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105 results for “Clock Gene”
Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics (Dataset)
<p>Complete dataset of <em>Clock</em> and <em>Adcyap1</em> alleles, distance matrices, and migration data used in the review and meta-analysis "<strong>Time trees and Clock genes: a Systematic Review and Comparative Analysis of Contemporary Avian Migration Genetics".</strong> </p>
Data from: Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis)
Clock genes exhibit substantial control over gene expression and ultimately life-histories using external cues such as photoperiod, and are thus likely to be critical for adaptation to shifting seasonal conditions and novel environments as species redistribute their ranges under climate change. Coding trinucleotide repeats (cTNRs) are found within several clock genes, and may be interesting targets of selection due to their containment within exonic regions and elevated mutation rates. Here, we conduct inter-specific characterization of the NR1D1 cTNR between Canada lynx and bobcat, and intra-specific spatial and environmental association analyses of neutral microsatellites and our functional cTNR marker, to investigate the role of selection on this locus in Canada lynx. We report signatures of divergent selection between lynx and bobcat, with the potential for hybrid-mediated gene flow in the area of range overlap. We also provide evidence that this locus is under selection across Canada lynx in eastern Canada, with both spatial and environmental variables significantly contributing to the explained variation, after controlling for neutral population structure. These results suggest that cTNRs may play an important role in the generation of functional diversity within some mammal species, and allow for contemporary rates of adaptation in wild populations in response to environmental change. We encourage continued investment into the study of cTNR markers to better understand their broader relevance to the evolution and adaptation of mammals.
Data from: Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis)
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Sexually dimorphic and clock-gene specific effects of artificial light at night on Drosophila behavioral rhythms
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Clock-linked genes underlie seasonal migratory timing in a diurnal raptor
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Data from: Temporal transcriptomics suggest that twin-peaking genes reset the clock
The mammalian suprachiasmatic nucleus (SCN) drives daily rhythmic behavior and physiology, yet a detailed understanding of its coordinated transcriptional programmes is lacking. To reveal the finer details of circadian variation in the mammalian SCN transcriptome we combined laser-capture microdissection and RNA-seq over a 24-hour light/dark cycle. We show that 7-times more genes exhibited a classic sinusoidal expression signature than previously observed in the SCN. Another group of 766 genes unexpectedly peaked twice, near both the start and end of the dark phase; this twin-peaking group is significantly enriched for synaptic transmission genes that are crucial for light-induced phase shifting of the circadian clock. 341 intergenic non-coding RNAs, together with novel exons of annotated protein-coding genes, including Cry1, also show specific circadian expression variation. Overall, our data provide an important chronobiological resource (www.wgpembroke.com/shiny/SCNseq/) and allow us to propose that transcriptional timing in the SCN is gating clock resetting mechanisms.
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.
Data from: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.
Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.
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>
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>
GWAS summary statistics pertaining to the publication "Mapping of the gene network that regulates glycan clock of ageing"
<p>Dataset pertaining to the publication "Mapping of the gene network that regulates IgG galactosylation". If you use this dataset, please cite the manuscript in order to fairly acknowledge the contribution of all participating studies and their sponsors.</p> <p>Data consists of three gzipped files corresponding to genome-wide association meta-analysis (GWAMA) of three IgG N-glycome traits describing the percentage of galactosylation: G0, G1 and G2. The files are tab-separated and contain genome-wide association meta-analysis data for the discovery studies. Summary data are given for the meta-analyses of over 15 million directly genotyped or imputed single variant polymorphisms corresponding to the HRC (Haplotype Reference Consortium) r1.1 reference panel. Meta-analysis estimates are corrected for inflation of test statistics using genomic control at the individual study level.</p>
Data from: Phenotypic correlates between clock genes and phenology among populations of Diederik cuckoo, Chrysococcyx caprius
<p>Dataset of Clock genes for Diederik Cuckoos collected as part of a migration genetics study.</p>
Data from: Clock gene evolution: seasonal timing, phylogenetic signal, or functional constraint?
Genetic determinants of seasonal reproduction are not fully understood, but may be important predictors of organism responses to climate change. We used a comparative approach to study the evolution of seasonal timing within a fish community in a natural common garden setting. We tested the hypothesis that allelic length variation in the PolyQ domain of a circadian rhythm gene, Clock1a, corresponded to interspecific differences in seasonal reproductive timing across five native and one introduced cyprinid fishes (n = 425 individuals) that co-occur in the Rio Grande, New Mexico, USA. Most common allele lengths were longer in native species that initiated reproduction earlier (Spearman's r = -0.70, p = 0.23). Clock1a allele length exhibited strong phylogenetic signal and earlier spawners were evolutionarily derived. Aside from length variation in Clock1a, all other amino acids were identical across native species, suggesting functional constraint over evolutionary time. Interestingly, the endangered Rio Grande silvery minnow (Hybognathus amarus) exhibited less allelic variation in Clock1a and observed heterozygosity was 2- to 6-fold lower than the five other (non-imperiled) species. Reduced genetic variation in this functionally important gene may impede this species' capacity to respond to ongoing environmental change.
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>
Dataset of scientific article: "Effect of miR-34a on expression of clock and clock-controlled genes in human cancer DLD1 and Lovo cells with different backgrounds in respect to p53 functionality and 17β-estradiol-mediated regulation"
<p>The dataset includes "raw" data used for the calculation of gene expression, wound healing test, fluorescence intensity, and MTS test.</p> <p> </p>
Clock Genes in Patients With Refractory Septic Shock (SeptiClock) - Pilot Study
ClinicalTrials.gov study NCT02044575. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Melatonin on Clock Genes in Parkinson's Disease
ClinicalTrials.gov study NCT04287543. IPD Sharing: YES. Countries: 1. Publications: 40.
Influence of Dairy Protein Breakfast on Glycemia, Weight Loss and Clock Genes in T2D
ClinicalTrials.gov study NCT03772067. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Metabolic Clock Genes During Fasting and After Food Intake in Type 2 Diabetics
ClinicalTrials.gov study NCT01939782. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Effect of Meal Frequency and Timing on Insulin Dose and Clock Gene in Type 2 Diabetic Patients
ClinicalTrials.gov study NCT02709915. IPD Sharing: NO. Countries: 1. Publications: 1.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.
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.