Journal of Biological Rhythms最新文献

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Biological Rhythms in Coronavirus Pneumonia Pathogenesis. 冠状病毒肺炎发病机制中的生物节律
IF 3 3区 生物学
Journal of Biological Rhythms Pub Date : 2026-10-01 Epub Date: 2026-06-16 DOI: 10.1177/07487304261449284
Huram Mok, Carrie Gierasch, Elaine Ostendorf, Aryaman Jaiswal, Avi J Adler, Alex Ganninger, Lola Wright, Andrew Ganninger, Carolyn Fox, Krzysztof Hyrc, Gregory Shao, Anna Eubanks, Brielle Patlin, Manoj Arra, Prisha Kumar, Janice Huss, Jeffrey A Haspel
{"title":"Biological Rhythms in Coronavirus Pneumonia Pathogenesis.","authors":"Huram Mok, Carrie Gierasch, Elaine Ostendorf, Aryaman Jaiswal, Avi J Adler, Alex Ganninger, Lola Wright, Andrew Ganninger, Carolyn Fox, Krzysztof Hyrc, Gregory Shao, Anna Eubanks, Brielle Patlin, Manoj Arra, Prisha Kumar, Janice Huss, Jeffrey A Haspel","doi":"10.1177/07487304261449284","DOIUrl":"10.1177/07487304261449284","url":null,"abstract":"<p><p>Night shift work is linked to more severe coronavirus pneumonia, suggesting that host resilience to these pathogens may depend on the timing of exposure. Here, we examined how the time of day influences the severity of coronavirus pneumonia in mice, using mouse hepatitis virus-1 (MHV-1) as a natural infection model. We found that the timing of infection influenced MHV-1 severity, with the highest mortality, peak viral load, and lung inflammation occurring with midday infection, which corresponds to the mid-rest phase in mice and is comparable with nighttime in humans. The time-of-day dependence in disease severity occurred prominently in males and was sensitive to global disruption of the clock gene <i>Bmal1</i>. Midday infection correlated with increased MHV-1 binding to and replication within alveolar macrophages (AM). Depleting AMs with clodronate or loading them with neutral liposomes before MHV-1 infection eliminated differences in pneumonia survival and peak viral load related to the timing of infection. These data suggest an immunologic rhythm underlying coronavirus outcomes, in which oscillations in \"first contact\" interactions between AMs and the virus shape subsequent pneumonia severity.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"549-570"},"PeriodicalIF":3.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13308194/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148264590","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}
引用次数: 0
RhythmInsight: An Interactive Web Platform for Circadian and Diurnal Rhythmic Analysis and Visualization. RhythmInsight:一个用于昼夜节律分析和可视化的交互式网络平台。
IF 3 3区 生物学
Journal of Biological Rhythms Pub Date : 2026-10-01 Epub Date: 2026-05-05 DOI: 10.1177/07487304261437377
Guohao Han, Xiaodie Wu, Xiaoyun Xiao, Tengfei Guo, Dan Li, Haisen Zhang, Dengke Gao, Chao Li, Aihua Wang, Hsu-Wen Chao, Yaping Jin, Huatao Chen
{"title":"RhythmInsight: An Interactive Web Platform for Circadian and Diurnal Rhythmic Analysis and Visualization.","authors":"Guohao Han, Xiaodie Wu, Xiaoyun Xiao, Tengfei Guo, Dan Li, Haisen Zhang, Dengke Gao, Chao Li, Aihua Wang, Hsu-Wen Chao, Yaping Jin, Huatao Chen","doi":"10.1177/07487304261437377","DOIUrl":"10.1177/07487304261437377","url":null,"abstract":"<p><p>Circadian rhythms are endogenous biological cycles with a period of approximately 24 h that integrate a wide range of physiological and behavioral processes in living organisms. In addition to circadian rhythms, many other biological processes also exhibit diurnal (24 h) rhythms driven by external environmental cues. With the significance of circadian and diurnal regulation becoming increasingly recognized, the field of chronobiology is exhibiting unprecedented growth in the life sciences and translational medicine. Over the past 2 decades, a variety of computational methods have been developed to detect and extract rhythmic signals from the time-series data of different species. However, existing rhythmic analysis tools are often fragmented, demand programming expertise, exhibit limited visualization capabilities, and impose inconsistent requirements on data types and sampling intervals. Therefore, there is an urgent need to establish a convenient and comprehensive tool for detecting and analyzing the circadian and diurnal rhythmicity. To meet this demand, RhythmInsight was developed as an open access, web-based platform for comprehensive analysis and visualization of