Search Results (161)

Increasingly frequent and severe drought events restrict global agricultural productivity. As sessile organisms, cereal crops have evolved phenotypic plasticity, drawing on drought escape (DE) and drought avoidance (DA) strategies to balance survival and reproduction. While the mechanisms governing photoperiodic flowering and drought responses are well characterized individually, their molecular intersection remains poorly understood. This review summarizes recent advances in the crosstalk between these two pathways. We highlight the divergent roles of core genetic hubs, such as florigen regulation, GIGANTEA (GI), DELLA proteins, and dual-function transcription factors (e.g., ZmCCT, Ghd7, Ppd-H1), and the breeding-selected alleles, including Green Revolution variants, that can partly uncouple stress tolerance from developmental penalties, though trade-offs often remain. Furthermore, we examine the internal networks driving this crosstalk, including circadian clock phase shifts, sugar and energy signaling through the trehalose-6-phosphate (T6P)-SNF1-related protein kinase 1 (SnRK1) module, and the antagonistic balance within phytohormone networks centered on abscisic acid (ABA). Finally, we propose that integrating epigenetic stress memory, systemic root-to-shoot signaling, and targeted CRISPR/Cas promoter engineering provides a useful conceptual framework for breeding climate-resilient, yield-stable crops. Full article

Background/Objectives: Circadian disruption resulting from factors such as jet lag, shift work, or aging leads to exaggerated inflammatory responses and increased disease susceptibility. However, the core dynamical mechanism by which circadian disruption exacerbates innate immune responses remains poorly understood. Methods: We develop an integrated mathematical model coupling the mammalian circadian clock with antigen-induced innate immune responses, incorporating key regulatory interactions including glucocorticoid modulation and pro-inflammatory positive feedback loops. Results: The model successfully recapitulates experimental data regarding homeostatic immune circadian oscillations and time-dependent gating of acute inflammatory responses. Dynamic analyses reveal that the circadian clock exerts its gating function by modulating the bistable characteristics within pro-inflammatory positive feedback loops. Circadian disruption, simulated as jet lag or age-related reduction in clock gene amplitude, reshapes this bistable landscape and prolongs residence duration in the pathological hyperinflammatory state. Conclusions: This shift not only amplifies acute cytokine bursts but also sustains exaggerated inflammatory activity, providing a mechanistic explanation for acute tissue injury and chronic low-grade inflammation (inflammaging) under these circadian disruption scenarios. Full article

Photobiomodulation (PBM) is a non-invasive therapeutic strategy that uses red and near-infrared (NIR) light in the 590–950 nm range to modulate the cellular and molecular pathways involved in retinal homeostasis. At the molecular level, PBM acts primarily through photon absorption by cytochrome c oxidase (CcO, complex IV of the mitochondrial electron transport chain), whose four metal centres—two copper (CuA and CuB) and two heme groups (heme a and heme a₃)—absorb light across approximately 600–1000 nm. Photon capture promotes photodissociation of inhibitory nitric oxide (NO) from the binuclear CuB–heme a₃ centre, accelerates electron transfer, restores the proton-motive force and increases ATP synthesis. These primary events trigger a coordinated molecular programme that includes (i) transient mitochondrial reactive oxygen species (ROS) bursts that activate the Nrf2/Keap1/ARE axis and upregulate phase II antioxidant enzymes (HO-1, NQO1, GCLC, SOD2, catalase, GPx); (ii) calcium- and cAMP-dependent secondary signalling that converges on PI3K/Akt, MAPK/ERK, AMPK and mTOR pathways; (iii) suppression of NF-κB-driven cytokine production (TNF-α, IL-1β, IL-6) and of NLRP3 inflammasome activation; (iv) downregulation of the HIF-1α/VEGF axis, particularly at 590 nm; (v) anti-apoptotic remodelling of the Bcl-2/Bax ratio with reduced cytochrome c release and caspase-3/9 activation; and (vi) PGC-1α/TFAM/NRF1-driven mitochondrial biogenesis, alongside restoration of fission/fusion homeostasis (Drp1, Mfn1/2, Opa1) and PINK1/Parkin-mediated mitophagy. Wavelength specificity has a defined molecular basis: 590 nm modulates VEGF signalling and RPE pump activity, 660 nm interacts with the CuB centre and enhances O₂ binding at CcO, and 850 nm is absorbed by CuA and supports electron entry into complex IV. A second molecular axis is the bidirectional crosstalk between PBM and the circadian system: mitochondrial respiration, ATP turnover and CcO activity oscillate over the 24 h cycle under the control of the BMAL1/CLOCK and PER/CRY core machinery, the NAD⁺/SIRT1–SIRT3 axis and REV-ERBα. Preliminary preclinical and human observations suggest that NIR-induced bioenergetic and functional gains may be coupled to this rhythm, with greater benefit reported when light is delivered in the morning window (≈08:00–11:00); this time dependence should be regarded as an emerging hypothesis rather than an established clinical principle. The clinical evidence is unevenly developed across indications. It is most robust for non-exudative age-related macular degeneration, where multiwavelength PBM (590/660/850 nm; Valeda Light Delivery System) has shown disease-modifying potential in randomized controlled trials (LIGHTSITE I–III and the LIGHTSITE IIIB extension), with sustained BCVA gains and reduced incidence of geographic atrophy over 24 months and beyond. Evidence for retinitis pigmentosa, central serous chorioretinopathy and, with red-light monotherapy, childhood myopia is at present limited to small or short-term studies and remains preliminary. This narrative review synthesizes the molecular machinery engaged by PBM, integrates clinical findings across retinal diseases and discusses how chronotherapeutic delivery of light, aligned with the molecular clock, may further optimize therapeutic efficacy. Full article

