bims-ciryme Biomed News
on Circadian rhythms and metabolism
Issue of 2022‒05‒29
24 papers selected by
Gabriela Da Silva Xavier
University of Birmingham

  1. Methods Mol Biol. 2022 ;2482 329-340
      In addition to diet quality and quantity, the "timing" of food intake recently emerged as a third key parameter in nutritional and metabolic health. The link between nutrition timing and metabolic homeostasis is in part due to the regulation of daily feeding:fasting cycles and metabolic pathways by the circadian clock. Preclinical feeding regimen studies in rodents are invaluable to further define the modalities of this relationship and get a better understanding of its mechanistic underpinnings. Time-restricted feeding (TRF) and caloric restriction (CR) are examples of feeding regimen at the crossroads of metabolic and circadian regulation. Here we propose methods to implement TRF and CR highlighting the parameters that are relevant to the study of circadian and metabolic health. We also provide methods to determine their impact on the output of the circadian clock by analyzing diurnal expression profiles using 24 h time-series collection as well as their impact on metabolic homeostasis using a glucose tolerance test (GTT).
    Keywords:  Circadian clock; Circadian rhythms; Intermittent fasting; Metabolism; Nutrition
  2. Methods Mol Biol. 2022 ;2482 301-310
      Indirect calorimetry probes the relationship between fuel consumed and energy produced, and in doing so provides an estimation of whole-body energy expenditure and fuel preference. When assayed continuously in real-time, rhythms appear and illuminate the temporal regulation of energy metabolism by the circadian clock. Here we describe a method for recording circadian energy metabolism in mice using indirect calorimetry-enabled metabolic cages, encompassing mouse entrainment, experimental design, data acquisition and analysis, troubleshooting of common problems, and important considerations. This method is adaptable to the end user's equipment and serves as an effective tool to study, for example, mutant mice, dietary interventions, drug treatments, or circadian disruption.
    Keywords:  Circadian clock; Circadian rhythm; Energy metabolism; In vivo recording; Indirect calorimetry; Metabolic cage; Real-time recording
  3. Biochem Soc Trans. 2022 May 23. pii: BST20210508. [Epub ahead of print]
      Lipids comprise a diverse group of metabolites that are indispensable as energy storage molecules, cellular membrane components and mediators of inter- and intra-cellular signaling processes. Lipid homeostasis plays a crucial role in maintaining metabolic health in mammals including human beings. A growing body of evidence suggests that the circadian clock system ensures temporal orchestration of lipid homeostasis, and that perturbation of such diurnal regulation leads to the development of metabolic disorders comprising obesity and type 2 diabetes. In view of the emerging role of circadian regulation in maintaining lipid homeostasis, in this review, we summarize the current knowledge on lipid metabolic pathways controlled by the mammalian circadian system. Furthermore, we review the emerging connection between the development of human metabolic diseases and changes in lipid metabolites that belong to major classes of lipids. Finally, we highlight the mechanisms underlying circadian organization of lipid metabolic rhythms upon the physiological situation, and the consequences of circadian clock dysfunction for dysregulation of lipid metabolism.
    Keywords:  T2D; circadian clock; lipid metabolism; lipidomics; metabolic disorders
  4. Methods Mol Biol. 2022 ;2482 217-242
      There is high interest in investigating the daily dynamics of gene expression in mammalian organs, for example, in liver. Such studies help to elucidate how and with what kinetics peripheral clocks integrate circadian signals from the suprachiasmatic nucleus, which harbors the circadian master pacemaker, with other systemic and environmental cues, such as those associated with feeding and hormones. Organ sampling around the clock, followed by the analysis of RNA and/or proteins, is the most commonly used procedure in assessing rhythmic gene expression. However, this method requires large cohorts of animals and is only applicable to behaviorally rhythmic animals whose phases are known. Real-time recording of gene expression rhythms using luciferase reporters has emerged as a powerful method to acquire continuous, high-resolution datasets from freely moving individual mice. Here, we share our experience and protocols with this technique, using the RT-Biolumicorder setup.