circadian and diurnal rhythms across various species and data types, including physiological, omics, and experimental data. RhythmInsight includes 3 modules: Rhythmic Analysis, Differential Rhythmicity Analysis, and Rhythmic Visualization. The Rhythmic Analysis module incorporates 9 algorithms (JTK_CYCLE, Cosinor, CircaCompare, meta2d, Lomb-Scargle, RAIN, ARSER, Fisher's G-test, and Robust G-test) to detect and characterize rhythmic signals. The Differential Rhythmicity Analysis module, based on CircaCompare, detects and compares rhythmic parameters (amplitude, phase, and the Midline Estimating Statistic of Rhythm) between 2 experimental conditions. The Rhythmic Visualization module provides powerful graphical tools, including line plots, fitted curves, heatmaps, polar plots, and boxplots, for the intuitive visualization of time-dependent trends. By integrating rhythmic algorithmic analysis with interactive visualization, RhythmInsight simplifies the analysis process and enhances accessibility for researchers without programming backgrounds, particularly experimental biologists and early-career scientists. RhythmInsight is freely available at https://RhythmInsight.com.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"663-677"},"PeriodicalIF":3.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838430","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}
引用次数: 0
The Ontogeny of Rhythms in Circadian Clock Gene Expression in Mouse Brain and Neuroimmune Tissues. 小鼠脑和神经免疫组织中生物钟基因表达节律的个体发生。
IF 3 3区 生物学
Journal of Biological Rhythms Pub Date : 2026-10-01 Epub Date: 2026-06-17 DOI: 10.1177/07487304261449282
Kiersten S Bell, Ruizhuo Chen, Aidan S Weitzner, Laura K Fonken
{"title":"The Ontogeny of Rhythms in Circadian Clock Gene Expression in Mouse Brain and Neuroimmune Tissues.","authors":"Kiersten S Bell, Ruizhuo Chen, Aidan S Weitzner, Laura K Fonken","doi":"10.1177/07487304261449282","DOIUrl":"10.1177/07487304261449282","url":null,"abstract":"<p><p>The circadian system coordinates daily physiology across nearly all tissues to temporally organize metabolism and maintain homeostasis. In the brain, circadian timing regulates neural activity, cellular function, and neuroimmune signaling, which is especially important during development. Yet, the ontogeny of circadian regulation during neurodevelopment remains poorly defined. Here, we characterized time-of-day variation in core clock and neuroimmune genes across multiple brain structures during early postnatal development, alongside circulating corticosterone concentrations. Using male and female C57BL mice housed in a standard light-dark cycle [12:12 light (150 lux)/dark (0 lux)], we measured the expression of <i>Per1</i>, <i>Per2</i>, and <i>Rev-erbα</i> in the suprachiasmatic nucleus, hippocampus, and medial prefrontal cortex, as well as in neuroimmune tissues (choroid plexus, meninges, and isolated microglia) across postnatal days (PND) 1-24. Across development, rhythms were seen in corticosterone concentrations and all brain regions, with increased amplitudes and gene-specific phase maturation toward adult-like timing by PND 24. Notably, the choroid plexus and meninges exhibited time-of-day differences in clock gene expression by PND 10-24. In contrast, isolated microglia did not display detectable time-of-day differences in clock gene expression; however, microglial phagocytic activity varied by time of day. Together, these findings demonstrate that circadian regulation of the brain emerges during the neonatal period, and the parameters of time-of-day differences are tissue- and gene-specific during development. In addition, functional rhythms may precede or occur independent of detectable transcriptional differences. This work establishes a developmental framework for circadian-neuroimmune interactions, with important implications for neuroimmune development and vulnerability. Given the neuroimmune system's role in shaping brain development, disruptions in these temporal processes may contribute to neurodevelopmental or mood disorders.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"615-635"},"PeriodicalIF":3.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13348823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148264545","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}
引用次数: 0
Influence of Diurnal Rhythms and Aging on Pupil Size Changes During Dark Adaptation in Mice. 昼夜节律和衰老对小鼠暗适应过程中瞳孔大小变化的影响。
