Entrainment of Circadian Programs

Heritable circadian period length in a wild bird population

Timing is essential, but circadian clocks, which play a crucial role in timekeeping, are almost unaddressed in evolutionary ecology. A key property of circadian clocks is their free-running period length (τ), i.e. the time taken for a full cycle under constant conditions. Under laboratory conditions, concordance of τ with the ambient light-dark cycle confers major fitness benefits, but little is known about period length and its implications in natural populations. We therefore studied natural variation of circadian traits in a songbird, the great tit (Parus major), by recording locomotor activity of 98 hand-raised, wild-derived individuals. We found, unexpectedly, that the free-running period of this diurnal species was significantly shorter than 24 h in constant dim light. We furthermore demonstrate, to our knowledge for the first time in a wild vertebrate, ample genetic variation and high heritability (h(2) = 0.86 ± 0.24), implying that period length is potentially malleable by micro-evolutionary change. The observed, short period length may be a consequence of sexual selection, as offspring from extra-pair matings had significantly shorter free-running periods than their half-siblings from within-pair matings. These findings position circadian clocks in the 'real world' and underscore the value of using chronobiological approaches in evolutionary ecology. Evolutionary ecologists study variation and its fitness consequences, but often have difficulties relating behavioural variation to physiological mechanisms. The findings presented here open the possibility that properties of internal, circadian clocks affect performance in traits that are relevant to fitness and sexual selection.

Phase misalignment between suprachiasmatic neuronal oscillators impairs photic behavioral phase shifts but not photic induction of gene expression

The ability of the circadian pacemaker within the suprachiasmatic nucleus (SCN) to respond to light stimulation in a phase-specific manner constitutes the basis for photic entrainment of circadian rhythms. The neural basis for this phase specificity is unclear. We asked whether a lack of synchrony between SCN neurons, as reflected in phase misalignment between dorsomedial (dmSCN) and ventrolateral (vlSCN) neuronal oscillators in the rat, would impact the ability of the pacemaker to respond to phase-resetting light pulses. Light pulses delivered at maximal phase misalignment between the vlSCN and dmSCN oscillators increased expression of Per1 mRNA, regardless of the circadian phase of the dmSCN. However, phase shifts of locomotor activity were only observed when the vlSCN and dmSCN were phase aligned at the time of stimulation. Our results fit a model in which a vlSCN oscillator phase gates its own response to light and in turn relays light information to a dmSCN oscillator. This model predicts that the phase misalignment that results from circadian internal desynchronization could preserve the ability of light to induce gene expression within the master circadian clock but impair its ability to induce behavioral phase shifts.

Photic entrainment of period mutant mice is predicted from their phase response curves

A fundamental property of circadian clocks is that they entrain to environmental cues. The circadian genes, Period1 and Period2, are involved in entrainment of the mammalian circadian system. To investigate the roles of the Period genes in photic entrainment, we constructed phase response curves (PRC) to light pulses for C57BL/6J wild-type, Per1(-/-), Per2(-/-), and Per3(-/-) mice and tested whether the PRCs accurately predict entrainment to non-24 light-dark cycles (T-cycles) and constant light (LL). The PRCs of wild-type and Per3(-/-) mice are similar in shape and amplitude and have relatively large delay zones and small advance zones, resulting in successful entrainment to 26 h T-cycles (T26), but not T21, with similar phase angles. Per1(-/-) mice have a high-amplitude PRC, resulting in entrainment to a broad range of T-cycles. Per2(-/-) mice also entrain to a wide range of T-cycles because the advance portion of their PRC is larger than wild types. Period aftereffects following entrainment to T-cycles were similar among all genotypes. We found that the ratio of the advance portion to the delay portion of the PRC accurately predicts the lengthening of the period of the activity rhythm in LL. Wild-type, Per1(-/-), and Per3(-/-) mice had larger delay zones than advance zones and lengthened (>24 h) periods in LL, whereas Per2(-/-) mice had delay and advance zones that were equal in size and no period lengthening in LL. Together, these results demonstrate that PRCs are powerful tools for predicting and understanding photic entrainment of circadian mutant mice.

Moonstruck primates: owl monkeys (Aotus) need moonlight for nocturnal activity in their natural environment

Primates show activity patterns ranging from nocturnality to diurnality, with a few species showing activity both during day and night. Among anthropoids (monkeys, apes and humans), nocturnality is only present in the Central and South American owl monkey genus Aotus. Unlike other tropical Aotus species, the Azara's owl monkeys (A. azarai) of the subtropics have switched their activity pattern from strict nocturnality to one that also includes regular diurnal activity. Harsher climate, food availability, and the lack of predators or diurnal competitors, have all been proposed as factors favoring evolutionary switches in primate activity patterns. However, the observational nature of most field studies has limited an understanding of the mechanisms responsible for this switch in activity patterns. The goal of our study was to evaluate the hypothesis that masking, namely the stimulatory and/or inhibitory/disinhibitory effects of environmental factors on synchronized circadian locomotor activity, is a key determinant of the unusual activity pattern of Azara's owl monkeys. We use continuous long-term (6-18 months) 5-min-binned activity records obtained with actimeter collars fitted to wild owl monkeys (n =  10 individuals) to show that this different pattern results from strong masking of activity by the inhibiting and enhancing effects of ambient luminance and temperature. Conclusive evidence for the direct masking effect of light is provided by data showing that locomotor activity was almost completely inhibited when moonlight was shadowed during three lunar eclipses. Temperature also negatively masked locomotor activity, and this masking was manifested even under optimal light conditions. Our results highlight the importance of the masking of circadian rhythmicity as a determinant of nocturnality in wild owl monkeys and suggest that the stimulatory effects of dim light in nocturnal primates may have been selected as an adaptive response to moonlight. Furthermore, our data indicate that changes in sensitivity to specific environmental stimuli may have been an essential key for evolutionary switches between diurnal and nocturnal habits in primates.

