Oscillating molecules and how they move circadian clocks across evolutionary boundaries

Contribution of membrane-associated oscillators to biological timing at different timescales

Environmental rhythms such as the daily light-dark cycle selected for endogenous clocks. These clocks predict regular environmental changes and provide the basis for well-timed adaptive homeostasis in physiology and behavior of organisms. Endogenous clocks are oscillators that are based on positive feedforward and negative feedback loops. They generate stable rhythms even under constant conditions. Since even weak interactions between oscillators allow for autonomous synchronization, coupling/synchronization of oscillators provides the basis of self-organized physiological timing. Amongst the most thoroughly researched clocks are the endogenous circadian clock neurons in mammals and insects. They comprise nuclear clockworks of transcriptional/translational feedback loops (TTFL) that generate ∼24 h rhythms in clock gene expression entrained to the environmental day-night cycle. It is generally assumed that this TTFL clockwork drives all circadian oscillations within and between clock cells, being the basis of any circadian rhythm in physiology and behavior of organisms. Instead of the current gene-based hierarchical clock model we provide here a systems view of timing. We suggest that a coupled system of autonomous TTFL and posttranslational feedback loop (PTFL) oscillators/clocks that run at multiple timescales governs adaptive, dynamic homeostasis of physiology and behavior. We focus on mammalian and insect neurons as endogenous oscillators at multiple timescales. We suggest that neuronal plasma membrane-associated signalosomes constitute specific autonomous PTFL clocks that generate localized but interlinked oscillations of membrane potential and intracellular messengers with specific endogenous frequencies. In each clock neuron multiscale interactions of TTFL and PTFL oscillators/clocks form a temporally structured oscillatory network with a common complex frequency-band comprising superimposed multiscale oscillations. Coupling between oscillator/clock neurons provides the next level of complexity of an oscillatory network. This systemic dynamic network of molecular and cellular oscillators/clocks is suggested to form the basis of any physiological homeostasis that cycles through dynamic homeostatic setpoints with a characteristic frequency-band as hallmark. We propose that mechanisms of homeostatic plasticity maintain the stability of these dynamic setpoints, whereas Hebbian plasticity enables switching between setpoints via coupling factors, like biogenic amines and/or neuropeptides. They reprogram the network to a new common frequency, a new dynamic setpoint. Our novel hypothesis is up for experimental challenge.

Temperature Profile and Adverse Outcomes After Discharge From the Intensive Care Unit

BACKGROUND

A predictive model that uses the rhythmicity of core body temperature (CBT) could be an easily accessible clinical tool to ultimately improve outcomes among critically ill patients.

OBJECTIVES

To assess the relation between the 24-hour CBT profile (CBT-24) before intensive care unit (ICU) discharge and clinical events in the step-down unit within 7 days of ICU discharge.

METHODS

This retrospective cohort study in a tertiary ICU at a single center included adult patients requiring acute invasive ventilation for more than 48 hours and assessed major clinical adverse events (MCAEs) and rapid response system activations (RRSAs) within 7 days of ICU discharge (MCAE-7 and RRSA-7, respectively).

RESULTS

The 291 enrolled patients had a median mechanical ventilation duration of 139 hours (IQR, 50-862 hours) and at admission had a median Acute Physiology and Chronic Health Evaluation II score of 22 (IQR, 7-42). At least 1 MCAE or RRSA occurred in 64% and 22% of patients, respectively. Independent predictors of an MCAE-7 were absence of CBT-24 rhythmicity (odds ratio, 1.78 [95% CI, 1.07-2.98]; P = .03), Sequential Organ Failure Assessment score at ICU discharge (1.10 [1.00-1.21]; P = .05), male sex (1.72 [1.04-2.86]; P = .04), age (1.02 [1.00-1.04]; P = .02), and Charlson Comorbidity Index (0.87 [0.76-0.99]; P = .03). Age (1.03 [1.01-1.05]; P = .006), sepsis at ICU admission (2.02 [1.13-3.63]; P = .02), and Charlson Comorbidity Index (1.18 [1.02-1.36]; P = .02) were independent predictors of an RRSA-7.

CONCLUSIONS

Use of CBT-24 rhythmicity can assist in stratifying a patient's risk of subsequent deterioration during general care within 7 days of ICU discharge.