IF 3 3区 生物学
Journal of Biological Rhythms Pub Date : 2026-10-01 Epub Date: 2026-05-20 DOI: 10.1177/07487304261448251
Yoshinori Iba, Yohei Yamashita, Taiga Hasegawa, Takumi Masui, Hiroyuki Wada
{"title":"Influence of Diurnal Rhythms and Aging on Pupil Size Changes During Dark Adaptation in Mice.","authors":"Yoshinori Iba, Yohei Yamashita, Taiga Hasegawa, Takumi Masui, Hiroyuki Wada","doi":"10.1177/07487304261448251","DOIUrl":"10.1177/07487304261448251","url":null,"abstract":"<p><p>During dark adaptation, pupil size changes in association with visual adaptation processes; however, the influence of diurnal phase (daytime vs nighttime) and aging on these changes remains unclear. In this study, we examined pupil size changes during dark adaptation across the daytime and nighttime in young, middle-aged, and aged C57BL/6N mice. In young mice, pupil size reached a maximum shortly after the onset of dark adaptation and then gradually decreased during the daytime, whereas it remained dilated during the nighttime. Furthermore, dopamine depletion induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) significantly attenuated the gradual pupillary constriction following pupil dilation during dark adaptation in the daytime, suggesting a possible involvement of dopaminergic signaling in the later phase of the response. In middle-aged mice, pupillary light reflex-evoked constriction was preserved; however, the early (rapid) phase of constriction following the initial dilation during daytime dark adaptation was impaired, whereas the later (delayed) phase remained largely comparable to that in young mice, suggesting age-related alterations in regulatory mechanisms rather than a loss of constriction capacity. Pharmacological analyses further suggested that distinct neural mechanisms may differentially contribute to these temporal phases. In aged mice, maximal pupil dilation during dark adaptation was significantly reduced during both the daytime and nighttime. In addition, aged mice exhibited distinct abnormalities in pupil dilation immediately after the onset of dark adaptation during the nighttime, indicating mechanisms that differ from those observed in middle-aged mice. Together, these results demonstrate that pupillary dynamics during dark adaptation are modulated by diurnal phase and progressively altered with aging. Thus, analysis of pupil dynamics during dark adaptation may provide a useful approach for detecting age-related changes in neural function.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"594-604"},"PeriodicalIF":3.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147972790","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}
引用次数: 0
Corrigendum to "Malcolm von Schantz". “对马尔科姆·冯·尚茨的更正”。
IF 3 3区 生物学
Journal of Biological Rhythms Pub Date : 2026-09-21 DOI: 10.1177/07487304261492496
{"title":"Corrigendum to \"Malcolm von Schantz\".","authors":"","doi":"10.1177/07487304261492496","DOIUrl":"https://doi.org/10.1177/07487304261492496","url":null,"abstract":"","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"7487304261492496"},"PeriodicalIF":3.0,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149016571","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}
引用次数: 0
Cell-Autonomous and Systemic Circadian Regulation of Gene Expression in Adipocytes. 脂肪细胞中基因表达的细胞自主和系统昼夜节律调节。
IF 3 3区 生物学
Journal of Biological Rhythms Pub Date : 2026-09-15 DOI: 10.1177/07487304261480978
Jennifer M Worthen, Armina-Lyn M Frederick, Phillip A Dumesic, Jennifer J Loros, Jay C Dunlap
{"title":"Cell-Autonomous and Systemic Circadian Regulation of Gene Expression in Adipocytes.","authors":"Jennifer M Worthen, Armina-Lyn M Frederick, Phillip A Dumesic, Jennifer J Loros, Jay C Dunlap","doi":"10.1177/07487304261480978","DOIUrl":"10.1177/07487304261480978","url":null,"abstract":"<p><p>Circadian clocks strongly influence adipocyte biology. Studying adipocyte circadian regulation in the absence of organismal cues isolates cell-autonomous clock control, providing insight into mechanisms relevant to metabolic disease. To resolve circadian core biological programs, we deeply sequenced bulk RNA from inguinal-derived, in vitro-differentiated adipocytes (IVDAs) over a 2.5-day circadian time-course and compared clock-controlled genes (CCGs) with existing mouse supraclavicular brown adipose tissue (BAT) and epididymal white adipose