VIVID interacts with the WHITE COLLAR complex and FREQUENCY-interacting RNA helicase to alter light and clock responses in Neurospora

The photoreceptor and PAS/LOV protein VIVID (VVD) modulates blue-light signaling and influences light and temperature responses of the circadian clock in Neurospora crassa. One of the main actions of VVD on the circadian clock is to influence circadian clock phase by regulating levels of the transcripts encoded by the central clock gene frequency (frq). How this regulation is achieved is unknown. Here we show that VVD interacts with complexes central for circadian clock and blue-light signaling, namely the WHITE-COLLAR complex (WCC) and FREQUENCY-interacting RNA helicase (FRH), a component that complexes with FRQ to mediate negative feedback control in Neurospora. VVD interacts with FRH in the absence of WCC and FRQ but does not seem to control the exosome-mediated negative feedback loop. Instead, VVD acts to modulate the transcriptional activity of the WCC.

Physiology of circadian entrainment

Mammalian circadian rhythms are controlled by endogenous biological oscillators, including a master clock located in the hypothalamic suprachiasmatic nuclei (SCN). Since the period of this oscillation is of approximately 24 h, to keep synchrony with the environment, circadian rhythms need to be entrained daily by means of Zeitgeber ("time giver") signals, such as the light-dark cycle. Recent advances in the neurophysiology and molecular biology of circadian rhythmicity allow a better understanding of synchronization. In this review we cover several aspects of the mechanisms for photic entrainment of mammalian circadian rhythms, including retinal sensitivity to light by means of novel photopigments as well as circadian variations in the retina that contribute to the regulation of retinal physiology. Downstream from the retina, we examine retinohypothalamic communication through neurotransmitter (glutamate, aspartate, pituitary adenylate cyclase-activating polypeptide) interaction with SCN receptors and the resulting signal transduction pathways in suprachiasmatic neurons, as well as putative neuron-glia interactions. Finally, we describe and analyze clock gene expression and its importance in entrainment mechanisms, as well as circadian disorders or retinal diseases related to entrainment deficits, including experimental and clinical treatments.

Effects of prd circadian clock mutations on FRQ-less rhythms in Neurospora

Rhythmic conidiation (spore formation) in Neurospora crassa provides a model system for investigating the molecular mechanisms of circadian rhythmicity. A feedback loop involving the frq, wc-1, and wc-2 gene products (FRQ/ WCC) is an important component of the mechanism; however, rhythmic conidiation can still be observed when these gene products are absent. The nature of the oscillator(s) that drives this FRQ-less rhythmicity (FLO) is an important question in Neurospora circadian biology. We have looked for interactions between FRQ/WCC and FLO by assaying the effects on FRQ-less rhythms of mutations known to affect the period in the presence of FRQ. We assayed 4 prd mutations (prd-1, prd-2, prd-3, and prd-4) under 2 conditions in frq(null) strains: long-period free-running rhythms in chol-1 strains grown without choline, and heat-entrainable rhythms in choline-sufficient conditions. We found effects of all 4 mutations on both types of FRQ-less rhythms. The greatest effects were seen with prd-1 and prd-2, which abolished free-running rhythms in the chol-1; frq(10) backgrounds and significantly affected entrained peak timing under heat-entrainment conditions in frq( 10) backgrounds. The prd-3 and prd-4 mutations had more subtle effects on period and stability of free-running rhythms in the chol-1; frq(10) backgrounds and had little effect on peak timing under heat-entrainment conditions in frq(10) backgrounds. These results, along with previously published evidence for effects of prd mutations on other FRQ-less rhythms, suggest that either there are common components shared between the FRQ/WCC oscillator and several FRQ-less oscillators or that there is a single oscillator driving all conidiation rhythms. We favor a model of the Neurospora circadian system in which a single FRQ-less oscillator drives conidiation and interacts with the FRQ/WCC feedback loop; the output or amplitude of the FRQ-less oscillator can be affected by many gene products and metabolic conditions that reveal FRQ-less rhythmicity. We propose that prd-1 and prd-2 are good candidates for components of the FRQ-less oscillator and that prd-3 and prd-4 act on the system mainly through effects on FRQ/WCC.

Velocity Response Curves Support the Role of Continuous Entrainment in Circadian Clocks

Circadian clocks drive endogenous oscillations in organisms across the tree of life. The Earth’s daily light/dark cycle entrains these clocks to the environment. Two major theories of light entrainment have been presented in the literature. The discrete theory emphasizes the instantaneous phase-shifting behavior of short pulses of light, and the continuous theory emphasizes changes to the period of oscillations in constant-light conditions. Historically, the primary tool for predicting and understanding discrete entrainment has been the PRC, which measures discrete adjustments to the clock’s phase. The authors present a unified theory, which relies on a velocity response curve (VRC), similar in shape to a PRC, but that describes continuous adjustments to the clock’s speed. The VRC explains data from both discrete and continuous light experiments and is therefore an invaluable tool to understand entrainment. The authors relate VRC features to specific entrainment behaviors, such as seasonal adjustments to the phase of entrainment. Furthermore, they estimate a VRC from PRC data and successfully reproduce additional PRC data. Finally, they entrain a VRC-based model to natural light/dark cycles, demonstrating the unified theory’s ability to predict clock behavior in the face of a fluctuating signal. The results indicate that a VRC-based model not only provides a comprehensive understanding of entrainment but also has excellent predictive capabilities.

