CosinorPy: a python package for cosinor-based rhythmometry

Moškon, Miha

doi:10.1186/s12859-020-03830-w

Cited by 61 publications

(70 citation statements)

References 19 publications

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“…The mean acrophase (the time at which the peak of a rhythm occurs) of 5 days was calculated for each animal, period and behaviour using the C osinor P y package [ 44 ]. Circular statistical analyses were conducted using the O riana software, v. 4 (Kovach Computing Wales, UK) [ 45 ].…”

Section: Methodsmentioning

confidence: 99%

Lifelong exposure to artificial light at night impacts stridulation and locomotion activity patterns in the cricketGryllus bimaculatus

et al. 2021

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Living organisms experience a worldwide continuous increase in artificial light at night (ALAN), negatively affecting their behaviour. The field cricket, an established model in physiology and behaviour, can provide insights into the effect of ALAN on insect behaviour. The stridulation and locomotion patterns of adult male crickets reared under different lifelong ALAN intensities were monitored simultaneously for five consecutive days in custom-made anechoic chambers. Daily activity periods and acrophases were compared between the experimental groups. Control crickets exhibited a robust rhythm, stridulating at night and demonstrating locomotor activity during the day. By contrast, ALAN affected both the relative level and timing of the crickets' nocturnal and diurnal activity. ALAN induced free-running patterns, manifested in significant changes in the median and variance of the activity periods, and even arrhythmic behaviour. The magnitude of disruption was light intensity dependent, revealing an increase in the difference between the activity periods calculated for stridulation and locomotion in the same individual. This finding may indicate the existence of two peripheral clocks. Our results demonstrate that ecologically relevant ALAN intensities affect crickets’ behavioural patterns, and may lead to decoupling of locomotion and stridulation behaviours at the individual level, and to loss of synchronization at the population level.

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Section: Methodsmentioning

confidence: 99%

Lifelong exposure to artificial light at night impacts stridulation and locomotion activity patterns in the cricketGryllus bimaculatus

et al. 2021

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“…A 2-or-more component model is useful when approximating a waveform that is not sinusoidal. It can describe waveforms with complex oscillatory dynamics that cannot be approximated with a single-component cosinor (Moškon, 2020). The 2-component cosinor is (Cornelissen, 2014) as follows:…”

Section: Data and Statistical Analysismentioning

confidence: 99%

Effect of circadian system disruption on the concentration and daily oscillations of cortisol, progesterone, melatonin, serotonin, growth hormone, and core body temperature in periparturient dairy cattle

Suárez-Trujillo

Hoàng

Robinson

et al. 2022

Journal of Dairy Science

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Metabolic, circadian, sleep, and reproductive systems are integrated and reciprocally regulated, but the understanding of the mechanism is limited. To study this integrated regulation, the circadian timing system was disrupted by exposing late pregnant nonlactating (dry) cows to chronic shifts in the light-dark phase, and rhythms of body temperature and circulating cortisol (CORT), progesterone (P4), serotonin (5HT), melatonin (MEL), and growth hormone (GH) concentrations were measured. Specifically, across 2 identical studies (1 and 2), at 35 d before expected calving (BEC) multiparous cows were assigned to control (CON; n = 24) and exposed to 16 h light and 8 h dark or phase shift (PS; n = 24) treatments and exposed to 6-h light-dark phase shifts every 3 d until parturition. All cows were exposed to control lighting after calving. Blood samples were collected in the first study at 0600 h on d 35 BEC, d 21 BEC, and 2 d before calving, and d 0, 2, 9, 15, and 22 postpartum (PP). A subset of cows (n = 6/group) in study 1 was blood sampled every 4 h over 48 h beginning on d 23 BEC, 9 BEC, and 5 PP. Body temperature was measured every 30 min (n = 8-16/treatment) for 48 h at 23 BEC and 9 BEC in both studies; and at 14 PP and 60 PP only in study 2. Treatment did not affect levels of CORT, GH, or P4 at 0600 h, but overall level of 5HT was lower and MEL higher in PS cows across days sampled. A 2-component versus single-component cosinor model better described [>coefficient of determination (R 2 );

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“…Rhythmicity and differential rhythmicity analyses were implemented in Python 3 using a recently developed CosinorPy package [ 41 ]. The reported significance values are adjusted for multiple testing using the Benjamini and Hochberg procedure.…”

Section: Methodsmentioning

confidence: 99%

Escherichia coli Affects Expression of Circadian Clock Genes in Human Hepatoma Cells

et al. 2021

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Recent research has indicated that dysbiosis of the gut microbiota can lead to an altered circadian clock of the mammalian host. Herein we developed an original system that allows real-time circadian studies of human HepG2 hepatoma cells co-cultured with bacteria. The HepG2 cells with stably integrated firefly luciferase reporter under the control of PERIOD2 promoter were co-cultured with E. coli strains isolated from human fecal samples from healthy individuals. The two E. coli strains differ in the phylogenetic group and the number of ExPEC virulence-associated genes: BJ17 has only two, and BJ23 has 15 of 23 tested. In the first 24 h, the E. coli BJ17 affected the HepG2 circadian clock more than BJ23. Cosinor analysis shows a statistically significant change in the amplitude of PER1 and 2 and the phase advance of PER3. A high percentage of necrotic and apoptotic cells occurred at 72 h, while a correlation between the number of ExPEC genes and the influence on the HepG2 core clock gene expression was observed. Our study reveals that the E. coli genetic background is important for the effect on the mammalian circadian clock genes, indicating possible future use of probiotic E. coli strains to influence the host circadian clock.

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CosinorPy: a python package for cosinor-based rhythmometry

Cited by 61 publications

References 19 publications

Lifelong exposure to artificial light at night impacts stridulation and locomotion activity patterns in the cricketGryllus bimaculatus

Lifelong exposure to artificial light at night impacts stridulation and locomotion activity patterns in the cricketGryllus bimaculatus

Effect of circadian system disruption on the concentration and daily oscillations of cortisol, progesterone, melatonin, serotonin, growth hormone, and core body temperature in periparturient dairy cattle

Escherichia coli Affects Expression of Circadian Clock Genes in Human Hepatoma Cells

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