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PubMed2004

Stability of atomic clocks based on entangled atoms.

We analyze the effect of realistic noise sources for an atomic clock consisting of a local oscillator that is actively locked to a spin-squeezed (entangled) ensemble of N atoms. We show that the use of entangled states can lead to an improvement of the long-term stability of the clock when the measurement is limited by decoherence associated with instability of the local oscillator combined with fluctuations in the atomic ensemble's Bloch vector. Atomic states with a moderate degree of entanglement yield the maximal clock stability, resulting in an improvement that scales as N(1/6) compared to the atomic shot noise level.

Journal Article↗

PubMed2005

High-accuracy optical clock via three-level coherence in neutral bosonic 88Sr.

An optical atomic clock scheme is proposed that utilizes two lasers to establish coherent coupling between the 5s2 1S0 ground state of 88Sr and the first excited state, 5s5p 3P0. The coupling is mediated by the broad 5s5p 1P1 state, exploiting the phenomenon of electromagnetically induced transparency. The effective linewidth of the clock transition can be chosen at will by adjusting the laser intensity. By trapping the 88Sr atoms in an optical lattice, long interaction times with the two lasers are ensured; Doppler and recoil effects are eliminated. Based on a careful analysis of systematic errors, a clock accuracy of better than 2 x 10(-17) is expected.

Journal Article↗

PubMed2006

Hyperpolarizability effects in a Sr optical lattice clock.

We report the observation of a higher-order frequency shift due to the trapping field in a (87)Sr optical lattice clock. We show that, at the magic wavelength of the lattice, where the first-order term cancels, the higher-order shift will not constitute a limitation to the fractional accuracy of the clock at a level of 10(-18). This result is achieved by operating the clock at very high trapping intensity up to 400 kW/cm(2) and by a specific study of the effect of the two two-photon transitions near the magic wavelength.

Journal Article↗

PubMed2006

Accurate optical lattice clock with 87Sr atoms.

We report a frequency measurement of the 1S0-3P0 transition of 87Sr atoms in an optical lattice clock. The frequency is determined to be 429 228 004 229 879(5) Hz with a fractional uncertainty that is comparable to state-of-the-art optical clocks with neutral atoms in free fall. The two previous measurements of this transition were found to disagree by about 2 x 10(-13), i.e., almost 4 times the combined error bar and 4 to 5 orders of magnitude larger than the claimed ultimate accuracy of this new type of clocks. Our measurement is in agreement with one of these two values and essentially resolves this discrepancy.

Journal Article↗

PubMed2004

Differential expression on a daily basis of plastid sigma factor genes from the moss Physcomitrella patens. Regulatory interactions among PpSig5, the circadian clock, and blue light signaling mediated by cryptochromes.

The nuclear-encoded plastid sigma factors are supposed to be a regulatory subunit of the multisubunit bacteria-type plastid RNA polymerase. We studied here whether or not three genes, PpSig1, PpSig2, and PpSig5 encoding plastid sigma factors, are controlled by the circadian clock and/or by blue light signaling in the moss Physcomitrella patens. Among the three PpSig genes, only PpSig5 was clearly controlled by the circadian clock. In contrast to the differential regulation on a daily timescale, a pulse of blue light induced the expression of all the three PpSig genes. This induction was significantly reduced in a knockout mutant that lacked the blue light photoreceptor cryptochromes PpCRY1a and PpCRY1b, indicating that PpCRY1a and/or PpCRY1b mediate the blue light signal that induces the expression of the PpSig genes. In a daily cycle of 12-h blue light/12-h dark, the timing of peak expression of PpSig5 and a chloroplast gene psbD, encoding the D2 subunit of photosystem II, advanced in the cryptochrome mutant relative to those in the wild type, suggesting the presence of regulatory interactions among the expression of PpSig5 and psbD, the circadian clock, and the blue light signaling mediated by the cryptochrome(s).

Amino Acid Sequence↗

PubMed2005

Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock.