Circadian rhythms impose temporal organization on immune function, shaping host responses to infection, injury, and chronic disease. While transcriptional control by core clock components such as CLOCK and BMAL1 has been extensively characterized, this paradigm alone cannot explain the rapid and dynamic nature of immune signaling. Emerging evidence identifies post-translational modifications (PTMs)—including phosphorylation, ubiquitination, and acetylation—as critical regulators that confer speed, reversibility, and specificity to inflammatory pathways. Here, we propose the concept of a “Chrono-PTM axis,” in which circadian timing and PTM-dependent signaling are functionally integrated to govern immune activation thresholds. We discuss how PTMs not only regulate core clock machinery but also temporally gate key innate immune pathways, including NF-κB signaling and inflammasome activation, thereby controlling cytokine production at multiple levels. Furthermore, we highlight the role of immunometabolism in supplying essential cofactors that couple cellular energetic states to PTM dynamics, linking metabolic oscillations to inflammatory outputs. Disruption of this axis contributes to the pathogenesis of autoimmune diseases, cancer, and tissue-specific inflammatory disorders. Finally, we outline emerging therapeutic opportunities targeting the Chrono-PTM axis, including chronotherapy and PTM-directed interventions, and identify critical gaps in temporal proteomics and translational studies. Elucidating the integration of circadian and post-translational regulation will provide a unifying framework for understanding immune homeostasis and may enable time-informed precision immunotherapy. Full article

The circadian clock is closely linked to glucose regulation, but the dynamical consequences of specific metabolic feedback pathways on core clock regulation remain incompletely understood. In this study, we developed a theoretical metabolic-circadian model incorporating a REV-ERB$\mathrm{\alpha }$-glucagon-glucose feedback pathway. The model extends a previously established mammalian circadian clock framework by introducing glucagon-mediated regulation of blood glucose and glucose-dependent modulation of Rev-erbα transcription. Using this model, we examined how the feedback pathway affects circadian oscillations, the sensitivity of period and amplitude to parameter perturbations, and phase-related responses under light stimulation and light–dark cycles. Simulations of the feedback-related parameters showed that the glucose-to-clock feedback strength had a marked effect on oscillation period and amplitude, motivating a further assessment of whether regular circadian dynamics were preserved under parameter perturbations. We therefore analyzed both one-parameter perturbations and simultaneous perturbations of all model parameters. For one-parameter scans, we quantified not only the oscillatory boundaries but also the period variation and the amplitude variation of Per and Rev-erbα within the oscillatory ranges. For simultaneous all-parameter perturbations, Latin hypercube sampling was used to compare coupled and uncoupled models under bounded perturbation ranges. The coupled model showed a higher fraction of regular circadian oscillations under local perturbations, mainly by reducing the probability of rhythm loss. We further examined phase responses and light–dark entrainment to assess how the feedback affects dynamical properties beyond period and amplitude. In the phase-response analysis, the feedback reduced excessive phase shifts in the model, suggesting a possible phase-response robustness effect in this theoretical framework. These theoretical results suggest that the REV-ERB$\mathrm{\alpha }$-glucagon-glucose feedback pathway may be relevant to circadian regulation under fasting-associated metabolic conditions. Full article