Biological clocks, some clock-related diseases, and medicinal plants

Progress in chronobiology thus far has been built on botanical field investigation records, experiments on the development of biological clocks, open questions, established rules, and molecular mechanisms. In this review, three clock-related diseases, namely cancer, Alzheimer's disease (AD), and depression, are discussed. Evidence-based mechanisms of action of active compounds, namely epigallocatechin-3-gallate (EGCG), curcumin, and melatonin, from three medicinal plants, Camellia sinensis K., Curcuma longa L., and Hypericum perforatum L., respectively, as potential therapies against cancer, AD, and depression, respectively, have been explained. Feedback loops of basic inputs and application outputs of various studies will lead to the development of chronobiology for applications in time-keeping, disease prevention, and control, and future agricultural practices.

mTOR Signaling, Translational Control, and the Circadian Clock

Almost all cellular processes are regulated by the approximately 24 h rhythms that are endogenously driven by the circadian clock. mRNA translation, as the most energy consuming step in gene expression, is temporally controlled by circadian rhythms. Recent research has uncovered key mechanisms of translational control that are orchestrated by circadian rhythmicity and in turn feed back to the clock machinery to maintain robustness and accuracy of circadian timekeeping. Here I review recent progress in our understanding of translation control mechanisms in the circadian clock, focusing on a role for the mammalian/mechanistic target of rapamycin (mTOR) signaling pathway in modulating entrainment, synchronization and autonomous oscillation of circadian clocks. I also discuss the relevance of circadian mTOR functions in disease.

Clinical chronobiology: a timely consideration in critical care medicine

A fundamental aspect of human physiology is its cyclical nature over a 24-h period, a feature conserved across most life on Earth. Organisms compartmentalise processes with respect to time in order to promote survival, in a manner that mirrors the rotation of the planet and accompanying diurnal cycles of light and darkness. The influence of circadian rhythms can no longer be overlooked in clinical settings; this review provides intensivists with an up-to-date understanding of the burgeoning field of chronobiology, and suggests ways to incorporate these concepts into daily practice to improve patient outcomes. We outline the function of molecular clocks in remote tissues, which adjust cellular and global physiological function according to the time of day, and the potential clinical advantages to keeping in time with them. We highlight the consequences of "chronopathology", when this harmony is lost, and the risk factors for this condition in critically ill patients. We introduce the concept of "chronofitness" as a new target in the treatment of critical illness: preserving the internal synchronisation of clocks in different tissues, as well as external synchronisation with the environment. We describe methods for monitoring circadian rhythms in a clinical setting, and how this technology may be used for identifying optimal time windows for interventions, or to alert the physician to a critical deterioration of circadian rhythmicity. We suggest a chronobiological approach to critical illness, involving multicomponent strategies to promote chronofitness (chronobundles), and further investment in the development of personalised, time-based treatment for critically ill patients.

Novel treatment strategies for chronic kidney disease: insights from the animal kingdom

Many of the >2 million animal species that inhabit Earth have developed survival mechanisms that aid in the prevention of obesity, kidney disease, starvation, dehydration and vascular ageing; however, some animals remain susceptible to these complications. Domestic and captive wild felids, for example, show susceptibility to chronic kidney disease (CKD), potentially linked to the high protein intake of these animals. By contrast, naked mole rats are a model of longevity and are protected from extreme environmental conditions through mechanisms that provide resistance to oxidative stress. Biomimetic studies suggest that the transcription factor nuclear factor erythroid 2-related factor 2 (NRF2) offers protection in extreme environmental conditions and promotes longevity in the animal kingdom. Similarly, during months of fasting, immobilization and anuria, hibernating bears are protected from muscle wasting, azotaemia, thrombotic complications, organ damage and osteoporosis - features that are often associated with CKD. Improved understanding of the susceptibility and protective mechanisms of these animals and others could provide insights into novel strategies to prevent and treat several human diseases, such as CKD and ageing-associated complications. An integrated collaboration between nephrologists and experts from other fields, such as veterinarians, zoologists, biologists, anthropologists and ecologists, could introduce a novel approach for improving human health and help nephrologists to find novel treatment strategies for CKD.

Influence of the nycthemeral cycle on the roosting behaviour of the Orange-winged Amazon

Environmental stimuli exert important effects on the expression of the endogenous rhythms. Daily movements of groups of parrots in response to the light/dark cycle have been studied by several researchers. However, the factors modifying the intrinsic rhythmicity of this behaviour remain little known. This study describes how the nychthemeral/circadian periodicity of roost daily movements of the Orange-winged Amazon Amazona amazonica is modified by weather factors. Numbers of parrots arriving or leaving the roosting site Ilha dos Papagaios were determined on a minute by minute basis. More parrots have significantly arrived at the roost after sunset than before, while more parrots have significantly left the roost before sunrise than after. The peak exodus of parrots occurred at 23 ± 5.24 minutes before sunrise, when the average light intensity was 1 lux. The peak influx of parrots occurred at 6 ± 6.1 minutes after sunset, when the average light intensity was 50 lux. By altering ambient light intensity, weather conditions have significantly influenced the arrival and departure times, with parrots leaving later and arriving earlier when conditions were overcast at the roost site.