Exposing Arabidopsis (Arabidopsis thaliana) plants to low temperature results in rapid induction of CBF1, 2, and 3 (CBF1-3; also known as DREB1B, C, and A, respectively), which encode transcriptional activators that induce expression of a battery of genes that increase plant freezing and chilling tolerance. Recently, it has been shown that basal levels of CBF3 transcripts and those of certain CBF-regulated genes exhibit circadian cycling. Here, we further explored the regulation of CBF1-3 by the circadian clock. The results indicated that the extent to which CBF1-3 transcripts accumulated in response to low temperature was dependent on the time of day that the plants were exposed to low temperature and that this was regulated by the circadian clock. The highest and lowest levels of cold-induced CBF1-3 transcript accumulation occurred at 4 and 16 h after subjective dawn, respectively. An analysis of CBF2 promoter-reporter gene fusions indicated that this control included transcriptional regulation. In addition, the cold responsiveness of RAV1 and ZAT12, genes that are cold induced in parallel with CBF1-3, was also subject to circadian regulation. However, whereas the maximum level of cold-induced RAV1 transcript accumulation occurred at the same time of day as did CBF1-3 transcripts, that of ZAT12 was in reverse phase, i.e. the highest level of cold-induced ZAT12 transcript accumulation occurred 16 h after subjective dawn. These results indicate that cold-induced expression of CBF1-3, RAV1, and ZAT12 is gated by the circadian clock and suggest that this regulation likely occurs through at least two nonidentical (though potentially overlapping) signaling pathways.

Arabidopsis↗

PubMed1996

Identification of an Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase/oxygenase activase (RCA) minimal promoter regulated by light and the circadian clock.

Transcription of the Arabidopsis thaliana gene encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase (RCA) is organ-specific, light-responsive, and regulated by the circadian clock. RCA is transcribed throughout the green parts of the plant, but not in roots and petals. Responses elicited by short pulses of light indicate that the light response is mediated, at least in part, by phytochrome. Analysis of transgenic tobacco and Arabidopsis carrying RCA 5' untranscribed regions fused to reporter genes (uidA, encoding beta-glucuronidase, or cat, encoding chloramphenicol acetyltransferase) indicate that elements sufficient to confer organ-specific, light-responsive, and clock-regulated transcription are localized within 317 base pairs upstream of the site of transcription initiation. A clock-responsive element sufficient to confer a low-amplitude (approximately 2-fold) circadian oscillation lies within 317 base pairs of the trascription start, but other elements necessary for high-amplitude (approximately 10-fold) circadian oscillation lie upstream of -317 and are removed by deletion from -970 to -317.

Arabidopsis↗

PubMed1967

Aspects of clock resetting in flowering of xanthium.

Flowering is induced in Xanthium strumarium by a single dark period exceeding about 8.3 hours in length (the critical night). To study the mechanism which measures this dark period, plants were placed in growth chambers for about 2 days under constant light and temperature, given a phasing dark period terminated by an intervening light period (1 min to several hrs in duration), and finally a test dark period long enough normally to induce flowering. In some experiments, light interruptions during the test dark period were given to establish the time of maximum sensitivity.If the phasing dark period was less than 5 hours long, its termination by a light flash only broadened the subsequent time of maximum sensitivity to a light flash, but the critical night was delayed. In causing the delay, the end of the intervening light period was acting like the dusk signal which initiated time measurement at the beginning of the phasing dark period.If the phasing dark period was 6 hours or longer, time of maximum sensitivity during the subsequent test dark period was shifted by as much as 10 to 14 hours. In this case the light terminating the phasing dark period acted as a rephaser or a dawn signal.Following a 7.5-hour phasing dark period, intervening light periods of 1 minute to 5 hours did not shift the subsequent time of maximum sensitivity, but with intervening light periods longer than 5 hours, termination of the light acts clearly like a dusk signal. The clock appears to be suspended during intervening light periods longer than 5 to 15 hours. It is restarted by a dusk signal. There is an anomaly with intervening light periods of 10 to 13 hours, following which time of maximum sensitivity is actually less than the usual 8 hours after dusk.Ability of the clock in Xanthium to be rephased, suspended, restarted, or delayed, depending always upon conditions of the experiment, is characteristic of an oscillating timer and may confer upon this plant its ability to respond to a single inductive cycle. It is suggested that phytochrome may influence only the phase of the clock and not other aspects of flowering such as synthesis of flowering hormone.

