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1,217 results for “circadian”
Parametric effects of light acting via multiple photoreceptors contribute to circadian entrainment in Drosophila melanogaster
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Data from: Circadian plasticity evolves through regulatory changes in a neuropeptide gene
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Size-selective mortality induces evolutionary changes in group risk-taking behavior and the circadian system in a fish
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Data from: Sporadic feeding regulates robust food entrainable circadian clocks in blind cavefish
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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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Dietary ketosis improves circadian dysfunction as well as motor symptoms in the BACHD mouse model of Huntington’s disease
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Supplementary code and visualisations for "Seizure pathways change on circadian and slower timescales in individual patients with focal epilepsy"
<p>MATLAB code and workspaces for reproducing the main results and figures of the paper "Seizure pathways change on circadian and slower timescales in individual patients with focal epilepsy." Additional supplementary visualisations for all patients are also provided as PDFs. </p> <p>The paper preprint is available on bioRxiv: https://www.biorxiv.org/content/10.1101/661371v2</p>
REV-ERBalpha mediates complement expression and circadian regulation of microglial synaptic phagocytosis
<p>The circadian clock has been shown to regulate various aspects of brain health including microglial and astrocyte activation. Here we report that deletion of the master clock protein BMAL1 induces robust increases in the expression of complement genes such as <i>C3, C4b </i>and <i>C1q</i> in the hippocampus. Loss of downstream REV-ERBa-mediated transcriptional repression led to increases in <i>C4b </i>in neurons and astrocytes as well as C3 protein in microglia and astrocytes. REV-ERBa deletion induced complement <i>C3/C4b </i>gene expression and increased microglial phagocytosis of synapses in the CA3 region of the hippocampus. Finally, we observed diurnal variation in the degree of microglial synaptic phagocytosis in wild type mice which was abrogated by REV-ERBα deletion. This work uncovers the BMAL1-REV-ERBa axis as a regulator of complement expression and synaptic phagocytosis in the brain, thereby illuminating a novel mechanism of synaptic regulation by the circadian clock.</p>
Data from: Genetic analysis of circadian responses to low frequency electromagnetic fields in Drosophila melanogaster
The blue-light sensitive photoreceptor cryptochrome (CRY) may act as a magneto-receptor through formation of radical pairs involving a triad of tryptophans. Previous genetic analyses of behavioral responses of Drosophila to electromagnetic fields using conditioning, circadian and geotaxis assays have lent some support to the radical pair model (RPM). Here, we describe a new method that generates consistent and reliable circadian responses to electromagnetic fields that differ substantially from those already reported. We used the Schuderer apparatus to isolate Drosophila from local environmental variables, and observe extremely low frequency (3 to 50 Hz) field-induced changes in two locomotor phenotypes, circadian period and activity levels. These field-induced phenotypes are CRY- and blue-light dependent, and are correlated with enhanced CRY stability. Mutational analysis of the terminal tryptophan of the triad hypothesised to be indispensable to the electron transfer required by the RPM reveals that this residue is not necessary for field responses. We observe that deletion of the CRY C-terminus dramatically attenuates the EMF-induced period changes, whereas the N-terminus underlies the hyperactivity. Most strikingly, an isolated CRY C-terminus that does not encode the Tryptophan triad nor the FAD binding domain is nevertheless able to mediate a modest EMF-induced period change. Finally, we observe that hCRY2, but not hCRY1, transformants can detect EMFs, suggesting that hCRY2 is blue light-responsive. In contrast, when we examined circadian molecular cycles in wild-type mouse suprachiasmatic nuclei slices under blue light, there was no field effect. Our results are therefore not consistent with the classical Trp triad-mediated RPM and suggest that CRYs act as blue-light/EMF sensors depending on trans-acting factors that are present in particular cellular environments.
