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Reorganisation of circadian activity and the pacemaker circuit under novel light regimes

Cite this dataset

Sharma, Pragya (2024). Reorganisation of circadian activity and the pacemaker circuit under novel light regimes [Dataset]. Dryad. https://doi.org/10.5061/dryad.djh9w0w7w

Abstract

Many environmental features are cyclic, with predictable changes across the day, seasons and latitudes. Additionally, anthropogenic, artificial light-induced changes in photoperiod or shiftwork-driven novel light/dark cycles also occur. Endogenous timekeepers or circadian clocks help organisms cope with such changes. The remarkable plasticity of clocks is evident in the waveforms of behavioural and molecular rhythms they govern. Despite detailed mechanistic insights into the functioning of the circadian clock, practical means to manipulate activity waveform are lacking. Previous studies using a nocturnal rodent model showed that novel light regimes caused locomotor activity to bifurcate such that mice showed two bouts of activity restricted to the dimly lit phases. Here, we explore the generalizability of these findings and leverage the genetic toolkit of Drosophila melanogaster to obtain mechanistic insights into this unique phenomenon. We find that dim scotopic illumination of specific durations induces circadian photoreceptor CRYPTOCHROME-dependent activity bifurcation in male flies. We show circadian re-organisation of the pacemaker circuit wherein the ‘evening’ neurons regulate the timing of both bouts of activity under novel light regimes. Our findings indicate that environmental regimes can be exploited to design light regimes to ease the circadian waveform into synchronising with challenging conditions. 

README: Reorganisation of circadian activity and the pacemaker circuit under novel light regimes

https://doi.org/10.5061/dryad.djh9w0w7w

Male *Drosophila melanogaster *were exposed to novel light regimes of LDimLDim. Data used to plot activity profiles of wild type flies under these regimes have been included in the dataset. The dataset also includes the values of bifurcation index which has been used to quantify and characterise the activity waveform under the novel light regimes. Activity profiles of mutant and transgenic flies along with their bifurcation index have also been included in the dataset.

Description of the data and file structure

Each of the CSV files corresponds to the data that has been used to plot the respective figures in the linked preprint.

The NA values in the cells in the datasets are only due to differences in the sample sizes among the treatements or genotypes and do not reflect any recorded data.

File name: Figure1_activity_profiles

Activity profiles of wild-type Drosophila melanogaster. Genotypes include w1118, outbred fly populations (controls) and Canton-S. Light regime: LDimLDim 5:7:5:7 (L = 70 lux, Dim = 1 lux). Average profiles were calculated by using the days when stable phases were attained and transients had subsided after a change in the light regime i.e. the first two days post the transfer to a new regime have been eliminated when calculating the average activity profiles. Activity profiles were obtained by averaging over five cycles for each individual and then across individuals. First column indicates the local time and is followed by the average activity level for each time bin (here, 15 mins). The genotype is indicate at the top and for each genotype the average activity level is listed along with the standard error of mean (the columns for which are labeled as mean activty and sem).

File name: Figure1_bifurcation_index

Bifurcation index of wild-type Drosophila melanogaster. Genotypes include w1118, outbred fly populations (controls) and Canton-S. Light regime: LDimLDim 5:7:5:7 (L = 70 lux, Dim = 1 lux). The total number of activity counts in each scotophase (SP1, SP2) and the daily total activity was calculated for each cycle. The activity counts in the lesser-active scotophase are doubled to provide an objective measure of bifurcation ranging from 0 to 1. If activity is perfectly bifurcated between the successive scotophases, the index should be a value of 1, BI = 1. The index enables quantification of the symmetry in the distribution of activity between the two bouts. The index is calculated for each of the 5 cycles for an individual. It is then averaged across cycles and this average value has been listed. The top row indicates the genotypes.

File name: Figure2_activity_profiles

Activity profiles of wild-type Drosophila melanogaster, outbred fly populations (controls). Light regimes: LDim 12:12 and LDimLDim (L = 70 lux, Dim = 1 lux) 5:7:5:7, 5:3:7:9, 5:5:5:9, 5:5:7:7, 7:5:7:5. Average profiles were calculated by using the days when stable phases were attained and transients had subsided after a change in the light regime i.e. the first two days post the transfer to a new regime have been eliminated when calculating the average activity profiles. Activity profiles were obtained by averaging over five cycles for each individual and then across individuals. First column indicates the local time and is followed by the average activity level for each time bin (here, 15 mins). The light regime is indicate at the top and for each of the light regimes the average activity level is listed along with the standard error of mean (the columns for which are labeled as mean activty and sem).

File name: Figure2_regimes_BI

Bifurcation index of wild-type Drosophila melanogaster, outbred fly populations (controls). Light regimes: LDimLDim (L = 70 lux, Dim = 1 lux) 5:7:5:7, 5:3:7:9, 5:5:5:9, 5:5:7:7, 7:5:7:5. The total number of activity counts in each scotophase (SP1, SP2) and the daily total activity was calculated for each cycle. The activity counts in the lesser-active scotophase are doubled to provide an objective measure of bifurcation ranging from 0 to 1. If activity is perfectly bifurcated between the successive scotophases, the index should be a value of 1, BI = 1. The index enables quantification of the symmetry in the distribution of activity between the two bouts. The index is calculated for each of the 5 cycles for an individual. It is then averaged across cycles and this average value has been listed. The top row indicates the light regimes.

