Hundreds of LncRNAs Display Circadian Rhythmicity in Zebrafish Larvae

Long noncoding RNAs (lncRNAs) have been shown to play crucial roles in various life processes, including circadian rhythms. Although next generation sequencing technologies have facilitated faster profiling of lncRNAs, the resulting datasets require sophisticated computational analyses. In particular, the regulatory roles of lncRNAs in circadian clocks are far from being completely understood. In this study, we conducted RNA-seq-based transcriptome analysis of zebrafish larvae under both constant darkness (DD) and constant light (LL) conditions in a circadian manner, employing state-of-the-art computational approaches to identify approximately 3220 lncRNAs from zebrafish larvae, and then uncovered 269 and 309 lncRNAs displaying circadian rhythmicity under DD and LL conditions, respectively, with 30 of them are coexpressed under both DD and LL conditions. Subsequently, GO, COG, and KEGG pathway enrichment analyses of all these circadianly expressed lncRNAs suggested their potential involvement in numerous biological processes. Comparison of these circadianly expressed zebrafish larval lncRNAs, with rhythmically expressed lncRNAs in the zebrafish pineal gland and zebrafish testis, revealed that nine (DD) and twelve (LL) larval lncRNAs are coexpressed in the zebrafish pineal gland and testis, respectively. Intriguingly, among peptides encoded by these coexpressing circadianly expressed lncRNAs, three peptides (DD) and one peptide (LL) were found to have the known domains from the Protein Data Bank. Further, the conservation analysis of these circadianly expressed zebrafish larval lncRNAs with human and mouse genomes uncovered one lncRNA and four lncRNAs shared by all three species under DD and LL conditions, respectively. We also investigated the conserved lncRNA-encoded peptides and found one peptide under DD condition conserved in these three species and computationally predicted its 3D structure and functions. Our study reveals that hundreds of lncRNAs from zebrafish larvae exhibit circadian rhythmicity and should help set the stage for their further functional studies.

A Comparative Study of Circadian Rhythmicity and Photoperiodism in Closely Related Species of Blow Flies: External Coincidence, Maternal Induction, and Diapause at Northern Latitudes

This review compares adult locomotor activity rhythms and photoperiodic induction of diapause in 3 common species of blow fly, Calliphora vicina, Lucilia sericata, and Protophormia terraenovae. Activity rhythms were broadly similar in all 3 species, although P. terraenovae is much less sensitive to constant light inducing arrhythmicity. Photoperiodic induction of diapause, on the other hand, varies more widely between species. C. vicina and L. sericata overwinter in a larval diapause induced by autumnal short days (long nights) acting both maternally and directly upon the larvae. P. terraenovae, on the other hand, shows an adult (reproductive) diapause induced by short daylength and low temperature experienced by the larvae. In the Nanda-Hamner protocol, C. vicina shows 3 clear peaks of high diapause incidence in cycle lengths close to 24, 48, and 72 h, without dampening and therefore suggesting a photoperiodic mechanism based on a self-sustained circadian oscillator acting in a clock of the external coincidence type. Entrainment of the locomotor activity rhythm to extended Nanda-Hamner photocycles, as well as to LD cycles close to the limits of the primary range of entrainment, demonstrates that overt circadian rhythmicity may act as ‘hands’ of the otherwise covert photoperiodic system, as suggested by Bünning, nearly 8 decades ago. In 24 h LD cycles, both locomotor activity rhythms and the photoperiodic oscillator are set to constant phase (CT 12) at light-off, so that the photoperiodic clock measures changes in nightlength by the coincidence (or not) of dawn light with a ‘photoinducible phase’ late in the subjective night (at about CT 21.5 h) as photoperiod changes with the seasons. Apparent differences between quantitative and qualitative photoperiodic responses are discussed.

