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1,217 results for “circadian”
Too hot or too disturbed? Temperatures more than hikers affect circadian activity of females in northern chamois
<p>This dataset contains: i) the activity level recorded by activity sensors for each 5-minutes boot for each individual, ii) the mean daily temperature assessed from ERA5 reanalysis combined with a micro-climate model, iii) the individual exposure to human disturbance for 62 adult female chamois monitored in the National Game and Hunting Reserve of Les Bauges massif (NGHRB), France, between June and September 2004-2020. This dataset is used in the analyses of the scientific paper “Too hot or too disturbed? Temperatures more than hikers affect circadian activity of females in northern chamois" (in prep).</p>
Transcriptomic analysis of light-induced genes in Nasonia vitripennis: possible implications for circadian light entrainment pathways
<p class="MDPI17abstract"><span>Circadian entrainment to the environmental day-night cycle is essential for the optimal use of environmental resources. In insects, opsin-based photoreception in the compound eye and ocelli, and CRYPTOCHROME1 (CRY1) in circadian clock neurons are thought to be involved in sensing photic information, but genetic regulation of circadian light entrainment in species without light-sensitive CRY1 remains unclear. To elucidate a possible CRY1-independent light transduction cascade, we analysed light-induced gene expression through RNA-sequencing in <em>Nasonia vitripennis</em>. Entrained wasps were subjected to a light pulse in the subjective night to reset the circadian clock and light-induced changes in gene expression were characterized at four different time points in wasp heads. We used co-expression, functional annotation, and transcription factor binding motif analyses to gain insight into the molecular pathways in response to acute light stimulus and form a hypothesis about the circadian light resetting pathway. Maximal gene induction was found after 2h of light stimulation (1432 genes), including the opsin <em>opblue</em> and the core clock genes <em>cry2</em> and <em>npas2</em>. Pathway and cluster analyses revealed light activation of glutamatergic and GABA-ergic neurotransmission, including CREB and AP-1 transcription pathway signalling. This suggests that circadian photic entrainment in <em>Nasonia</em> may require pathways that are similar to mammals. We propose a model for hymenopteran circadian light resetting that involves opsin-based photoreception, glutamatergic neurotransmission, and gene induction of <em>cry2</em> and <em>npas2</em> to reset the circadian clock.</span></p>
The Feasibility of Home-Based Measurement of Circadian Timing for Veterans With TBI and Insomnia
ClinicalTrials.gov study NCT05665764. IPD Sharing: YES. Countries: 1. Publications: 0.
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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Reprogramming feedback strength in gibberellin biosynthesis highlights conditional regulation by the circadian clock and carbon dioxide
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Transcriptomic analysis of light-induced genes in Nasonia vitripennis: possible implications for circadian light entrainment pathways
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Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus
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Anabaena circadian clock behavior under nitrogen-poor conditions from single-cell measurements of fluorescence intensity
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Size-selective mortality induces evolutionary changes in group risk-taking behavior and the circadian system in a fish
<p>1. Intensive and trait-selective mortality of fish and wildlife can cause evolutionary changes in a range of life-history and behavioral traits. These changes might in turn alter the circadian system due to coevolutionary mechanisms or correlated selection responses both at behavioral and molecular levels, with knock-on effects on daily physiological processes and behavioral outputs.</p> <p>2. We examined the evolutionary impact of size-selective harvesting on group risk-taking behavior and the circadian system in a model fish species. We exposed zebrafish (<em>Danio rerio</em>) to either large or small size-selective harvesting relative to a control over five generations, followed by eight generations during which harvesting halted to remove maternal effects.</p> <p>3. Size-selective mortality affected fine-scale timing of behaviors. In particular, small size-selective mortality, typical of specialized fisheries and gape-limited predators targeting smaller size classes, increased group risk-taking behavior during feeding and after simulated predator attacks. Moreover, small size-selective mortality increased early peaks of daily activity as well as extended self-feeding daily activity to the photophase compared to controls. By contrast large size-selective mortality, typical of most wild capture fisheries, only showed an almost significant effect of decreasing group risk-taking behavior during the habituation phase and no clear changes in fine-scale timing of daily behavioral rhythms compared to controls.</p> <p>4. We also found changes in the molecular circadian core clockwork in response to both size selective mortality treatments. These changes disappeared in the clock output pathway because both size-selected lines showed similar transcription profiles. This switch downstream to the molecular circadian core clockwork also resulted in similar overall behavioral rhythms (diurnal swimming and self-feeding in the last hours of darkness) independent of the underlying molecular clock.</p> <p>5. To conclude, our experimental harvest left an asymmetrical evolutionary legacy in group risk-taking behavior and in fine-scale daily behavioral rhythms. Yet, the overall timing of activity showed evolutionary resistance probably maintained by a molecular switch. Our experimental findings suggest that size-selective mortality can have consequences for behavior and physiological processes.</p>
