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PubMed1996

Use of a high stringency differential display screen for identification of retinal mRNAs that are regulated by a circadian clock.

We report here the initiation of a systematic screen to identify clock-controlled mRNAs from the retina of Xenopus laevis using mRNA differential display. Xenopus retina contains an endogenous circadian clock located within the photoreceptor layer. The retinal block controls many aspects of physiology, including gene transcription. This screen uses differential display, a PCR based procedure, to compare retinal mRNA populations at different times of day in constant darkness, for identification of messages that exhibit rhythmic expression. Out of approx. 2000 mRNAs that we have screened to date, we have identified four candidates for clock-controlled mRNAs. Initial characterization of one of these PCR products shows that it recognizes a pair of mRNA bands on Northern blots that exhibit high amplitude rhythms. This pair of messages is called RM1 and shows peak levels of expression in the subjective night. In situ hybridization shows that this clock-controlled message is specifically localized to the clock containing photoreceptor cell layer within the retina. Identification of new messages that are under the control of the circadian clock has broad relevance in retinal physiology and provides an opportunity to gain insight into the molecular mechanism of vertebrate circadian control.

Animals↗
PubMed2002

A switch from diurnal to nocturnal activity in S. ehrenbergi is accompanied by an uncoupling of light input and the circadian clock.

The subterranean mole rat Spalax ehrenbergi superspecies represents an extreme example of adaptive visual and neuronal reorganization. Despite its total visual blindness, its daily activity rhythm is entrainable to light-dark cycles, indicating that it can confer light information to the clock. Although most individuals are active during the light phase under laboratory conditions (diurnal animals), some individuals switch their activity period to the night (nocturnal animals). Similar to other rodents, the Spalax circadian clock is driven by a set of clock genes, including the period (sPer) genes. In this work, we show that diurnal mole rats express the Per genes sPer1 and sPer2 with a peak during the light period. Light can synchronize sPer gene expression to an altered light-dark cycle and thereby reset the clock. In contrast, nocturnal Spalax express sPer2 in the dark period and sPer1 in a biphasic manner, with a light-dependent maximum during the day and a second light-independent maximum during the night. Although sPer1 expression remains light inducible, this is not sufficient to reset the molecular clockwork. Hence, the strict coupling of light, Per expression, and the circadian clock is lost. This indicates that Spalax can dissociate the light-driven resetting pathway from the central clock oscillator.

Animals↗
PubMed2026

Sex-specific biological aging clocks across organs and omics.

Sex differentially shapes aging, neurodevelopment and neurodegenerative diseases such as Alzheimer's disease (AD). However, most biological aging clocks (artificial intelligence-predicted age minus chronological age) were trained on sex-pooled samples and implicitly assume sex invariance.Here we developed 38 sex-specific biological aging clocks across 15 organ systems. We first demonstrate the importance of sex-stratified training for constructing sex-specific healthy normative references and then reveal marked divergence between female and male clocks. Key genetic parameters and Mendelian randomization results indicate that organ-specific aging liability and its relationships to cardiometabolic, endocrine and mental traits are configured differently in females and males. Proteomic analyses identify distinct, organ-resolved synaptic, immune, vascular and metabolic networks that differentially track female and male biological aging. In longitudinal survival analyses, sex-specific clocks predict whole-body systemic diseases and all-cause mortality in a sex-dependent and organ-dependent manner. Further analyses reveal sex-dependent associations between the brain aging clock and cognitive decline trajectory during a preclinical AD clinical trial. Sex-stratified clocks may offer distinct value by defining biological age against sex-appropriate normative references and revealing sex-dependent genetic, molecular and clinical signatures that pooled models may obscure. Meanwhile, sex-pooled and sex-interaction approaches remain valuable, as human aging and disease also share fundamental biological similarities between females and males. Together, these findings reveal sex-specific biological aging signatures in aging, AD and systemic health, highlighting the need for explicitly sex-stratified modeling approaches.

Journal Article↗
PubMed2001

Light regulation of circadian clock-controlled gene expression in rice.