    Keywords:  Circadian rhythms; Feeding rhythms; Gene expression regulation; Luciferase; Mouse liver; Peripheral oscillators; RT-Biolumicorder; Real-time bioluminescence recording; Transcription
  5. Methods Mol Biol. 2022 ;2482 169-179
      Isolation of primary hepatocytes and culturing these cells ex vivo provides a powerful platform to model liver physiology in vivo. Primary hepatocytes can be cultured for several days, the circadian clock can be synchronized, and these primary cells can be utilized for functional gene regulation analysis and metabolic studies. In this chapter, we describe detailed methodology for isolation of viable primary hepatocytes, techniques for culturing these cells, methods for synchronization of the circadian clock, transfection and luciferase reporter analysis, as well as glucose production assays as a functional readout of metabolic state.
    Keywords:  Clock-controlled gene expression; Glucose production assays; Luciferase reporter assays; Primary hepatocyte cell culture; Primary hepatocyte isolation; Synchronization of the circadian clock
  6. Methods Mol Biol. 2022 ;2482 211-215
      Rhythmic locomotor activity is a commonly used readout of general circadian function in animals. For instance, measuring the activity of rodents in their home cages can provide information about circadian phase and period in response to genetic, pharmacological, and environmental manipulations. Herein, the use of infrared light sensors to measure circadian locomotor activity is described. Furthermore, we provide information about data handling, analysis and software use as well as points to consider when performing the experiment.
    Keywords:  Actogram; Circadian rhythm; ClockLab; Infrared motion detectors; Locomotor activity; Vitalview
  7. Methods Mol Biol. 2022 ;2482 137-152
      In mammals, molecular circadian clocks not only exist in the suprachiasmatic nucleus (SCN) but in almost all organ systems. Intriguingly, tissue clocks can operate in both isolated tissues and cell lines with endocrine signals mediating the circadian expression of local transcriptomes. This can be demonstrated by treating tissue explants with endocrine cues in a phase- and dose-dependent manner. In this chapter we provide an overview of methods to study the effects of candidate hormonal time cues on tissue clock resetting. We propose an experimental procedure based on an in vitro setup consisting of several consecutive steps in which organotypic tissue cultures or cells can be used. Our approach targets the potential resetting mechanism at three levels: the hormone, the direct clock gene target, and the tissue clock response.
    Keywords:  Hormones; In vitro; Peripheral circadian clocks; Phase resetting; Screening
  8. Neurosci Res. 2022 May 18. pii: S0168-0102(22)00148-1. [Epub ahead of print]
      Circadian rhythms are defined as approximately 24-hour oscillations in physiology and behavior. In mammals, the suprachiasmatic nucleus (SCN) of the hypothalamus is known as the central circadian clock. Based on current understanding, circadian rhythms are believed to be generated by transcription-translation feedback loops (TTFL) involving several clock genes and their protein products. However, several studies have shown that circadian oscillation in single SCN cells is still detectable in several clock gene deficient mice. These results suggest that there might be some oscillatory mechanisms without TTFL in mammalian cells. Other important aspects of circadian rhythms include neuronal circuits in the brain that regulate timing of physiological functions. Especially, functional output pathways from the SCN that regulate sleep and wakefulness have not been identified. In this review, I describe recent findings on circadian rhythm in the SCN, and of neuronal mechanisms that control circadian clock regulated sleep and wakefulness in mice.
    Keywords:  Circadian rhythm; Clock gene; Neuronal network; Sleep; Suprachiasmatic nucleus
  9. Cell Rep. 2022 May 24. pii: S2211-1247(22)00617-9. [Epub ahead of print]39(8): 110844
      Calcium signaling is pivotal to the circadian clockwork in the suprachiasmatic nucleus (SCN), particularly in rhythm entrainment to environmental light-dark cycles. Here, we show that a small G-protein Gem, an endogenous inhibitor of high-voltage-activated voltage-dependent calcium channels (VDCCs), is rapidly induced by light in SCN neurons via the calcium (Ca2+)-mediated CREB/CRE transcriptional pathway. Gem attenuates light-induced calcium signaling through its interaction with VDCCs. The phase-shift magnitude of locomotor activity rhythms by light, at night, increases in Gem-deficient (Gem-/-) mice. Similarly, in SCN slices from Gem-/- mice, depolarizing stimuli induce larger phase shifts of clock gene transcription rhythms that are normalized by the application of an L-type VDCC blocker, nifedipine. Voltage-clamp recordings from SCN neurons reveal that Ca2+ currents through L-type channels increase in Gem-/- mice. Our findings suggest that transcriptionally activated Gem feeds back to suppress excessive light-evoked L-type VDCC activation, adjusting the light-induced phase-shift magnitude to an appropriate level in mammals.
