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1,217 results for “circadian”
Temperature-dependent fold-switching mechanism of the circadian clock protein KaiB
<p>Derived data accompanying publication of <em>Temperature-dependent fold-switching mechanism of the circadian clock protein KaiB</em> (Zhang et al., PNAS 2024).</p> <p> </p> <p>This dataset contains data for fold-switching of KaiB from simulations performed using the Upside coarse-grained model (Jumper et al. PLoS Comput. Bio 2017). Files contained include collective variables, kinetic quantities (committors), and initial structures used to seed unbiased simulations. These data should be sufficient recreate the analysis shown in the associated publicaion. Raw trajectory files have not been deposited due to their size; contact the author (Spencer Guo) to request.</p>
Arabidopsis thaliana circadian mRNA-seq gene expression processed tables from Romanowski et al., TPJ 2020.
<p>This dataset is an add-on for Romanowski et al., TPJ 2020 (https://doi.org/10.1111/tpj.14776) containing processed files for the circadian RNAseq data in tab delimited txt format.</p> <p><br> Here, you can the raw counts file, the normalized CPM values, and the full JTK result (without recalculated circadian phases, just the original ones). All genes with a read density > 0.05 in at least one timepoint were considered expressed. The read density is calculated as the amount of reads divided by the effective length of a gene (total reads / length). Genes rd file is also included.</p> <p>Some useful notes:<br> 1) Counts were assigned using ASpli and the AtRTDv2 annotation (34,212 genes).<br> 2) After filtering by rd we had a total of 18,503 expressed genes.<br> 3) 13,256 genes passed the QL F-tests.<br> 4) 9,127 genes were rhythmic according to JTK_cycle. </p> <p>For detailed protocols, please see Romanowski et al., TPJ 2020 (https://doi.org/10.1111/tpj.14776)</p> <p>The RNA-seq raw data supporting the conclusions of this article have been deposited in ArrayExpress (Kolesnikov et al., 2015) at EMBL-EBI (www.ebi.ac.uk/arrayexpress), under accession numbers E-MTAB-7933.</p> <p>All relevant custom r scripts are available at https://github.com/aromanowski/Circadian_rhythms_and_alternative_splicing</p>
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>
Two metabolomics data sets (mouse kidney, mouse plasma), generated for the publication Bignon et al., 2023: "Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock".
<p><strong>Publication: </strong>Bignon Y, Wigger L, Ansermet C, Weger BD, Lagarrigue S, Centeno G, Durussel F, Götz L, Ibberson M, Pradervand S, Quadroni M, Weger M, Amati F, Gachon F, Firsov D. Multiomics reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock. J Clin Invest. 2023 Mar 2:e167133. doi: 10.1172/JCI167133. Epub ahead of print. PMID: 36862511.</p> <p> </p> <p><strong>Abstract: </strong> Circadian rhythmicity in renal function suggests rhythmic adaptations in renal metabolism. To decipher the role of the circadian clock in renal metabolism, we studied diurnal changes in renal metabolic pathways using integrated transcriptomic, proteomic, and metabolomic analysis performed on control mice and mice with inducible deletion of the circadian clock regulator Bmal1 in the renal tubule (cKOt). With this unique resource, we demonstrated that ~30% RNAs, ~20% proteins and ~20% metabolites are rhythmic in kidneys of control mice. Several key metabolic pathways including NAD+ biosynthesis, fatty acid transport, carnitine shuttle,and b-oxidation displayed impairments in kidneys of cKOt, resulting in a perturbed mitochondrial activity. Carnitine reabsorption from the primary urine was one of the most impacted processes with a ~50% reduction in plasma carnitine levels and a parallel systemic decrease in tissues carnitine content. This suggests that the circadian clock in the renal tubule controls both kidney and systemic physiology.</p> <p> </p> <p><strong>This record contains two separate mass-spectrometry metabolomics data sets associated with this study:</strong></p> <ol> <li>Metabolic profile of renal tubules, MS/MS data, Metabolon, Morrisville, NC (N=60)</li> <li>Metabolic profile of blood plasma, MS/MS data, Biocrates, Innsbruck, Austria (N=60)</li> </ol> <p>For each data set, original data as received from the platforms and processed data as used in the data analysis are provided. Preprocessing of kidney data included removal of metabolites with more than 80% missing data values, median normalization, imputation and glog2 transformation. Preprocessing of plasma data included filtering of metabolites with any missing data and log2 transformation. Details of data processing are available in the STAR*methods of the publication.</p> <p> </p> <p><strong>Data sets in other repositories associated with the same study:</strong></p> <p>Additional data sets (transcriptomics, proteomics) pertaining to the same study have been deposited in public repositories:</p> <ul> <li>Gene Expression Omnibus (NCBI GEO), GSE216252</li> <li>PRIDE Archive (EMBL-EBI), PXD036803</li> </ul> <p> </p>