Nocturnal illumination dimmer than starlight altered the circadian rhythm of adult locomotor activity of a fruit fly

The effects of nocturnal irradiance tenfold dimmer than starlight intensity on the locomotor activity rhythm of Drosophila jambulina were investigated in two types of light-dark (12 h:12 h) cycles, in which light intensity of the photophase was 10 lux while that of the scotophase was either 0 lux for control flies or 0.0006 lux for experimental flies. Activity onset in the experimental flies was approximately 5.4 h prior to lights-on, so it occurred around midnight. However, activity onset of the control flies coincided almost with the lights-on. Nevertheless, activity offset was the same in both groups, occurring at lights-off. Duration of the active phase (alpha) and activity passes/fly/cycle (APC) in the experimental flies was far greater than in controls. After-effects of the nocturnal illumination of the light-dark cycles when the flies were transferred to constant darkness were evident as the period of the free-running rhythm was shortened, alpha was lengthened, and APC was enhanced in the experimental compared to control flies. Thus, very low photic sensitivity of these flies appears to be a physiological adaptation to dim-light ambiance in its natural breeding site in the field.

The role of the neuropeptides PACAP and VIP in the photic regulation of gene expression in the suprachiasmatic nucleus

Previously, we have shown that mice deficient in either vasoactive intestinal peptide (VIP) or pituitary adenylate cyclase-activating polypeptide (PACAP) exhibit specific deficits in the behavioral response of their circadian system to light. In this study, we investigated how the photic regulation of the molecular clock within the suprachiasmatic nucleus (SCN) is altered by the loss of these closely-related peptides. During the subjective night, the magnitude of the light-induction of FOS and phosphorylated mitogen-activated protein kinase (p-MAPK) immunoreactive cells within the SCN was significantly reduced in both VIP- and PACAP-deficient mice when compared with wild-type mice. The photic induction of the clock gene Period1 (Per1) in the SCN was reduced in the VIP- but not in the PACAP-deficient mice. Baselines levels of FOS, p-MAPK or Per1 in the night were not altered by the loss of these peptides. In contrast, during the subjective day, light exposure increased the levels of FOS, p-MAPK and Per1 in the SCN of VIP-deficient mice, but not in the other genotypes. During this phase, baseline levels of these markers were reduced in the VIP-deficient mice compared with untreated controls. Finally, the loss of either neuropeptide reduced the magnitude of the light-evoked increase in Per1 levels in the adrenals in the subjective night without any change in baseline levels. In summary, our results indicate that both VIP and PACAP regulate the responsiveness of cells within the SCN to the effects of light. Furthermore, VIP, but not PACAP, is required for the appropriate temporal gating of light-induced gene expression within the SCN.

Accelerated re-entrainment to advanced light cycles in BALB/cJ mice

Circadian rhythms in mammals are coordinated by the suprachiasmatic nuclei (SCN) of the hypothalamus, which are most potently synchronized to environmental light-dark cycles. Large advances in the light-dark cycle typically yield gradual advances in activity rhythms on the order of 1-2h per day until re-entrainment is complete due to limitations on the circadian system which are not yet understood. In humans, this delay until re-entrainment is accomplished is experienced as jetlag, with accompanying symptoms of malaise, decreased cognitive performance, sleep problems and gastrointestinal distress. In these experiments, locomotor rhythms of BALB/cJ mice monitored by running wheels were shown to re-entrain to large 6- or 8-hour shifts of the light-dark cycle within 1-2 days, as opposed to the 5-7 days required for C57BL/6J mice. A single-day 6-hour advance of the LD cycle followed by release to constant darkness yielded similar phase shifts, demonstrating that exaggerated re-entrainment is not explained by masking of activity by the light-dark cycle. Responses in BALB/cJ mice were similar when monitored instead by motion detectors, indicating that wheel-running exercise does not influence the magnitude of responses. Neither brief (15 min) light exposure late during subjective nighttime nor 6-hour delays of the light-dark cycle produced exaggerated locomotor phase shifts, indicating that BALB/cJ mice do not merely experience enhanced sensitivity to light. Fos protein was expressed in cells of the SCN following acute light exposure at ZT10 of their previous light-dark cycle, a normally non-responsive time in the circadian cycle, but only in BALB/cJ (and not C57BL/6J) mice that had been subjected two days earlier to a single-day 6-hour advance of the light-dark cycle, indicating that their SCN had been advanced by that treatment. BALB/cJ mice may thus serve as a useful comparative model for studying molecular and physiological processes that limit responsiveness of circadian clocks to photic input.

Non‐Parametric Entrainment by Natural Twilight in the Microchiropteran Bat,Hipposideros SpeorisInside a Cave

The study aimed to determine the influence of repeated natural dawn and dusk twilight pulses in entraining the circadian flight activity rhythm of the microchiropteran bat, Hipposideros speoris, free-running in constant darkness in a natural cave. The bats were exposed to repeated dawn or dusk twilight pulses at eight circadian phases. All bats exposed to dawn twilight pulses were entrained by advancing transients, and the stable entrainment was reached when the onset of activity occurred about 12 h before the lights-on of the pulses, irrespective of the initial phase at which the bats were exposed to twilight. All bats exposed to dusk twilight pulses, however, were entrained by delaying transients, and the stable entrainment was reached when the onset of activity occurred about 1.6 h after the lights-on of the pulses. The entrainment caused by dawn and dusk twilight pulses is discussed in the context of the postulated two photoreceptors: the short wavelength sensitive (S) photoreceptors mediating entrainment via dusk twilight, and the medium wavelength sensitive (M) photoreceptors mediating entrainment via dawn twilight.

