems that their death is programmed cell death. Dae-Young Lee. Reactive Oxygen Species regulates proliferative and apoptotic pathways, and aberrant regulation of proliferation and apoptosis is essential in tumerigenesis.

Another way to explore circadian rhythms and cell division, is to look at circadian rhythms and ageing including genomic instability, telomeres, epigenetic alterations group processes, loss of proteostasis, deregulated nutrient-sensing affects, mitochondrial dysfunction, cellular senescence, impairment of stem cells, and inflammation and consequently perturbed communication between the individual cells. These issues are explored by S S Fonesca 2015. For example  in humans, telomerase activity declines with age limiting the replicative life and affecting function of cells. For example, if telomere shortening occurs in hematopoietic stem cells, their function and engraftment ability are significantly compromised. The enzyme TERT and its activity were found to be under circadian control in mice. Circadian expression of TERT mRNA is hardwired to the circadian oscillator via direct regulation by the BMAL1 and CLOCK heterodimer.

What is also useful to consider is what applies in the case of species with weak circadian rhythms (e.g the naked molerat, c.elegans, hydra and human fish).  These species can be very long lived, resistant to cancer and in some cases have increased regenerative capacity.  This is further explored in another positing.


Is the Circadian-Redox Link Supporting The Sleep-Wake Cycle?

Daily rhythms of sleep and metabolism in mammals are driven by a biological clock in the suprachiasmatic nucleus (SCN), a structure in the brain made up of 20,000 neurons, all of which can keep daily (circadian) time individually. If the SCN is to be a robust, but sensitive, timing system, the neurons must synchronize precisely with one another and adjust their rhythms to those of the environment…Each SCN neuron generates intrinsic rhythmicity through interlocking feedback loops involving a set of “core clock genes” and their protein products. Cell autonomous rhythms are synchronized at the level of cell populations. The SCN exerts top-down control over other brain regions and peripheral oscillators while receiving feedback from them. Thus, the circadian control system is a hierarchical network, involving “elementary clocks” in individual cells, “ensemble clocks” in cell populations, coupling between central and peripheral oscillators, and interactions with external input….. Each section has its distinct role, but harmonizes with the other sections via a precise phase relationship.  J. Z. Li  2014

In mammals global SCN redox state has been found to undergo an autonomous circadian rhythm. Redox state is relatively reduced in daytime, when neuronal activity is high, and oxidized during night-time, when neurons are relatively inactive. Redox modulates neuronal excitability via tight coupling: imposed reducing or oxidizing shifts immediately alter membrane excitability. Whereas an intact transcription–translation oscillator is necessary for the redox oscillation, metabolic modulation of excitability is too rapid to be under clockwork control.  It has been hypothesised that redox state and neuronal activity are coupled nontranscriptional circadian oscillators in SCN neurons…  The self-sustained circadian rhythms of SCN redox state that required the molecular clockwork. and dynamic regulation of SCN excitability appears to be closely tied to metabolism that engages the clockwork machinery. T A Wang 2012.  Energetic fluctuation in the central nervous system has been considered to be a consequence of the neuronal activity. However, new findings suggest that changes in cellular metabolic state can be the cause, rather than the result, of the neuronal activity. M U Gillette 2014.  Also see C B Peek 2012.   There are also links between the redox state and the membrane excitability of SCN neurons, given that oxidizing and reducing agents can produce hyperpolarization and depolarization, respectively. Redox-dependent modulation of K+ channel conductance is believed to underlie these oscillations. M L Fanjul-Moles 2016.