Circadian ontogenetic metabolomics atlas: an interactive resource with insights from rat plasma, tissues, and feces
<p>LC–MS instrumental files in mzXML format for metabolomics (HILICp, HILICn, HSST3p, HSST3n) and lipidomics platforms (LIPp, LIPn), including metadata for study samples, method blanks, quality control samples, and serial dilution samples. The instrumental files were acquired for each LC–MS platform as part of a study focused on creating a circadian ontogenetic metabolomics atlas of rat plasma, tissues, and feces. The original paper is accessible at http://doi.org/10.1007/s00018-025-05783-w</p>
Anabaena circadian clock behavior under nitrogen-poor conditions from single-cell measurements of fluorescence intensity
<p>Circadian clock arrays in multicellular filaments of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120 display remarkable spatio-temporal coherence under nitrogen-replete conditions. To shed light on the interplay between circadian clocks and the formation of developmental patterns, we followed the expression of a clock-controlled gene under nitrogen deprivation, at the level of individual cells. Our experiments showed that differentiation into heterocysts took place preferentially within a limited interval of the circadian clock cycle, that gene expression in different vegetative intervals along a developed filament was discoordinated, and that the circadian clock was active in individual heterocysts. Furthermore, Anabaena mutants lacking the kaiABC genes encoding the circadian clock core components produced heterocysts but failed in diazotrophy. Therefore, genes related to some aspect of nitrogen fixation, rather than early or mid-heterocyst differentiation genes, are likely affected by the absence of the clock. A bioinformatics analysis supports the notion that RpaA may play a role as master regulator of clock outputs in Anabaena, the temporal control of differentiation by the circadian clock and the involvement of the clock in proper diazotrophic growth. Together, these results suggest that under nitrogen-deficient conditions, the clock coherent unit in Anabaena is reduced from a full filament under nitrogen-rich conditions to the vegetative cell interval between heterocysts.</p>
F I G U R E 2 Fitted logistic curves with 95 in Circadian and seasonal flight activity differences between the sexes of the biocontrol agent Eadya daenerys (Hymenoptera: Braconidae) and the impact of host size on adult emergence
F I G U R E 2 Fitted logistic curves with 95% confidence intervals for the effect of Paropsisterna agricola beetle prepupal weight (mg) for three post-beetle prepupal outcomes (dead beetle prepupa, beetle or E. daenerys wasp).
F I G U R E 3 in Circadian and seasonal flight activity differences between the sexes of the biocontrol agent Eadya daenerys (Hymenoptera: Braconidae) and the impact of host size on adult emergence
F I G U R E 3 Host beetle prepupal weight (mg) (using both Paropsisterna agricola <80 mg and Paropsis charybdis>80 mg) and the head capsule width (mm) of laboratory-reared Eadya daenerys across both host species (n = 96).
F I G U R E 1 in Circadian and seasonal flight activity differences between the sexes of the biocontrol agent Eadya daenerys (Hymenoptera: Braconidae) and the impact of host size on adult emergence
F I G U R E 1 Weekly adult total malaise trap counts for three paropsine leaf beetle hosts of E. daenerys at Runnymede for the 2015/2016 season.
F I G U R E 4 in Circadian and seasonal flight activity differences between the sexes of the biocontrol agent Eadya daenerys (Hymenoptera: Braconidae) and the impact of host size on adult emergence
F I G U R E 4 Head capsule width (mm) of adult Eadya daenerys (left) reared in the laboratory on Paropsisterna agricola (n = 179) or (right) collected in the field (n = 253).