Journal Article↗

PubMed1981

Temperature Compensation of Circadian Period Length in Clock Mutants of Neurospora crassa.

Temperature compensation of circadian period length in 12 clock mutants of Neurospora crassa has been examined at temperatures between 16 and 34 degrees C. In the wild-type strain, below 30 degrees C (the "breakpoint" temperature), the clock is well-compensated (Q(10) = 1), while above 30 degrees C, the clock is less well-compensated (Q(10) = 1.3). For mutants at the frq locus, mutations that shorten the circadian period length (frq-1, frq-2, frq-4, and frq-6) do not alter this temperature compensation response. In long period frq mutants (frq-3, frq-7, frq-8), however, the breakpoint temperature is lowered, and the longer the period length of the mutants the lower the breakpoint temperature. Long period mutants at other loci exhibit other types of alterations in temperature compensation-e.g. chr is well-compensated even above 30 degrees C, while prd-3 has a Q(10) significantly less than 1 below 30 degrees C. Prd-4, a short period mutant, has several breakpoint temperatures. Among four double mutants examined, the only unusual interaction between the individual mutations occurred with chr prd, which had an unusually low Q(10) value of 0.86 below 27 degrees C. There was no correlation between circadian period length and growth rate. These strains should be useful tools to test models for the temperature compensation mechanism.

Journal Article↗

PubMed1990

Steps linking the photosynthetic light reactions to the biological clock require calcium.

The effect of modifying calcium concentration on the expression of the photosynthesis circadian rhythm was examined in Euglena gracilis, Klebs strain Z. Expression of the oxygen evolution rhythm required the presence of both extracellular and intracellular calcium. Several treatments were found to uncouple the rate of the light reactions from the biological clock. In the presence of these chemical agents, the rate of oxygen evolution increased steadily throughout the light portion of the light/dark cycle, instead of showing a peak of activity in the middle of the light cycle. Oxygen evolution was uncoupled from the biological clock when extracellular calcium concentrations were altered by the presence of EGTA or LaCl(3). Uncoupling was also observed when intracellular calcium concentrations were disrupted by the use of Ca(2+) channel blockers, the intracellular Ca(2+) antagonist 8-(diethylamino)-octyl-3,4,5-trimethoxybenzoate, or by disrupting expression of the inositol trisphosphate system. Uncoupling was also observed when the diacylglycerol signaling system, which activates kinase C, was inhibited by acridine orange. The inhibition was reversed by the presence of phorbol esters which activate the kinase. It was concluded that both the inositol trisphosphate and diacylglycerol signaling systems were required for the expression of the oxygen evolution rhythm generated by the biological clock.

Journal Article↗

PubMed2006

FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock.

Temperature compensation contributes to the accuracy of biological timing by preventing circadian rhythms from running more quickly at high than at low temperatures. We previously identified quantitative trait loci (QTL) with temperature-specific effects on the circadian rhythm of leaf movement, including a QTL linked to the transcription factor FLOWERING LOCUS C (FLC). We have now analyzed FLC alleles in near-isogenic lines and induced mutants to eliminate other candidate genes. We showed that FLC lengthened the circadian period specifically at 27 degrees C, contributing to temperature compensation of the circadian clock. Known upstream regulators of FLC expression in flowering time pathways similarly controlled its circadian effect. We sought to identify downstream targets of FLC regulation in the molecular mechanism of the circadian clock using genome-wide analysis to identify FLC-responsive genes and 3503 transcripts controlled by the circadian clock. A Bayesian clustering method based on Fourier coefficients allowed us to discriminate putative regulatory genes. Among rhythmic FLC-responsive genes, transcripts of the transcription factor LUX ARRHYTHMO (LUX) correlated in peak abundance with the circadian period in flc mutants. Mathematical modeling indicated that the modest change in peak LUX RNA abundance was sufficient to cause the period change due to FLC, providing a molecular target for the crosstalk between flowering time pathways and circadian regulation.