Using transgenic rice seedlings expressing a firefly luciferase (luc) gene under the control of a rice CAB (chlorophyll a/b binding protein) promoter, we demonstrated how light affects circadian clocks in the transcription of the CAB gene. Rhythmic luc expression was observed for more than 5 d under constant light and dark (DD) conditions after light/dark entrainment. After a light pulse was applied at different time points in DD various temporal patterns of CAB gene expression were individually observed. We first examined two distinct properties related to the entrainment mechanism of the circadian clock: fluence-rate dependence of free-running periods (FRPs) and phase resetting by a light pulse. Although fluence-rate dependent shortening of FRP was demonstrated, the FRP in DD was almost equal to that in constant light of a middle fluence-rate, indicating that this fluence-rate dependence may not fully describe the entrainment of the circadian clock in rice. Typical phase responses of the circadian clock by a single light pulse were also observed at the transcriptional level in rice seedlings. Thus, the phase resettings upon the light/dark transitions of daily cycles may be sufficient to explain the entrainment mechanisms of rice. We have further demonstrated that, in addition to having a gating effect to acute response, a light pulse can activate the circadian clock-controlled CAB1R gene expression at the first circadian peak in a phase-dependent manner. This suggests that light activates circadian clock activity in the diurnal CAB gene expression under daily light/dark cycles.

Circadian Rhythm↗
PubMed2004

Insight into molecular core clock mechanism of embryonic and early postnatal rat suprachiasmatic nucleus.

Rhythmicity of the rat suprachiasmatic nucleus (SCN), a site of the circadian clock, develops prenatally. A molecular clockwork responsible for the rhythmicity consists of clock genes and their negative and positive transcriptional-translational feedback loops. The aim of the present study was to discover the development of the clockwork during ontogenesis. Daily profiles of Per1, Per2, Cry1, Bmal1, and Clock mRNA in the SCN of fetuses at the embryonic day (E)19 and of newborn rats at the postnatal day (P)3 and P10 were assessed by the in situ hybridization method. In addition, daily profiles of PER1, PER2, and CRY1 proteins at E19 were assessed by immunohistochemistry. As early as at E19, all the studied clock genes were already expressed in the SCN. However, no SCN rhythm in their expression was detected; Per1, Cry1, and Clock mRNA levels were low, whereas Bmal1 mRNA levels were high and Per2 mRNA levels were medium. Moreover, no rhythms of PER1, PER2, and CRY1 were detectable, as no immunoreactive cells were present at E19. At P3, rhythms in Per1, Per2, Cry1, and Bmal1, but not in Clock mRNA, were expressed in the SCN. The rhythm matured gradually; at P10, the amplitude of Per1, Per2, and Bmal1 mRNA rhythms was more pronounced than at P3. Altogether, the data show a gradual development of both the positive and negative elements of the molecular clockwork, from no detectable rhythmicity at E19 to highly developed rhythms at P10.

Animals↗
PubMed1998

Glyceraldehyde-3-phosphate dehydrogenase is regulated on a daily basis by the circadian clock.

Circadian clocks function to govern a wide range of rhythmic activities in organisms. An integral part of rhythmicity is the daily control of target genes by the clock. Here we describe the sequence and analysis of a novel clock-controlled gene, ccg-7, showing similarity to glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme widely used as a constitutive control in a variety of systems. That ccg-7 encodes GAPDH was confirmed by demonstrating that in vitro synthesized CCG-7 possesses GAPDH activity. Rhythms in both ccg-7 mRNA accumulation and CCG-7 (GAPDH) activity are observed in a clock wild-type strain where the peak in GAPDH activity lags several hours behind the peak in ccg-7 mRNA accumulation in the late night. Together with our previous observation that ccg-7 mRNA is not developmentally regulated, we show that ccg-7 is not induced by environmental stresses such as glucose or nitrogen deprivation (which also trigger development), heat shock, or osmotic stress. Thus, the finding that GAPDH is clock-regulated points to a specific role for the circadian clock in controlling aspects of general metabolism and provides evidence for circadian regulation of a gene found in most living organisms.

Amino Acid Sequence↗
PubMed2002

The p42/44 mitogen-activated protein kinase pathway couples photic input to circadian clock entrainment.

