Research focused on Alzheimer's disease (AD) 'biomarker clocks' seeks to identify ages at which AD pathological landmarks occur (e.g., initiation of amyloid accumulation) and are meaningfully related to disease outcomes (e.g., symptom onset). However, the statistical approach for assessing the association between age at biomarker-clock event and remaining time to clinical symptom onset can create a structural artifact. We term it here the 'countdown paradox', because the remaining time to symptom onset shrinks as the age at biomarker-clock event increases, which may result in inaccurate associations between age at biomarker-clock event and the remaining time. We conducted analyses to examine this issue with simulation studies and theoretical results, and also examined it empirically using five biomarkers in two longitudinal AD-related cohorts (BIOCARD and ADNI): (1) CSF Abeta42/Abeta40, (2) CSF p-tau181, (3) plasma p-tau181, (4) amyloid PET, and (5) plasma p-tau217. As an alternative analytic approach to the standard approach, we used a time-varying effect analysis that evaluates the association between biomarker-clock events and symptom onset on the 'age' time scale, avoiding the structural coupling between predictor and outcome. This analytic approach generates clinically relevant insights on the prognostic value of biomarker-clock events. Under simulated null scenarios in which the biomarker was generated independent of symptom onset, the standard analysis produced false-positive rates up to 100% and hazard ratios above 1, regardless of the true effect direction, whereas the time-varying analysis maintained type I error near the nominal 5%. Moreover, in analyses of both the BIOCARD and ADNI cohorts, the standard analysis produced uniformly significant associations for ages at biomarker-clock events, based on all five biomarkers (hazard ratios 1.94-3.34, all P < 0.01), comparable to the pattern predicted by the countdown paradox and reported in the literature. The time-varying analysis showed a different pattern for the effect of age at biomarker-clock events: for all biomarkers investigated, a younger age at biomarker-clock events is associated with a higher hazard for symptom onset on the age scale, conveying the opposite prognostic message implied by the standard analysis. These findings suggest that the standard biomarker-clock analysis may generate inaccurate associations and even reverse the apparent direction of the age effect, inverting the resulting prognostic message. A time-varying effect analysis avoids this by relating the age at a biomarker-clock event to clinical onset, with important implications for interpreting prior biomarker-clock studies.
Lateral root formation starts with priming, predisposing subsets of pericycle cells with the potential of future lateral root formation through semi-periodic elevations in auxin (signalling). While various mechanisms have been suggested, one frequently suggested hypothesis proposes a genetic, cell-autonomous root clock akin to the clock underlying vertebrate somitogenesis. Still, while gene expression variations were observed, so far this clock has not been proven. From a functional and evolutionary perceptive it is furthermore an open question whether lateral root priming is not more likely to arise from an emergent tissue level process similar to phyllotaxis. To help settle this debate in this study I use general knowledge of oscillator dynamics and simple models of auxin signalling to underline the unlikelihood of a root clock driving lateral root priming. I show how within a single cell oscillations are limited to a small parameter domain, with constraints intensifying due to the presence of multiple AUX/IAA and ARF types as well as auxin export. Furthermore, I demonstrate how non-meristem based oscillations, due to a lack of memory of oscillator phase, can not drive periodic prebranch site formation, and periodic inputs are insufficient to induce phase differences. Combined this underlines the unlikelihood of a root clock driving lateral root priming.
Low-frequency electron paramagnetic resonance (EPR) spectroscopy proves large sample space and special selectivity to hyperfine spin related transitions in molecules. For instance, the hyperfine clock transition in endohedral phosphorus fullerene (P@C60), which has been proposed for solid-state chip-scale atomic clocks (CSACs), is at the low frequency of 239 MHz. To probe this clock transition, we have developed a dedicated low-frequency EPR spectrometer. Comprehensive characterization of its core components confirms that the spectrometer fulfills the essential sensitivity requirements for clock transition measurements. The limited spin concentration of the available P@C60 sample allowed only the detection of a faint suspected signal. Several pathways were identified to enhance the signal to a level sufficient for its development as a frequency reference.