Data from: The bear circadian clock doesn't 'sleep' during winter dormancy
Background: Most biological functions are synchronized to the environmental light:dark cycle via a circadian timekeeping system. Bears exhibit shallow torpor combined with metabolic suppression during winter dormancy. We sought to confirm that free-running circadian rhythms of body temperature (Tb) and activity were expressed in torpid grizzly (brown) bears and that they were functionally responsive to environmental light. We also measured activity and ambient light exposures in denning wild bears to determine if rhythms were evident and what the photic conditions of their natural dens were. Lastly, we used cultured skin fibroblasts obtained from captive torpid bears to assess molecular clock operation in peripheral tissues. Circadian parameters were estimated using robust wavelet transforms and maximum entropy spectral analyses. Results: Captive grizzly bears housed in constant darkness during winter dormancy expressed circadian rhythms of activity and Tb. The rhythm period of juvenile bears was significantly shorter than that of adult bears. However, the period of activity rhythms in adult captive bears was virtually identical to that of adult wild denning bears as was the strength of the activity rhythms. Similar to what has been found in other mammals, a single light exposure during the bear's active period delayed subsequent activity onsets whereas these were advanced when light was applied during the bear's inactive period. Lastly, in vitro studies confirmed the expression of molecular circadian rhythms with a period comparable to the bear's own behavioral rhythms. Conclusions: Based on these findings we conclude that the circadian system is functional in torpid bears and their peripheral tissues even when housed in constant darkness, is responsive to phase-shifting effects of light, and therefore, is a normal facet of torpid bear physiology.
Data from: Developmental exposure to PCB153 (2,2',4,4',5,5'-hexachlorobiphenyl) alters circadian rhythms and the expression of clock and metabolic genes
Polychlorinated biphenyls (PCBs) are highly persistent and ubiquitously distributed environmental pollutants. Based on their chemical structure, PCBs are classified into non-ortho-substituted and ortho-substituted congeners. Ortho-substituted PCBs are structurally similar to dioxin and their toxic effects and mode of action are well established. In contrast, very little is known about the effects of non-ortho-substituted PCBs, particularly during early development. The objective of this study is to investigate the effects of exposure to an environmentally prominent ortho-substituted PCB (2,2',4,4',5,5'-hexachlorobiphenyl; PCB153) on zebrafish embryos. We exposed zebrafish embryos to either DMSO or three different concentrations of PCB153 starting from 4 hours post-fertilization (hpf) to 120 hpf. We quantified gross morphological changes, behavioral phenotypes, gene expression changes and circadian behavior in the larvae. There were no developmental defects during the exposure period, but starting at 7 dpf, we observed spinal deformity in the 10 μM PCB153 treated group. A total of 633, 2227, and 3378 differentially expressed genes were observed in 0.1, 1 and 10 μM PCB153 treated embryos, respectively. Of these, 301 genes were common to all treatment groups. KEGG pathway analysis revealed enrichment of genes related to circadian rhythm, FoxO signaling and insulin resistance pathways. Behavioral analysis revealed that PCB153 exposure significantly alters circadian behavior. Disruption of circadian rhythms has been associated with the development of metabolic and neurological diseases. Thus, understanding the mechanisms of action on environmental chemicals in disrupting circadian regulation of metabolism is essential for preventing or mitigating chemical-induced metabolic disease.
Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock gene vrille
<p><strong>Background</strong>: Tracing the association between insect cold tolerance and latitudinally and locally varying environmental conditions, as well as key morphological traits and molecular mechanisms, is essential for understanding the processes involved in adaptation. We explored these issues in two closely-related species, Drosophila montana and Drosophila flavomontana, originating from diverse climatic locations across several latitudes on the coastal and mountainous regions of North America. We also investigated the association between sequence variation in one of the key circadian clock genes, vrille, and cold tolerance in both species. Finally, we studied the impact of vrille on fly cold tolerance and cold acclimation ability by silencing it with RNA interference in D. montana.</p> <p><strong>Results</strong>: We performed a principal component analysis (PCA) on variables representing bioclimatic conditions on the study sites and used latitude as a proxy of photoperiod. PC1 separated the mountainous continental sites from the coastal ones based on temperature variability and precipitation, while PC2 arranged the sites based on summer and annual mean temperatures. Cold tolerance tests showed D. montana to be more cold-tolerant than D. flavomontana and chill coma resistance (CT<sub>min</sub>) of this species showed an association with PC2. Chill coma recovery time (CCRT) of both species improved towards northern latitudes, and in D. flavomontana this trait was also associated with PC1. D. flavomontana flies were darkest in the coast and in the northern mountainous populations, but coloration showed no linkage with cold tolerance. Body size decreased towards cold environments in both species, but only within D. montana populations largest flies showed fastest recovery from cold. Finally, both the sequence analysis and RNAi study on vrille suggested this gene to play an essential role in D. montana cold resistance and acclimation, but not in recovery time.