Circadian clock controlled gene expression in soybean seeds
ABSTRACT: Microarray expression profiling was used to identify genes expressed in developing soybean (Glycine max) seeds that are controlled by the circadian clock. Plants with developing seeds were entrained to 12hour light: 12 hour dark cycles and sampled in constant light conditions. Overall design: Soybean seeds entrained to 12 hour-light:12 hour dark photocycles were harvested after 24 hours of constant light and temperature conditions. Timepoint 24h represents subjective dawn. To minimize developmental variation, flowers were marked as they opened and seeds were harvested from marked pods after 5 weeks. There are two replicate samples at each time point, and each sample consists of 8 seeds collected from three diffferent plants.
Project description:Microarray expression profiling was used to identify genes expressed in developing soybean (Glycine max) seeds that are controlled by the circadian clock. Plants with developing seeds were entrained to 12hour light: 12 hour dark cycles and sampled in constant light conditions. Soybean seeds entrained to 12 hour-light:12 hour dark photocycles were harvested after 24 hours of constant light and temperature conditions. Timepoint 24h represents subjective dawn. To minimize developmental variation, flowers were marked as they opened and seeds were harvested from marked pods after 5 weeks. There are two replicate samples at each time point, and each sample consists of 8 seeds collected from three diffferent plants.
Project description:Setaria viridis (A10.1) circadian expression after light or temperature entrainment Overall design: Plants were grown under either 12 hour photocycles (12h light/12h dark) or 12 hour thermocycles (12h 32 deg C/ 12h 22 deg C) then sampled every 2 hours for 48 hours under constant light and constant temperature conditions (32 deg C). Photocycle entrained samples are labeled LDHH-F, and thermocycle entrained samples are entrained LLHC-F.
Project description:Mice lacking the CLOCK protein have a relatively subtle circadian phenotype, including a slightly shorter period in constant darkness, differences in phase resetting after 4-hour light pulses in the early and late night, and a variably advanced phase angle of entrainment in a light-dark (LD) cycle. The present series of experiments was conducted to more fully characterize the circadian phenotype of Clock(-/-) mice under various lighting conditions. A phase-response curve (PRC) to 4-hour light pulses in free-running mice was conducted; the results confirm that Clock(-/-) mice exhibit very large phase advances after 4-hour light pulses in the late subjective night but have relatively normal responses to light at other phases. The abnormal shape of the PRC to light may explain the tendency of CLOCK-deficient mice to begin activity before lights-out when housed in a 12-hour light:12-hour dark lighting schedule. To assess this relationship further, Clock(-/-) and wild-type control mice were entrained to skeleton lighting cycles (1L:23D and 1L:10D:1L:12D). Comparing entrainment under the 2 types of skeleton photoperiods revealed that exposure to 1-hour light in the morning leads to a phase advance of activity onset (expressed the following afternoon) in Clock(-/-) mice but not in the controls. Constant light typically causes an intensity-dependent increase in circadian period in mice, but this did not occur in CLOCK-deficient mice. The failure of Clock(-/-) mice to respond to the period-lengthening effect of constant light likely results from the increased functional impact of light falling in the phase advance zone of the PRC. Collectively, these experiments reveal that alterations in the response of CLOCK-deficient mice to light in several paradigms are likely due to an imbalance in the shape of the PRC to light.
Project description:The ability to change colour rapidly is widespread among ectotherms and has various functions including camouflage, communication and thermoregulation. The process of colour change can occur as an aperiodic event or be rhythmic, induced by cyclic environmental factors or regulated by internal oscillators. Despite the importance of colour change in reptile ecology, few studies have investigated the occurrence of a circadian rhythm in lizard pigmentation. Additionally, although colour change also entails changes in near-infrared reflectance, which may affect thermoregulation, little research has examined this part of the spectrum. We tested whether the bearded dragon lizard, Pogona vitticeps, displays an endogenous circadian rhythm in pigmentation changes that could be entrained by light/dark (LD) cycles and how light affected the relative change in reflectance in both ultraviolet-visible and near-infrared spectra. We subjected 11 lizards to four photoperiodic regimens: LD 12:12; LD 6:18; LD 18:6 and DD; and measured their dorsal skin reflectance at 3-hour intervals for 72 hours after a habituation period. A proportion of lizards displayed a significant rhythm under constant darkness, with maximum reflectance occurring in the subjective night. This endogenous rhythm synchronised to the different artificial LD cycles, with maximum reflectance occurring during dark phases, but did not vary in amplitude. In addition, the total ultraviolet-visible reflectance in relation to the total near-infrared reflectance was significantly higher during dark phases than during light phases. We conclude that P. vitticeps exhibits a circadian pigmentation rhythm of constant amplitude, regulated by internal oscillators and that can be entrained by light/dark cycles.
Project description:To explore daily rhythms of ocular gene expression in adult mice we performed the following experiments: i) Mice were entrained to a 12:12-hr light-dark (LD) cycle for 3 weeks. Then mice were transferred to constant darkness (DD) or remained in LD and eyes were collected at four-hour intervals over a three-day period; ii) Bmal1-/- mice and wild-type littermates were entrained to a 12:12-hr LD cycle for 3 weeks and eyes were collected at four-hour intervals over a one-day period in LD.