Effects of Temperature, Photoperiod, and Light Intensity on the Eclosion Rhythm of the High-Altitude Himalayan Strain ofDrosophila ananassae

Eclosion rhythm of the high-altitude Himalayan strain of Drosophila ananassae from Badrinath (altitude 5123 m) was temperature-dependent and at 21 degrees C, it was entrained by cycles of 12h light: 12h darkness (LD 12:12) and free-ran in constant darkness, however, it was arrhythmic at 13 degrees C or 17 degrees C under identical experimental conditions (Khare, P. V., Barnabas, R. J., Kanojiya, M., Kulkarni, A. D., Joshi, D. S. (2002). Temperature dependent eclosion rhythmicity in the high altitude Himalayan strains of Drosophila ananassae. Chronobiol. Int. 19:1041-1052). The present studies were designed to see whether or not these strains could be entrained at 13 degrees C, 17 degrees C, and 21 degrees C by two types of LD cycles in which the photoperiod at 100 lux intensity varied from 6h to 18h, and the light intensity of LD 14:10 cycles varied from 0.001 lux to 1000 lux. All LD cycles entrained this strain at 21 degrees C but not at 13 degrees C or 17 degrees C. These results demonstrate that the entrainment of eclosion rhythm depends on the ambient temperature and not on the photoperiod or light intensity of LD cycles. Thus the temperature has taken precedence over the light in the entrainment process of eclosion rhythm of the high altitude Himalayan strain of D. ananassae. This may be the result of natural selection in response to the environmental temperature at Badrinath that resembles that of the sub-Arctic region but the photoperiod or light intensity are of the subtropical region.

Natural Twilight Phase‐Response Curves for the Cave‐Dwelling Bat,Hipposideros Speoris

Phase-response curves (PRCs) for the circadian rhythm of flight activity of the microchiropteran bat (Hipposideros speoris) were determined in a cave, employing discrete natural dawn and dusk twilight pulses. These PRCs are reported for the first time for any circadian system and they are unlike other PRCs constructed for nocturnal mammals. Dawn and dusk twilight pulses evoked advance and delay phase shifts, respectively. Advance phase shifts were followed by 3 to 4 advancing transients and a subsequent shortening of free-running period (tau); whereas, the delay phase shifts were instantaneous without any transients but with a subsequent lengthening of tau.

Effects of Photophase and Altitude on Oviposition Rhythm of the Himalayan Strains ofDrosophila Ananassae

The effects of varying photophase and altitude of origin on the phase angle difference (Psi) of the circadian rhythm of oviposition during entrainment to light-dark (LD) cycles and the aftereffects of such photophases on the period of the free-running rhythm (tau) in constant darkness (DD) were evaluated in two Himalayan strains of Drosophila ananassae, the high-altitude (HA) strain from Badrinath (5,123 m above sea level=ASL) and the low-altitude (LA) strain from Firozpur (179 m ASL). The Psi (i.e., the hours from lights-on of the LD cycle to oviposition median) of both strains was determined in LD cycles in which the photophase at 100 lux varied from 6 to 18 h/24 h. The HA strain was entrained by all LD cycles except the one with 6 h photophase in which it was weakly rhythmic, but the LA strain was entrained by only three LD cycles with photophases of 10, 12, and 14 h, but photophases of 6, 8, 16, and 18 h rendered it arrhythmic. Lights-off transition of LD cycles was the phase-determining signal for both strains as oviposition medians of the HA strain occurred approximately 6 h prior to lights-off, while those of the LA strain occurred approximately 1 h after lights-off. The Psi of the HA strain increased from approximately 2 h in 8 h photophase to approximately 11 h in 18 h photophase, while that of the LA strain increased from approximately 11 h in 10 h photophase to approximately 15 h in 14 h photophase. The aftereffects of photophase of the prior entraining LD cycles on tau in DD were determined by transferring flies from LD cycles to DD. The tau of the HA strain increased from approximately 19 to approximately 25 h when transferred to DD from LD 8:16 and LD 18:6 cycles, respectively, whereas the tau of the LA strain increased from approximately 26 to approximately 28 h when transferred to DD from LD 10:14 and LD 14:10 cycles, respectively. Thus, these results demonstrate that the photophases of entraining LD cycles and the altitude of origin affected several parameters of entrainment and the period of the free-running rhythm of these strains.