It is clear that there is a rhythmic pattern in cell function and cycles of energy utilization in accordance with a daily rhythm, while sleep plays a crucial role in maintaining metabolic homeostasis. However, the mechanism of bidirectional communication between the sleep centers and the circadian pacemaker, and their regulation of diverse metabolic networks is still unclear… Redox state may impact on transcriptional activity of clock components and neuronal activity within the master pacemaker in mammals, the suprachiasmatic nuclei (SCN) interestingly, in turn circadian clocks also control the cellular redox status, since expression levels of many reactive oxygen species (ROS) responsive genes, or antioxidant enzymes, are frequently regulated by the clock genes. Consequently, mechanistic interactions between redox and circadian components suggest that the redox state of a cell and clocks are influenced and regulated by each other… The neural circuits involved in the regulation of sleep‐wake states and circadian rhythms are becoming established, as are the vital roles of circadian and homeostatic processes in regulation of the sleep and arousal‐promoting circuitry. Intriguingly, there is physiological evidence that indicate sleep centers can also regulate the circadian pacemaker. In addition, sleep plays a role in the clearance of potentially neurotoxic waste products from the central nervous system, and thereby maintains metabolic homeostasis. Circadian clocks regulate different aspects of sleep, suggesting that redox and metabolism may affect sleep homeostasis through their impact on the state of the circadian system. However, the exact mechanism by which sleep‐wake centers communicate with the SCN and metabolic cycles has not been untangled…Recent studies indicate that the circadian rhythm of redox state controls excitability in SCN neurons. Consequently, it can be speculated that redox homeostasis and neuronal activity are coupled non‐transcriptional circadian oscillators intertwined in neuronal physiology. S Ray 2016 .    Europa Project.  

The most recent findings on how the sleep-wake cycle may be driven by the circadian-redox coupling can be found in in an article on ‘Cross‐talk between circadian clocks, sleep‐wake cycles, and metabolic networks’ by S Ray and A B Reddy 2016.

The Entrainment of Circadian Rhythms by Redox

Evidence indicates that the circadian rhythms of crayfish are controlled by a distributed circadian system that includes four pairs of coupled oscillators, and two extraretinal circadian photoreceptors sensitive to blue light, which are involved in photic entrainment. In the crayfish studies have demonstrated that these oscillators express clock proteins similar to those found in the Drosophila. In addition, the brain and the sixth abdominal ganglion extraretinal receptors express CRY. It has been proposed that the blue light-induced photo-entrainment of some rhythms in crayfish, particularly ERG amplitude and activity rhythms, are mediated by CRY. The changes produced by light intensity and photoperiod length in ROS and the antioxidant rhythms of crayfish inhabiting different latitudes suggest that a photo-oxidative redox signal may be contributing to this animal’s entrainment to latitudinal photoperiodic changes using similar signaling pathways as aquatic vertebrates to activate CCG transcription.

In Drosophila it has been proposed that CRY activation involves intramolecular electron transfer and presumably subsequent conformational changes; thus, the cellular redox status also regulates the transfer of photic information and CRY stability  Results suggest that cellular redox status and electron transfer modulate the light-dependent activation of CRY, which in turn affects the subsequent transmission of the light signal to TIM and the degradation of CRY itself, with the subsequent clock resetting.

In zebrafish cells, the light-induced redox changes stimulating intracellular mitogen- activated protein kinase (MAPK) signalling that transduces photic signals to zCry1a gene transactivation. Importantly, light also drives the production of intracellular ROS, such as H2O2 , that leads to an altered redox status and increases intracellular catalase activity by stimulating catalase transcription, an event which occurs after the maximum expression of the zCry1a gene has been reached. This increased catalase activity diminishes light induced cellular ROS levels, resulting in decreased zCry1a transcription and creating a negative feedback loop. Thus, this altered redox state triggers the transduction of photic signals that regulate and synchronize the circadian clock. M L Fanjul-Moles 2015. 