In mammals, the suprachiasmatic nuclei (SCN) of the hypothalamus function as the major biological clock. SCN-dependent rhythms of physiology and behavior are regulated by changes in the environmental light cycle. Currently, the second messenger signaling events that couple photic input to clock entrainment have yet to be well characterized. Recent work has revealed that photic stimulation during the night triggers rapid activation of the p42/44 mitogen activated protein kinase (MAPK) pathway in the SCN. The MAPK signal transduction pathway is a potent regulator of numerous classes of transcription factors and has been shown to play a role in certain forms of neuronal plasticity. These observations led us to examine the role of the MAPK pathway in clock entrainment. Here we report that pharmacological disruption of light-induced MAPK pathway activation in the SCN uncouples photic input from clock entrainment, as assessed by locomotor activity phase. In the absence of photic stimulation, transient disruption of MAPK signaling in the SCN did not alter clock-timing properties. We also report that signaling via the Ca(2+)/calmodulin kinase pathway functions upstream of the MAPK pathway, coupling light to activation of the MAPK pathway. Together these results delineate key intracellular signaling events that underlie light-induced clock entrainment.

Animals↗
PubMed2000

Developmental progression of clock face drawing in children.

The clock drawing test has been routinely administered by many neuropsychologists as part of their testing battery with the adult population. Our study investigated the development of clock face drawing in normal children ages 6 to 12 years. Conceptualization of time and construction of the clock face were assessed by an adapted scoring system developed as part of the investigation. As a group, the results indicated an upward progression with regard to the concept of time through age 8 and clock construction through age 12. Results further demonstrated that number reversals were more frequent among left-handers but were no longer evident by age 7 regardless of handedness. It also was determined that left visuospatial neglect specific to the upper quadrant was relatively common in 6- and 7-year olds but not evidenced by age 8. Given the pattern of the findings, it is likely that the neglect was secondary to poor planning and not a visuo-spatial deficit. In general, development of clock face drawing most closely paralleled that of frontal lobe maturation. Implications of these findings and the usefulness of clock face drawing with the pediatric population are presented.

Age Factors↗
PubMed2005

Effects of light and food schedules on liver and tumor molecular clocks in mice.

BACKGROUND: Disrupted circadian coordination accelerates malignant growth, but the molecular mechanism is unclear. METHODS: Healthy or Glasgow osteosarcoma-bearing mice (n = 162) were synchronized with light and darkness over 2-3 weeks, submitted to an 8-hour advance onset of light every 2 days (chronic jet lag) to disrupt circadian coordination, or submitted to chronic jet lag and meal timing to prevent molecular clock alteration. The expression of molecular clock genes and of the cell cycle genes c-Myc and p53 in liver and tumor was determined with quantitative reverse transcription-polymerase chain reaction at six circadian times over a 24-hour period of light and darkness and analyzed with analysis of variance and cosinor. Tumor weight was measured daily over the course of the experiment. All statistical tests were two-sided. RESULTS: In synchronized mice, mean mRNA levels of clock genes Rev-erbalpha, Per2, and Bmal1 varied by 206-, four-, and 26-fold, respectively, over the 24 hours in healthy mouse liver; by 36-, 35-, and 32-fold in the livers of tumor-bearing mice; and by 9.4-, 5.5-, and sixfold in tumor tissue (P = .046 to <.001). In mice subjected to chronic jet lag, the periodic changes were dampened and the clock gene rhythms were temporally shifted in liver and ablated in tumor, and tumor growth was accelerated. Meal timing reversed the chronic jet lag-induced alterations in Rev-erbalpha and Per2 expression in liver and of all three clock genes in tumor and slowed tumor growth. Tumor growth differed as a function of light and feeding schedules (P = .04). No obvious rhythm was detected for p53 or c-Myc in liver or tumor tissues of synchronized mice. In healthy mice subjected to chronic jet lag, the mean level of p53 expression was cut in half (P = .002), and a 12-fold circadian variation in c-Myc mRNA level (P = .03) was induced in the liver of healthy mice, whereas complex expression patterns were found in the liver and tumor of tumor-bearing mice. CONCLUSIONS: Altered light-dark or feeding schedules modified the expression of molecular clock genes and genes involved in carcinogenesis and tumor progression.