D-box binding protein (DBP) is a high-amplitude proline- and acidic amino acid-rich basic leucine zipper (PAR bZIP) transcription factor that functions as a key circadian output regulator downstream of the core molecular clock. Although DBP is widely recognized as a clock-controlled gene, its broader role in converting circadian timing into tissue-specific physiological programs remains incompletely integrated. In this review, we synthesize current evidence supporting DBP as a context-dependent D-box-centered regulatory node. We first summarize the upstream mechanisms that establish rhythmic Dbp expression, including CLOCK–BMAL1-dependent transcription, promoter-level amplification, signaling-dependent modulation, and post-translational control of DBP stability. We then discuss how DBP, together with related PAR bZIP activators and the opposing repressor E4 promoter-binding protein 4/nuclear factor interleukin 3 regulated (E4BP4/NFIL3), regulates D-box-mediated transcriptional output. Finally, we examine tissue-selective DBP functions in hepatic metabolism, pancreatic β-cell secretory competence, neural and behavioral regulation, reproductive neuroendocrine timing, and T helper 9 (Th9)-associated antitumor immunity. Across these systems, DBP does not act as a universal circadian effector; rather, its function depends on chromatin accessibility, cofactor availability, competing transcription factors, and local signaling context. We also highlight the current limits of human translational evidence and propose that DBP-centered signatures may be useful for interpreting circadian output failure in disease. Overall, DBP provides a mechanistically informative framework for understanding how circadian time is transformed into organ-specific physiological function and pathological vulnerability. Full article

Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by impaired metabolic flexibility, oxidative stress, and disruption of the temporal coordination of hepatic processes. Obesogenic diets contribute to this dysfunction by altering redox homeostasis and autophagy, thereby promoting lipid accumulation and cellular stress. In this study, we investigated whether grape seed proanthocyanidin extract (GSPE), a polyphenol-rich compound with antioxidant properties, can modulate these alterations in a time-dependent manner. Male Fischer 344 rats were fed a standard or cafeteria diet and supplemented with GSPE (25 mg/kg) at the onset of the active phase (ZT12). Liver samples were collected across four Zeitgeber times to evaluate circadian-related proteins, autophagy markers, antioxidant responses, lipid content, and metabolomic profiles. Cafeteria feeding disrupts hepatic homeostasis, reducing BMAL1 protein levels, altering the temporal organization of autophagy markers, and impairing redox regulation. GSPE did not restore core clock protein expression but induced a pronounced, time-specific activation of the NRF2/HO-1 axis, with a marked increase in HO-1 at the onset of the active phase. This effect was associated with a metabolic shift toward amino acid-related pathways linked to redox balance. These findings indicate that GSPE enhances antioxidant defenses in a time-dependent manner, improving redox–metabolic coordination under obesogenic conditions. Full article

Circadian rhythms are fundamental regulators of skeletal homeostasis, coordinating osteoblast and osteoclast activity through tightly controlled temporal programs. Disruption of these rhythms, whether through environmental misalignment or genetic perturbation of core clock components, alters bone formation, enhances resorption, and contributes to skeletal fragility. This review synthesizes current knowledge on circadian regulation of bone biology across in vivo, ex vivo, and in vitro model systems, highlighting how each platform reveals distinct aspects of rhythmic gene expression, cellular function, and tissue-level remodeling. We critically evaluate the strengths and limitations of these models, outline key controversies such as the interpretation of global clock-gene knockouts, and discuss the emerging relevance of human-derived systems including iPSC-based models, organoids, and microphysiological “bone-on-chip” platforms. Integrative approaches that combine multiple model systems provide the most reliable framework for understanding circadian control of bone and for identifying targets for chronotherapeutic intervention. Advancing human-relevant models and refining temporal experimental design will be essential for translating circadian biology into clinical strategies for metabolic bone diseases. Full article