Circadian rhythms in a nutshell

Living organisms on this planet have adapted to the daily rotation of the earth on its axis. By means of endogenous circadian clocks that can be synchronized to the daily and seasonal changes in external time cues, most notably light and temperature, life forms anticipate environmental transitions, perform activities at biologically advantageous times during the day, and undergo characteristic seasonal responses. The effects of transmeridian flight and shift work are stark reminders that although modern technologies can create "cities that never sleep" we cannot escape the recalcitrance of endogenous clocks that regulate much of our physiology and behavior. Moreover, malfunctions in the human circadian timing system are implicated in several disorders, including chronic sleep disorders in the elderly, manic-depression, and seasonal affective disorders (SAD or winter depression). Recent progress in understanding the molecular mechanisms underlying circadian rhythms has been remarkable. In its most basic form, circadian clocks are comprised of a set of proteins that, by virtue of the design principles involved, generate a self-sustaining transcriptional-translational feedback loop with a free-running period of about 24 h. One or more of the clock components is acutely sensitive to light, resulting in an oscillator that can be synchronized to local time. This review provides an overview of the roles circadian clocks play in nature, how they might have arisen, human health concerns related to clock dysfunction, and mainly focuses on the clockworks found in Drosophila and mice, the two best studied animal model systems for understanding the biochemical and cellular bases of circadian rhythms.

A differential response of two putative mammalian circadian regulators, mper1 and mper2, to light

A mouse gene, mper1, having all the properties expected of a circadian clock gene, was reported recently. This gene is expressed in a circadian pattern in the suprachiasmatic nucleus (SCN). mper1 maintains this pattern of circadian expression in constant darkness and can be entrained to a new light/dark cycle. Here we report the isolation of a second mammalian gene, mper2, which also has these properties and greater homology to Drosophila period. Expression of mper1 and mper2 is overlapping but asynchronous by 4 hr. mper1, unlike period and mper2, is expressed rapidly after exposure to light at CT22. It appears that mper1 is the pacemaker component which responds to light and thus mediates photic entrainment.

Circadian and ultradian clock-controlled rhythms in unicellular microorganisms

The time structure of a biological system is at least as intricate as its spatial structure. Whereas we have detailed information about the latter, our understanding of the former is still rudimentary. As techniques for monitoring intracellular processes continuously in single cells become more refined, it becomes increasingly evident that periodic behaviour abounds in all time domains. Circadian timekeeping dominates in natural environments. Here the free-running period is about 24 h. Circadian rhythms in eukaryotes and prokaryotes allow predictive matching of intracellular states with environmental changes during the daily cycles. Unicellular organisms provide excellent systems for the study of these phenomena, which pervade all higher life forms. Intracellular timekeeping is essential. The presence of a temperature-compensated oscillator provides such a timer. The coupled outputs (epigenetic oscillations) of this ultradian clock constitute a special class of ultradian rhythm. These are undamped and endogenously driven by a device which shows biochemical properties characteristic of transcriptional and translational elements. Energy-yielding processes, protein turnover, motility and the timing of the cell-division cycle processes are all controlled by the ultradian clock. Different periods characterize different species, and this indicates a genetic determinant. Periods range from 30 min to 4 h. Mechanisms of clock control are being elucidated; it is becoming evident that many different control circuits can provide these functions.

A novel circadianly expressed Drosophila melanogaster gene dependent on the period gene for its rhythmic expression

The Drosophila melanogaster period (per) gene is required for expression of endogenous circadian rhythms of locomotion and eclosion. per mRNA is expressed with a circadian rhythm that is dependent on Per protein; this feedback loop has been proposed to be essential to the central circadian pacemaker. This model would suggest the Per protein also controls the circadian expression of other genetic loci to generate circadian behavior and physiology. In this paper we describe Dreg-5, a gene whose mRNA is expressed in fly heads with a circadian rhythm nearly identical to that of the per gene. Dreg-5 mRNA continues to cycle in phase with that of per mRNA in conditions of total darkness and also when the daily feeding time is altered. Like per mRNA, Dreg-5 mRNA is not expressed rhythmically in per null mutant flies. Dreg-5 encodes a novel 298 residue protein and Dreg-5 protein isoforms also oscillate in abundance with a circadian rhythm. The phase of Dreg-5 protein oscillation, however, is different from that of Per protein expression, suggesting that Dreg-5 and per have common translational but different post-translational control mechanisms. These results demonstrate that the per gene is capable of modulating the rhythmic expression of other genes; this activity may form the basis of the output of circadian rhythmicity in Drosophila.