Fig. 2 in Preliminary observations on the circadian variation in site fidelity in Atelopus hoogmoedi (Lescure, 1974) (Anura, Bufonidae)
Fig. 2. Geographical overview of the study area. (A) Map of the Iwokrama Forest Reserve and its location in Guyana (top right corner). The red line crossing Iwokrama corresponds to the Linden-Lethem Road. (B) Relief map of the Iwokrama Mountains with Turu Falls represented by a black triangle (N 4°24.770' W 58°47.061'). (C) Portion of the trail between Turu Falls camp and the Linden-Lethem Road monitored, with dots corresponding to Atelopus individuals (from A1 - N 4°24.742', W 58°47.130' to A14 - N 4°24.750', W 58°47.128'). A and B from Kok et al. (2013).
Fig. 3 in Preliminary observations on the circadian variation in site fidelity in Atelopus hoogmoedi (Lescure, 1974) (Anura, Bufonidae)
Fig. 3. Substrate (shrub or leaf litter) use in Atelopus hoogmoedi during the day (light grey) and night (dark grey) at Turu Falls, Guyana. As indicated, substrate use was significantly different after dark.
Fig. 1 in Preliminary observations on the circadian variation in site fidelity in Atelopus hoogmoedi (Lescure, 1974) (Anura, Bufonidae)
Fig. 1. (A) Orange and (B) Yellow color morphs of Atelopus hoogmoedi, both encountered at the studied locality in the Iwokrama Mountains, Guyana. (C) Typical breeding habitat of A. hoogmoedi in the Iwokrama Mountains. Photos by PJRK.
Mechano-circadian simulation results
<p>Simulation results associated with the manuscript, "Computational modeling establishes mechanotransduction as a potent modulator of the mammalian circadian clock". See README file for descriptions of individual results files. All are stored as .m files for use in MATLAB. README reproduced below for easy access:</p> <ul> <li>bayesianAnalysis.mat: This should be loaded after initializing UQLab and before running any of the scripts. It contains all the results from MCMC for Bayesian parameter estimation in a single variable, `myBayesianAnalysis`.</li> <li>pSol_MAP.mat: This can be loaded for running simulations using only the maximum a posteriori parameters, contains a single variable `pSol`.</li> <li>SobolAnalysis.mat: results of Sobol sensitivity analysis stored in single variable `SobolAnalysis` for use with UQLab.</li> <li>circStored.mat: Contains variable `circStoreCell` to generate phase diagrams in CircadianAnalysis file.</li> <li>BranchesStored.mat: Contains variable `BranchesStored` with the coordinates of Hopf bifurcation curves in the MRTF-YAP/TAZ phase plane. Generated by ddeBifCircadian.m, for use with CircadianAnalysis.m.</li> <li>nMechCircStored.mat and nMechBranches.mat: Alterative versions of the above, corresponding to tests of different coupling Hill coefficients [1,1.5,2,3,4.5]</li> <li>StiffnessTests.mat: results from population level simulations for Figure 4, with substrate stiffnesses [0.1, 0.3, 1, 3, 10, 30, 100, 300, 1e7]. Data stored in single variable `popSeq`, generated by MechanoCircadian_main.m</li> <li>WTTests.mat: tests from Abenza et al for Figure 5, population level data in single variable `popSeq`, see MechanoCircadian_main.m for more details</li> <li>StiffnessTestsYAPMutant.mat: same as stiffnessTests above, but for YAP mutant 5SA-YAP (see settings in MechanoCircadian_main.m)</li> <li>StiffnessTestsLaminMutant.mat: same as stiffnessTests above, but for YAP mutant 5SA-YAP (see settings in MechanoCircadian_main.m)</li> <li>AltMutantTests.mat: tests for Figure S5, all at substrate stiffness = 30 kPa. 6 populations, corresponding to 0.5x YAP mutant, 2x YAP mutant, 4x YAP mutant, 1.5x NPC opening (Lamin mutant), 3x NPC opening (Lamin mutant), 5x NPC opening (Lamin mutant) - all stored in `popSeq` as above</li> </ul>
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>
Figure 1 in Circadian and seasonal variations in the metabolism of carbohydrates in Aegla ligulata (Crustacea: Anomura: Aeglidae)
Figure 1. Circadian and seasonal variations of haemolymphatic glucose levels in Aegla ligulata Bond-Buckup and Buckup, 1994, males and females. Data are given as mean ± SEM. The number of animals at each point varied between 15 and 20. The same letter denotes significantly different means (P<0.05). * denotes significantly different means of the spring (Sep, Oct and Nov), winter (Jun, Jul and Aug), summer (Dec, Jan and Feb) and autumn (Mar, Apr and May). Numbers 1, 2 and 3 stand for the collection times: 0600, 1200 and 1800 h, respectively.