    Keywords:  CP: Neuroscience; Gem; RGK; circadian clock; light-induced; phase-shift; small G-protein; suprachiasmatic nucleus; voltage-dependent calcium channels
  10. J Neurosci. 2022 May 23. pii: JN-RM-2337-21. [Epub ahead of print]
      The suprachiasmatic nucleus (SCN) is the master circadian clock of mammals, generating and transmitting an internal representation of environmental time that is produced by the cell-autonomous transcriptional/post-translational feedback loops (TTFL) of the 10,000 neurons and 3,500 glial cells. Recently, we showed that TTFL function in SCN astrocytes alone is sufficient to drive circadian timekeeping and behaviour, raising questions about the respective contributions of astrocytes and neurons within the SCN circuit. We compared their relative roles in circadian timekeeping in mouse SCN explants, of either sex. Treatment with the glial-specific toxin fluorocitrate revealed a requirement for metabolically competent astrocytes for circuit-level timekeeping. Recombinase-mediated genetically complemented Cryptochrome (Cry) proteins in Cry1- and/or Cry2-deficient SCN, were used to compare the influence of the TTFLs of neurons or astrocytes in the initiation of de novo oscillation or in pacemaking. While neurons and astrocytes both initiated de novo oscillation and lengthened period equally, their kinetics were different: astrocytes taking twice as long. Furthermore, astrocytes could shorten period, but not as potently as neurons. Chemogenetic manipulation of Gi- and Gq-coupled signalling pathways in neurons acutely advanced or delayed ensemble phase, respectively. In contrast, comparable manipulations in astrocytes were without effect. Thus, astrocytes can initiate SCN rhythms and bi-directionally control SCN period, albeit with lower potency than neurons. Nevertheless, their activation does not influence SCN phase. The emergent SCN properties of high amplitude oscillation, initiation of rhythmicity, pacemaking and phase are differentially regulated: astrocytes and neurons sustain the ongoing oscillation, but its phase is determined by neurons.Significance Statement:The hypothalamic suprachiasmatic nucleus (SCN) encodes and disseminates time-of-day information to allow mammals to adapt their physiology to daily environmental cycles. Recent investigations have revealed a role for astrocytes, in addition to neurons, in regulation of this rhythm. Using pharmacology, genetic complementation and chemogenetics, we compared the abilities of neurons and astrocytes in determining the emergent SCN properties of high amplitude oscillation, initiation of rhythmicity, pacemaking and determination of phase. These findings parameterise the circadian properties of the astrocyte population in the SCN, and reveal the types of circadian information astrocytes and neurons can contribute within their heterogeneous cellular network.
  11. Cell Mol Life Sci. 2022 May 27. 79(6): 318
      Misaligned feeding may lead to pancreatic insufficiency, however, whether and how it affects circadian clock in the exocrine pancreas is not known. We exposed rats to a reversed restricted feeding regimen (rRF) for 10 or 20 days and analyzed locomotor activity, daily profiles of hormone levels (insulin, glucagon, and corticosterone) in plasma, and clock gene expression in the liver and endocrine and exocrine pancreas. In addition, we monitored responses of the exocrine pancreatic clock in organotypic explants of mPer2Luc mice in real time to acetylcholine, insulin, and glucocorticoids. rRF phase-reversed the clock in the endocrine pancreas, similar to the clock in the liver, but completely abolished clock gene rhythmicity and significantly downregulated the expression of Cpb1 and Cel in the exocrine pancreas. rRF desynchronized the rhythms of plasma insulin and corticosterone. Daily profiles of their receptor expression differed in the two parts of the pancreas and responded differently to rRF. Additionally, the pancreatic exocrine clock responded differently to treatments with insulin and the glucocorticoid analog dexamethasone in vitro. Mathematical simulation confirmed that the long-term misalignment between these two hormonal signals, as occurred under rRF, may lead to dampening of the exocrine pancreatic clock. In summary, our data suggest that misaligned meals impair the clock in the exocrine part of the pancreas by uncoupling insulin and corticosterone rhythms. These findings suggest a new mechanism by which adverse dietary habits, often associated with shift work in humans, may impair the clock in the exocrine pancreas and potentially contribute to exocrine pancreatic insufficiency.