Analysis of Variance↗
PubMed2006

Conserved expression profiles of circadian clock-related genes in two Lemna species showing long-day and short-day photoperiodic flowering responses.

The Lemna genus is a group of monocotyledonous plants with tiny, floating bodies. Lemna gibba G3 and L. paucicostata 6746 were once intensively analyzed for physiological timing systems of photoperiodic flowering and circadian rhythms since they showed obligatory and sensitive photoperiodic responses of a long-day and a short-day plant, respectively. We attempted to approach the divergence of biological timing systems at the molecular level using these plants. We first employed molecular techniques to study their circadian clock systems. We developed a convenient bioluminescent reporter system to monitor the circadian rhythms of Lemna plants. As in Arabidopsis, the Arabidopsis CCA1 promoter produced circadian expression in Lemna plants, though the phases and the sustainability of bioluminescence rhythms were somewhat diverged between them. Lemna homologs of the Arabidopsis clock-related genes LHY/CCA1, GI, ELF3 and PRRs were then isolated as candidates for clock-related genes in these plants. These genes showed rhythmic expression profiles that were basically similar to those of Arabidopsis under light-dark conditions. Results from co-transfection assays using the bioluminescence reporter and overexpression effectors suggested that the LHY and GI homologs of Lemna can function in the circadian clock system like the counterparts of Arabidopsis. All these results suggested that the frame of the circadian clock appeared to be conserved not only between the two Lemna plants but also between monocotyledons and dicotyledons. However, divergence of gene numbers and expression profiles for LHY/CCA1 homologs were found between Lemna, rice and Arabidopsis, suggesting that some modification of clock-related components occurred through their evolution.

Araceae↗
PubMed2004

Clock drawing errors in dementia: neuropsychological and neuroanatomical considerations.

OBJECTIVES: A clock drawing test scoring system is presented to explore the neuropsychological/neuroanatomic components underlying clock drawing in patients initially diagnosed with Alzheimer disease, ischemic vascular dementia associated with white matter alterations, and Parkinson disease. METHODS: Fourteen clock drawing test errors were scored to create 4 clock drawing test subscales that assess different underlying cognitive operations. RESULTS: In the command condition, errors on the Time subscale were correlated with impairment on executive control measures. In the copy condition, errors on the Perseveration/Pull to Stimulus subscale was also correlated with executive control measures. Patients presenting with mild (low) magnetic resonance imaging white matter alterations, significant (high) white matter alterations, and Parkinson disease were compared. In the command condition, the low white matter alterations group made fewer total errors than the Parkinson disease group. In the copy condition, the low white matter alterations group made fewer errors on the Time, Spatial Layout, and Perseveration/Pull to Stimulus clock drawing test subscales than the high white matter alterations or Parkinson disease groups. Few differences were noted between the high white matter alterations and Parkinson disease groups. DISCUSSION: Our data suggest that heavy demands on executive control associated with the interruption of large-scale cortical-subcortical neural networks underlie impairment in clock drawing in mild dementia.

Aged↗
PubMed2001

The Neurospora circadian clock: simple or complex?

The fungus Neurospora crassa is being used by a number of research groups as a model organism to investigate circadian (daily) rhythmicity. In this review we concentrate on recent work relating to the complexity of the circadian system in this organism. We discuss: the advantages of Neurospora as a model system for clock studies; the frequency (frq), white collar-1 and white collar-2 genes and their roles in rhythmicity; the phenomenon of rhythmicity in null frq mutants and its implications for clock mechanisms; the study of output pathways using clock-controlled genes; other rhythms in fungi; mathematical modelling of the Neurospora circadian system; and the application of new technologies to the study of Neurospora rhythmicity. We conclude that there may be many gene products involved in the clock mechanism, there may be multiple interacting oscillators comprising the clock mechanism, there may be feedback from output pathways onto the oscillator(s) and from the oscillator(s) onto input pathways, and there may be several independent clocks coexisting in one organism. Thus even a relatively simple lower eukaryote can be used to address questions about a complex, networked circadian system.

