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307 results for “circadian rhythms”
Adaptive Introgression in Modern Human Circadian Rhythm Genes Datasets
<p><strong>README:</strong></p> <p>Modern human genetic data with evidence of adaptive introgression from Neanderthals or Denisovans within circadian rhythm genes. The data was generated from the phased gnomAD 1KGP + HGDP callset (Koenig <em>et al</em>., 2024) and introgressed segments were identified by SPrime (Browning <em>et al</em>., 2018). Genes of interest were downloaded from the Circadian Genome Database (CGDB) (Li <em>et al</em>., 2017). Additional variants, haplotypes, and genes that have been previously reported to influence circadian rhythm or chronotype that are thought to be derived from Neanderthals and Denisovans were compiled from Dannemann & Kelso (2017), McArthur et al. (2021), Dannemann et al. (2022), and Velazquez-Arcelay et al. (2023).</p> <p><strong>SPrime ND_Match Files</strong></p> <p>Raw SPrime identified files that we used for our entire analysis. These were modified to include the archaic allele, archaic allele frequency, and average introgressed segment allele frequency. Note that these have been lifted over (Hinrichs <em>et</em> <em>al</em>., 2006) from GRCh38 (hg38) to GRCh37 (hg19) coordinates to match the genome builds of the archaic samples used in our study. As such, any manually generated variant IDs (chromosome:position:ReferenceAllele_AlternativeAllele naming convention) may no longer match the position they are currently sitting on as they were generated with hg38 coordinates. However, all of these were subsequently filtered out of our final results and any proper SNP IDs (dbSNP labels) will be accurate.</p> <p><strong>Supplementary Tables</strong></p> <p>All supplementary tables have an associated README as the first sheet that explains in detail the contents.</p> <p><strong>NEXUS Files</strong></p> <p>NEXUS files were used to generate haplotype networks in PopArt (Leigh & Bryant, 2015). There is a larger, master haplotype file and a smaller subset file. The larger file contains 668 haplotypes from all populations generated in the phased gnomAD 1KGP + HGDP callset (Koenig <em>et al</em>., 2024) for the <em>SUSD1 </em>core haplotype. The smaller subset file is the top 50 haplotypes and ties based on frequency, all Oceanic haplotypes with frequencies of at least 2, and the Neanderthal and Denisovan haplotypes for <em>SUSD1</em>. </p> <p><strong>TRAITS file</strong></p> <p>Accompanies the NEXUS files to create pie graphs for the haplotype network and contains frequency counts of number of haplotypes per region.</p>
Data for: Altered Circadian Rhythm, Sleep, and Rhodopsin 7-Dependent Shade Preference During Diapause in Drosophila Melanogaster
<p>To survive adverse environments, many animals enter a dormant state such as hibernation, dauer, or diapause. Various Drosophila species undergo adult reproductive diapause in response to cool temperatures and/or short day-length. While it is known that flies are less active during diapause, an in-depth understanding of diapause effects on circadian rhythms and sleep is lacking. Here we show that, in diapause-inducing conditions, Drosophila melanogaster exhibit altered circadian activity profiles, including a severely reduced morning activity peak and an advanced evening activity peak. Consequently, the flies have a single activity peak at a time similar to when non-diapausing flies have a siesta. Temperatures ≤15 °C, rather than short day-length, primarily drive the behavior. At cool temperatures, flies also rapidly enter a deep sleep state that lacks the sleep cycles of flies at higher temperatures and requires particularly high levels of stimulation for arousal. Furthermore, we show that at 18–25 °C, flies prefer to siesta in the shade, a preference that is virtually eliminated at 10 °C. Resting in the shade is driven by an aversion to blue light, sensed by rhodopsin 7 (Rh7) outside of the eyes. Flies at 10 ˚C show neuronal markers of elevated sleep pressure, including increased expression of Bruchpilot and elevated Ca2+ in the R5 ellipsoid body neurons. Therefore, sleep pressure might overcome blue light aversion. Thus at temperatures known to cause reproductive arrest, preserve germline stem cells, and extend lifespan, Drosophila melanogaster are prone to deep sleep and exhibit dramatically altered - yet rhythmic - daily activity patterns.</p>
Data for: Altered Circadian Rhythm, Sleep, and Rhodopsin 7-Dependent Shade Preference During Diapause in Drosophila Melanogaster
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Data from: Molecular circadian rhythms are robust in marine annelids lacking rhythmic behavior