tissue (eWAT) circadian time-course datasets. Using Phase Set Enrichment Analysis (PSEA), we report that 21% of the protein-coding transcriptome is rhythmic in IVDAs. Intrinsic circadian regulation governs key processes in energy metabolism, molecular transport, and transcription. Integration with in vivo datasets reveals that BAT and IVDAs exhibit more cohesive rhythmic pathways than does eWAT, clustering around the late-night early-morning transition. To explore how these pathways may be regulated, we reexamine a recent interscapular BAT cistrome dataset. Using in vitro-differentiated adipocyte (IVDA) transcription factors that are phase-aligned (≤4 h) with in vivo as input, motif enrichment analysis reveals 2 temporally distinct regulatory programs: an early E-box activator ARNT-family/bHLH-PAS program is enriched for transcriptional regulation, RNA metabolism, and signaling pathways, and a late nuclear receptor-associated program is enriched for energy metabolism, phospholipid biosynthesis, mitochondrial function, extracellular matrix (ECM) organization, and nuclear receptor signaling. Overall, we identify novel rhythmic transcripts and define cell-autonomous circadian programs in adipocytes whose timing is further sculpted by systemic cues in vivo. Because obesity is associated with adipocyte hypertrophy and hyperplasia, processes likely influenced by circadian regulation, these findings advance our understanding of clock-controlled adipocyte metabolism and its contribution to metabolic dysfunction.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"7487304261480978"},"PeriodicalIF":3.0,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148976843","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}
引用次数: 0
The Circadian System and Chronic Kidney Disease Risk: Epidemiological Evidence. 昼夜节律系统和慢性肾脏疾病风险:流行病学证据。
IF 3 3区 生物学
Journal of Biological Rhythms Pub Date : 2026-09-09 DOI: 10.1177/07487304261477969
Jing Zhang, Dat Thien Tran, Tala El Ghoul, Magdalena Żebrowska, Susanne Strohmaier, Dilara Gülmez, Manfred Hecking, Eva S Schernhammer
{"title":"The Circadian System and Chronic Kidney Disease Risk: Epidemiological Evidence.","authors":"Jing Zhang, Dat Thien Tran, Tala El Ghoul, Magdalena Żebrowska, Susanne Strohmaier, Dilara Gülmez, Manfred Hecking, Eva S Schernhammer","doi":"10.1177/07487304261477969","DOIUrl":"https://doi.org/10.1177/07487304261477969","url":null,"abstract":"<p><p>Chronic kidney disease (CKD) affects roughly 10% of the world's population, and growing evidence suggests that disruption of the circadian system-now recognized as an important regulator of numerous physiological pathways, may contribute to impaired kidney function and increased CKD risk. This narrative review aims to synthesize the existing literature on the association between determinants of circadian rhythm (shift work, artificial light at night [ALAN], melatonin) as well as sleep health and CKD risk. Three databases (PubMed, Web of Science, and Embase) were searched for original articles published from 1966 through 28 February 2026. A total of 34 studies examined the association between circadian factors and CKD risk: 7 on shift work, 2 on ALAN, 4 on melatonin, 4 on chronotype, 2 on social jetlag, 2 on insomnia, and 18 on sleep duration. Taken together, these studies offer consistent evidence that shift work, evening chronotype, prolonged social jetlag, and both short and long sleep duration are associated with elevated CKD risk. Given the potential implications for early detection, risk stratification, and targeted behavioral interventions, future research should employ standardized approaches and improved measures using, for example, actigraphy, to clarify causal pathways and strengthen the evidence base.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"7487304261477969"},"PeriodicalIF":3.0,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148919918","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}
引用次数: 0
Daylight, Daily Rhythms, and Downstream Physiology: A Translational Study in Diurnal Nile Grass Rats (Arvicanthis niloticus). 日光、每日节律和下游生理:尼罗河草鼠(Arvicanthis niloticus)的翻译研究。
IF 3 3区 生物学
Journal of Biological Rhythms Pub Date : 2026-09-07 DOI: 10.1177/07487304261480753
Antony B Kim, Katrina Linning-Duffy, Melanie Balbach, Nolan Lucera, Marshall Delgado, Nikhil Kummur, Huishi Toh, Luisa Caldas, Lily Yan