Robust food anticipatory activity in BMAL1-deficient mice

Food availability is a potent environmental cue that directs circadian locomotor activity in rodents. Even though nocturnal rodents prefer to forage at night, daytime food anticipatory activity (FAA) is observed prior to short meals presented at a scheduled time of day. Under this restricted feeding regimen, rodents exhibit two distinct bouts of activity, a nocturnal activity rhythm that is entrained to the light-dark cycle and controlled by the master clock in the suprachiasmatic nuclei (SCN) and a daytime bout of activity that is phase-locked to mealtime. FAA also occurs during food deprivation, suggesting that a food-entrainable oscillator (FEO) keeps time in the absence of scheduled feeding. Previous studies have demonstrated that the FEO is anatomically distinct from the SCN and that FAA is observed in mice lacking some circadian genes essential for timekeeping in the SCN. In the current study, we optimized the conditions for examining FAA during restricted feeding and food deprivation in mice lacking functional BMAL1, which is critical for circadian rhythm generation in the SCN. We found that BMAL1-deficient mice displayed FAA during restricted feeding in 12hr light:12hr dark (12L:12D) and 18L:6D lighting cycles, but distinct activity during food deprivation was observed only in 18L:6D. While BMAL1-deficient mice also exhibited robust FAA during restricted feeding in constant darkness, mice were hyperactive during food deprivation so it was not clear that FAA consistently occurred at the time of previously scheduled food availability. Taken together, our findings suggest that optimization of experimental conditions such as photoperiod may be necessary to visualize FAA in genetically modified mice. Furthermore, the expression of FAA may be possible without a circadian oscillator that depends on BMAL1.

Strong resetting of the mammalian clock by constant light followed by constant darkness

The mammalian molecular circadian clock in the suprachiasmatic nuclei (SCN) regulates locomotor activity rhythms as well as clocks in peripheral tissues (Reppert and Weaver, 2002; Ko and Takahashi, 2006). Constant light (LL) can induce behavioral and physiological arrhythmicity by desynchronizing clock cells in the SCN (Ohta et al., 2005). We examined how the disordered clock cells resynchronize by probing the molecular clock and measuring behavior in mice transferred from LL to constant darkness (DD). The circadian locomotor activity rhythms disrupted in LL become robustly rhythmic again from the beginning of DD, and the starting phase of the rhythm in DD is specific, not random, suggesting that the desynchronized clock cells are quickly reset in an unconventional manner by the L/D transition. By measuring mPERIOD protein rhythms, we showed that the SCN and peripheral tissue clocks quickly become rhythmic again in phase with the behavioral rhythms. We propose that this resetting mechanism may be different from conventional phase shifting, which involves light induction of Period genes (Albrecht et al., 1997; Shearman et al., 1997; Shigeyoshi et al., 1997). Using our functional insights, we could shift the circadian phase of locomotor activity rhythms by 12 h using a 15 h LL treatment: essentially producing phase reversal by a single light pulse, a feat that has not been reported previously in wild-type mice and that has potential clinical utility.

Rhythmic conidiation in constant light in vivid mutants of Neurospora crassa

In Neurospora crassa, a circadian rhythm of conidiation (asexual spore formation) can be seen on the surface of agar media. This rhythm has a period of 22 hr in constant darkness (D/D). Under constant illumination (L/L), no rhythm is visible and cultures show constant conidiation. However, here we report that strains with a mutation in the vivid (vvd) gene, previously shown to code for the photoreceptor involved in photo-adaptation, exhibit conidiation rhythms in L/L as well as in D/D. The period of the rhythm of vvd strains ranges between 6 and 21 hr in L/L, depending upon the intensity of the light, the carbon source, and the presence of other mutations. Temperature compensation of the period also depends on light intensity. Dark pulses given in L/L shift the phase of the rhythm. Shifts from L/L to D/D show unexpected after effects; i.e., the short period of a vvd strain in L/L gradually lengthens over 2-3 days in D/D. The rhythm in L/L requires the white collar (wc-1) gene, but not the frequency (frq) gene. FRQ protein shows no rhythm in L/L in a vvd strain. The conidiation rhythm in L/L in vvd is therefore driven by a FRQ-less oscillator (FLO).

Activation of TGF-beta/activin signalling resets the circadian clock through rapid induction of Dec1 transcripts

The circadian clock is reset by external time cues for synchronization to environmental changes. In mammals, the light-input signalling pathway mediated by Per gene induction has been extensively studied. On the other hand, little is known about resetting mechanisms that are independent of Per induction. Here we show that activation of activin receptor-like kinase (ALK), triggered by TGF-beta, activin or alkali signals, evoked resetting of the cellular clock independently of Per induction. The resetting was mediated by an immediate-early induction of Dec1, a gene whose physiological role in the function of the circadian clock has been unclear. Acute Dec1 induction was a prerequisite for ALK-mediated resetting and upregulation was dependent on SMAD3, which was phosphorylated for activation in response to the resetting stimuli. Intraperitoneal injection of TGF-beta into wild-type or Dec1-deficient mice demonstrated that Dec1 has an essential role in phase-shift of clock gene expression in the kidney and adrenal gland. These results indicate that ALK-SMAD3-Dec1 signalling provides an input pathway in the mammalian molecular clock.

S-Phase and M-Phase Timing Are under Independent Circadian Control in the Dinoflagellate Lingulodinium

In many phytoplankton species, cell division (mitosis) usually occurs at defined times of day. This timing is also observed under constant conditions, indicating that it is regulated by a circadian clock rather than by a simple response to the light-dark cycle. For those algae with cell cycles longer than a day, the clock opens a window of opportunity for mitosis at a particular time of day through which cells in an appropriate phase of the cell cycle can pass. Although the timing of mitosis is generally studied due to ease of measurement, for some phytoplankton the timing of S-phase is also circadian. This thus raises the possibility that mitosis is not directly gated by the clock but occurs instead at a defined interval (a constant G2 length) following a circadian controlled S-phase. To determine if the clock exercises independent control over the timing of both S- and M-phase, we measured the timing of both S- and M-phase in cultures of the dinoflagellate Lingulodinium grown under a variety of different photoperiods. We interpret the phase angles of both rhythms, in particular those resulting in a change in the length of G2, as an indication that the clock independently regulates the timing of S-phase and mitosis.