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Genetic variation and phenotypic plasticity in circadian rhythms of an armed beetle, Gnatocerus cornutus (Tenebrionidae)
<p>Circadian rhythms, their free-running periods and strength of the rhythm are often used as indicators of biological clocks, and there is evidence that the free-running periods of circadian rhythm are not affected by environmental factors like temperature. However, there are few studies of environmental effects on the power of rhythms and it is not clear if temperature compensation is universal. Additionally, genetic variation and phenotypic plasticity in biological clocks are important for understanding the evolution of biological rhythm, but genetic and plastic effects are rarely investigated. Here, we used 18 isofemale lines (genotypes) of <i>Gnatocerus cornutus</i> to assess rhythms of locomotor activity, while also testing for temperature effects. We found that total activity and power of circadian rhythm were affected by interactions between sex and genotype or sex, genotype and temperature, so that while males tended to be more active and showed greater increases in activity, this effect varied across both genotypes and temperatures. The period of activity only varied by genotype and was thus independent of temperature. The complicated genotype-sex-environment interactions we recorded stress the importance of investigating circadian activity in more integrated ways.</p>
Developmental pyrethroid exposure disrupts molecular pathways for MAP kinase and circadian rhythms in mouse brain
<p><span>Neurodevelopmental disorders (NDDs) are a category of pervasive disorders of the developing nervous system with few or no recognized biomarkers. A significant portion of the risk for NDDs, including attention deficit hyperactivity disorder (ADHD), is contributed by the environment, and exposure to pyrethroid pesticides during pregnancy has been identified as a potential risk factor for NDD in the unborn child. We recently showed that low-dose developmental exposure to the pyrethroid pesticide deltamethrin in mice causes male-biased changes to ADHD- and NDD-relevant behaviors as well as the striatal dopamine system. Here, we used an integrated multiomics approach to determine the broadest possible set of biological changes in the mouse brain caused by developmental pyrethroid exposure (DPE). Using a litter-based, split-sample design, we exposed mouse dams during pregnancy and lactation to deltamethrin (3 mg/kg or vehicle every 3 days) at a concentration well below the EPA-determined benchmark dose used for regulatory guidance. We raised male offspring to adulthood, euthanized them, and pulverized and divided whole brain samples for split-sample transcriptomics, kinomics and multiomics integration. Transcriptome analysis revealed alterations to multiple canonical clock genes, and kinome analysis revealed changes in the activity of multiple kinases involved in synaptic plasticity, including the mitogen-activated protein (MAP) kinase ERK. Multiomics integration revealed a dysregulated protein-protein interaction network containing primary clusters for MAP kinase cascades, regulation of apoptosis, and synaptic function. These results demonstrate that DPE causes a multi-modal biophenotype in the brain relevant to ADHD and identifies new potential mechanisms of action.</span></p>
Circadian and circatidal rhythms of protein abundance in the California mussel (Mytilus californianus)
<p>Coastal habitats fluctuate with the 12.4 h tidal and 24 h light/dark cycle to predictably alter conditions such as air exposure, temperature, and food availability. Intertidal sessile bivalves exhibit behavioral and physiological adjustments to minimize the challenges of this environment. We investigated a high-resolution time course of the changes in protein abundance in the gill tissue of the intertidal mussel <i>Mytilus californianus</i> in a simulated tidal environment of 12:12 h light:dark cycles and a matching 6:6 h high:low tide cycle within each 12 h period. Approximately 38% of detected proteins showed significant rhythms in their abundances, with diversity in the phases of rhythmic isoforms. The circadian rhythm was dominant in protein abundance changes, particularly with oxidative metabolism. A tidal cycle elicited changes within functional groups, including in cytoskeletal proteins, chaperones, and oxidative stress proteins. In addition to protein abundance changes, we found the possibility for post-translational modifications driving rhythms, including methylation, mitochondrial peptide processing (proteolysis), and acylation. Dynamic changes in the proteome across functional categories demonstrate the importance of the tidal environment in entraining cellular processes, confirming that differential expression studies should not assume a static baseline of cellular conditions in intertidal organisms.</p>
