Journal of Biological Rhythms最新文献

{"title":"Validation and TaqMan Conversion of a Molecular Chronotype Assessment Approach.","authors":"Alberto Biscontin, Antonella Russo, Davide Marnetto, Luca Pagani, Rodolfo Costa, Sara Montagnese","doi":"10.1177/07487304241298404","DOIUrl":"10.1177/07487304241298404","url":null,"abstract":"<p><p>The present study aimed to develop a TaqMan genotyping card for molecular chronotype assessment based on a predictive panel of 35 previously identified genetic variants. A reliable TaqMan assay was successfully developed for 33 out of the 35 chronotype-predictive variants. The resulting TaqMan genotyping card was utilized to genetically characterize 196 new individuals (in addition to the previously studied 96) and the Morningness-Eveningness Questionnaire was utilized for their phenotypical chronotype assessment. The predictive panel performance was validated on (a) a group of morning and evening individuals (logistic regression model), (b) a representative sample of the original study population also including intermediate chronotypes (linear regression model) and, (c) 25,986 individuals from the Estonian Biobank, for whom Munich Chronotype Questionnaire scores were available. The validation of the morningness-eveningness logistic regression model on 25 morning and 21 evening types resulted in a predictive value of 72%, confirming the reliability of the predictive panel and the success of its conversion into a TaqMan genotyping card. By contrast, the inclusion of intermediate individuals in the model led to a significant decrease in predictive performance (45% on 100 individuals [25 morning, 54 intermediate, and 21 evening]), with intermediate types being the most affected. No significant associations were observed between the genotype panel and chronotype in the Estonian Biobank sample. In conclusion, our genotyping card might represent a promising molecular chronotyping tool for the Italian population. Its performance in other populations is worthy of further study.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"19-26"},"PeriodicalIF":2.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142739687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Feeding- and Light-Cycle Synergistically Regulate Mouse Blood Pressure Daily Rhythm via <i>Bmal1</i>-Dependent and Independent Mechanisms.","authors":"Tianfei Hou, Wen Su, Aaron N Chacon, An-Hsuan Lin, Zhenheng Guo, Ming C Gong","doi":"10.1177/07487304241302510","DOIUrl":"10.1177/07487304241302510","url":null,"abstract":"<p><p>Cardiovascular health requires the orchestration of the daily rhythm of blood pressure (BP), which responds to changes in light exposure and dietary patterns. Whether rhythmic light and feeding can modulate daily BP rhythm directly or via modulating intrinsic core clock gene <i>Bmal1</i> is unknown. Using inducible global <i>Bmal1</i> knockout mice (iBmal1KO), we explored the impact of rhythmic light, rhythmic feeding, or their combination on various physiological parameters. Daily rhythms of BP, heart rate, and locomotor activity were monitored via radiotelemetry, while food intake patterns were tracked using the BioDAQ system. Respiratory exchange ratio (RER) and energy expenditure (EE) were assessed through indirect calorimetry. In addition, spectrum analysis was employed to analyze spontaneous baroreflex sensitivity and heart rate variability, and urinary norepinephrine excretion was quantified using high-performance liquid chromatography (HPLC). Neither rhythmic feeding nor rhythmic light alone was sufficient to reinstate the daily BP rhythm in arrhythmic iBmal1KO mice. However, combining the light and feeding cues in synchrony partially restored the daily BP rhythm. Interestingly, rhythmic feeding alone robustly reinstated RER and EE rhythms, even without rhythmic light. Similar to BP, the partial reinstatement of the daily rhythms in heart rate and locomotor activity was observed only when rhythmic light and feeding were applied in tandem. Rhythmic light by itself did not restore the light-dark phase difference in baroreflex sensitivity, urinary norepinephrine excretion, or the daily rhythm of heart rate variability. However, rhythmic feeding, alone or in combination with rhythmic light, successfully reinstated the light-dark phase differences in these parameters. In the absence of <i>Bmal1</i>, the synergy between rhythmic light and feeding can partially restore daily BP rhythm.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"76-90"},"PeriodicalIF":2.