Fig. 3 in Circadian activity patterns of the Red fox (Vulpes vulpes) and the Stone marten (Martes foina) in agricultural landscape of Northwestern Bulgaria during autumn-winter period
Fig. 3. Stone marten (Martes foina) and Red fox (Vulpes vulpes) daily activity patterns in protected area "Zlatiyata", Northwestern Bulgaria.
Fig. 2 in Circadian activity patterns of the Red fox (Vulpes vulpes) and the Stone marten (Martes foina) in agricultural landscape of Northwestern Bulgaria during autumn-winter period
Fig. 2. Stone marten, Martes foina (left) and Red fox, Vulpes vulpes (right) captured in protected area "Zlatiyata", Northwestern Bulgaria.
Data Sharing Practices in the MRC Circadian Mental Health Network.
<p>This dataset supports the research conducted within the MRC Circadian Mental Health Network which assesses data sharing practices among Principal Investigators' publications in 2023. This work aims to identify trends, challenges, and inform future recommendations and policies based on the findings. The dataset includes various files that detail the methodology, data collected, and analyses performed.</p> <p> </p> <p><strong>Repository Contents:</strong></p> <ol> <li> <p><strong>Methods and Analysis Report - Data Sharing Practices in the MRC CMHN.pdf</strong></p> <ul> <li>This report provides the methodologies used for selecting and assessing research papers within the network, along with detailed results, tables, and discussions from the evaluation.</li> </ul> </li> <li> <p><strong>CMHN_All_Data.xlsx</strong></p> <ul> <li>An Excel workbook containing: <ul> <li><strong>Sheet 1</strong>: All data and variables collected and analysed for this project.</li> <li><strong>Sheet 2</strong>: A README file that explains each variable and its values.<br><br></li> </ul> </li> </ul> </li> <li> <p><strong>CMHN DataType Scoring.xlsx</strong></p> <ul> <li>An Excel workbook detailing: <ul> <li><strong>Sheet 1</strong>: All datatypes, both code and datasets, evaluated in this study.</li> <li><strong>Sheet 2</strong>: A README explaining the variables evaluated and their specific values.<br><br></li> </ul> </li> </ul> </li> <li> <p><strong>CMHN Data Extraction Survey.pdf</strong></p> <ul> <li>A copy of the Microsoft Form used to systematically evaluate data-sharing practices from selected publications, describing the structured data extraction process used.<br><br></li> </ul> </li> <li> <p><strong>CMHN DataType Scoring Survey.pdf</strong></p> <ul> <li>A Microsoft Form used to assess the types of data (code and datasets) shared.<br><br></li> </ul> </li> <li> <p><strong>Data_CSV_Code.csv</strong></p> <ul> <li>This file is the original, uncleaned dataset directly extracted from the initial response data of the Microsoft Form used in the project. It served as the primary dataset for all subsequent data analysis and code execution within the study.<br><br></li> </ul> </li> <li> <p><strong>CMHN Code.Rmd</strong></p> <ul> <li>An R Markdown file containing the code used for data analysis; predominantly descriptive statistics due to the limited number of papers with shared data.</li> </ul> </li> </ol> <p><strong><br>Recommended Use:</strong> For comparative purposes or further analysis, researchers are encouraged to utilise the cleaned datasets available in "CMHN_All_Data.xlsx" and "CMHN DataType Scoring.xlsx."<br><br><strong>Contact:</strong> For further inquiries, please email us at <a href="mailto:bio_rdm@ed.ac.uk" target="_blank" rel="noopener">bio_rdm@ed.ac.uk</a>.</p>
Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus
<p>This dataset contains the genome assembly and associated annotation of the Patagonian Blennie (<em>Eleginops maclovinus</em>), the closest extant taxon to the Antarctic notothenioid radiation. In addition to the characterization of the <em>E. maclovinus </em>genome, the dataset includes a description of circadian rhythm orthologs for <em>E. maclovinus</em>, other notothenenioid taxa, and teleost outgroups, as well as a copy of the bioinformatic scripts used for the assembly, annotation, and other downstream analysis.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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