    Keywords:  Circadian clock; Dexamethasone; Insulin; Misaligned feeding; Pancreas; mPer2Luc mouse
  12. Methods Mol Biol. 2022 ;2482 353-371
      Circadian rhythms are daily oscillations in physiology and gene expression that are governed by a molecular feedback loop known as the circadian clock. In Drosophila melanogaster, the core clock consists of transcription factors clock (Clk) and cycle (cyc) which form protein heterodimers that activate transcription of their repressors, period (per) and timeless (tim). Once produced, protein heterodimers of per/tim repress Clk/cyc activity. One cycle of activation and repression takes approximately ("circa") 24-h ("diem") and repeats even in the absence of external stimuli. The circadian clock is active in many cells throughout the body; however, tracking it dynamically represents a challenge. Traditional fluorescent reporters are slowly degraded and consequently cannot be used to assess dynamic temporal changes exhibited by the circadian clock. The use of rapidly degraded fluorescent protein reporters containing destabilized GFP (dGFP) that report transcriptional activity in vivo at a single-cell level with ~1-h temporal resolution can circumvent this problem. Here we describe the use of circadian clock reporter strains of Drosophila melanogaster, ClockPER and ClockTIM, to track clock transcriptional activity using the intestine as a tissue of interest. These methods may be extended to other tissues in the body.
    Keywords:  Circadian clock; Circadian rhythms; Drosophila melanogaster; Intestine; Regeneration; Transcriptional reporters
  13. Methods Mol Biol. 2022 ;2482 15-34
      Circadian rhythms are part of the body's clock, which regulates several physiological and biochemical variables according to the 24-h cycle. Ample evidence indicated disturbance of the circadian clock leads to an increased susceptibility to several diseases. Therefore, a great effort has been made to find small molecules that regulate circadian rhythm by high-throughput methods. Having crystal structures of core clock proteins, makes them amenable to structure-based drug design studies. Here, we describe virtual screening methods that can be utilized for the identification of small molecules regulating the activity of core clock protein Cryptochrome 1.
    Keywords:  Circadian rhythm; Cryptochrome; Docking; Drug discovery; Virtual screening
  14. Front Endocrinol (Lausanne). 2022 ;13 876752
      Background: Circadian misalignment between behaviors such as feeding and endogenous circadian rhythms, particularly in the context of shiftwork, is associated with poorer cardiometabolic health. We examined whether insulin and leptin levels differ between dayshift versus nightshift nurses, as well as explored whether the timing of food intake modulates these effects in nightshift workers.Methods: Female nurses (N=18; 8 dayshift and 10 nightshift) completed daily diet records for 8 consecutive days. The nurses then completed a 24-h inpatient stay, during which blood specimens were collected every 3 h (beginning at 09:00) and meals were consumed at regular 3-h intervals (09:00, 12:00, 15:00, and 18:00). Specimens were analyzed for insulin and leptin levels, and generalized additive models were used to examine differences in mean insulin and leptin levels.
    Results: Mean insulin and leptin levels were higher in nightshift nurses by 11.6 ± 3.8 mU/L (p=0.003) and 7.4 ± 3.4 ng/ml (p=0.03), respectively, compared to dayshift nurses. In an exploratory subgroup analysis of nightshift nurses, predominately eating at night (21:00 - 06:00) was associated with significantly higher insulin and leptin levels than consuming most calories during the daytime (06:00 - 21:00).
    Conclusions: In our study of hospital nurses, working the nightshift was associated with higher insulin and leptin levels, and these effects were driven by eating predominately at night. We conclude that although nightshift work may raise insulin and leptin levels, eating during the daytime may attenuate some of the negative effects of nightshift work on metabolic health.