Recent increase in reported cases of Bundibugyo virus (species Orthoebolavirus bundibugyoense) in the Democratic Republic of the Congo and Uganda highlight the importance of understanding their evolutionary dynamics. We analyzed publicly available genomes obtained from the Pathoplexus database representing 3 medically relevant species of the Orthoebolavirus genus: Ebola virus (n = 3,388), Zaire virus (n = 166), and Bundibugyo virus (n = 49). We investigated whether genetic divergence is associated with sampling time utilizing root-to-tip regression analyses derived from temporally calibrated phylogenies as an indicator of molecular clock behavior. Sudan virus (R2 = 0.855) and Ebola virus (R2 = 0.709) exhibited significant temporal structures between sampling time and genetic divergence. Bundibugyo virus displayed strong clock-like behavior after exclusion of 2026 genomes (R2 = 0.983), which showed a marked substitution deficit relative to the historical molecular clock and deviated substantially from the inferred regression. Date randomization tests supported the presence of temporal signal across all datasets (p < 0.001), indicating that the temporal signals exceeded expectations under a null model without temporal structure. These results provide a comparative assessment of the temporal structures across 3 medically relevant Orthoebolavirus species. While historical genomes largely conformed to molecular clock expectations, the inclusion of genomes from the ongoing 2026 Bundibugyo virus outbreak deviated from these projections, suggesting an alternative evolutionary process for 2026 Bundibugyo virus, such as viral persistence in immune-privileged anatomical sites of previously infected individuals or an independent zoonotic spillover event in an alternative species, in which the virus evolved within its natural reservoir prior to human infection.
Organisms adjust their physiology and behavior in response to seasonal changes. The current working model indicates that the circadian clock is involved in this process, but the molecular mechanisms mediating the integration of seasonal cues are still unclear. Notably, the circadian neuropeptide pigment-dispersing factor (PDF), an output of the circadian clock, has been shown to alter its expression and activity in response to seasonal changes to facilitate seasonal adaptations in insects. Here, we show that the alternative splicing of a circadian clock gene, timeless (tim), regulates the seasonal responses through PDF in Drosophila melanogaster. We found that tim-sc, the predominant isoform in winter, is regulated by photoperiod, while the canonical tim-l isoform is not. In addition, we demonstrated that tim-sc is used to maintain physiology and behavior in a "winter lock" state by modulating PDF. Our results support a role of isoform-specific characteristics in providing circadian clock components with the ability to modulate seasonal physiology.
Mammals exhibit a circadian rhythm of bladder capacity, but whether this rhythm can be maintained through intrinsic bladder mechanisms independently of central clock-driven behavioral rhythms remains unclear. Here, we addressed this question using Bmal1 conditional knockout mice lacking central clock function in the brain. Under constant darkness, these mice lost behavioral rhythmicity but largely retained circadian variation in bladder capacity together with bladder clock gene expression. Transcriptomic analyses further identified diurnal variation in bladder extracellular matrix-related factors, suggesting a potential molecular basis for bladder capacity rhythmicity. These findings indicate that the bladder harbors a peripheral circadian mechanism that contributes to the circadian regulation of bladder capacity and provides insight into the role of peripheral clock mechanisms in bladder pathophysiology.
Alcohol use disorder (AUD) is a leading cause of morbidity and mortality worldwide, characterized by cycles of heightened craving and excessive, uncontrolled consumption of alcohol despite progressive decline in physical and mental health. Voluntary alcohol consumption is influenced by a variety of environmental and genetic factors, including circadian clock genes, whose effects are modulated in a sex-specific manner. The sex-specific role of clock genes in alcohol drinking was identified through selective ablation of Bmal1 and Per2 from neurons of the mouse striatum; however, the contribution of specific striatal subregions to the observed drinking behavior remains unclear. Thus, alcohol intake and preference were investigated in male and female mice with a conditional knockout of Bmal1 or Per2 from cells in the nucleus accumbens (NAc), a key area of the brain's reward center. Alcohol consumption and preference were increased in male and female mice with a conditional knockout of Bmal1, whereas the deletion of Per2 increased consumption and preference in males only. The changes in alcohol consumption can be attributed to the manipulation of the circadian clock genes in the NAc exclusively, because affective behaviors were largely unchanged. The results show that Bmal1 and Per2 in the NAc are negative regulators of alcohol drinking in mice, with sex-dependent differences in their effects.