Acute respiratory distress syndrome (ARDS) is a high-mortality condition lacking targeted treatments. Emerging evidence indicates that circadian rhythm disruption is a key factor in the development of ARDS. Core clock proteins control essential processes, including alveolar–capillary barrier function, inflammation, and tissue repair. The intensive care unit (ICU) environment and underlying illness create double hits that impair biological clocks, leading to a cycle of excessive inflammation and organ damage. This review highlights the central role of circadian rhythms in ARDS. Despite strong preclinical evidence, there are still many challenges for clinical application, including a lack of high-quality human studies and uncertainty about the optimal timing of interventions. Incorporating biological rhythm stabilization into multimodal ARDS management is a prerequisite step toward precision medicine. Future research should focus on mechanistic and translational studies to confirm the safety and effectiveness of chronomedicine in improving long-term patient outcomes. Full article

Circadian rhythms are ~24 h cycles regulated by an internal molecular clock. Disruption of this timing system has been implicated in numerous diseases, including the advancement of cancers and declines in function associated with aging. In recent years, scientists have identified various small molecules that can modulate core circadian clock proteins and pathways, providing potential therapeutic strategies to correct circadian dysfunction. This review presents a thorough overview of circadian clock mechanisms and highlights known small-molecule modulators. We describe how these compounds were discovered (through high-throughput screening and rational design) and categorize them based on their molecular targets. This review also summarizes key findings in cancer models, where clock-modulating compounds affect tumor metabolism, cell proliferation, and responsiveness to treatments, as well as in aging models, where strengthening circadian function may enhance metabolic health and longevity. Additionally, we cover clinical and preclinical studies involving these molecules and address challenges such as off-target effects and the complex nature of clock regulation. Finally, we outline future directions, emphasizing the development of new chronotherapeutics and the incorporation of circadian modulation into interventions for cancer and aging. Full article

Circadian clocks generate daily rhythms of gene expression that influence physiology, disease, and responses to therapeutics, yet how circadian transcription differs between juvenile and adult organisms remains unresolved. Here, we used genome-wide eXcision Repair sequencing (XR-seq) to quantify transcription-coupled repair as an indirect, high-sensitivity measure of transcription. We profiled the brain, liver, kidney, and testis from juvenile and adult C57BL6/J mice across a 24 h cycle and show that XR-seq enables sensitive circadian transcription mapping. In all organs except the testis, rhythmic transcription phases clustered near dawn and dusk. While core clock gene rhythms are largely preserved between juveniles and adults, rhythms of many clock-controlled genes differ markedly by age. Rhythmic genes are strongly organ-specific yet their overlap between ages is limited, indicating substantial developmental changes in circadian control. Together, these data provide a multi-organ map of juvenile versus adult circadian transcription and indicate that adult therapeutic schedules may not translate to juveniles. Full article

Soybean (Glycine max) is a critically important crop for oil, protein, feed, and food security in China. Expanding soybean cultivation into high-latitude regions represents one of the most direct and effective strategies to increase total production. In the present study, we employed KASP (Kompetitive Allele-Specific PCR) marker technology to systematically analyze 18 variant loci across 14 flowering-time genes in 443 soybean germplasm accessions adapted to high-latitude conditions in Arctic Village (Beiji Cun), Mohe City (>53° N), northeastern China. Our results revealed clear functional-tier-dependent selection gradients: key mutation sites (frequency > 96%) in upstream photoreceptors and core circadian clock genes, such as E2 and GmPRR3a, were nearly fixed in the population, whereas downstream flowering genes such as GmFT5b and GmFT2b remained under dynamic selection. Combinatorial analysis of early-maturity allelic variants identified 178 distinct genotype combinations, including six dominant types (n ≥ 10). Field phenotypic analysis demonstrated that the cumulative number of early-maturity alleles was significantly negatively correlated with flowering time, with specific allele combinations such as FT5a^A + FKF1b-hap3^T exhibiting particularly strong flower-promoting effects. A set of 80 highly enriched super-early-maturity accessions, including extreme materials such as MHL22002, were identified, providing valuable genetic resources and a theoretical framework for elucidating the flowering regulatory mechanisms of high-latitude soybean and for breeding super-early-maturing varieties. Full article