    Keywords:  Leptin; circadian misalignment; insulin; meal timing; shiftwork
  15. Nat Struct Mol Biol. 2022 May 23.
      Mammalian circadian oscillators are built on a feedback loop in which the activity of the transcription factor CLOCK-BMAL1 is repressed by the PER-CRY complex. Here, we show that murine Per-/- fibroblasts display aberrant nucleosome occupancy around transcription start sites (TSSs) and at promoter-proximal and distal CTCF sites due to impaired histone H2A.Z deposition. Knocking out H2A.Z mimicked the Per null chromatin state and disrupted cellular rhythms. We found that endogenous mPER2 complexes retained CTCF as well as the specific H2A.Z-deposition chaperone YL1-a component of the ATP-dependent remodeler SRCAP and p400-TIP60 complex. While depleting YL1 or mutating chaperone-binding sites on H2A.Z lengthened the circadian period, H2A.Z deletion abrogated BMAL1 chromatin recruitment and promoted its proteasomal degradation. We propose that a PER2-mediated H2A.Z deposition pathway (1) compacts CLOCK-BMAL1 binding sites to establish negative feedback, (2) organizes circadian chromatin landscapes using CTCF and (3) bookmarks genomic loci for BMAL1 binding to impinge on the positive arm of the subsequent cycle.
  16. Proc Natl Acad Sci U S A. 2022 May 31. 119(22): e2115725119
      Significance The moon provides highly reliable time information to organisms. Whereas sunlight is known to set daily animal timing systems, mechanistic insight into the impact of moonlight on such systems remains scarce. We establish that the marine bristleworm Platynereis dumerilii times the precise hours of mass spawning by integrating lunar light information into a plastic daily timing system able to run with circadian (∼24 h) or circalunidian (∼24.8 h) periodicity. The correct interpretation of moonlight is mediated by the interplay of two light sensors: a cryptochrome and a melanopsin ortholog provide information on light valence and moonrise time, respectively. Besides its ecological relevance, our work provides a plausible explanation for long-standing observations of light intensity-dependent differences in circadian clock periods.
    Keywords:  chronobiology; marine biology; molecular clock; moon light; reproduction
  17. Exp Gerontol. 2022 May 19. pii: S0531-5565(22)00145-0. [Epub ahead of print] 111837
      Calorie restriction (CR) and time-restricted eating (TRE) are distinctly different dietary management strategies with overlapping health outcomes. After two years of CR, healthy participants in the Comprehensive Assessment of Long-Term Effects of Reducing Intake of Energy (CALERIE) study showed significant weight-loss relative to the ad libitum intake control group and achieved 12% CR on average. Preclinical rodent studies have shown that sustaining a consistent eating interval of 8-12 h between the first and last calories of each day-without reducing daily calorie intake-can impart health benefits that partly overlap with those imparted by CR. Preclinical CR protocols often inadvertently restrict eating interval, and conversely, clinical studies of TRE often inadvertently result in modest CR. Other factors related to daily timing of food intake, such as breakfast skipping, and early food intake also impact health outcomes. These observations have raised the possibility that CR protocols can be further optimized by adopting relevant aspects of eating patterns to boost weight loss and health outcomes. With a goal to inform CR protocols that aim to optimize eating patterns, the objective of this secondary analysis was to test aspects of daily timing of food intake associated with greater weight loss in the CALERIE study participants. We found no difference in the daily time window of energy intake between the CR and control arms. In the CALERIE trial, weight change was used as a proxy for adherence to CR, and hence we used linear models to test the relationships among CR, weight loss, and temporal aspects of daily eating pattern. We found that CR alone could explain 41% of the variance in weight loss. We tested the contribution of eating interval, time to 50% daily calorie intake, and day-to-day shifts in the time of the first (breakfast) or last meal consumed. We found that eating interval and variation in the timing of the first and last meals significantly influenced weight loss after controlling for CR. Our models suggest that shorter eating intervals are associated with greater CR (1% of the variance explained) and facilitate additional weight loss. Our models suggest that less day to day variation in first mealtime is directly associated with weight loss (6% of the variance explained). More regular first meal timing is also associated with greater CR (2% of the variance explained). Likewise, regular timing of the last daily meal is directly associated with weight loss (1% of the variance explained) and greater CR (1% of the variance explained). The time to 50% of daily calorie intake or consuming half the caloric intake earlier in the day is associated with additional CR (2% of the variance explained). In summary, these secondary analyses on CALERIE data suggest that - in order to maximize CR and weight loss - future CR protocols should encourage participants to adopt consistent timing of their first and last meals, a shorter eating window, and earlier consumption of food.