Circadian Rhythm↗
PubMed2005

The PAS/LOV protein VIVID supports a rapidly dampened daytime oscillator that facilitates entrainment of the Neurospora circadian clock.

A light-entrainable circadian clock controls development and physiology in Neurospora crassa. Existing simple models for resetting based on light pulses (so-called nonparametric entrainment) predict that constant light should quickly send the clock to an arrhythmic state; however, such a clock would be of little use to an organism in changing photoperiods in the wild, and we confirm that true, albeit dampened, rhythmicity can be observed in extended light. This rhythmicity requires the PAS/LOV protein VIVID (VVD) that acts, in the light, to facilitate expression of an oscillator that is related to, but distinguishable from, the classic FREQUENCY/WHITE-COLLAR complex (FRQ/WCC)-based oscillator that runs in darkness. VVD prevents light resetting of the clock at dawn but, by influencing frq RNA turnover, promotes resetting at dusk, thereby allowing the clock to run through the dawn transition and take its phase cues from dusk. Consistent with this, loss of VVD yields a clock whose performance follows the simple predictions of earlier models, and overexpression of VVD restores rhythmicity in the light and sensitivity of phase to the duration of the photoperiod.

Circadian Rhythm↗
PubMed1992

The Neurospora circadian clock-controlled gene, ccg-2, is allelic to eas and encodes a fungal hydrophobin required for formation of the conidial rodlet layer.

The Neurospora crassa clock-controlled gene (ccg-2) is transcriptionally activated by the circadian clock in a time-of-day-specific manner. Transcript and sequence analyses of ccg-2 reveal that the predicted Ccg-2 polypeptide bears significant similarity to a class of low-molecular-weight, cysteine-rich, hydrophobic proteins (hydrophobins), first identified in Schizophyllum, and including the product of the developmentally regulated Aspergillus gene, rodletless, required for spore surface rodlets. Allelism between ccg-2 and easily wettable (eas) (one of the first developmental genetic loci identified in Neurospora) was predicted on the basis of this similarity, their close genetic linkage, and previous findings demonstrating that eas mutants lack rodlets. In this study allelism is confirmed experimentally by showing that (1) transformation of an eas mutant strain with ccg-2 DNA results in phenotypic complementation, including restoration of surface rodlets, (2) inactivation of the ccg-2 gene, by RIP, results in an eas phenotype including loss of rodlet fascicles, and (3) the original eas strain has dramatically reduced levels of ccg-2 mRNA. Thus, the clock-controlled ccg-2 gene encodes an integral component of fungal asexual spores important for spore dispersal. The dramatic reduction of ccg-2 expression in the eas mutant has no apparent effect on the normal operation of the circadian clock, confirming that there is no feedback of this clock output on the oscillator itself. These data, in conjunction with the previous observation that ccg-2 is light induced, serve to focus attention on the dual interacting role of light and the circadian clock in the regulation of fungal spore development.

Alleles↗
PubMed2006

Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock.

The circadian clock of the honey bee is implicated in ecologically relevant complex behaviors. These include time sensing, time-compensated sun-compass navigation, and social behaviors such as coordination of activity, dance language communication, and division of labor. The molecular underpinnings of the bee circadian clock are largely unknown. We show that clock gene structure and expression pattern in the honey bee are more similar to the mouse than to Drosophila. The honey bee genome does not encode an ortholog of Drosophila Timeless (Tim1), has only the mammalian type Cryptochrome (Cry-m), and has a single ortholog for each of the other canonical "clock genes." In foragers that typically have strong circadian rhythms, brain mRNA levels of amCry, but not amTim as in Drosophila, consistently oscillate with strong amplitude and a phase similar to amPeriod (amPer) under both light-dark and constant darkness illumination regimes. In contrast to Drosophila, the honey bee amCYC protein contains a transactivation domain and its brain transcript levels oscillate at virtually an anti-phase to amPer, as it does in the mouse. Phylogenetic analyses indicate that the basal insect lineage had both the mammalian and Drosophila types of Cry and Tim. Our results suggest that during evolution, Drosophila diverged from the ancestral insect clock and specialized in using a set of clock gene orthologs that was lost by both mammals and bees, which in turn converged and specialized in the other set. These findings illustrate a previously unappreciated diversity of insect clockwork and raise critical questions concerning the evolution and functional significance of species-specific variation in molecular clockwork.