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11835536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142948951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thinking Outside the Clock: Using the Whole Genome to Understand the Role of Circadian Rhythms in Human Health.","authors":"Danae Penichet","doi":"10.1177/07487304241308633","DOIUrl":"10.1177/07487304241308633","url":null,"abstract":"","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"4-6"},"PeriodicalIF":2.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142915142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How Light at Night Sets the Circalunar Clock in the Marine Midge <i>Clunio marinus</i>.","authors":"Carolina M Peralta, Eric Feunteun, Julien Guillaudeau, Dušica Briševac, Tobias S Kaiser","doi":"10.1177/07487304241286936","DOIUrl":"10.1177/07487304241286936","url":null,"abstract":"<p><p>Many organisms inhabiting the interface between land and sea have evolved biological clocks corresponding to the period of the semilunar (14.77 days) or the lunar (29.53 days) cycle. Since tidal amplitude is modulated across the lunar cycle, these circasemilunar or circalunar clocks not only allow organisms to adapt to the lunar cycle, but also to specific tidal situations. Biological clocks are synchronized to external cycles via environmental cues called <i>zeitgebers</i>. Here, we explore how light at night sets the circalunar and circasemilunar clocks of <i>Clunio marinus</i>, a marine insect that relies on these clocks to control timing of emergence. We first characterized how moonlight intensity is modulated by the tides by measuring light intensity in the natural habitat of <i>C. marinus</i>. In laboratory experiments, we then explored how different moonlight treatments set the phase of the clocks of two <i>C. marinus</i> strains, one with a lunar rhythm and one with a semilunar rhythm. Light intensity alone does not affect the phase of the lunar rhythm. Presenting moonlight during different 2-h or 4-h windows during the night shows that (1) the required duration of moonlight is strain-specific, (2) there are strain-specific moonlight sensitivity windows and (3) timing of moonlight can shift the phase of the lunar rhythm to stay synchronized with the lowest low tides. Experiments simulating natural moonlight patterns confirm that the phase is set by the timing of moonlight. Simulating natural moonlight at field-observed intensities leads to the best synchronization. Taken together, we show that there is a complex and strain-specific integration of intensity, duration and timing of light at night to precisely entrain the lunar and semilunar rhythms. The observed fine-tuning of the rhythms under natural moonlight regimes lays the foundation for a better chronobiological and genetic dissection of the circa(semi)lunar clock in <i>C. marinus</i>.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"91-110"},"PeriodicalIF":2.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142590687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Incorporating Physical Activity in a New Two-Oscillator Model of Circadian Activity in Nocturnal and Diurnal Mammals.","authors":"Anouk W van Beurden, Johanna H Meijer, Jos H T Rohling","doi":"10.1177/07487304241303554","DOIUrl":"10.1177/07487304241303554","url":null,"abstract":"<p><p>In both diurnal and nocturnal species, the neurons in the suprachiasmatic nucleus (SCN) generate a daily pattern in which the impulse frequency peaks at midday and is lowest during the night. This pattern, common to both day-active and night-active species, has led to the long-standing notion that their functional difference relies merely on a sign reversal in SCN output. However, recent evidence shows that the response of the SCN to the animal's physical activity is opposite in nocturnal and diurnal animals. This finding suggests the presence of additional differences in the circadian system between nocturnal and diurnal species. We therefore attempted to identify these differences in neuronal network organization using the A-B two-oscillator model, which is comprised of Poincaré like oscillators. Based on this model, we infer that in diurnal animals the feedback from physical activity acts on neuronal subpopulations in the SCN that do not receive light input; in contrast, in nocturnal animals, physical activity acts on light-receptive neurons in the SCN in order to produce high-amplitude circadian rhythms.