{"title":"Daylight, Daily Rhythms, and Downstream Physiology: A Translational Study in Diurnal Nile Grass Rats (<i>Arvicanthis niloticus</i>).","authors":"Antony B Kim, Katrina Linning-Duffy, Melanie Balbach, Nolan Lucera, Marshall Delgado, Nikhil Kummur, Huishi Toh, Luisa Caldas, Lily Yan","doi":"10.1177/07487304261480753","DOIUrl":"10.1177/07487304261480753","url":null,"abstract":"<p><p>The circadian system evolved under natural light-dark cycles, while modern humans spend much of their time indoors under electric lighting that differs substantially from daylight in intensity, spectral composition, and temporal structure. How such lighting environments influence the circadian system has not been systematically examined in a diurnal animal model under ecologically relevant conditions. In this study, we used the diurnal Nile grass rat (<i>Arvicanthis niloticus</i>) to assess daily locomotor rhythms across 4 lighting conditions designed to approximate common human exposure scenarios: rectangular daylight (D65‑R; ~5600 lux), semi‑sigmoidal daylight mimicking natural intensity dynamics (D65‑S; matched peak intensity with ~50% lower cumulative energy), fluorescent indoor light (F12; ~150 lux), and fluorescent light supplemented with a 1‑h midday daylight pulse (F12 + D65‑P). Using a within‑subject design (<i>n</i> = 8), male grass rats were housed under each condition for 2 weeks. D65‑R produced the highest daytime activity levels and the strongest day-night activity ratio, consistent with robust circadian entrainment. Despite matching peak intensity, D65‑S did not yield comparable circadian outcomes, indicating that cumulative photon exposure, rather than peak intensity alone, contributes to entrainment strength. Notably, the addition of a 1‑h midday daylight pulse (D65-P) partially increased circadian amplitude under otherwise fluorescent conditions, with higher periodogram amplitude relative to F12 alone. A separate cohort of males was exposed to D65-R or F12 for 6 weeks (<i>n</i> = 10/condition) to assess physiological outcomes, including metabolic and reproductive measures. Compared with the D65-R group, the F12 group showed a higher diabetic rate (10% vs. 40%) and reduced sperm motility (45 ± 6 vs. 19 ± 1%), consistent with potential downstream correlates of circadian rhythm disruption. Together, these findings demonstrate that lighting conditions characteristic of indoor environments produce weaker circadian organization than daylight-equivalent lighting in a diurnal rodent, which underscore the importance of light quality in shaping circadian rhythms and downstream physiological processes.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"7487304261480753"},"PeriodicalIF":3.0,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13556272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148900603","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}
引用次数: 0
CHORD: Resolving 12-h Transcriptomic Rhythms Into Harmonic, Autonomous, and Intersection Origins. 和弦:解决12小时转录组节律成谐波,自主和交叉起源。
IF 3 3区 生物学
Journal of Biological Rhythms Pub Date : 2026-09-07 DOI: 10.1177/07487304261480190
Peigen Chen, Yun Liu, Xiaoting Zhang
{"title":"CHORD: Resolving 12-h Transcriptomic Rhythms Into Harmonic, Autonomous, and Intersection Origins.","authors":"Peigen Chen, Yun Liu, Xiaoting Zhang","doi":"10.1177/07487304261480190","DOIUrl":"https://doi.org/10.1177/07487304261480190","url":null,"abstract":"<p><p>A 12-h (12-h) periodicity in a transcriptomic series is routinely reported as a \"12-h rhythm,\" yet a single 12-h spectral peak can arise from 3 mechanistically distinct processes: the second harmonic of a non-sinusoidal 24-h waveform (a harmonic), an autonomous 12-h oscillator with its own phase (such as the IRE1<math><mrow><mi>α</mi></mrow></math>-XBP1s ER-stress cycle), or the apparent 12-h when 2 anti-phase 24-h processes combine as synthesis minus degradation (an intersection). These origins carry opposite biological meanings but are indistinguishable to standard detectors such as JTK_CYCLE, RAIN, and Cosinor. To resolve the origin of 12-h rhythms, Circadian Harmonic Oscillation Resolution and Disentanglement (CHORD) detects 12-h periodicity and resolves it into this ternary taxonomy. Detection fuses 4 tests through the Cauchy Combination Test; disentanglement rests on 4 complementary statistics, each tied to one identifiable model feature and combined by a calibrated