Critically ill patients requiring treatment in the intensive care unit (ICU) suffer from muscle weakness that persists for years. As compared with healthy subjects, skeletal muscle of patients biopsied five years post-ICU revealed an abnormal transcriptome partially associated with poor muscle strength. We now hypothesized that skeletal muscle of long-term ICU survivors is "epigenetically aged", as determined by a muscle-specific epigenetic clock, and that such accelerated epigenetic aging contributes to their long-term muscle weakness. Muscle DNA-methylation data from former ICU patients at 5-year follow-up (N = 118) and healthy controls (N = 160), aged 18-89 years, were analyzed by the MEATv2 epigenetic clock. First, epigenetic age (DNAmAge), epigenetic minus chronological age (AADiff) and epigenetic age acceleration (AAResid) were compared between 97 former patients and 97 controls, propensity score-matched for age and sex. Next, the impact of any muscle-specific epigenetic aging of ICU survivors was investigated, via multivariable models, as a potential contributor to the altered transcriptome and reduced muscle strength. Former ICU patients showed a significantly higher muscle DNAmAge, AADiff, and AAResid than matched controls. In adjusted models, higher muscle DNAmAge, AADiff, or AAResid did not substantially contribute to differentially expressed muscle RNAs in former patients as compared with controls and was not associated with the poor long-term muscle strength. In conclusion, five years after ICU discharge, former patients showed accelerated epigenetic aging in skeletal muscle. However, the muscle-specific epigenetic clock did not capture molecular changes that are associated with long-term muscle weakness, which highlights the need for other muscle-specific biological predictors of age-related physical impairment. Trail Registration: ClinicalTrials.gov: NCT00512122.
There are extensive ongoing efforts to slow or even reverse human aging, such as with epigenetic cellular reprogramming, thymus rejuvenation or senolytics. In parallel, new and diverse metrics-known as biological clocks-have been discovered and shown to track the pace of aging in an individual and their organs, tissues and cells. These clocks have multiple potential use cases, including identifying people at high risk of disease, serving as a foundation for prevention or early detection, and determining whether lifestyle factors or an intervention can modulate the aging process. This review provides a critical appraisal of the progress that is being made with biological clocks and how they might ultimately help understand pathobiology, reduce the burden of disease and extend healthspan.
"Omic" aging clocks(ACs) represent an established predictor of biological-age(BA)/all-cause-mortality(ACM); however, they are expensive and lack interpretability/explainability. We developed a Blood-Biochemistry Age Clock(BBAC) composed of 11 routine blood biomarkers. The AC functions by transforming the individual's levels of blood biomarkers to years added/subtracted according to "biomarker-ACM risk-profile". The BBAC and PhenoAge were calculated for individuals of the UKB cohort and the results were associated with ACM and disease incidence(eight common chronic diseases) using univariant/multivariate Cox mortality analysis. The BBAC calculation procedure was further optimised. Mortality analysis was likewise performed on NHANES dataset with additional ACs(PCAge/LinAge) serving as predictors. Comparisons between ACs were done using Akaike Information Criterion(AIC). In univariate ACM prediction on UKB cohort BBAC outperformed PhenoAge(AIC= 910749.6 vs. 912914.9). Similarly, BBAC was a better univariate disease incidence predictor(lower AIC). In multivariate ACM prediction PhenoAge exceeded BBAC(AIC= 890855.6 vs. 893294.4). Nevertheless, the optimized version of BBAC was better in predicting ACM in uni(BBAC/PhenoAge AIC= 154165.7/155217.6) as well as in multivariant setting(BBAC/PhenoAge AIC= 151006.9/151031.9). For multivariant disease incidence prediction the results were mixed. On the NHANES cohort BBAC and PhenoAge performed similarly, while PCAge and LinAge achieved the best mortality prediction power. BBAC is an explainable/interpretable AC with good ACM prediction ability.