Stress Resistance

The circadian-redox link could have major implications for the understanding of the sleep-wake cycle in terms of a rhythmic metabolism which overlays nutrition and stress resistance to biotic and abiotic cues.  In 2015 it was reported that the master immune regulator NPR1 (non-expressor of pathogenesis-related gene 1) of Arabidopsis is a sensor of the plant’s redox state and regulates transcription of core circadian clock genes even in the absence of pathogen challenge. Surprisingly, acute perturbation in the redox status triggered by the immune signal salicylic acid does not compromise the circadian clock but rather leads to its reinforcement. M Zhou 2015.  Proteins made by the morning genes suppress the evening genes at the beginning of the day, but as the proteins start to build up within the cell they eventually turn themselves off. The subsequent drop in morning protein levels near the end of the day in turn activates the “evening” genes, creating a continuous 24-hour loop. Plants treated with salicylic acid activated both their ‘morning’ clock genes and their ‘evening’ clock genes more strongly. Researchers identified a gene called NPR1 that links the two clocks, allowing them to work together. Like a molecular thermostat, NPR1 senses changes in the plants’ reactive oxygen species clock, and responds by turning up both the ‘morning’ and the ‘evening’ genes in the other clock. The end result was that the plants’ immune systems were even more prepared for fungal attack in the morning but more susceptible to infection at night — presumably to minimize interference between pathogen defence and growth, which mainly occurs in the pre-dawn hours

Circadian Rhythms have been implicated in Seizures and Anaesthesia

Time-of-day factors such as sleep and circadian rhythms are well known to influence expression of seizures.  Studies in humans have shown an association between seizures and alterations in sleep-wake states. In patients with common forms of idiopathic generalized epilepsy, tonic, and tonic-clonic seizures are more frequently seen in sleep, whereas all other generalized semiologic seizure types including clonic, myoclonic, absence and atonic occur more frequently out of wakefulness, suggesting circadian rhythms control distinct mechanisms of neuronal hyperexcitability that may result in seizures.  Jason R. Gerstner 2014.

Following general anaesthesia, people are often confused about the time of day and experience sleep disruption and fatigue. It has been hypothesized that these symptoms may be caused by general anaesthesia affecting the circadian clock.

The Role of Circadian Rhythms in Neurogenesis

Recent studies suggest that cellular circadian clocks may regulate adult neurogenesis and survival of newly formed neurons, although circadian studies of neurogenesis in vitro are lacking. During adult neurogenesis, multipotent neural stem cells self-renew and differentiate to generate neurons.   The core circadian clock proteins that serve in the timing mechanism are found throughout the hippocampus  and impairing their normal expression causes deficits in habituation, exploratory behavior, and learning. Cry 1-/-2-/- mice exhibit impaired recognition memory, increased anxiety, and lack of time-place associations , although no deficits in working or long-term memory formation were reported. In contrast, Bmal1-/- mice show a diminished learning ability and have previously been reported to display phenotypes associated with accelerated aging . Per2-/- mice showed impaired trace-fear memory, suppressed long-term potentiation (LTP), and diminished CREB phosphorylation . Equivalent effects were observed in mPer1-/- mice in which spatial memory, CREB activation, and LTP declined, further suggesting that Per genes have additional effects on hippocampal functions, perhaps independent of their role in circadian timing.  A Malik  2015

The observed circadian regulation of adult hippocampal neurogenesis (Bouchard-Cannon et al., 2013) could complement circadian regulation of dendritic spine formation and stabilization (Liston et al., 2013), allowing for more efficient reintegration of new neurons into the adult brain.  S Brown 2014

 Circadian Rhythms, Neuronal Activity and Memory

Neural rhythms operate on time scales that vary from milliseconds to seconds, synchronize the forebrain and are mediated by neurotransmitter systems such as acetylcholine, norepinephrine, and serotonin (Woolf et al., 2010). The neurotransmitter systems further fluctuate according to endogenous, circadian rhythms that also fluctuate according to the season of the year, which ultimately leads to an enormous range of time scales spanning between 8 and 10 orders of magnitude or even more if atomic fluctuations are included.. SR Hameroff – ‎2014.

The activity of place cells in hippocampus has previously been shown to be modulated at a circadian time-scale, entrained by a behavioral stimulus, but not entrained by light.   The frequency of hippocampal theta rhythm is modulated on a circadian period and is entrained by food availability. The frequency of theta-band hippocampal EEG varies with a circadian period in freely moving animals and that this periodicity mirrors changes in the firing rate of hippocampal neurons. Theta activity serves, therefore, as a proxy of circadian-modulated hippocampal neuronal activity… . Robert Munn et al 2015.

