RhythmicAlly: Your R and Shiny–Based Open-Source Ally for the Analysis of Biological Rhythms

Abhilash, Lakshman; Sheeba, Vasu

doi:10.1177/0748730419862474

Cited by 34 publications

(28 citation statements)

References 20 publications

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“…To estimate rates of re-entrainment to 6-h advance and delay, we marked phases of offset for each fly on each day for all 12 populations using RhythmicAlly (Abhilash and Sheeba, 2019). We then calculated the daily phase relationship as phase of offset of activity – phase of offset of thermophase.…”

Section: Methodsmentioning

confidence: 99%

“…Raw DAM data was scanned and monitor files were saved in 20-min bins. These data files were analysed using RhythmicAlly (Abhilash and Sheeba, 2019). Individual profiles were downloaded and were re-organised to 1-h bins.…”

Section: Methodsmentioning

confidence: 99%

“…For TC 06:18, ψ CoM was computed without the angle doubling transformation. FRP of flies experiencing constant conditions post aforementioned entrainment regimes was quantified using the chi-square periodogram implemented in RhythmicAlly (Abhilash and Sheeba, 2019).…”

Section: Methodsmentioning

confidence: 99%

“…From the 1-h binned profiles, we also computed total activity in a morning window (ZT01-06) and an evening window (ZT06-11) to assess the individual contributions of morning and evening bouts of activity to potential differences in temperature sensitivity. FRP for all these flies under constant darkness at 19 and 28 °C were assessed in RhythmicAlly (Abhilash and Sheeba, 2019) using the chi-squared periodogram. Similar analyses were performed to estimate FRP of flies under DD at 25 °C.…”

Section: Methodsmentioning

confidence: 99%

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Activity/rest rhythms of Drosophila populations selected for divergent eclosion timing under temperature cues

Abhilash

Arshad

Sheeba

2019

Preprint

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2rhythms. We found that in response to simulated jetlag with temperature cycles, late 3 3 chronotypes (populations selected for predominant emergence during dusk) indeed re-entrain 3 4 faster than early chronotypes (populations selected for predominant emergence during dawn), 3 5 thereby indicating enhanced sensitivity of the activity/rest clock to temperature cues in these 3 6 stocks (entrainment is the synchronisation of internal rhythms to cyclic environmental time-3 7 cues). Additionally, we found that late chronotypes show higher plasticity of phases across 3 8 regimes, day-to-day stability in phases and amplitude of entrainment, all indicative of 3 9 enhanced temperature sensitive activity/rest rhythms. Our results highlight remarkably 4 0 similar organisation principles between emergence and activity/rest rhythms.4 1

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Activity/rest rhythms of Drosophila populations selected for divergent eclosion timing under temperature cues

Abhilash

Arshad

Sheeba

2019

Preprint

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“…153 Locomotor activity rhythm assay: 154 Individual virgin male flies (4-6 days old) were housed in glass tubes (length 65mm, diameter Activity data analysis 160 Raw data obtained from the DAM system were scanned and binned into activity counts of 161 15 minute intervals. Data was analysed using the CLOCKLAB software (Actimetrics, 162 Wilmette, IL) or RhythmicAlly (Abhilash & Sheeba, 2019). Values of period and power of 163 rhythm were calculated for a period of 7-10 days using the Chi-square periodogram with a 164 cut-off of p=0.05.…”

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confidence: 99%

Gap junction protein INNEXIN2 modulates the period of free-running rhythms inDrosophila melanogaster