Extent and character of circadian gene expression in Drosophila melanogaster: identification of twenty oscillating mRNAs in the fly head

BACKGROUND

Although mRNAs expressed with a circadian rhythm have been isolated from many species, the extent and character of circadianly regulated gene expression is unknown for any animal. In Drosophila melanogaster, only the period (per) gene, an essential component of the circadian pacemaker, is known to show rhythmic mRNA expression. Recent work suggests that the encoded Per protein controls its own transcription by an autoregulatory feedback loop. Per might also control the rhythmic expression of other genes to generate circadian behavior and physiology. The goals of this work were to evaluate the extent and character of circadian control of gene expression in Drosophila, and to identify genes dependent on per for circadian expression.

RESULTS

A large collection of anonymous, independent cDNA clones was used to screen for transcripts that are rhythmically expressed in the fly head. 20 of the 261 clones tested detected mRNAs with a greater than two-fold daily change in abundance. Three mRNAs were maximally expressed in the morning, whereas 17 mRNAs were most abundant in the evening--when per mRNA is also maximally expressed (but when the flies are inactive). Further analysis of the three 'morning' cDNAs showed that each has a unique dependence on the presence of a light-dark cycle, on timed feeding, and on the function of the per gene for its oscillation. These dependencies were different from those determined for per and for a novel 'evening' gene. Sequence analysis indicated that all but one of the 20 cDNAs identified previously uncloned genes.

CONCLUSIONS

Diurnal control of gene expression is a significant but limited phenomenon in the fly head, which involves many uncharacterized genes. Diurnal control is mediated by multiple endogenous and exogenous mechanisms, even at the level of individual genes. A subset of circadianly expressed genes are predominantly or exclusively dependent on per for their rhythmic expression. The per gene can therefore influence the expression of genes other than itself, but for many rhythmically expressed genes, per functions in conjunction with external inputs to control their daily expression patterns.

Conformational study of the Thr-Gly repeat in the Drosophila clock protein, PERIOD

Recent results with the Drosophila melanogaster period gene suggest that the apparently conserved repetitive motif (Thr-Gly)n encoded by this gene may play an important role in the temperature compensation of the circadian clock. We have therefore initiated both a theoretical and experimental conformational analysis of (Thr-Gly)n peptides. By using a build-up method, it is clear that the hexapeptide (Thr-Gly)3 represents a 'conformational monomer' and generates a stable type II or type III beta-turn. Circular dichroism and nuclear magnetic resonance spectra of synthetic (Thr-Gly)3 and poly(Thr-Gly) peptides revealed that these peptides exhibit flexible conformations, especially in more polar environments and at higher temperatures. We speculate that this flexibility may illuminate our understanding of both the molecular mechanism of temperature compensation and the systematic geographical distribution within Europe of the Thr-Gly length polymorphism in D. melanogaster.

Analysis of period mRNA cycling in Drosophila head and body tissues indicates that body oscillators behave differently from head oscillators

The period (per) gene is thought to be part of the Drosophila circadian pacemaker. The circadian fluctuations in per RNA and protein that constitute the per feedback loop appear to be required for pacemaker function, and have been measured in head neuronal tissues that are necessary for locomotor activity and eclosion rhythms. The per gene is also expressed in a number of neuronal and nonneuronal body tissues for which no known circadian phenomena have been described. To determine whether per might affect some circadian function in these body tissues, per RNA cycling was examined. These studies show that per RNA cycles in the same phase and amplitude in head and body tissues during light-dark cycles. One exception to this is the lack of per RNA cycling in the ovary, which also appears to be the only tissue in which PER protein is primarily cytoplasmic. In constant darkness, however, the amplitude of per RNA cycling dampens much more quickly in bodies than in heads. Taken together, these results indicate that circadian oscillators are present in head and body tissues in which PER protein is nuclear and that these oscillators behave differently.