Project description:Circadian rhythms can be entrained by a light-dark (LD) cycle and can also be reset pharmacologically, for example, by the CK1?/? inhibitor PF-670462. Here, we determine how these two independent signals affect circadian timekeeping from the molecular to the behavioral level. By developing a systems pharmacology model, we predict and experimentally validate that chronic CK1?/? inhibition during the earlier hours of a LD cycle can produce a constant stable delay of rhythm. However, chronic dosing later during the day, or in the presence of longer light intervals, is not predicted to yield an entrained rhythm. We also propose a simple method based on phase response curves (PRCs) that predicts the effects of a LD cycle and chronic dosing of a circadian drug. This work indicates that dosing timing and environmental signals must be carefully considered for accurate pharmacological manipulation of circadian phase.CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e57; doi:10.1038/psp.2013.34; published online 17 July 2013.
Project description:Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions. Results provide insight into circadian gene expression patterns in normal urinary bladder. Analysis of urinary bladder in wild-type C57BL/6 females sacrificed every 4 hours at six time points (n=2 for each time (CT 0, 4, 8, 12 and 20)) under constant darkness after acclimation for 2 weeks under 12-hour light and 12-hour dark conditions.
Project description:Circadian clocks allow the temporal compartmentalization of biological processes. In Arabidopsis, circadian rhythms display organ specificity but the underlying molecular causes have not been identified. We investigated the mechanisms responsible for the similarities and differences between the clocks of mature shoots and roots in constant conditions and in light : dark cycles. We developed an imaging system to monitor clock gene expression in shoots and light- or dark-grown roots, modified a recent mathematical model of the Arabidopsis clock and used this to simulate our new data. We showed that the shoot and root circadian clocks have different rhythmic properties (period and amplitude) and respond differently to light quality. The root clock was entrained by direct exposure to low-intensity light, even in antiphase to the illumination of shoots. Differences between the clocks were more pronounced in conditions where light was present than in constant darkness, and persisted in the presence of sucrose. We simulated the data successfully by modifying those parameters of a clock model that are related to light inputs. We conclude that differences and similarities between the shoot and root clocks can largely be explained by organ-specific light inputs. This provides mechanistic insight into the developing field of organ-specific clocks.
Project description:Background Circadian rhythms across mammalian tissues are coordinated by a master clock in the suprachiasmatic nucleus (SCN) that is principally entrained by light-dark cycles. Prior investigations have shown, however, that time-restricted feeding (TRF)—daily alternation of fasting and food availability—synchronizes peripheral clocks independent of the light-dark cycle and of the SCN. This has led to the idea that downstream peripheral clocks are entrained indirectly by food intake rhythms. However, TRF is not a normal eating pattern, and it imposes non-physiologic long fasts that rodents do not typically experience. Therefore, we tested whether normal feeding patterns can phase-shift or entrain peripheral tissues by measuring circadian rhythms of the liver, kidney, and submandibular gland in mPer2Luc mice under different food schedules. Results We employed home cage feeders to first measure ad libitum food intake and then to dispense 20-mg pellets on a schedule mimicking that pattern. In both conditions, PER2::LUC bioluminescence peaked during the night as expected. Surprisingly, shifting the scheduled feeding by 12?h advanced peripheral clocks by only 0–3?h, much less than predicted from TRF protocols. To isolate the effects of feeding from the light-dark cycle, clock phase was then measured in mice acclimated to scheduled feeding over the course of 3 months in constant darkness. In these conditions, peripheral clock phases were better predicted by the rest-activity cycle than by the food schedule, contrary to expectation based on TRF studies. At the end of both experiments, mice were exposed to a modified TRF with food provided in eight equally sized meals over 12?h. In the light-dark cycle, this advanced the phase of the liver and kidney, though less so than in TRF with ad libitum access; in darkness, this entrained the liver and kidney but had little effect on the submandibular gland or the rest-activity cycle. Conclusions These data suggest that natural feeding patterns can only weakly affect circadian clocks. Instead, in normally feeding mice, the central pacemaker in the brain may set the phase of peripheral organs via pathways that are independent of feeding behavior.
Project description:Circadian rhythmicity, the 24-hour cycle responsive to light and dark, is determined by periodic oscillations in gene transcription. This phenomenon has broad ramifications in physiologic function. Recent work has disclosed more cycles in gene transcription, and to the uncovering of these we apply a novel signal processing methodology known as the pencil method and compare it to conventional parametric, nonparametric, and statistical methods.<label>METHODS</label>In order to assess periodicity of gene expression over time, we analyzed a database derived from livers of mice entrained to a 12-hour light/12-hour dark cycle. We also analyzed artificially generated signals to identify differences between the pencil decomposition and other alternative methods.<label>RESULTS</label>The pencil decomposition revealed hitherto-unsuspected oscillations in gene transcription with 12-hour periodicity. The pencil method was robust in detecting the 24-hour circadian cycle that was known to exist, as well as confirming the existence of shorter-period oscillations. A key consequence of this approach is that orthogonality of the different oscillatory components can be demonstrated. thus indicating a biological independence of these oscillations, that has been subsequently confirmed empirically by knocking out the gene responsible for the 24-hour clock.<label>CONCLUSION</label>System identification techniques can be applied to biological systems and can uncover important characteristics that may elude visual inspection of the data.<label>SIGNIFICANCE</label>The pencil method provides new insights on the essence of gene expression and discloses a wide variety of oscillations in addition to the well-studied circadian pattern. This insight opens the door to the study of novel mechanisms by which oscillatory gene expression signals exert their regulatory effect on cells to influence human diseases.