The circadian-controlled mitogen-activated protein kinase (MAPK) and cAMP signal transduction pathway plays critical roles in the consolidation of hippocampus-dependent memory. KL Eckel-Mahan – ‎2012 and Jason R. Gerstner et al 2010.

Per1-knockout animals are severely handicapped in a hippocampus-dependent long-term spatial learning paradigm.  A Jilg 2010. 

The presence of gamma-band activity in many LFP measurements under stimulation led to the idea that gamma-band oscillations serve as a ‘clock’ signal for the purpose of temporally encoding information (Hopfield, 1995Buzsaki and Chrobak, 1995Jefferys et al., 1996Buzsaki and Draguhn, 2004Buzsaki, 2006Bartos et al., 2007Fries et al., 2007Hopfield, 2004). The ‘clock’ theory of gamma combined with the pervasiveness of gamma oscillations have given rise to the theory that the brain uses gamma oscillations to synchronize different regions of the brain for the purpose of ‘binding’ information about a stimulus (Gray and Singer, 1989Singer and Gray, 1995).

Researchers at Harvard University have also found that circadian genes play a vital role in mammalian brain development and plasticity— that is, the ability of the brain to learn from, and physically change in response to, environmental experiences. Mice deficient for the core circadian gene ‘Clock’ had significantly delayed and prolonged plasticity in the visual system.,“They found a cell-intrinsic Clock may control the normal trajectory of brain development”.Kobayashi et al., 2015.   It has been found that the plasticity  of a very small number of neurons helps run the biological clock in Drosphila.  Daily changes in the s-LNv cell and that the axon termini grows and retracts every 24 hours.  This plasticity is required for both maintaining circadian rhythms and season adaptation.   Blau 2015.

Circadian Rhythms and Behavioural Change

The Clock PER2 is rhythmically expressed in the straitum and cerebullum, and it’s expression is linked with the daily fluctuations in extracellular dopamine levels and D2 receptor activity.   It has been suggested that neural oscillations in the cerebellum and striatum and the synchrony between them are modulated by time of day, & these are influenced by dopamine manipulation.   Thomas C Watson, ‎Stella Koutsikou, ‎Richard Apps  2015.

The loss of cryptochromes change physiology, and dysfunction of cryptochromes may change mood. On the basis of the data presented above, CRY2 appears to be “a mood gene.” Success in the resetting has been hypothesized to improve lowered mood in the depressed, whereas failure in the resetting may deepen a depressive episode any time of the year, especially in the spring. Here, the overarching link might be the circadian clock protein NR1D1. T Partonen 2015…CRY1 Variations Impacts on the Depressive Relapse Rate in a Sample of Bipolar Patients. A Drago, 2015.

Mice carrying a dominant-negative mutation of the Clock gene show sleep disturbances, but also manic-like behavior, which can be reversed by lithium, a common mood-stabilizing drug.

Circadian Rhythms and Neurodegeneration

The most immediate way for the clock to influence neurodegeneration is by circadian control over the expression of pro-neurodegenerative factors. This has been reported for several relevant genes in various rodent tissues. For example, presenilin-2, which regulates the cleavage of amyloid precursor protein (APP), is a direct target of CLOCK/BMAL1 transcriptional regulation, and is expressed with a strong circadian rhythm. TDP-43 is the principal pathogenic protein in tau-negative fronto-temporal dementia (FTLD-TDP) and in many forms of ALS, and at the transcript level is very highly circadian in mouse brain, as well as in liver and kidney. Similarly, α-synuclein and γ-synuclein are rhythmic in various tissues and the synuclein-interacting protein synphilin shows a strong circadian cycle in brain….Similarly, mutations in FUS are associated with forms of FTD and ALS and again this gene is expressed with a very strong circadian rhythm in adrenal gland, liver and brain. At a transcriptional level, therefore, clock mechanisms may contribute to pro-neurodegenerative processes by elevating expression levels of the naturally occurring form of the protein on a recurrent daily basis, incurring progressive risk throughout the lifespan.