Analysis of period mRNA cycling in Drosophila head and body tissues indicates that body oscillators behave differently from head oscillators

The period (per) gene is thought to be part of the Drosophila circadian pacemaker. The circadian fluctuations in per RNA and protein that constitute the per feedback loop appear to be required for pacemaker function, and have been measured in head neuronal tissues that are necessary for locomotor activity and eclosion rhythms. The per gene is also expressed in a number of neuronal and nonneuronal body tissues for which no known circadian phenomena have been described. To determine whether per might affect some circadian function in these body tissues, per RNA cycling was examined. These studies show that per RNA cycles in the same phase and amplitude in head and body tissues during light-dark cycles. One exception to this is the lack of per RNA cycling in the ovary, which also appears to be the only tissue in which PER protein is primarily cytoplasmic. In constant darkness, however, the amplitude of per RNA cycling dampens much more quickly in bodies than in heads. Taken together, these results indicate that circadian oscillators are present in head and body tissues in which PER protein is nuclear and that these oscillators behave differently.

Circadian rhythms of cyanobacteria: monitoring the biological clocks of individual colonies by bioluminescence

Reproducible circadian rhythms of bioluminescence from individual colonies of cyanobacteria (Synechococcus sp. strain PCC 7942) has been observed. Phenotypic monitoring of colonies on agar plates will enable us to genetically analyze the molecular mechanism of the circadian clock of cyanobacteria by screening for clock mutants. By the introduction of a bacterial luciferase gene, we previously developed a transformed cyanobacterial strain (AMC149) that expresses luciferase as a bioluminescent reporter of the circadian clock. In liquid culture, AMC149 expresses a rhythm of bioluminescence that displays the same behavior as circadian rhythms in higher eukaryotes. Improvements in the technique for administering the reporter enzyme's substrate (decanal) and a highly sensitive photon-counting camera allow monitoring the bioluminescence of single colonies. Individual colonies on agar plates displayed a rhythmicity which is essentially the same as that previously reported for liquid cultures.

Interactions between Light and the Circadian Clock in the Regulation of CAT2 Expression in Arabidopsis

In Arabidopsis seedlings germinated and grown in continuous light, CAT2 mRNA abundance peaks 1 d after imbibition, consistent with the role of catalase in detoxifying H2O2 generated during the [beta]-oxidation of fatty acids stored in the seed. A second peak of CAT2 mRNA abundance, of lower amplitude than the initial peak, appears 6 d after imbibition and may be associated with the development of photosynthetic competence and induction of photorespiration. This second peak in steady-state CAT2 mRNA abundance is regulated by light and is not seen in etiolated seedlings. CAT2 mRNA accumulation is induced by exposure to high-fluence blue or far-red light but not by red light. In addition, light induction is unaffected by several mutations that block blue light-mediated inhibition of hypocotyl elongation (blu1, blu2, blu3, hy4), suggesting phytochrome involvement. When etiolated seedlings are transferred to continuous white light, CAT2 mRNA rapidly (within 30 min) accumulates. It is interesting that in these seedlings CAT2 mRNA abundance undergoes pronounced oscillations with a circadian (24 h) periodicity, indicating control by the endogenous circadian clock. No such oscillations are detected in CAT2 mRNA abundance in etiolated seedlings prior to illumination. Control of CAT2 expression by the circadian clock is also seen in 5-week-old plants grown in a light-dark cycle and transferred either to continuous dark or to continuous light; in continuous light the circadian oscillations in CAT2 mRNA abundance persist for at least five circadian cycles, indicating the robustness of this circadian rhythm.

Oscillating behavior of carbohydrate granule formation and dinitrogen fixation in the cyanobacterium Cyanothece sp. strain ATCC 51142

It has been shown that some aerobic, unicellular, diazotrophic cyanobacteria temporally separate photosynthetic O2 evolution and oxygen-sensitive N2 fixation. Cyanothece sp. ATCC strain 51142 is an aerobic, unicellular, diazotrophic cyanobacterium that fixes N2 during discrete periods of its cell cycle. When the bacteria are maintained under diurnal light-dark cycles, N2 fixation occurs in the dark. Similar cycling is observed in continuous light, implicating a circadian rhythm. Under N2-fixing conditions, large inclusion granules form between the thylakoid membranes. Maximum granulation, as observed by electron microscopy, occurs before the onset of N2 fixation, and the granules decrease in number during the period of N2 fixation. The granules can be purified from cell homogenates by differential centrifugation. Biochemical analyses of the granules indicate that these structures are primarily carbohydrate, with some protein. Further analyses of the carbohydrate have shown that it is a glucose polymer with some characteristics of glycogen. It is proposed that N2 fixation is driven by energy and reducing power stored in these inclusion granules. Cyanothece sp. strain ATCC 51142 represents an excellent experimental organism for the study of the protective mechanisms of nitrogenase, metabolic events in cyanobacteria under normal and stress conditions, the partitioning of resources between growth and storage, and biological rhythms.