Amino Acid Motifs↗
PubMed2002

The circadian clock that controls gene expression in Arabidopsis is tissue specific.

The expression of CHALCONE SYNTHASE (CHS) expression is an important control step in the biosynthesis of flavonoids, which are major photoprotectants in plants. CHS transcription is regulated by endogenous programs and in response to environmental signals. Luciferase reporter gene fusions showed that the CHS promoter is controlled by the circadian clock both in roots and in aerial organs of transgenic Arabidopsis plants. The period of rhythmic CHS expression differs from the previously described rhythm of chlorophyll a/b-binding protein (CAB) gene expression, indicating that CHS is controlled by a distinct circadian clock. The difference in period is maintained in the wild-type Arabidopsis accessions tested and in the de-etiolated 1 and timing of CAB expression 1 mutants. These clock-affecting mutations alter the rhythms of both CAB and CHS markers, indicating that a similar (if not identical) circadian clock mechanism controls these rhythms. The distinct tissue distribution of CAB and CHS expression suggests that the properties of the circadian clock differ among plant tissues. Several animal organs also exhibit heterogeneous circadian properties in culture but are believed to be synchronized in vivo. The fact that differing periods are manifest in intact plants supports our proposal that spatially separated copies of the plant circadian clock are at most weakly coupled, if not functionally independent. This autonomy has apparently permitted tissue-specific specialization of circadian timing.

Acyltransferases↗
PubMed2000

Cryptochromes are required for phytochrome signaling to the circadian clock but not for rhythmicity.

The circadian clock is entrained to the daily cycle of day and night by light signals at dawn and dusk. Plants make use of both the phytochrome (phy) and cryptochrome (cry) families of photoreceptors in gathering information about the light environment for setting the clock. We demonstrate that the phytochromes phyA, phyB, phyD, and phyE act as photoreceptors in red light input to the clock and that phyA and the cryptochromes cry1 and cry2 act as photoreceptors in blue light input. phyA and phyB act additively in red light input to the clock, whereas cry1 and cry2 act redundantly in blue light input. In addition to the action of cry1 as a photoreceptor that mediates blue light input into the clock, we demonstrate a requirement of cry1 for phyA signaling to the clock in both red and blue light. Importantly, Arabidopsis cry1 cry2 double mutants still show robust rhythmicity, indicating that cryptochromes do not form a part of the central circadian oscillator in plants as they do in mammals.

Base Sequence↗
PubMed2006

The proteasome-dependent degradation of CKB4 is regulated by the Arabidopsis biological clock.

Most organisms have evolved an internal timing mechanism, the circadian clock, that is able to generate and maintain 24 h rhythmic oscillation in molecular, biochemical and metabolic activities. In Arabidopsis, the clock-dependent synchronization of physiology with the environment is essential for successful growth and development. The mechanisms of the Arabidopsis clockwork have been described as transcriptional feedback loops at the core of the oscillator. However, an increasing body of evidence points towards a key role of post-translational regulation of clock components as an essential mechanism of circadian function. Here, we identify CKB4, a CK2 regulatory subunit, as a component of the Arabidopsis circadian system. We demonstrate that the nuclear-localized CKB4 protein exists in vivo as different isoforms, resulting from phosphorylation on serine residues. Our findings show that the phosphorylated isoforms are the preferred substrate for ubiquitination and degradation by the proteasome pathway. We provide evidence of the involvement of the biological clock in the circadian regulation of CKB4 protein abundance, which itself is important for an accurate control of circadian period by the clock. Overexpression of CKB4 results in elevated CK2 overall activity and period-shortening of clock-controlled genes peaking at different phase angles. Restriction of CKB4 protein phosphorylation and/or degradation to specific phases within the circadian cycle might provide the cell with a fine-tuning mechanism to selectively regulate the CK2 phosphorylation activity on specific substrates.

Amino Acid Sequence↗