Arabidopsis↗

PubMed2006

The molecular basis of temperature compensation in the Arabidopsis circadian clock.

Circadian clocks maintain robust and accurate timing over a broad range of physiological temperatures, a characteristic termed temperature compensation. In Arabidopsis thaliana, ambient temperature affects the rhythmic accumulation of transcripts encoding the clock components TIMING OF CAB EXPRESSION1 (TOC1), GIGANTEA (GI), and the partially redundant genes CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). The amplitude and peak levels increase for TOC1 and GI RNA rhythms as the temperature increases (from 17 to 27 degrees C), whereas they decrease for LHY. However, as temperatures decrease (from 17 to 12 degrees C), CCA1 and LHY RNA rhythms increase in amplitude and peak expression level. At 27 degrees C, a dynamic balance between GI and LHY allows temperature compensation in wild-type plants, but circadian function is impaired in lhy and gi mutant plants. However, at 12 degrees C, CCA1 has more effect on the buffering mechanism than LHY, as the cca1 and gi mutations impair circadian rhythms more than lhy at the lower temperature. At 17 degrees C, GI is apparently dispensable for free-running circadian rhythms, although partial GI function can affect circadian period. Numerical simulations using the interlocking-loop model show that balancing LHY/CCA1 function against GI and other evening-expressed genes can largely account for temperature compensation in wild-type plants and the temperature-specific phenotypes of gi mutants.

Acclimatization↗

PubMed1997

Attenuation of phytochrome A and B signaling pathways by the Arabidopsis circadian clock.

In higher plants, environmental cues such as light signals are integrated with circadian clock signals to control precisely the daily rhythms observed for many biological functions. We have used a fusion of the promoter of a chlorophyll a/b binding protein gene, CAB2, with firefly luciferase (cab2::luc) to monitor the detailed kinetics of transcription in response to photoreceptor activation in Arabidopsis. Using this marker in phototransduction and circadian-dysfunctional mutants, we studied how signals from phytochrome and the circadian clock are integrated for the regulation of CAB2 transcription. Results from these mutant studies demonstrate that similar expression features, namely, the acute and circadian responses, are present in both etiolated and green seedlings and that the acute and circadian responses are genetically separable. We also demonstrate that persistent Pfr signaling occurs in red light-pulsed etiolated seedlings, which suggests that the circadian clock antagonizes Pfr-mediated signal transduction. Based on these genetic studies, we propose a model for the regulation of CAB2 transcription in which individual photoreceptors and phototransduction components have been assigned to specific pathways for the regulation of discrete kinetic components of the CAB2 expression pattern.

Arabidopsis↗

PubMed2001

Implementation of the beam reversal technique on compact cesium clocks: towards an improvement in accuracy.

We report the evaluation of the residual phase difference deltaphi in a short (18 cm) Ramsey cavity by implementing the beam reversal technique to an optically pumped cesium beam clock. Deltaphi is measured to be 21 +/- 1.5 microrad, allowing a more accurate evaluation of the frequency performances of this small cesium clock. Finally, the clock accuracy is equal to 1.1 x 10(-13).

Journal Article↗

PubMed2001

Melastomeae come full circle: biogeographic reconstruction and molecular clock dating.

Rhexia, with 11 species in the Coastal Plain province of North America, is the only temperate zone endemic of the tropical eudicot family Melastomataceae. It is a member of the only pantropical tribe of that family, Melastomeae. Based on the chloroplast gene ndhF, we use a fossil-calibrated molecular clock to address the question of the geographic origin and age of Rhexia. Sequences from 37 species in 21 genera representing the tribe's geographical range were analyzed together with five outgroups. To obtain better clade support, another chloroplast region, the rpl16 intron, was added for 24 of the species. Parsimony analysis of the combined data and maximum-likelihood analysis of ndhF alone indicate that the deepest split is between Rhexia plus its sister group, a small Central American genus, and all other Melastomeae. Old World Melastomeae are monophyletic and nested within New World Melastomeae. Although likelihood-ratio tests of clock and nonclock substitution models for the full or moderately pruned datasets rejected the clock, these models yielded identical topologies (for 30 taxa) with few significantly different branch lengths as assessed by a Student's t-test. Age estimates obtained were 22 million years ago (Mya) for the divergence of Rhexia from its sister group, 12 Mya for the dispersal of Melastomeae from the New World to West Africa, and 1 Mya for the diversification of Melastoma in Southeast Asia. The only other genus of Melastomeae to have reached Southeast Asia from Africa or Madagascar is Osbeckia. The age and geographic distribution of fossils, which come from Miocene sites throughout Eurasia, suggest that Melastomeae once ranged from Eurasia across Beringia to North America from whence they reached South America and subsequently Africa and Southeast Asia. Climate deterioration led to their extinction in the Northern Hemisphere, with Rhexia possibly surviving in Coastal Plain refugia.