Glucagon-like peptide-1 receptor agonists (GLP-1RAs) have transformed the management of type 2 diabetes and obesity, yet their actions extend beyond glycemic control and weight loss. This narrative review synthesizes current preclinical and clinical evidence examining the bidirectional relationship between glucagon-like peptide-1 (GLP-1) receptor agonists and circadian biology. A structured literature search was conducted in PubMed using combinations of the terms ‘GLP-1,’ ‘circadian,’ ‘chronobiology,’ ‘sleep,’ ‘obesity,’ and ‘type 2 diabetes’ through January 2026. Accumulating evidence indicates that GLP-1 physiology is closely coupled to circadian timing systems and sleep–wake regulation. In this narrative review, we synthesize emerging data that reframe GLP-1RAs as chronometabolic modulators, acting at the intersection of metabolism, circadian biology, and sleep. We review circadian control of GLP-1 secretion by intestinal L-cells, emphasizing the role of core clock genes and the vulnerability of incretin rhythms to circadian misalignment from shift work, nocturnal light exposure, and sleep loss. We then examine GLP-1 receptor signaling within central and peripheral clock networks, including feedback effects on hypothalamic and hepatic circadian regulation. Emerging data suggest that GLP-1 signaling is under circadian regulation and may, in turn, influence central and peripheral clock systems. Comparative discussion of semaglutide, liraglutide, and tirzepatide highlights agent-specific pharmacokinetics and emerging clinical data linking GLP-1RA therapy to sleep outcomes, particularly obstructive sleep apnea. Finally, we outline translational opportunities for chronotherapy and precision medicine, positioning GLP-1RAs as integrative tools for metabolic and sleep-related disease rather than purely weight-centric therapies. We propose that GLP-1 receptor agonists may function as chronometabolic modulators, with potential implications for personalized chronopharmacological strategies in metabolic disease. Full article

Background: Hepatocellular carcinoma (HCC) stands as a prevalent global health issue with increasing incidence and mortality rates. Hepatocellular carcinoma (HCC) exhibits profound molecular and clinical heterogeneity, which limits the effectiveness of current therapeutic strategies. Circadian rhythm disruption has been implicated in metabolic reprogramming, proliferation, and immune modulation in cancer, but its role in shaping HCC heterogeneity remains poorly defined. Methods: Four public HCC transcriptomic cohorts (TCGA-LIHC, CHCC, LIRI, LICA) were integrated using RMA normalization and ComBat for batch correction. Consensus clustering based on 31 core circadian clock genes (CCGs) identified robust molecular subtypes. Multi-omics characterization—including genomic alterations, pathway activity (GSEA/GSVA), immune microenvironment profiling (CIBERSORT, EPIC, MCP-counter, xCell), and drug-sensitivity prediction (pRRophetic/oncoPredict)—was performed to delineate subtype-specific biological properties. A nine-gene CCG-based RiskScore model was constructed using LASSO Cox regression to internally validate subtype robustness and intra-subtype risk stratification. Results: Using consensus clustering of 31 core CCGs in TCGA-LIHC and three independent validation cohorts (CHCC, LIRI, LICA), we identified three reproducible subtypes—Cluster-1 (metabolic–quiescent), Cluster-2 (transition–intermediate), and Cluster-3 (proliferation–inflammatory)—which were recapitulated across cohorts and showed distinct overall survival (Cluster-3 worst; log-rank p values significant across datasets). Multi-omic characterization revealed that Cluster-3 exhibits the highest tumor mutational burden and CNV burden with enrichment of TP53/AXIN1/TERT alterations, strong activation of cell-cycle, E2F, and G2M programs, and an immune-hot yet immunosuppressed microenvironment enriched for TAMs, Tregs and MDSCs. By contrast, Cluster-1 shows relative genomic stability, dominant hepatic metabolic signatures (fatty-acid oxidation, bile-acid and xenobiotic metabolism) and an immune-cold phenotype. Single-cell mapping linked ALAS1 expression to malignant hepatocytes predominating in Cluster-1, whereas NONO and CSNK1D localized to stromal (CAFs/TECs) and both malignant/immune compartments respectively in Cluster-3, providing a cellular mechanism for subtype-specific metabolism, angiogenesis and immune modulation. Finally, a nine-gene CCG-based RiskScore validated prognostic stratification and drug-sensitivity predictions indicated subtype-specific therapeutic vulnerabilities (notably increased predicted TKI sensitivity in Cluster-3). Conclusion: In conclusion, this study proposes a robust circadian rhythm-based molecular classification of hepatocellular carcinoma, revealing three biologically and clinically distinct subtypes characterized by divergent genomic alterations, metabolic programs, immune microenvironment states, and prognostic patterns. By integrating bulk and single-cell transcriptomic data, we identify subtype-specific roles of key circadian regulators—including ALAS1, NONO, and CSNK1D—in shaping tumor metabolism, proliferation, stromal remodeling, and immune suppression. These findings highlight circadian dysregulation as a potential upstream factor associated with HCC heterogeneity and provide a conceptual framework for developing subtype-tailored mechanistic studies and circadian-informed therapeutic strategies. Full article