</p> <p><strong>Conclusions</strong>: Our study demonstrates the complexity of insect cold tolerance and emphasizes the need to trace its association with multiple environmental variables and morphological traits to identify potential agents of natural selection. It also shows that a circadian clock gene vrille is essential both for short- and long-term cold acclimation, potentially elucidating the connection between circadian clock system and cold tolerance.</p> <p> </p>
Dataset - Monitoring and Analyzing of Circadian and Ultradian Locomotor Activity Based on Raspberry-Pi
<p>Dataset of the raw data used for the figures in the article "Monitoring and Analyzing of Circadian and Ultradian Locomotor Activity Based on Raspberry-Pi", published by Electronics, Special Issue on Raspberry-Pi.</p> <p>Description:</p> <p>-fig 6-7, raw data of one Gammarus setosus used for actogram and spectral analysis;</p> <p>-fig 10-board temp-current, raw data of the board temperature recorded by PT100 and current in mA;</p> <p>-fig10-12-13 chamber-cpu temp, raw data of the chamber temperature and cpu temperature.</p>
Data from: Optimal sampling interval for characterisation of the circadian rhythm of body temperature in homeothermic animals using periodogram and cosinor analysis
<p>Core body temperature (T<sub>c</sub>) is a critical aspect of homeostasis in birds and mammals and is increasingly used as a biomarker of the fitness of an animal to its environment. Periodogram and cosinor analysis can be used to estimate the characteristics of the circadian rhythm of T<sub>c</sub> from data obtained on loggers that have limited memory capacity and battery life. This data set contains five days of core body temperature, measured by loggers implanted into the abdominal cavity, in nine species of birds and mammals.</p>
Plant circadian clock control of Medicago truncatula nodulation involving regulation of Nodule Cysteine-Rich genes
<p>Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcriptional factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of Nodule-specific Cysteine Rich peptides (NCRs) that have the LHY-bound conserved Evening Element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.</p>
Survival of extreme heat related to circadian cycle and sex in bees
<p>The pollination services provided by insects have been a crucial part of evolution and survival for many species, including humans. For bees to be efficient pollinators they must survive the environmental insults they face daily. Thus, looking into the short- and long-term effects of heat exposure on bee performance provides us with a foundation for investigating how stress can affect insect pollination. Solitary bees are a great model for investigating the effects of environmental stress on pollinators because the vast majority of insect pollinator species are solitary rather than social. One of the most pervasive environmental stressors to insects is temperature. Here we investigated how a one-hour heat shock affected multiple metrics of performance in the alfalfa leafcutting bee, <em>Megachile rotundata</em>. We found that a short heat shock (1hr at 45ºC) can delay adult emergence in males but not females. Bee pupae were rather resilient to a range of high temperature exposures that larvae did not survive. Following heat shock (1hr at 50ºC), adult bees were drastically less active than untreated bees, and this reduction in activity was evident over several days. Heat shock also led to a decrease in bee survival and longevity. Additionally, we found a connection between starvation survival after heat shock and time of exposure, where bees exposed in the morning survived longer than those exposed in the afternoon, when they would normally experience heat shock in the field. These data suggest that there is an unexplored daily/circadian component to the stress response in bees likely similar to that seen in flies, nematodes, and plants which is constitutive or preemptive rather than restorative. Taken together our data indicates that single heat shock events have strong potential to negatively impact multiple life history traits correlated with reproduction and fitness.</p>
Data from: Cyclin dependent kinase 5 (CDK5) regulates the circadian clock
<p>Circadian oscillations emerge from transcriptional and post-translational feedback loops. An important step in generating rhythmicity is the translocation of clock components into the nucleus, which is regulated in many cases by kinases. In mammals, the kinase promoting the nuclear import of the key clock component Period 2 (PER2) is unknown. We observed that the cyclin-dependent kinase 5 (CDK5) regulates the mammalian clock involving phosphorylation of PER2. Knock-down of Cdk5 in the suprachiasmatic nuclei (SCN), the main coordinator site of the mammalian circadian system, shortened the free-running period in mice. CDK5 phosphorylated PER2 at serine 394 (S394) in a diurnal fashion. This facilitated interaction with Cryptochrome 1 (CRY1) and nuclear entry of the PER2-CRY1 complex. Taken together, we found that CDK5 drives nuclear entry of PER2, which is critical for establishing an adequate circadian period of the circadian cycle. Therefore, CDK5 is critically involved in the regulation of the circadian clock.</p>