Dynamic physiological and transcriptome changes reveal a po-tential relationship between the circadian clock and salt stress response in Ulmus pumila
<p>Despite the important role the circadian clock plays in numerous critical physiological responses in plants, such as hypocotyl elongation, leaf movement, stomatal opening, flowering, and stress responses, there have been no investigations into the effect of the circadian clock on physiological and transcriptional networks under salt stress. <em>Ulmus pumila</em> L.—a major tree species used for timber, shelter, food, medicine, fodder, and ecological protection—has been reported to tolerate 100~150 mM NaCl treatment. We performed a time-course physiological and transcriptome analysis of 2-years-old <em>U. pumila</em> seedlings under salt treatment to dissect the physiological regulation and potential relationship between the circadian clock and the salt stress response. Seedlings in 150 mM NaCl treatment exhibited salt-induced physiological enhancement compared to the control group. A total of 7,009 unigenes were identified under salt stress, of which 283 unigenes were identified as circadian rhythm genes and 16 unigenes were differentially expressed (circadian rhythm-related DEGs). Further analysis of dynamic expression changes revealed that DEGs involved in four crucial pathways—photosynthesis, thiamine metabolism, abscisic acid synthesis and metabolism, and the hormone-MAPK signal crosstalk pathway—are closely related to the circadian clock. Finally, we constructed a co-expression network between the circadian clock and these four crucial pathways. Our results help shed light on the molecular link between the circadian clock and salt stress tolerance in <em>U. pumila</em>.</p>
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>
Data from: Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock
<p>Circadian clocks are composed of molecular oscillators that pace rhythms of gene expression to the diurnal cycle. Therein, transcriptional-translational negative feedback loops (TTFLs) generate oscillating levels of transcriptional repressor proteins that regulate their own gene expression. In the filamentous fungus Neurospora crassa, the proteins Frequency (FRQ), the FRQ-interacting RNA helicase (FRH) and Casein-Kinase I (CK1) form the FFC complex that represses expression of genes activated by the White-Collar complex (WCC). A key question concerns how FRQ orchestrates molecular interactions at the core of the clock despite containing little predicted tertiary structure. We present the reconstitution and biophysical characterization of FRQ and the FFC in unphosphorylated and highly phosphorylated states. Site-specific spin labeling and pulse-dipolar ESR spectroscopy provides domain-specific structural details on the full-length, 989-residue intrinsically disordered FRQ and the FFC. FRQ contains a compact core that associates and organizes FRH and CK1 to coordinate their roles in WCC repression. FRQ phosphorylation increases conformational flexibility and alters oligomeric state but the changes in structure and dynamics are non-uniform. Full-length FRQ undergoes liquid-liquid phase separation (LLPS) to sequester FRH and CK1 and influence CK1 enzymatic activity. Although FRQ phosphorylation favors LLPS, LLPS feeds back to reduce FRQ phosphorylation by CK1 at higher temperatures. Live imaging of Neurospora hyphae reveals FRQ foci characteristic of condensates near the nuclear periphery. Analogous clock repressor proteins in higher organisms share little position-specific sequence identity with FRQ; yet, they contain amino-acid compositions that promote LLPS. Hence, condensate formation may be a conserved feature of eukaryotic circadian clocks. </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>
Shedding light on the threespine stickleback circadian clock
<p>The circadian clock is an internal timekeeping system shared by most organisms, and knowledge about its functional importance and evolution in natural environments is still needed. Here, we investigated the circadian clock of wild-caught threespine sticklebacks (<i>Gasterosteus aculeatus</i>) at the behavioural and molecular levels. While their behaviour, ecology, and evolution are well studied, information on their circadian rhythms are scarce. We quantified the daily locomotor activity rhythm under a light-dark cycle (LD) and under constant darkness (DD). Under LD, all fish exhibited significant daily rhythmicity, while under DD, only 18% of individuals remained rhythmic. This interindividual variation suggests that the circadian clock controls activity only in certain individuals. Moreover, under LD, some fish were almost exclusively nocturnal, while others were active around the clock. Furthermore, the most nocturnal fish were also the least active. These results suggest that light masks activity (i.e. suppresses activity without entraining the internal clock) more strongly in some individuals than others. Finally, we quantified the expression of five clock genes in the brain of sticklebacks under DD using qPCR. We did not detect circadian rhythmicity, which could either indicate that the clock molecular oscillator is highly light-dependent, or that there was an oscillation but that we were unable to detect it. Overall, our study suggests that a strong circadian control on behavioural rhythms may not necessarily be advantageous in a natural population of sticklebacks and that the daily phase of activity varies greatly between individuals because of a differential masking effect of light.</p>