Bacterial circadian programs

Twenty years ago, it was widely believed that prokaryotes were too "simple" to have evolved circadian programs. Since that time, however, the cyanobacterial circadian system has progressed from a curiosity to a major model system for analyzing clock phenomena. In addition to globally regulating gene expression, cyanobacteria are one of the only systems in which the adaptive fitness of a circadian system has been rigorously evaluated. Moreover, cyanobacteria are the only clock system in which all essential proteins of the core oscillator have been crystallized and structurally determined, namely, the KaiA, KaiB, and KaiC proteins. A biochemical oscillator can be reconstituted in vitro with these three purified Kai proteins and displays the key properties of temperature-compensated rhythmicity. This result spectacularly demonstrates that a strictly posttranslational clock is sufficient to elaborate circadian phenomena and that a transcription-translation feedback loop is not obligatory. The conjunction of structural information on essential clock proteins with a defined system that reconstitutes circadian oscillations in vitro leads to a turning point whereby biophysical and biochemical approaches bring analyses of circadian clock-work to an unprecedented level of molecular detail.

Circadian entrainment of Neurospora crassa

The circadian clock evolved under entraining conditions, yet most circadian experiments and much circadian theory are built around free-running rhythms. The interpretation of entrainment experiments is certainly more complex than that of free-running rhythms due to the relationship between exogenous and endogenous cycles. Here, we systematically describe entrainment in the simplest of the traditional eukaryotic model systems in circadian research, Neurospora crassa. This fungus forms a mass of spores (bands of conidia) each day. Over a wide range of photoperiods, these bands begin to appear at midnight, suggesting integration of neither dawn nor dusk signals alone. However, when symmetrical light/dark cycles (T cycles, each with 50% light) are applied, dusk determines the time of conidiation with a uniform, period-dependent delay in phase. This "forced" synchronization appears to be specific for the zeitgeber light because similar experiments, but using temperature, result in systematic entrainment, with bands appearing relatively later in shorter cycles and earlier in longer cycles. We find that the molecular mechanism of entrainment primarily concerns posttranscriptional regulation. Finally, we have used Neurospora to investigate acute effects of zeitgeber stimuli known as "masking."

Systems biology of mammalian circadian clocks

Systems Biology is a natural extension of molecular biology and can be defined as biology after identification of key gene(s). Systems-biological research is hence seen as a multistage process, beginning with the comprehensive identification and quantitative analysis of individual system components and their networked interactions and leading to the ability to control existing systems toward the desired state and design new ones based on an understanding of structure and underlying dynamical principles. In this chapter, we take mammalian circadian clocks as a model system and describe systems-biological approaches, including the identification of clock-controlled genes, clock-controlled cis elements, and clock transcriptional circuits driven by functional genomics; the parameter change of clock components followed by quantitative measurement; and the dynamic and quantitative perturbation of the clock and its application to one of the fundamental but yet-unsolved questions: singularity behavior of clocks. As perspective for systems-biological investigations, we also introduce the system-level dynamical questions related to the core of clocks, including delay, nonlinearity, temperature-compensation and synchronization of mammalian circadian oscillator(s), and the system-level information problems related to clocks in the environment, including the internal representation of light change through perfect adaptation and internal representation of day length through photoperiodism in mammals.

Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler

METHOD

The objective of the present article is to propose and evaluate a probabilistic approach based on Bayesian networks for modelling non-homogeneous and non-linear gene regulatory processes. The method is based on a mixture model, using latent variables to assign individual measurements to different classes. The practical inference follows the Bayesian paradigm and samples the network structure, the number of classes and the assignment of latent variables from the posterior distribution with Markov Chain Monte Carlo (MCMC), using the recently proposed allocation sampler as an alternative to RJMCMC.

RESULTS

We have evaluated the method using three criteria: network reconstruction, statistical significance and biological plausibility. In terms of network reconstruction, we found improved results both for a synthetic network of known structure and for a small real regulatory network derived from the literature. We have assessed the statistical significance of the improvement on gene expression time series for two different systems (viral challenge of macrophages, and circadian rhythms in plants), where the proposed new scheme tends to outperform the classical BGe score. Regarding biological plausibility, we found that the inference results obtained with the proposed method were in excellent agreement with biological findings, predicting dichotomies that one would expect to find in the studied systems.

AVAILABILITY

Two supplementary papers on theoretical (T) and experi-mental (E) aspects and the datasets used in our study are available from http://www.bioss.ac.uk/associates/marco/supplement/

Circadian entrainment aftereffects in suprachiasmatic nuclei and peripheral tissues in vitro

Circadian rhythms are endogenous 24-h rhythms. The suprachiasmatic nuclei (SCN) of the mammalian hypothalamus serve as the master circadian pacemaker, entraining peripheral organs which also demonstrate circadian rhythms. Entrainment to LD cycles of non-24 h duration (T-cycles) induces aftereffects on period that act to bring the intrinsic period closer to the entraining cycle. Both parametric effects, such as changes in endogenous period, and non-parametric effects of light, such as instantaneous phase shifts, act synergistically to accomplish entrainment of the SCN. It is not yet known if entrainment of peripheral oscillators similarly involves both parametric and non-parametric effects. In this study, mPer2(Luc) knockin mice were entrained to either long or short T-cycles, placed into constant darkness (DD) for 3 days to measure behavioral free-running period (FRP), and then PER2::LUC bioluminescence from SCN, spleen, esophagus, lung and thymus was measured in vitro. The FRP of SCN samples was negatively correlated with the FRP of behavioral rhythms, replicating prior results in mPer1-Luc mice. The FRP of the four peripheral oscillators tested did not correlate with behavioral rhythm FRP. Evidence that the SCN may entrain peripheral tissues by shifting phase relationships was observed, in that the phase of PER2::LUC in the SCN relative to peripheral tissues and also to the onset of behavioral activity varied between groups. Our study suggests that aftereffects on FRP may be an emergent property of the system that cannot be explained by the period changes in the system components. Further, we demonstrate that the phase relationship between the rhythm in PER2 in the SCN and these peripheral tissues is altered following T-cycle entrainment.