As with autophagy, the capacity of cells to quality-control, degrade and clear unwanted proteins varies across the circadian cycle, thereby limiting the ability of the cell to deal with mis-folded monomers, toxic intermediates and aggregates alike. Disturbance of this circadian programme in neurons would enhance their susceptibility to a pre-existing neurodegenerative state.

A significant source of damage to pro-neurodegenerative proteins arises from oxidative stress, and circadian influences on the redox state of a cell are manifest in several ways. First, as with autophagy and proteasomal pathways, transcriptomic and proteomic analyses  have shown that the expression of oxidative metabolic enzymes and antioxidant factors is modulated by the circadian system in both liver and brain. The ability of cells to deal with the consequences of dysfunctional mitochondria is therefore clock-gated.  M H Hastings 2013.

Circadian Rhythms may also interact with prions e.g  the messenger RNA for the prion protein is regulated in the rat brain in a marked circadian manner not only in the suprachiasmatic nuclei, the principal site for the generation of mammalian circadian rhythms, but also in other forebrain regions. F R Cagampang 1999.   In mice devoid of protein prions  there is an alteration in both circadian activity rhythms and patterns.  I Tobler 1996.

Rhythms as Phase Transitions?

It has been argued that the collective rhythmicity of circadian clocks may be best obtained by studying it at its outset, that is treating it as a kind of phase transition or bifurcation or self-synchronization transition (Y Kuramoto 1984).  Working within the framework of a mean-field model, Winfree discovered that such oscillator populations can exhibit a remarkable cooperative phenomenon. As the variance of the frequencies is reduced, the oscillators remain incoherent, each running near its natural frequency, until a certain threshold is crossed. Then the oscillators begin to synchronize spontaneously… Winfree pointed out that this phenomenon is strikingly reminiscent of a thermodynamic phase transition, but the oscillators align in time, not space.  In addition, biological clocks can be stopped by relatively mild perturbations – with a stimulus of appropriate timing and duration can drive the clock to a “phase singularity,”  – a point at which phase is ambiguous and near which phase takes on all values.   S Strogatz 2016.

Evidence of phase transitions is being widely explored in the field of neurobiology e.g  R Kozma and W J Freeman 2016G Werner 2009,  J D Cowan 2013A de Andrade Costa Beggs 2015 and Plenz 2003, 2004; Haldeman and Beggs 2005; Plenz and Thiagarajan 2007.  Also see F D Ludin 2015.   In experiments on coordinated biological motion, clear evidence for critical slowing down, a key feature of nonequilibrium phase transitions, has found. J P Scholz 1987.

The neural criticality hypothesis states that the brain may be poised in a critical state at a boundary between different types of dynamics. Theoretical and experimental studies show that critical systems often exhibit optimal computational properties, suggesting the possibility that criticality has been evolutionarily selected as a useful trait for our nervous system. Evidence for criticality has been found in cell cultures, brain slices, and anesthetized animals. Yet, inconsistent results were reported for recordings in awake animals and humans, and current results point to open questions about the exact nature and mechanism of criticality, as well as its functional role….If a system has a continuous phase transition, then the system can reside exactly at the transition point between two phases…systems at criticality are believed to have optimal memory and information processing capabilities.  Janina Hesse 2014

Pattern of spontaneous neuronal activity near a critical point of a phase transition is a characteristic property that can be used to identify the bifurcation mechanism of the transition. Bursts and avalanches are precursors of a first-order phase transition, paroxysmal-like spikes of activity precede a second-order phase transition caused by a saddle-node bifurcation, while irregular spindle oscillations represent spontaneous activity near a second-order phase transition caused by a supercritical Hopf bifurcation.. results support the idea that collective behavior of neuronal networks may have universal properties that do not depend on details of single neuron dynamics. K.-E. Lee 2013