    Keywords:  Breakfast; CALERIE; Calorie restriction; Time restriction; Weightloss
  18. Methods Mol Biol. 2022 ;2399 277-341
      The temporal dynamics in biological systems displays a wide range of behaviors, from periodic oscillations, as in rhythms, bursts, long-range (fractal) correlations, chaotic dynamics up to brown and white noise. Herein, we propose a comprehensive analytical strategy for identifying, representing, and analyzing biological time series, focusing on two strongly linked dynamics: periodic (oscillatory) rhythms and chaos. Understanding the underlying temporal dynamics of a system is of fundamental importance; however, it presents methodological challenges due to intrinsic characteristics, among them the presence of noise or trends, and distinct dynamics at different time scales given by molecular, dcellular, organ, and organism levels of organization. For example, in locomotion circadian and ultradian rhythms coexist with fractal dynamics at faster time scales. We propose and describe the use of a combined approach employing different analytical methodologies to synergize their strengths and mitigate their weaknesses. Specifically, we describe advantages and caveats to consider for applying probability distribution, autocorrelation analysis, phase space reconstruction, Lyapunov exponent estimation as well as different analyses such as harmonic, namely, power spectrum; continuous wavelet transforms; synchrosqueezing transform; and wavelet coherence. Computational harmonic analysis is proposed as an analytical framework for using different types of wavelet analyses. We show that when the correct wavelet analysis is applied, the complexity in the statistical properties, including temporal scales, present in time series of signals, can be unveiled and modeled. Our chapter showcase two specific examples where an in-depth analysis of rhythms and chaos is performed: (1) locomotor and food intake rhythms over a 42-day period of mice subjected to different feeding regimes; and (2) chaotic calcium dynamics in a computational model of mitochondrial function.
    Keywords:  Biological clocks; Circadian and ultradian rhythms; Lyapunov exponent; Phase space reconstruction; Power spectrum analysis; Synchrosqueezing; Wavelet; Wavelet coherence
  19. Cells. 2022 May 11. pii: 1613. [Epub ahead of print]11(10):
      Circadian clocks control many vital aspects of physiology from the sleep-wake cycle to metabolism. The circadian clock operates through transcriptional-translational feedback loops. The normal circadian signaling relies on a 'master clock', located in the suprachiasmatic nucleus (SCN), which synchronizes peripheral oscillators. Glucocorticoid receptor (GR) signaling has the ability to reset the phase of peripheral clocks. It has been shown that maternal exposure to glucocorticoids (GCs) can lead to modification of hypothalamic-pituitary-adrenal (HPA) function, impact stress-related behaviors, and result in a hypertensive state via GR activation. We previously demonstrated altered circadian rhythm signaling in the adrenal glands of offspring exposed to the synthetic GC, dexamethasone (Dex). Results from the current study show that prenatal exposure to Dex affects circadian rhythm gene expression in a brain region-specific and a sex-specific manner within molecular oscillators of the amygdala, hippocampus, paraventricular nucleus, and prefrontal cortex, as well as the main oscillator in the SCN. Results also show that spontaneously hypertensive rats (SHR) exhibited dysregulated circadian rhythm gene expression in these same brain regions compared with normotensive Wistar-Kyoto rats (WKY), although the pattern of dysregulation was markedly different from that seen in adult offspring prenatally exposed to GCs.
    Keywords:  amygdala; fetal programming; hypertension; paraventricular nucleus; spontaneously hypertensive rat (SHR); suprachiasmatic nucleus (SCN)
  20. Methods Mol Biol. 2022 ;2482 35-54
      Experiments that compare rhythmic properties across different genetic alterations and entrainment conditions underlie some of the most important breakthroughs in circadian biology. A robust estimation of the rhythmic properties of the circadian signals goes hand in hand with these discoveries. Widely applied traditional signal analysis methods such as fitting cosine functions or Fourier transformations rely on the assumption that oscillation periods do not change over time. However, novel high-resolution recording techniques have shown that, most commonly, circadian signals exhibit time-dependent changes of periods and amplitudes which cannot be captured with the traditional approaches. In this chapter we introduce a method to determine time-dependent properties of oscillatory signals, using the novel open-source Python-based Biological Oscillations Analysis Toolkit (pyBOAT). We show with examples how to detect rhythms, compute and interpret high-resolution time-dependent spectral results, analyze the main oscillatory component, and to subsequently determine these main components' time-dependent instantaneous period, amplitude, and phase. We introduce step-by-step how such an analysis can be done by means of the easy-to-use point-and-click graphical user interface (GUI) provided by pyBOAT or executed within a Python programming environment. Concepts are explained using simulated signals as well as experimentally obtained time series.