Ramakrishnan

Sheeba

2020

Preprint

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30The circadian neuronal circuit of Drosophila melanogaster is made up of about 150 neurons, 31 distributed bilaterally and distinguished into 7 clusters. Multiple lines of evidence suggest 32 that coherent rhythms in behaviour are brought about when these clusters function as a 33 network. Although chemical modes of communication amongst circadian neurons have 34 been well-studied, there has been no report of communication via electrical synapses made 35 up of gap junctions. Here, we report for the first time that gap junction proteins -Innexins 36 play crucial roles in determining the period of free-running activity rhythms in flies. Our 37 experiments reveal the presence of gap junction protein INNEXIN2 in the ventral lateral 38 neurons. RNA-interference based knockdown of its expression in circadian pacemakers 39 slows down the speed of locomotor activity rhythm. Concomitantly, we find alterations in 40 the oscillation of a core-clock protein PERIOD and in the output molecule Pigment 41 Dispersing Factor in the circadian pacemaker neuron network. 42 43 44 45 membrane potential, activity-rest. 46 47 48 150 neurons distributed bilaterally in the brain. Based on their location, they can be divided 53 into lateral neurons (LN) and dorsal neurons (DN). The lateral neurons are further divided 54 into the small ventral lateral neurons (s-LNv), large ventral lateral neurons (l-LNv), the 55 lateral dorsal neurons (LNd) and the lateral posterior neurons (LPN). The dorsal cluster of 56 neurons are further divided into 3 groups as dorsal neurons 1-3 (DN1-3) (reviewed in 57 Sheeba, 2008). 58 Each of these neurons have a ticking molecular clock composed of a self-sustained 59 transcriptional translational feedback loop (TTFL) made up of four core clock genes Clock, 60 Cycle, Period and Timeless. The period of these molecular oscillations in mRNA and protein 61 within the pacemaker circuit in the fly brain mirror the period of rhythmic activity-rest 62 behaviour reviewed in (Hardin, 2005). Although molecular circadian clocks in individual 63 neurons can be thought of as ticking cell autonomously due to the precisely timed cycling of 64 their mRNA and proteins, one interesting question that remains to be fully understood is 65 how these distinct neuronal clusters, with distinct intrinsic periodicities (Yoshii et al., 2009) 66 together bring about one coherent period of the behavioural activity rhythm. Early studies 67 of Drosophila clock neuronal network have shown that under constant darkness and 68 constant temperature (DD 25 °C), s-LNv neurons and clocks in these cells are necessary and 69 sufficient for the persistence of activity-rest rhythms (Helfrich-Förster, 1998, Renn et al., 70 1999). s-LNv release neuropeptide Pigment Dispersing factor (PDF) in the dorsal part of the 71 brain via their projections in a time-of-day dependent manner (Park et al., 2000). Lack of 72 PDF results in arrhythmicity of activity-rest rhythms under constant conditions (Renn et al., 73 1999) suggesting that PDF is necessary for persistence...

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Astrocytic circadian clock control of energy expenditure by transcriptional stress responses in the ventromedial hypothalamus

Mendoza-Viveros

Marmolejo-Gutierrez

Cid-Castro

et al. 2023

Glia

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Hypothalamic circuits compute systemic information to control metabolism.Astrocytes residing within the hypothalamus directly sense nutrients and hormones, integrating metabolic information, and modulating neuronal responses.Nevertheless, the role of the astrocytic circadian clock on the control of energy balance remains unclear. We used mice with a targeted ablation of the core-clock gene Bmal1 within Gfap-expressing astrocytes to gain insight on the role played by this transcription factor in astrocytes. While this mutation does not substantially affect the phenotype in mice fed normo-caloric diet, under high-fat diet we unmasked a thermogenic phenotype consisting of increased energy expenditure, and catabolism in brown adipose and overall metabolic improvement consisting of better glycemia control, and body composition. Transcriptomic analysis in the ventromedial hypothalamus revealed an enhanced response to moderate cellular stress, including ER-stress response, unfolded protein response and autophagy.We identified Xbp1 and Atf1 as two key transcription factors enhancing cellular stress responses. Therefore, we unveiled a previously unknown role of the astrocytic circadian clock modulating energy balance through the regulation of cellular stress responses within the VMH. † Deceased.

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RhythmicAlly: Your R and Shiny–Based Open-Source Ally for the Analysis of Biological Rhythms

Cited by 34 publications

References 20 publications

Activity/rest rhythms of Drosophila populations selected for divergent eclosion timing under temperature cues

Activity/rest rhythms of Drosophila populations selected for divergent eclosion timing under temperature cues

Gap junction protein INNEXIN2 modulates the period of free-running rhythms inDrosophila melanogaster

Astrocytic circadian clock control of energy expenditure by transcriptional stress responses in the ventromedial hypothalamus

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