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"27-35"},"PeriodicalIF":2.9,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834329/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detecting Rhythmic Gene Expression in Single-cell Transcriptomics.","authors":"Bingxian Xu, Dingbang Ma, Katharine Abruzzi, Rosemary Braun","doi":"10.1177/07487304241273182","DOIUrl":"10.1177/07487304241273182","url":null,"abstract":"<p><p>An autonomous, environmentally synchronizable circadian rhythm is a ubiquitous feature of life on Earth. In multicellular organisms, this rhythm is generated by a transcription-translation feedback loop present in nearly every cell that drives daily expression of thousands of genes in a tissue-dependent manner. Identifying the genes that are under circadian control can elucidate the mechanisms by which physiological processes are coordinated in multicellular organisms. Today, transcriptomic profiling at the single-cell level provides an unprecedented opportunity to understand the function of cell-level clocks. However, while many cycling detection algorithms have been developed to identify genes under circadian control in bulk transcriptomic data, it is not known how best to adapt these algorithms to single-cell RNA seq data. Here, we benchmark commonly used circadian detection methods on their reliability and efficiency when applied to single-cell RNA seq data. Our results provide guidance on adapting existing cycling detection methods to the single-cell domain and elucidate opportunities for more robust and efficient rhythm detection in single-cell data. We also propose a subsampling procedure combined with harmonic regression as an efficient strategy to detect circadian genes in the single-cell setting.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"581-593"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hierarchy or Heterarchy of Mammalian Circadian Timekeepers?","authors":"William Bechtel","doi":"10.1177/07487304241286573","DOIUrl":"10.1177/07487304241286573","url":null,"abstract":"<p><p>Mammalian circadian biologists commonly characterize the relation between circadian clocks as hierarchical, with the clock in the suprachiasmatic nucleus at the top of the hierarchy. The lineage of research since the suprachiasmatic nucleus (SCN) was first identified as <i>the clock</i> in mammals has challenged this perspective, revealing clocks in peripheral tissues, showing that they respond to their own zeitgebers, coordinate oscillations among themselves, and in some cases modify the behavior of the SCN. Increasingly circadian timekeepers appear to constitute a heterarchical network, with control distributed and operating along multiple pathways. One reason for the continued invocation of hierarchy in mammalian circadian biology is that it is difficult to understand how a heterarchical system could operate effectively so as to maintain the organism. Evolved mechanisms, however, need not respect hierarchy and those that have survived have demonstrated the ability of heterarchical organizaton to maintain organisms.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"513-534"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142500939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Combination of Topological Data Analysis and Mathematical Modeling Improves Sleep Stage Prediction From Consumer-Grade Wearables.","authors":"Minki P Lee, Dae Wook Kim, Caleb Mayer, Olivia Walch, Daniel B Forger","doi":"10.1177/07487304241288607","DOIUrl":"10.1177/07487304241288607","url":null,"abstract":"<p><p>Wearable devices have become commonplace tools for tracking behavioral and physiological parameters in real-world settings. Nonetheless, the practical utility of these data for clinical and research applications, such as sleep analysis, is hindered by their noisy, large-scale, and multidimensional characteristics. Here, we develop a neural network algorithm that predicts sleep stages by tracking topological features (TFs) of wearable data and model-driven clock proxies (CPs) reflecting the circadian propensity for sleep. To evaluate its accuracy, we apply it to motion and heart rate data from the Apple Watch worn by young subjects undergoing polysomnography (PSG) and compare the predicted sleep stages with the corresponding ground truth PSG records. The neural network that includes TFs and CPs along with raw wearable data as inputs shows improved performance in classifying Wake/REM/NREM sleep. For example, it shows significant improvements in identifying REM and NREM sleep (AUROC/AUPRC improvements >13% and REM/NREM accuracy improvement of 12%) compared with the neural network using only raw data inputs. We find that this improvement is mainly attributed to the heart rate TFs. To further validate our algorithm on a different population, we test it on elderly subjects from the Multi-ethnic Study of Atherosclerosis cohort. This confirms that TFs and CPs contribute to the improvements in Wake/REM/NREM classification. We next compare the performance of our algorithm with previous state-of-the-art wearable-based sleep scoring algorithms and find that our algorithm outperforms them within and across different populations. This study demonstrates the benefits of combining topological data analysis and mathematical modeling to extract hidden inputs of neural networks from puzzling wearable data.