Circadian rhythms and sleep are known regulators of neurodevelopment, yet the mechanisms by which they influence neuronal circuit formation remain unclear. In Caenorhabditis elegans, postembryonic development comprises four larval stages separated by developmentally timed sleep (DTS) and is regulated by homologs of circadian clock genes. Here, we leverage the well-defined male mating circuitry to investigate how developmental timing and sleep affect neurodevelopment. We found that males exhibit accelerated development with altered DTS patterns and reduced quiescence. Surprisingly, perturbing DTS does not impair male mating, suggesting that developmental sleep is not essential for functional circuit formation in this context. Disruption of the clock gene homolog ces-2 resulted in delayed and variable development in both sexes. In males, these timing defects were associated with reduced mating abilities and decreased synaptic connectivity within the mating circuitry. Together, our findings support the presence of conserved molecular machinery that coordinates developmental rhythms and provide insight into how such rhythms influence neurodevelopment.
Schizophrenia (SCZ) is a severe and chronic neuropsychiatric disorder associated with substantially shortened life expectancy and early onset of age-related comorbidities. Mounting evidence from physical health, brain structure, and cognitive function suggests that SCZ may involve accelerated biological aging. This review focuses on three core aging-related biomarkers, namely, epigenetic clocks, telomere dynamics, and the senescence-associated secretory phenotype (SASP), with the aim of systematically characterizing biological aging features in SCZ. Collectively, available studies point to altered epigenetic aging, telomere attrition, and enhanced pro-inflammatory profiles in SCZ, although findings remain inconsistent because of methodological heterogeneity, tissue specificity, and predominantly cross-sectional study designs. Oxidative stress and chronic low-grade inflammation are proposed to serve as a central hub that links these aging-related processes and may contribute to a self-sustaining pathological loop that accelerates systemic aging. Future longitudinal multi-omics studies and tissue-specific analyses are warranted to clarify causal relationships, identify dynamic aging trajectories, and explore modifiable intervention targets. Understanding the mechanistic links between SCZ and accelerated aging may provide novel insights into disease pathophysiology and facilitate the development of innovative strategies to mitigate age-related comorbidities and improve long-term health outcomes in this vulnerable population.
Sunlight exposure has shaped the evolutionary biology of most life forms through circadian entrainment. Full-spectrum sunlight regulates circadian rhythms, modulates gut and skin microbiomes, influences the gut-brain-skin axis, and drives dermal melanin and vitamin D synthesis. The skin acts as the body's largest photoreceptive organ and neuroendocrine hub. Melanocytes, keratinocytes, and immune cells in the skin translate photons into hormonal, metabolic, and neuronal signals. Melanin, present across vertebrate tissues, bacteria, and fungi, is a unifying photoreceptive molecule whose redox properties and signaling within the melanocortin pathway bridge host and microbial photic cues. Light signals the suprachiasmatic nucleus, triggering hypothalamic-pituitary-adrenal glucocorticoid release and peripheral clock expression throughout the gut-brain-skin axis, influencing rhythmic gastrointestinal functions, short-chain fatty acid production, and vagal feedback to the brain. Microbial photoreceptors, including melanin, flavins, and cryptochromes, extend the photoneuroendocrinology into the holobiont, revealing a shared molecular pathway through which light calibrates the host-microbe interactions. Shift work, nocturnal blue light, sun avoidance, abnormal feeding times, and circadian desynchrony disrupt the gut-brain-skin axis, resulting in dysbiosis, intestinal and skin epithelial barrier dysfunction, shifts in immune signaling, and metabolic disorders. Vitamin D intersects with these pathways, yet its possible circadian regulation remains unknown. This review synthesizes evidence positioning host and microbial melanin as the key signaling molecule of the melanocortin pathway, which is inherently circadian-regulated, governing metabolic and immune homeostasis across the gut-brain-skin axis. We outline mechanistic models and research gaps, and propose that reframing melanin as a holobiont photoreceptor opens therapeutic opportunities across dermatology, gastroenterology, and neuroendocrinology.