Characterizing the modern light environment and its influence on circadian rhythms
<p>Humans have largely supplanted natural light cycles with a variety of electric light sources and schedules misaligned with day-night cycles. Circadian disruption has been linked to a number of disease processes, but the extent of circadian disruption among the population is unknown. In this study, we measured light exposure and wrist temperature among residents of an urban area during each of the four seasons, as well as light illuminance in nearby outdoor locations. Daily light exposure was significantly lower for individuals, compared to outdoor light sensors, across all four seasons. There was also little seasonal variation in the realized photoperiod experienced by individuals, with the only significant difference occurring between winter and summer. We tested the hypothesis that differential light exposure impacts circadian phase timing, detected via the wrist temperature rhythm. To determine the influence of light exposure on circadian rhythms, we modeled the impact of morning and nighttime light exposure on the timing of the maximum wrist temperature. We found that morning and nighttime light exposure had significant but opposing impacts on maximum wrist temperature timing. Our results demonstrate that, within the range of exposure seen in everyday life, nighttime light can delay the onset of the maximum wrist temperature, while morning light can lead to earlier onset. Our results demonstrate that humans are minimizing natural seasonal differences in light exposure, and that circadian shifts and disruptions may be a more regular occurrence in the general population than is currently recognized.</p>
Arginine-vasopressin expressing neurons in the murine suprachiasmatic nucleus exhibit a circadian rhythm in network coherence in vivo
<p>The suprachiasmatic nucleus (SCN) is composed of functionally distinct subpopulations of GABAergic neurons which form a neural network responsible for synchronizing most physiological and behavioral circadian rhythms in mammals. To date, little is known regarding which aspects of SCN rhythmicity are generated by individual SCN neurons, and which aspects result from neuronal interaction within a network. Here, we utilize in vivo miniaturized microscopy to measure fluorescent GCaMP-reported calcium dynamics in arginine vasopressin (AVP)-expressing neurons in the intact SCN of awake, behaving mice. We report that SCN AVP neurons exhibit periodic, slow calcium waves which we demonstrate, using in vivo electrical recordings, likely reflect burst firing. Further, we observe substantial heterogeneity of function in that AVP neurons exhibit unstable rhythms and relatively weak rhythmicity at the population level. Network analysis reveals that correlated cellular behavior, or coherence, among neuron pairs also exhibited stochastic rhythms with about 33% of pairs rhythmic at any time. Unlike single-cell variables, coherence exhibited a strong rhythm at the population level with time of maximal coherence among AVP neuronal pairs at CT/ZT 6 and 9, coinciding with the timing of maximal neuronal activity for the SCN as a whole. These results demonstrate robust circadian variation in the coordination between stochastically rhythmic neurons and interactions between AVP neurons in the SCN may be more influential than single-cell activity in the regulation of circadian rhythms. Furthermore, they demonstrate that cells in this circuit, like those in many other circuits<span></span>, exhibit profound heterogenicity of function over time and space.</p>
Hydrobates spp. – Circadian locomotor output cycles kaput (Clock) gene poly-glutamine repeats
<p>Annual cues in the environment result in physiological changes that allow organisms to time reproduction during periods of optimal resource availability. Understanding how circadian rhythm genes sense these environmental cues and stimulate the appropriate physiological changes in response is important for determining the adaptability of species, especially in the advent of changing climate. A first step involves characterizing the environmental correlates of natural variation in these genes. Band-rumped and Leach's storm-petrels (<em>Hydrobates</em> spp.) are pelagic seabirds that breed across a wide range of latitudes. Importantly, some populations have undergone allochronic divergence, in which sympatric populations use the same breeding sites at different times of year. We investigated the relationship between variation in key functional regions of four genes that play an integral role in the cellular clock mechanism – <em>Clock, Bmal1, Cry2 </em>and<em> Per2</em> – with both breeding season and absolute latitude in these two species complexes. We discovered that allele frequencies in two genes, <em>Clock</em> and <em>Bmal1</em>, differed between seasonal populations in one archipelago, and also correlated with absolute latitude of breeding colonies. These results indicate that variation in these circadian rhythm genes may be involved in allochronic speciation, as well as adaptation to photoperiod at breeding locations.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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.
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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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OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.