Serotonergic potentiation of dark pulse-induced phase-shifting effects at midday in hamsters

In mammals, resetting of the suprachiasmatic clock (SCN) by behavioral activation or serotonin (5-HT) agonists is mimicked by dark pulses, presented during subjective day in constant light (LL). Because behavioral resetting may be mediated in part by 5-HT inputs to the SCN, here we determined whether 5-HT system can modulate dark-induced phase-shifts in Syrian hamsters housed in LL. Two hours of darkness at mid-subjective day (circadian time 6; CT-6) resulted in increased concentrations of 5-HT in the SCN tissue and induction of c-FOS expression in the raphe nuclei. Injections of the 5-HT(1A/7) agonist +8-OH-DPAT or dark pulses at CT-6 induced phase-advances of the wheel-running activity rhythm and down-regulated the expression of the clock genes Per1-2 and c-FOS in the SCN in a similar way. The combination of both treatments [+8-OH-DPAT + dark pulses], however, resulted in larger phase-advances, while associated molecular changes were not significantly modified, except for the gene Dbp, in comparison to +8-OH-DPAT or dark pulses alone. Dark resetting was blocked by pre-treatment with a 5-HT(7) antagonist, but not with a 5-HT(1A) antagonist. The additive phase-shifts of two different cues to reset the SCN clock open wide the gateway for non-photic shifting, leading to new strategies in chronotherapy.

Comparative study of circadian oscillatory network models of Drosophila

The circadian clock of Drosophila is a model pathway for research in biological clock mechanisms, both with traditional experimental approaches and with emerging systems biology approaches utilizing mathematical modeling and in silico computer simulation. Dynamic diurnal oscillations are achieved by the complex interaction of components as a system, and mathematical reconstruction has proven to be an invaluable means of understanding such systematic behavior. In this study, we implemented eight published models of the Drosophila circadian clock in Systems Biology Markup Language (SBML) for comparative systems biology studies using E-Cell Simulation Environment version 3, to examine the system-level requirements for the clock mechanism to be robust, by calculating the period and amplitude sensitivity coefficients with simulation experiments. While all models were generally robust as determined by the network topology of the oscillatory feedback loop structure, existing models place relatively strong emphasis on transcription regulation, although this is a limitation on robustness. We suggest that more comprehensive modeling including protein phosphorylation, polymerization, and nuclear transport with regard to amplitude sensitivity will be necessary for understanding the light entrainment and temperature compensation of circadian clocks.

The PAS/LOV protein VIVID controls temperature compensation of circadian clock phase and development in Neurospora crassa

Circadian clocks are cellular timekeepers that regulate aspects of temporal organization on daily and seasonal time scales. To allow accurate time measurement, the period lengths of clocks are conserved in a range of temperatures--a phenomenon known as temperature compensation. Temperature compensation of circadian clock period aids in maintaining a stable "target time" or phase of clock-controlled events. Here we show that the Neurospora protein VIVID (VVD) buffers the circadian system against temperature fluctuations. In vvd-null mutants, the circadian period of clock-controlled events such as asexual sporulation (conidiation) is temperature compensated, but the phase of this clock time marker is not. Consistent with delayed conidiation at lower temperatures in vvd(KO) strains, the levels of vvd gene products in the wild type increase with decreasing temperatures. Moreover, vvd(C108A) mutants that lack the light function of VVD maintain a dark activity that transiently influences the phase of conidiation, indicating that VVD influences the time of conidiation downstream from the clock. FREQUENCY (FRQ) phosphorylation is altered in a vvd(KO) strain, suggesting a mechanism by which VVD can influence the timing of clock-controlled processes in the dark. Thus, temperature compensation of clock-controlled output is a key factor in maintaining temperature compensation of the entire circadian system.

Phase resetting and phase singularity of an insect circannual oscillator

In circadian rhythms, the shape of the phase response curves (PRCs) depends on the strength of the resetting stimulus. Weak stimuli produce Type 1 PRCs with small phase shifts and a continuous transition between phase delays and advances, whereas strong stimuli produce Type 0 PRCs with large phase shifts and a distinct break point at the transition between delays and advances. A stimulus of an intermediate strength applied close to the break point in a Type 0 PRC sometimes produces arrhythmicity. A PRC for the circannual rhythm was obtained in pupation of the varied carpet beetle, Anthrenus verbasci, by superimposing a 4-week long-day pulse (a series of long days for 4 weeks) over constant short days. The shape of this PRC closely resembles that of the Type 0 PRC. The present study shows that the PRC to 2-week long-day pulses was Type 1, and that a 4-week long-day pulse administered close to the PRC's break point induced arrhythmicity in pupation. It is, therefore, suggested that circadian and circannual oscillators share the same mode in phase resetting to the stimuli.