Data from: Natural Zeitgebers under temperate conditions cannot compensate for the loss of a functional circadian clock in timing of a vital behavior in Drosophila
<p><span>The adaptive significance of adjusting behavioral activities to the right time of the day seems obvious but is under debate. Our data provides evidence that proper timing of eclosion, a vital behavior of the fruit fly <em>Drosophila melanogaster</em>, requires a functional molecular clock under quasi-natural conditions. </span></p> <p><span>We compared eclosion profiles and assessed eclosion rhythmicity in wildtype flies (CS) and clock-related mutant strains <em>(per<sup>01</sup></em>, <em>pdf<sup>01</sup></em>, <em>han<sup>5304</sup></em>) under laboratory and outdoor conditions. In the laboratory, flies were entrained in either light-dark cycle (LD12:12) or warm (25°C)-cold (16°C) cycle (WC12:12), and tested under entrainment or constant conditions using TriKinetics Drosophila Eclosion Monitors. For outdoor assays, a WEclMon system was used and experiments were performed between July-Octobre 2014 and July-Octobre 2016. </span></p> <p><span>Flies with a defective molecular clock showed impaired rhythmicity and gating under natural temperate conditions in Würzburg/Germany even in the presence of a full complement of abiotic Zeitgebers. We also found that eclosion rhythmicity cannot be entrained by daily cycles in relative humidity. Low relative humidity also did not or only weakly affect the ability of the flies to eclose and unfold their wings.</span></p> <p><span>Our results suggest that the presence of natural Zeitgebers is not sufficient, and a functional molecular clock is required to induce stable temporal eclosion patterns in flies under temperate conditions with considerable day-today variation in light intensity and temperature. Temperate Zeitgebers are, however, sufficient to functionally rescue a loss of PDF-signalling.</span></p> <p><span>The data set belongs to the publication:</span></p> <p><em><span>Ruf F, Mitesser O, Mungwa ST, Horn M, Rieger D, Hovestadt T, and Wegener C (2021) Natural Zeitgebers Under Temperate Conditions Cannot Compensate for the Loss of a Functional Circadian Clock in Timing of a Vital Behavior in Drosophila. </span>Journal of Biological Rhythms 36: 271–285. DOI: 10.1177/0748730421998112.</em></p>
Data for: Pericytes' Circadian Clock Affects Endothelial Cells' Synchronization and Angiogenesis in a 3D Tissue Engineered Scaffold
<p>Raw data set and analysis files for Mastrullo et al., Frontiers in Pharmacology, 2022 <strong>DOI:</strong> 10.3389/fphar.2022.867070 </p>
Estimates of circadian period for family lines of Boechera stricta
<p>Circadian clocks confer adaptation to predictable 24-h fluctuations in the exogenous environment, but it has yet to be determined what ecological factors maintain natural genetic variation in endogenous circadian period outside of the hypothesized optimum of 24 h. We estimated quantitative genetic variation in circadian period in leaf movement in 30 natural populations of the <em>Arabidopsis </em>relative<em> Boechera stricta </em>sampled within only 1° of latitude but across an elevation gradient spanning 2460−3300 m in the Rocky Mountains. Measuring ~3800 plants from 473 maternal families (7−20 per population), we found that genetic variation was of similar magnitude among vs. within populations, with population means varying between 21.9−24.9 h and maternal family means within populations varying by up to ~6 h. After statistically accounting for spatial autocorrelation at a habitat extreme, we found that elevation explained a significant proportion of genetic variation in circadian period, such that higher-elevation populations had shorter mean period lengths and reduced intrapopulation ranges. Environmental data indicate that these spatial trends could be related to steep regional climatic gradients in temperature, precipitation, and their intra-annual variability. Our findings suggest that spatially fine-grained environmental heterogeneity contributes to naturally occurring genetic variation in circadian traits in wild populations.</p>
The intestinal circadian clock drives microbial rhythmicity to maintain gastrointestinal homeostasis
<p><strong>Diurnal (<em>i.e.</em>, 24-hour) oscillations of the gut microbiome have been described in various species including mice and humans. However, the driving force behind these rhythms remains less clear. In this study, we differentiate between endogenous and exogenous time cues driving microbial rhythms.</strong> <strong>Our results demonstrate that fecal microbial oscillations are maintained in mice kept in the absence of light, supporting a role of the host’s circadian system rather than representing a diurnal response to environmental changes. Intestinal epithelial cell-specific ablation of the core clock gene <em>Bmal1</em> disrupts rhythmicity of microbiota. Targeted metabolomics functionally link intestinal clock-controlled bacteria to microbial-derived products, in particular branched-chain fatty acids and secondary bile acids. Microbiota transfer from intestinal clock-deficient mice into germ-free mice altered intestinal gene expression, enhanced lymphoid organ weights and suppressed immune cell recruitment. These results highlight the importance of functional intestinal clocks for circadian microbiota composition and function, which is required to balance the host’s gastrointestinal homeostasis. </strong></p>
Figure 1 in Circadian activity patterns and temporal overlap among cracids (Aves: Cracidae) within a vegetation mosaic in the Pantanal of Rio Negro, Brazil
Figure 1. Study area and location of the 90 camera trap stations in the Pantanal of Rio Negro, Aquidauana, Mato Grosso do Sul, Brazil.
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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.
OpenNeuro
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.