multinomial classifier. On a held-out benchmark, CHORD separates autonomous from driven 12 h at area under the curve (AUC) 0.83 and a genuine oscillator from an intersection at 0.93. An interventional test anchors the classifier to biology: in a liver-specific XBP1 knockout, the hepatic 12-h program collapses when the IRE1-XBP1 clock is ablated (knockout/wild-type ratio 0.27) while the 24-h circadian clock is preserved (0.91). The canonical autonomous genes are 12-h dominant with little 24 h, which a single series cannot resolve, so CHORD abstains and the intervention resolves them; the confidently classified autonomous set also collapses more than the driven set (0.47 vs. 0.62). Because the program is strongly coregulated, a correlation-adjusted test keeps the program-versus-driven collapse significant (<math><mrow><mi>p</mi><mo>=</mo><mn>00</mn><mo>.</mo><mn>045</mn></mrow></math>); this validation covers the autonomous arm in liver only. An identifiability budget shows that 12-h signal-to-noise, not sampling density, bounds classification. CHORD reframes ultradian transcriptomics from whether a 12-h rhythm exists to what kind it is.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"7487304261480190"},"PeriodicalIF":3.0,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148900611","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}
引用次数: 0
Feeding a Diurnal Rodent at Night Induces Weight Loss and Body Temperature Reduction Without Food-Anticipatory Activity. 在夜间喂养昼行性啮齿类动物可以在没有食物预期活动的情况下减轻体重和降低体温。
IF 3 3区 生物学
Journal of Biological Rhythms Pub Date : 2026-08-25 DOI: 10.1177/07487304261471802
Victor Y Zhang, G J Kenagy, Cassidy Austin, Horacio O de la Iglesia
{"title":"Feeding a Diurnal Rodent at Night Induces Weight Loss and Body Temperature Reduction Without Food-Anticipatory Activity.","authors":"Victor Y Zhang, G J Kenagy, Cassidy Austin, Horacio O de la Iglesia","doi":"10.1177/07487304261471802","DOIUrl":"10.1177/07487304261471802","url":null,"abstract":"<p><p>An important component of behavioral plasticity is the ability of animals to shift the timing of daily or seasonal activities to accommodate changing physical and biotic conditions, a phenomenon known as temporal niche switching. Temporal niche switching in response to experimentally altered food availability in the laboratory is often accompanied by locomotor activity that anticipates the time of daily food access (\"food-anticipatory activity\" = FAA), which reflects the plasticity of the mammalian circadian system. Most FAA studies have been conducted in nocturnal rodents, reporting robust anticipatory increases in locomotor activity and physiological variables such as body temperature before food presentation, but this kind of plasticity has not been tested in strictly diurnal species. In the present study, we show that the diurnal antelope ground squirrel (AGS; <i>Ammospermophilus leucurus</i>) fails to exhibit FAA when subjected to temporally restricted food access. We centered 8 h of food restriction either in the middle of the active/light phase (daytime feeding; DF) or the rest/dark phase (nighttime feeding; NF). In contrast to findings in nocturnal rodents, NF AGSs did not show FAA, lost body mass, decreased overall wheel-running activity, and exhibited decreases in body temperature, with 2 animals becoming hypothermic. DF squirrels ate more than NF squirrels, had greater activity levels, and maintained normal body temperature. These results indicate that exclusive nighttime food availability was not sufficient to support normal energy balance in this strictly diurnal rodent. Thus, whereas negative energy balance can promote shifts toward daytime activity in some nocturnal mammals, AGS did not show the reciprocal shift toward nighttime activity when food was restricted to the dark phase. This suggests that, relative to nocturnal species, strictly diurnal mammals may have a limited capacity to compensate behaviorally and physiologically for food availability during the rest phase of the circadian cycle.</p>","PeriodicalId":15056,"journal":{"name":"Journal of Biological Rhythms","volume":" ","pages":"7487304261471802"},"PeriodicalIF":3.0,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13509486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148813146","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}
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