A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock

Circadian clocks rhythmically coordinate biological processes in resonance with the environmental cycle. The clock function relies on negative feedback loops that generate 24-h rhythms in multiple outputs. In Arabidopsis thaliana, the clock component TIMING OF CAB EXPRESSION1 (TOC1) integrates the environmental information to coordinate circadian responses. Here, we use chromatin immunoprecipitation as well as physiological and luminescence assays to demonstrate that proper photoperiodic phase of TOC1 expression is important for clock synchronization of plant development with the environment. Our studies show that TOC1 circadian induction is accompanied by clock-controlled cycles of histone acetylation that favor transcriptionally permissive chromatin structures at the TOC1 locus. At dawn, TOC1 repression relies on the in vivo circadian binding of the clock component CIRCADIAN CLOCK ASSOCIATED1 (CCA1), while histone deacetylase activities facilitate the switch to repressive chromatin structures and contribute to the declining phase of TOC1 waveform around dusk. The use of cca1 late elongated hypocotyl double mutant and CCA1-overexpressing plants suggests a highly repressing function of CCA1, antagonizing H3 acetylation to regulate TOC1 mRNA abundance. The chromatin remodeling activities relevant at the TOC1 locus are distinctively modulated by photoperiod, suggesting a mechanism by which the clock sets the phase of physiological and developmental outputs.

The Neurospora crassa circadian clock

The filamentous fungus Neurospora crassa is one of a handful of model organisms that has proven tractable for dissecting the molecular basis of a eukaryotic circadian clock. Work on Neurospora and other eukaryotic and prokaryotic organisms has revealed that a limited set of clock genes and clock proteins are required for generating robust circadian rhythmicity. This molecular clockwork is tuned to the daily rhythms in the environment via light- and temperature-sensitive pathways that adjust its periodicity and phase. The circadian clockwork in turn transduces temporal information to a large number of clock-controlled genes that ultimately control circadian rhythms in physiology and behavior. In summarizing our current understanding of the molecular basis of the Neurospora circadian system, this chapter aims to elucidate the basic building blocks of model eukaryotic clocks as we understand them today.

Sildenafil accelerates reentrainment of circadian rhythms after advancing light schedules

Mammalian circadian rhythms are generated by a master clock located in the suprachiasmatic nuclei and entrained by light-activated signaling pathways. In hamsters, the mechanism responsible for light-induced phase advances involves the activation of guanylyl cyclase, cGMP and its related kinase (PKG). It is not completely known whether interference with this pathway affects entrainment of the clock, including adaptation to changing light schedules. Here we report that cGMP-specific phosphodiesterase 5 is present in the hamster suprachiasmatic nuclei, and administration of the inhibitor sildenafil (3.5 mg/kg, i.p.) enhances circadian responses to light and decreases the amount of time necessary for reentrainment after phase advances of the light-dark cycle. These results suggest that sildenafil may be useful for treatment of circadian adaptation to environmental changes, including transmeridian eastbound flight schedules.

Phase responses in the circannual rhythm of the varied carpet beetle, Anthrenus verbasci, under naturally changing day length

In the varied carpet beetle, Anthrenus verbasci, we examined the effects on the circannual pupation rhythm of a short-day or long-day pulse under naturally changing day length at a constant 20 degrees C. A short-day pulse for 4 weeks caused a prominent phase delay or advance under constant long days, but had little or no effect on the phase under naturally changing day length between 4 August and 24 November. A long-day pulse for 4 weeks given under naturally changing day length caused a phase shift in the first pupation group, as under constant short days. A long-day pulse given on 4 August, 1 September, or 29 September caused a phase delay, and a pulse given on 27 October or 24 November caused a phase advance. Pupation was least synchronous just before the transition from delaying to advancing. However, the magnitude of phase delays was much smaller under natural day length than under short days. In the second pupation group, larvae pupated at the same time as in the control experiment without a long-day pulse, and this result can be attributed to entrainment to the geophysical year by long days in spring and summer.

Monitoring and analyzing Drosophila circadian locomotor activity

In the 1970s, the intriguing discovery of autonomous circadian rhythmicity at the behavioral level in Drosophila set the starting point for one of the most remarkably rapid advancements in the understanding of the genetic and molecular bases of a complex behavioral trait. To this end, the design of appropriate electronic devices, apt to continuously monitor behavioral activity, has proven to be fundamental to such progress. In particular, most of the mutational screens performed to date in the search for genes involved in circadian rhythmicity were based on monitoring Drosophila mutants for alterations in the circadian pattern of locomotor activity. Many different experimental paradigms, based on the use of circadian locomotor activity monitors, have been developed. Experiments can be designed to determine (1) the natural period, (2) the capacity to adapt to day-night cycles with photoperiods of differing length, and (3) the phase of the circadian activity cycles with respect to the entraining stimulus. Here we describe some of the rationale and the steps required to set up experiments to monitor circadian locomotor activity in Drosophila. Suggestions for the statistical analysis of the data obtained in such experiments are also provided.

Constitutive activation of the ERK-MAPK pathway in the suprachiasmatic nuclei inhibits circadian resetting

Circadian entrainment involves photic stimulation of the suprachiasmatic molecular oscillator, including activation of the ERK/MAP kinase, which is phosphorylated endogenously during the day and in response to light during the night. We aimed to disrupt the diurnal cycle of ERK phosphorylation by in vivo transfection of a constitutively active form of MEK, a MAPK kinase. This procedure did not affect normal circadian parameters, but completely inhibited light-induced phase advances. Therefore, circadian regulation of the ERK pathway is not essential for the normal mechanism of the biological clock, but it is fundamental as an interface with environmental entrainment by light.