File name: Figure3_activity_profiles

Activity profiles of cry01 *and its background control *w1118 *under LDimLDim 5:7:5:7 with the bright light of 70 lux, dim light of 1 lux, and bright light of 700 lux with dim light of 10 lux. The file also includes the activity profiles of flies with *cry knocked down in the circadian clock neurons and their respective parental controls under LDimLDim 5:7:5:7. Profiles of fly lines with two different cryRNAi constructs on the second and third chromosomes are depicted in the upper (VDRC-KK 103414) and lower (VDRC-GD 738) panels, respectively. First column indicates the local time and is followed by the average activity level for each time bin (here, 15 mins). The light regime is indicate at the top and for each genotype under each of the light regimes the average activity level is listed along with the standard error of mean (the columns for which are labeled as mean activty and sem). The genotype and light regimes are indicated at the top, low indicates L = 70 lux and dim = 1 lux and high indicates L = 700 lux and dim = 1 lux.

File name: Figure3_BI

Bifurcation index of cry01 *and its background control *w1118 *under LDimLDim 5:7:5:7 with the bright light of 70 lux, dim light of 1 lux, and bright light of 700 lux with dim light of 10 lux. The file also includes bifurcation index of flies with *cry knocked down in the circadian clock neurons and their respective parental controls under LDimLDim 5:7:5:7. The total number of activity counts in each scotophase (SP1, SP2) and the daily total activity was calculated for each cycle. The activity counts in the lesser-active scotophase are doubled to provide an objective measure of bifurcation ranging from 0 to 1. If activity is perfectly bifurcated between the successive scotophases, the index should be a value of 1, BI = 1. The index enables quantification of the symmetry in the distribution of activity between the two bouts. The index is calculated for each of the 5 cycles for an individual. It is then averaged across cycles and this average value has been listed. The genotype and light regimes are indicated at the top, low indicates L = 70 lux and dim = 1 lux and high indicates L = 700 lux and dim = 1 lux.

File name: Figure4_activity_profiles

Activity profiles of null mutants of the circadian genes, period *(per01), timeless (*tim01), clock *(*clkjrk) and cycle *(*cyc01) under LDimLDim 5:7:5:7 (L = 70 lux, Dim = 1 lux). Canton-S *(*CS) is the genetic background for per01, clkjrk and cyc01 *while *w1118 *is the genetic background for *tim01. First column indicates the local time and is followed by the average activity level for each time bin (here, 15 mins). For each of the genotypes the average activity level is listed along with the standard error of mean (the columns for which are labeled as mean activty and sem).

File name: Figure4_BI

Bifurcation index of null mutants of the circadian genes, period *(per01), timeless (*tim01), clock *(*clkjrk) and cycle *(*cyc01) under LDimLDim 5:7:5:7 (L = 70 lux, Dim = 1 lux). Canton-S *(*CS) is the genetic background for per01, clkjrk and cyc01 *while *w1118 *is the genetic background for *tim01. The total number of activity counts in each scotophase (SP1, SP2) and the daily total activity was calculated for each cycle. The activity counts in the lesser-active scotophase are doubled to provide an objective measure of bifurcation ranging from 0 to 1. If activity is perfectly bifurcated between the successive scotophases, the index should be a value of 1, BI = 1. The index enables quantification of the symmetry in the distribution of activity between the two bouts. The index is calculated for each of the 5 cycles for an individual. It is then averaged across cycles and this average value has been listed. The genotypes are indicated at the top.

File name: Figure4_CoM_ZT

Mean phase of activity of each of the two bouts of activity in zeitgeber time (ZT00 = 10am, beginning of the first photophase) of null mutants of the circadian genes, period *(per01), timeless (*tim01), clock *(*clkjrk) and cycle *(*cyc01) under LDimLDim 5:7:5:7 (L = 70 lux, Dim = 1 lux). Canton-S *(*CS) is the genetic background for per01, clkjrk and cyc01 *while *w1118 *is the genetic background for *tim01. The mean phase of activity was calculated for each of the two activity bouts, under SP1 are listed the mean phase values of activity during the first scotophase and under SP2 are listed the mean phase values of activity during the second scotophase. The circular mean phase of activity within the scotophases was also quantified to measure the centrality of activity on the time axis. It considers and quantifies the overall activity waveform.

File name: Figure5_activity_profiles

Activity profiles of flies with DBT s expressed in circadian clock neurons or subsets of the circuit under LDimLDim 5:7:5:7 (L = 70 lux, Dim = 1 lux). Activity profiles of flies with all circadian clock neurons expressing the DBT s, activity profiles of flies with only the PDF+ve circadian neurons expressing the DBT s and activity profiles of flies with only the dorsolateral (LNds) circadian neurons expressing DBT s have been tabulated. At the top are the genotypes. The respective controls and their activity profiles have also been listed. First column indicates the local time and is followed by the average activity level for each time bin (here, 15 mins). For each of the genotypes the average activity level is listed along with the standard error of mean (the columns for which are labeled as mean activty and sem).

File name: Figure5_CoM_degrees

Mean phase of activity of each of the two bouts of activity in degrees of flies with all circadian clock neurons expressing the DBT s, activity profiles of flies with only the PDF+ve circadian neurons expressing the DBT s and activity profiles of flies with only the dorsolateral (LNds) circadian neurons expressing DBT s have been tabulated. The mean phase of activity was calculated for each of the two activity bouts, under SP1 are listed the mean phase values of activity during the first scotophase and under SP2 are listed the mean phase values of activity during the second scotophase. The circular mean phase of activity within the scotophases was also quantified to measure the centrality of activity on the time axis. It considers and quantifies the overall activity waveform.

Methods

Data was collected using Drosophila activity monitors. The activity counts have been normalised by the total amount of activity in a day and the percentage values have been plotted in activity profiles. The same activity profiles have been provided in the dataset. Bifurcation index has been calculated using raw activity counts. The details of which can be found in the associated preprint. Values of bifurcation index plotted in each of figures have also been included in the dataset.

Funding

Jawaharlal Nehru Centre for Advanced Scientific Research