Time to put a spotlight on out-patient chronotherapy for depression

Summary The challenge of identifying efficacious out-patient treatments for depression is amplified by the increasing desire to find interventions that reduce the time to sustained improvement. One potential but underexplored option is triple chronotherapy (TCT). To date, use of TCT has been largely restricted to specialist units or in-patients. Recent research demonstrates that it may be possible to undertake sleep deprivation in out-patient settings, raising the possibility of delivering TCT to broader populations of individuals with depression. Emerging evidence suggests that out-patient TCT is a high-benefit, low-risk intervention but questions remain about how to target TCT and its mechanisms of action. Like traditional antidepressants, TCT probably acts through several pathways, especially the synchronisation of the ‘master clock’. Availability of reliable and valid methods of out-patient measurement of intra-individual circadian rhythmicity and light exposure are rate-limiting steps in the wider dissemination of TCT.

A High Cattle-Grazing Density Alters Circadian Rhythmicity of Temperature, Heart Rate, and Activity as Measured by Implantable Bio-Loggers

Six cows managed under extensive grazing conditions were used to study the effect of moving the animals to a higher grazing density on the circadian rhythms of temperature (T), heart rate (HR), and activity (ACT), which were recorded by implantable bio-loggers. Cows were maintained at a density of 1.5 livestock units per hectare (LSUs/ha; low density, LD) until they were moved to a grazing area at 128 LSUs/ha (high density, HD). Animals were implanted subcutaneously with a T, HR, and ACT bio-logger, which was programmed to record data at 5-min intervals. For each animal, cosinor rhythmometry (the study of circadian rhythms by fitting a sine wave to a time series) was applied to the data recorded over 5 days in LD and HD. Mean Midline Estimating Statistic of Rhythm (MESOR; the average value around which the variable oscillates), amplitude (difference between the peak and the mean value of a wave), and acrophase (timing of peak activity) were calculated and evaluated statistically. Differences between mean day and nighttime values, and mean LD and HD values were calculated. Cows presented cosinor curves that fit a 24-h rhythm (p < 0.001) in T, HR, and ACT at both densities. MESOR (T: 37.98 vs. 38.02°C; HR: 69.12 vs. 65.91 bpm; ACT: 49.39 vs. 40.41 mg, for LD and HD, respectively) and amplitude (T: 0.28 vs. 0.28°C; HR: 4.12 vs. 3.14 bpm; ACT: 18.14 vs. 11.28 mg, respectively) did not differ significantly between the two densities; however, significant (p < 0.05) differences between densities occurred in the acrophase of the three variables; specifically, the T acrophase was 2 h later at HD (22:45 h) than LD (20:45 h), and HR (LD: 19:51; HD: 16:49 h) and ACT acrophases 3 and 2 h earlier at HD than LD (LD: 14:47; HD: 12:49 h), respectively. T and ACT differed significantly (p < 0.01) between daytime (mean ± SE; 37.92 ± 0.19°C, 40.39 ± 4.74 mg) and nighttime (38.14 ± 0.17°C, 29.93 ± 5.66 mg). In conclusion, our study suggests that a high animal grazing density might exacerbate the social competence for valuable resources for animals, resulting in shifting the circadian rhythmicity of temperature, heart rate, and activity of the cows, advancing or delaying their acrophases.

Modeling the Influence of Chronic Sleep Restriction on Cortisol Circadian Rhythms, with Implications for Metabolic Disorders

Chronic sleep deficiency is prevalent in modern society and is associated with increased risk of metabolic and other diseases. While the mechanisms by which chronic sleep deficiency induces pathophysiological changes are yet to be elucidated, the hypothalamic–pituitary–adrenal (HPA) axis may be an important mediator of these effects. Cortisol, the primary hormone of the HPA axis, exhibits robust circadian rhythmicity and is moderately influenced by sleep and wake states and other physiology. Several studies have explored the effects of acute or chronic sleep deficiency (i.e., usually from self-selected chronic sleep restriction, CSR) on the HPA axis. Quantifying long-term changes in the circadian rhythm of cortisol under CSR in controlled conditions is inadequately studied due to practical limitations. We use a semi-mechanistic mathematical model of the HPA axis and the sleep/wake cycle to explore the influence of CSR on cortisol circadian rhythmicity. In qualitative agreement with experimental findings, model simulations predict that CSR results in physiologically relevant disruptions in the phase and amplitude of the cortisol rhythm. The mathematical model presented in this work provides a mechanistic framework to further explore how CSR might lead to HPA axis disruption and subsequent development of chronic metabolic complications.

Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

Background In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear. Results We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean. Conclusions These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.