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"535-553"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Reindeer Circadian Clock Is Rhythmic and Temperature-compensated But Shows Evidence of Weak Coupling Between the Secondary and Core Molecular Clock Loops.","authors":"Daniel Appenroth, Chandra S Ravuri, Sara K Torppa, Shona H Wood, David G Hazlerigg, Alexander C West","doi":"10.1177/07487304241283066","DOIUrl":"10.1177/07487304241283066","url":null,"abstract":"<p><p>Circadian rhythms synchronize the internal physiology of animals allowing them to anticipate daily changes in their environment. Arctic habitats may diminish the selective advantages of circadian rhythmicity by relaxing daily rhythmic environmental constraints, presenting a valuable opportunity to study the evolution of circadian rhythms. In reindeer, circadian control of locomotor activity and melatonin release is weak or absent, and the molecular clockwork is reportedly non-functional. Here we present new evidence that the circadian clock in cultured reindeer fibroblasts is rhythmic and temperature-compensated. Compared with mouse fibroblasts, however, reindeer fibroblasts have a short free-running period, and temperature cycles have an atypical impact on clock gene regulation. In reindeer cells, <i>Per2</i> and <i>Bmal1</i> reporters show rapid responses to temperature cycles, with a disintegration of their normal antiphasic relationship. The antiphasic <i>Per2-Bmal1</i> relationship re-emerges immediately after release from temperature cycles, but without complete temperature entrainment and with a marked decline in circadian amplitude. Experiments using <i>Bmal1</i> promoter reporters with mutated RORE sites showed that a reindeer-like response to temperature cycles can be mimicked in mouse or human cell lines by decoupling <i>Bmal1</i> reporter activity from ROR/REV-ERB-dependent transcriptional regulation. We suggest that weak coupling between core and secondary circadian feedback loops accounts for the observed behavior of reindeer fibroblasts in vitro. Our findings highlight diversity in how the thermal environment affects the temporal organization of mammals living under different thermoenergetic constraints.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"554-567"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sex-Related Variation in Circadian Rhythms in the Bumble Bee <i>Bombus terrestris</i>.","authors":"Ozlem Gonulkirmaz-Cancalar, Guy Bloch","doi":"10.1177/07487304241283863","DOIUrl":"10.1177/07487304241283863","url":null,"abstract":"<p><p>Mating success depends on many factors, but first of all, a male and a female need to meet at the same place and time. The circadian clock is an endogenous system regulating activity and sex-related behaviors in animals. We studied bumble bees (<i>Bombus terrestris</i>) in which the influence of circadian rhythms on sexual behavior has been little explored. We characterized circadian rhythms in adult emergence and locomotor activity under different illumination regimes for males and gynes (unmated queens). We developed a method to monitor adult emergence from the pupal cocoon and found no circadian rhythms in this behavior for either males or gynes. These results are not consistent with the hypothesis that the circadian clock regulates emergence from the pupa in this species. Consistent with this premise, we found that both gynes and males do not show circadian rhythms in locomotor activity during the first 3 days after pupal emergence, but shortly after developed robust circadian rhythms that are readily shifted by a phase delay in illumination regime. We conclude that the bumble bees do not need strong rhythms in adult emergence and during early adult life in their protected and regulated nest environment, but do need strong activity rhythms for timing flights and mating-related behaviors. Next, we tested the hypothesis that the locomotor activity of males and gynes have a similar phase, which may improve mating success. We found that both males and gynes have strong endogenous circadian rhythms that are entrained by the illumination regime, but males show rhythms at an earlier age, their rhythms are stronger, and their phase is slightly advanced relative to that of gynes. An earlier phase may be advantageous to males competing to mate a receptive gyne. Our results are consistent with the hypothesis that sex-related variations in circadian rhythms is shaped by sexual selection.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"594-606"},"PeriodicalIF":2.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11613518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}