Circadian rhythm entrainment of the jewel wasp, Nasonia vitripennis, by antagonistic interactions of multiple spectral inputs
<p>Circadian light entrainment in some insects is regulated by blue-light sensitive cryptochrome (CRY) protein that is expressed in the clock neurons, but this is not the case in hymenopterans. The hymenopteran clock does contain CRY, but it appears to be light-insensitive. Therefore, we investigated the role of retinal photoreceptors in the photic entrainment of the jewel wasp <em>Nasonia</em> <em>vitripennis</em>. Application of monochromatic light stimuli at different light intensities caused phase shifts in the wasp's circadian activity from which an action spectrum with three distinct peaks was derived. Electrophysiological recordings from the compound eyes and ocelli revealed the presence of three photoreceptor classes, with peak sensitivities at 340 nm (ultraviolet), 450 nm (blue), and 530 nm (green). An additional photoreceptor class in the ocelli with sensitivity maximum at 560–580 nm (red) was found. Whereas a simple sum of photoreceptor spectral sensitivities could not explain the action spectrum of the circadian phase shifts, modelling of the action spectrum indicates antagonistic interactions between pairs of spectral photoreceptors, residing in the compound eyes and the ocelli. Our findings imply that the photic entrainment mechanism in <em>N</em>. <em>vitripennis</em> encompasses the neural pathways for measuring the absolute luminance as well as the circuits mediating colour opponency. </p>
Data and supplementary information: Effects of lithium on locomotor activity and circadian rhythm of honey bees
<p>Data and supplementary files for publication:</p><p>Erdem, B., Arslan, O.C., Sevin, S. Gozen, A. G., Agosto-Rivera, J. L., Tugrul, G., & Alemdar, H. (2023). Effects of lithium on locomotor activity and circadian rhythm of honey bees. <i>Scientific Reports</i>, <i>13,</i> 19861. https://doi.org/10.1038/s41598-023-46777-7</p><p> </p><p>AcuteExp_Dark_ActivityData.xlsx - Total LMA counts of acute experiment in dark condition.</p><p>AcuteExp_Light_ActivityData.xlsx - Total LMA counts of acute experiment in light condition.</p><p>ChronicExp_ActivityData.xlsx - Total LMA counts of the chronic experiment.</p><p>ChronicExp_MortalityData.xlsx - Mortality data of the chronic experiment.</p><p>ChronicExp_PeriodRhytmData.xlsx - Defines rhythmic and arrhythmic individuals and the circadian periods (h) of the rhythmic individuals in chronic experiment.</p><p>LD_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the 12 h light / 12 h dark condition.</p><p>DD_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the constant dark condition.</p><p>LL_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the constant light condition.<br>In the double-plotted actograms, NR indicates "non-rhythmic" individuals.</p>
The Effects of Light Therapy on Circadian Rhythms, Sleep, and Mood in Postpartum Depression
ClinicalTrials.gov study NCT02769858. IPD Sharing: NO. Countries: 1. Publications: 1.
Safety and Efficacy of VEC-162 on Circadian Rhythm in Healthy Adult Volunteers
ClinicalTrials.gov study NCT00490945. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Sleep and Circadian Rhythm Biomarkers of Postoperative Delirium
ClinicalTrials.gov study NCT06052397. IPD Sharing: YES. Countries: 1. Publications: 10.
Circadian Rhythms and Time Perception in Healthy Adults During Constant Wakefulness
ClinicalTrials.gov study NCT07294781. IPD Sharing: YES. Countries: 1. Publications: 3.
Circadian Rhythms of Aqueous Humor Dynamics in Humans
ClinicalTrials.gov study NCT00572936. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Feasibility of Bright Light Therapy on Fatigue, Sleep and Circadian Activity Rhythms in Lung Cancer Survivors
ClinicalTrials.gov study NCT02954809. IPD Sharing: NO. Countries: 1. Publications: 5.
Genetic variation and phenotypic plasticity in circadian rhythms of an armed beetle, Gnatocerus cornutus (Tenebrionidae)
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Circadian rhythm entrainment of the jewel wasp, Nasonia vitripennis, by antagonistic interactions of multiple spectral inputs
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Sex-specific expression of circadian rhythms enables allochronic speciation
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Circadian and circatidal rhythms of protein abundance in the California mussel (Mytilus californianus)
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Data from: Investigation of the effect of temperature and colonial air on the ontogeny of circadian rhythms in young worker honey bees Apis mellifera
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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