Oxidative alcohol metabolism in the liver relies on sequential enzymatic reactions involving alcohol dehydrogenase (ADH), cytochrome P450 2E1 (CYP2E1), and aldehyde dehydrogenase (ALDH) isozymes. However, the circadian regulation of these enzymes, their susceptibility to genetic, environmental, and metabolic disruption, and their functional implications toward alcohol-mediated tissue injury remain incompletely defined. To address this gap, we performed a comprehensive integrative analysis of the publicly available circadian transcriptome datasets spanning genetic clock disruption, acute sleep deprivation, chronic high-fat diet feeding, and occupational shift work to systematically characterize the temporal regulation and disruption vulnerability of the major alcohol-metabolizing enzymes. Mouse tissue-cycling analyses revealed pronounced gene- and tissue-specific diurnal regulation, with Adh1 oscillating primarily in adipose tissues; Cyp2e1 and mitochondrial Aldh2 cycling broadly across kidney, aorta, lung, adrenal gland, and liver; and cytosolic Aldh1b1 being uniformly arrhythmic. In the liver, Cyp2e1 and Aldh2 exhibited robust ~24 h oscillations that peaked during the light/resting phase, while Adh1 showed inconsistent rhythmicity and Aldh1b1 remained arrhythmic. Notably, Cyp2e1 and Aldh2 rhythms persisted in Bmal1 knockout and Clock mutant livers under light–dark conditions, despite complete loss of core clock gene oscillations, yet were abolished in constant darkness, revealing that systemic zeitgeber cues can mask the loss of intrinsic clock function to maintain apparent rhythmicity in these metabolic genes. Systematic cross-paradigm comparison established a novel gene-specific vulnerability hierarchy. Aldh2 was found to be most disrupted by environmental and metabolic perturbations, with acute sleep deprivation eliminating its rhythmicity and temporal expression pattern and a Western-style high-fat diet inducing pronounced phase delays and rhythm loss relative to low-fat diet controls. Both disruptions paralleled alterations in hepatocyte nuclear factor 4α (Hnf4a), newly implicating HNF4α as a potential mediator of ALDH2 circadian instability. In humans, ALDH2 and CYP2E1 exhibited conserved but phase-inverted circadian rhythms across multiple tissues relative to mice, and, importantly, night-shift workers showed markedly dampened and phase-shifted ALDH2 rhythms in peripheral blood mononuclear cells, providing the molecular link between occupational circadian misalignment and impaired acetaldehyde detoxification. Collectively, our detailed and innovative analytical approach reveals gene- and tissue-specific circadian regulation of alcohol-metabolizing enzymes, identifies ALDH2 as uniquely vulnerable to circadian misalignment, underscores the importance of circadian timing for optimal hepatic detoxification and resistance to tissue injury, and suggests that monitoring circadian rhythms could help tailor individualized advice on alcohol consumption for shift workers and populations with irregular sleep schedules, informing precision medicine approaches for alcohol-related disorders. Full article