    Keywords:  Circadian clocks; Data analysis; Nonstationary signals; Oscillations; Spectral analysis; Synchronization; Time series analysis; Wavelets
  21. Methods Mol Biol. 2022 ;2482 341-351
      Organisms exhibit daily changes of physiology and behavior to exert homeostatic adaptations to day-night cycles. The cyclic fluctuation also takes place at transcriptional levels, giving rise to rhythmic gene expression. Central to this oscillatory transcription is the core clock machinery which constitutes a circuit of transcriptional-translational feedback and achieves circadian functions accordingly. Chromatin immunoprecipitation provides understanding of such mechanisms that clock and non-clock transcription factors along with co-regulators and chromatin modifications dictate circadian epigenome through cyclic alterations of chromatin structures and molecular functions in a concerted fashion. Besides, innovation of high-throughput sequencing technology has broadened our horizon and renewed perspectives in circadian research. This article summarizes the methodology of a chromatin immunoprecipitation experiment in light of circadian rhythm research.
    Keywords:  Circadian rhythms; DNA shearing; Dual cross-linking; Histone marks; Transcription factors
  22. Methods Mol Biol. 2022 ;2482 181-189
      Oscillatory output from the suprachiasmatic nuclei (SCN) of the hypothalamus communicates time-of-day information to the brain and body. The SCN's intrinsic ~24-h rhythm can be measured in the neuronal firing rate both in vivo and in vitro, where it continues unperturbed. This robust reporter of endogenous physiology in the SCN brain slice can be widely used to study dynamic changes in SCN physiology, its changing sensitivity to phase-altering signals, and underlying mechanisms. To provide relevant and reproducible data, care must be taken to ensure health of the SCN brain slice. The methods detailed here have been proven to produce healthy, long-lived brain slices.
    Keywords:  Circadian rhythm; Electrophysiology; Oscillator; Phase; Single unit; Suprachiasmatic nucleus
  23. Methods Mol Biol. 2022 ;2482 81-94
      Circadian rhythms are fundamental to biology and medicine and today these can be studied at the molecular level in high-throughput fashion using various omic technologies. We briefly present two resources for the study of circadian omic (e.g. transcriptomic, metabolomic, proteomic) time series. First, BIO_CYCLE is a deep-learning-based program and web server that can analyze omic time series and statistically assess their periodic nature and, when periodic, accurately infer the corresponding period, amplitude, and phase. Second, CircadiOmics is the larges annotated repository of circadian omic time series, containing over 260 experiments and 90 million individual measurements, across multiple organs and tissues, and across 9 different species. In combination, these tools enable powerful bioinformatics and systems biology analyses. The are currently being deployed in a host of different projects where they are enabling significant discoveries: both tools are publicly available over the web at: .
    Keywords:  Amplitude; Bioinformatics; Circadian; Omic; Period; Phase; Rhythms; Transcriptomic
  24. Methods Mol Biol. 2022 ;2482 153-167
      Circadian clocks can be found in nearly all eukaryotic organisms, as well as certain bacterial strains, including commensal microbiota. Exploring intercellular coupling among cell-autonomous circadian oscillators is crucial for understanding how cellular ensembles generate and sustain coherent circadian rhythms on the tissue level, and thus, rhythmic organ functions. Here we describe a protocol for studying intercellular coupling among peripheral circadian oscillators using three-dimensional spheroid cultures in order to measure coupling strength within peripheral clock networks. We use cell spheroids to simulate in vivo tissue integrity, as well as to increase complexity of cell-cell interactions and the abundance of potential coupling factors. Circadian rhythms are monitored using live-cell imaging of spheroids equipped with circadian reporters over several days.
    Keywords:  Bioluminescence recording; Circadian rhythms; Fluorescence microscopy; Intercellular coupling; Live-cell imaging; Luciferase reporter; Peripheral clocks; Time series analysis