Calibration↗

PubMed1993

Melatonin and the circadian clock in mink: effects of daily injections of melatonin on circadian rhythm of locomotor activity and autoradiographic localization of melatonin binding sites.

The present study examines a putative effect of exogenous melatonin on the circadian organization of the mink. Two approaches were used to determine first whether entrainment of free-running rhythms of locomotor activity in constant darkness can be obtained by daily melatonin injections, thus demonstrating a control of melatonin on the clock generating circadian rhythms, the suprachiasmatic nucleus of the hypothalamus. Entrainment was never obtained in the 8 vehicle-injected females and 7 out of the 8 melatonin injected-ones. In 3 females free-running in constant darkness, a phase advance followed by a few days of transient effect was observed when melatonin injections coincided with the onset of activity. However, the comparison of the regression of the daily activity onset related to successive days by covariance analysis revealed that true entrainment was effective in only 1 female. Second, we examined the distribution of melatonin binding sites within the brain of juvenile and adult mink using an in vitro autoradiographic procedure with [125I]2-iodomelatonin. No binding sites were observed in the suprachiasmatic nucleus of any of the animals. However, all animals displayed a high density of melatonin binding sites in the pars tuberalis of the pituitary. The relation between a modulatory control of melatonin on the circadian clock and the presence and density of melatonin binding sites in the clock is discussed. In mink, melatonin does not seem to act as an internal Zeitgeber.

Animals↗

PubMed1998

Pituitary adenylate cyclase activating peptide (PACAP) in the retinohypothalamic tract: a daytime regulator of the biological clock.

The retinohypothalamic tract (RHT) relays photic information from the eyes to the brain biological clock in the suprachiasmatic nucleus (SCN). Activation of this pathway by light plays a role in adjusting circadian timing to light exposure at night. Here we report a new signaling pathway by which the RHT regulates circadian timing in the daytime as well. Using dual-immunocytochemistry for PACAP and the in vivo tracer Cholera toxin subunit B (ChB), intense PACAP immunoreactivity (PACAP-IR) was observed in retinal afferents at the rat SCN as well as in the intergeniculate leaflet (IGL) of the thalamus. This PACAP-IR was nearly lost upon bilateral eye enucleation. PACAP afferents originated from ganglion cells distributed throughout the retina. The phase of circadian rhythm measured as SCN neuronal activity in vitro was significantly advanced by application of PACAP-38 during the subjective day, but not at night. The effect is channelled to the clock via a PACAP 1 receptor-cAMP signaling mechanism. Thus, in addition to its role in nocturnal regulation by glutamatergic neurotransmission, the RHT can adjust the biological clock by a PACAP-cAMP-dependent mechanism during the daytime.

Animals↗

PubMed1994

Circadian clock mutants of cyanobacteria.

A diverse set of circadian clock mutants was isolated in a cyanobacterial strain that carries a bacterial luciferase reporter gene attached to a clock-controlled promoter. Among 150,000 clones of chemically mutagenized bioluminescent cells, 12 mutants were isolated that exhibit a broad spectrum of periods (between 16 and 60 hours), and 5 mutants were found that show a variety of unusual patterns, including arrhythmia. These mutations appear to be clock-specific. Moreover, it was demonstrated that in this cyanobacterium it is possible to clone mutant genes by complementation, which provides a means to genetically dissect the circadian mechanism.

Circadian Rhythm↗