Theory provides precise predictions on signatures of critical slowing down near the bifurcation to spiking. It has also been shown that 1) the transition to spiking dynamically corresponds to a critical transition exhibiting slowing down, 2) the scaling laws suggest a saddle-node bifurcation governing slowing down, and 3) these precise scaling laws can be used to predict the bifurcation point from a limited window of observation. This demonstrates scaling laws of critical slowing down in an experiment. The decrease in recovery rate as a result of critical slowing down upon approaching the spiking threshold is likely to have implications on information processing in neurons…identical scaling of these statistics in both type 1 and type 2 neurons suggested by analysis could indicate a universal mechanism by which tuning the bifurcation occurs. Beyond single neurons, shifts to different dynamical regimes also occur on a larger spatial scale in neuronal systems. Such transitions of cortical network dynamics can be quite subtle and occur, for example, under physiologic conditions in the course of wake and sleep, or are exemplified by the rapid transitions to pathologic seizure states in epilepsy . A tipping point at the network level has also recently been described as ‘coherence potential’ in the ongoing avalanche dynamics of awake monkeys and in vitro. It will be interesting to explore whether these network transitions exhibit similar scaling laws Christian Meisel 2015

Dramatic switching of brain activity to a new state is observed in both healthy and pathological cases, for example during wake–sleep and wake–anaesthesia cycles, and at seizure onset. It has been proposed recently by Jirsa et al. that different bifurcation types may be responsible for these neural state transitions

Ermentrout and Cowan, and more recently Bressloff, have explored diffusion-driven Turing instabilities in the Wilson–Cowan neural field equations supporting formation of stationary activity patterns that have been likened to visual hallucinations. E Negahbani 2014.  These hallucinations are called “phosphenes” can be experienced as part of entry into sleep, awakening, or as part of lucid dreaming.

Species with weak circadian rhythms

However again it would be useful to consider what mechanisms are operating in mammal with weak circadian rhythms i.e the naked molerat.  How is the brain effected when circadian rhythms are weak, and potentially weakly coupled with redox/the metabolism.  Although it should be remembered that redox (including peroxiredoxins which are found in molerats) can also oscillate to a 24 hr rhythm. Alternatively it may be the case that if some species were found to have no circadian (TTFL) rhythms, that redox oscillations may become prolonged.  This may move the species away from a rhythmic cycle of moving in and out of a conscious state.  Sleep is known to be influenced by temperature, as well as environmental timing cues or zeitgebers. Closely related to the onset of sleep and wakefulness is the endogenous circadian temperature cycle. It has been found that the Naked Mole-Rat has a distinct temperature and activity rhythm that is not coupled to environmental conditions. More surprisingly, there is an inverse relationship between the two measures. When temperature is at its lowest (nadir), activity is at its highest and vice versa.  Scripps Research.  J Davis Walton 1994.   Research is currently being taken into sleep patterns of other species which are thought to lack robust circadian clocks e.g the Hydra.

Further Thoughts

In view of the possible influence of the circadian-redox coupling on morphogenesis/neurogenesis, could this mechanism in early development also lead to the stimulation of the brain into a continuous sleep-wake cycle and the human perception of consciousness?


Copyright Nina Schuller 2016 (although this has drawn on the work of many people and so has been referenced throughout).

The Physics

Circadian rhythms have been modelled in several ways.  This has included as:

The implications for health and our place in the universe

Evidence of phase transitions is being widely explored in the field of neurobiology .

Self organised criticality models may also be useful in considering this approach, as dramatic switching of brain activity to a new state is observed in both healthy and pathological cases – for example during wake–sleep and wake–anaesthesia cycles, and at seizure onset. It has been proposed that different bifurcation types may be responsible for these neural state transitions.

So the physics of circadian rhythms could provide a basis for why the circadian rhythms-redox coupling is implicated in the sleep-wake cycle, and the reason for neural integration of space-time as there are phase transition models of an expanding universe.

The physics of circadian rhythms may also provide an explanation for why circadian rhythms are deeply implicated in morphogenesis (i.e the forming of cells, tissues, organs, etc). For it may be the case that they generating matter as temporal dissipative structures.

The FKPP equation could be useful for exploring this further.

October 2016. This article merely joins up other peoples work into an overall system.  These works have been referenced so it is clear that others have provided the individual pieces of evidence that have been used to shape a specific systems approach.    











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