In the original publication [...].
Post Covid-19 Condition (PCC) can fluctuate over time, yet, no in-depth investigation of the heterogeneous PCC trajectories that can exist in children and young people (CYP) has been undertaken. We aim to examine associations between PCC trajectories in CYP over 2-years following infection and (i) factors prior to the COVID-19 pandemic/infection including socio-demographic variables (e.g., age, sex, ethnicity), health and educational needs status and (ii) factors subsequent to infection including the nature, number, functional impact and severity of symptoms, as well as mental health and wellbeing. 943 PCR-test positive CYP (enrolled January-March 2021) were followed-up over two-years (till January-March 2023). Five PCC trajectory groups were specified: (i) chronic, (ii) recovered, (iii) fluctuating, (iv) late onset and (v) never PCC. These groups were compared in terms of factors at baseline using multinomial logistic regression and concurrent health during the two-year period using Chi-Square/Fisher's Exact tests. Baseline factors prior to the pandemic/infection such as female sex, older age, poorer pre-infection mental and physical health, prior healthcare use, and educational needs were strongly and consistently associated with adverse PCC trajectories. Compared to those aged 11-to-14-years at infection, those aged 15-to-17-years had a 2.44 (95%CI:1.39,4.26) higher risk of being in the chronic group (compared to the never group). Similarly, the risk of being in the fluctuating group was 1.57 (95%CI:1.04,2.37), the recovered group was 2.08 (95%CI:1.10,3.92) and the late-onset group was 1.50 (95%CI:1.08,2.07). Other sociodemographic factors, such as ethnicity and region of residence, had more modest and inconsistent associations. PCC trajectories differed by concurrent number, frequency, functional impact and severity of symptoms and mental health. CYP with chronic PCC consistently reported a higher median number of symptoms (5+) compared to the other groups (median symptoms ≤ 3). Mental health and wellbeing, of the chronic PCC group was also consistently worse (e.g., 41% of the chronic group consistently were classified as 'cases' on the Strengths and Difficulties scale vs 17%-to-2% of the other groups). There were consistent differences between PCC trajectories, in terms of sex, age, pre-infection mental and physical health, healthcare use, and educational needs. Understanding factors associated with PCC trajectory heterogeneity in CYP and how these trajectories differ over time can help with treatment planning.
Human aging is a heterogeneous, multi-system process that spans molecular, tissue, and physiological decline. In this issue of Cell, Li et al. integrate clinical data, multi-omics, and organ-associated signatures to construct a multi-layer framework for quantifying biological aging across scales.
Biological ageing is a heterogeneous process that shapes susceptibility to chronic disease. However, whether ageing patterns diverge within clinically defined type 2 diabetes (T2D) subgroups remains unclear. We investigated whether epigenetic age acceleration (EAA) differs across T2D phenotypes and whether these patterns relate to subsequent renal vulnerability. We included 607 multi-ethnic Asians with recent-onset T2D previously classified into three clinically distinct subgroups: mild obesity-related diabetes (MOD), mild age-related diabetes with insulin insufficiency (MARD-II), and severe insulin-resistant diabetes with relative insulin insufficiency (SIRD-RII). EAA was quantified using multiple epigenetic clocks. Kidney function was assessed longitudinally using eGFR slope over a median follow-up of 7.3 years, serving as a maker of cumulative systemic ageing burden. SIRD-RII, despite being chronologically younger, showed accelerated ageing across multiple second-generation clocks, whereas MARD-II, despite being chronologically older, showed comparatively lower levels of EAA. Among all epigenic clocks examined, GrimAge2logA1c was both highest in SIRD-RII and the only clock associated with kidney function decline (eGFR slope, β [SE] = -0.113 [0.040], p = 4.77 × 10-3). Epigenome-wide analyses identified subgroup-specific, glucose-responsive loci associated with accelerated ageing. Hypomethylation at TXNIP (cg19693031) characterised the SIRD-RII subgroup and was associated with both faster ageing pace and kidney function decline. Exploratory longitudinal within-person changes in glucose-linked epigenetic ageing were correlated with changes in TXNIP methylation within SIRD-RII (r = -0.901, p = 1.93 × 10-6). These findings suggest that T2D subgroups represent distinct epigenetic ageing phenotypes that may be associated with renal vulnerability. Integrating epigenetic ageing metrics with clinical stratification may enhance identification of individuals at risk for accelerated systemic ageing, informing geroscience-guided intervention strategies early in disease development.
Aging is accompanied by the progressive deterioration of circadian clock function, characterized by reduced amplitude, increased period variability, and impaired metabolic coupling. Declining intracellular nicotinamide adenine dinucleotide (NAD+) levels and SIRT1 activity have been implicated as key mediators of age-associated circadian disruption. Ergothioneine (EGT), a diet-derived antioxidant with longevity-associated effects, has recently been reported to improve healthspan and modulate redox metabolism. However, its effects on the circadian clock remain unclear. Here, we examined whether EGT mitigates age-related decline in circadian rhythmicity using PER2::LUC mouse embryonic fibroblasts (MEFs). Chronic EGT treatment enhanced the amplitude of the PER2::LUC rhythm in a dose-dependent manner without markedly altering the baseline period length. Aging-associated NAD+ decline was modeled using FK866, a NAMPT inhibitor that depletes intracellular NAD+, which reduced rhythm amplitude, lengthened the period, and increased cycle-to-cycle variability. Notably, co-treatment with EGT significantly restored rhythm amplitude, attenuated FK866-induced period lengthening, and reduced period variability. Biochemical analyses revealed that EGT increased the NAD+/NADH ratio under basal conditions and significantly elevated both NAD+ levels and the NAD+/NADH ratio under FK866-induced NAD+ depletion. This effect was not attributable solely to cytoprotection. This study demonstrates that EGT enhances circadian rhythm robustness and counteracts NAD+-depletion-induced clock dysfunction. EGT may ameliorate age-related circadian decline by improving intracellular redox balance and NAD+ metabolism. Given that EGT crosses the blood-brain barrier, it may represent a novel nutritional strategy to preserve circadian function during aging.
The epitranscriptome has been mapped in extraordinary detail, and metabolic-labeling assays have begun to measure how fast modifications turn over at the population level - yet the per-molecule residence time of a mark, how long it remains on an individual RNA once written, is rarely recovered. I argue that this variable deserves a name and a place beside the ones we already quantify. I propose to treat the persistence of a mark as an independent clock - mark dwell time, the average time a modification remains on an RNA molecule - running in parallel to the clock of RNA decay. The two clocks are logically distinct, and their relationship, not either alone, determines whether a modification behaves as a static "birthmark" written once for the life of the transcript or a "dynamic switch" written and erased within it. The central claim is that steady-state stoichiometry is degenerate with respect to this distinction: a site reported as "30% methylated" is equally consistent with 30% of molecules permanently marked and with every molecule marked 30% of the time, and no measurement of level alone can separate them. Arranging the major marks - A-to-I editing, m6A, pseudouridine, m5C, and ac4C - in relation to a birthmark-to-switch spectrum exposes how much of their assumed dynamics rests on inference rather than measurement. I close with a constructive roadmap: crossing metabolic RNA pulse-chase with modification-specific, ideally single-molecule, detection to read a mark's level on surviving RNA of known age, and so constrain dwell time directly.
The hypothalamic radial-glia-like tanycyte population plays important and intertwined roles in metabolism, reproduction, and seasonality. Although these processes are circadian-regulated, the role of the molecular clock in tanycytes themselves has not yet been examined. We report that clock genes cycle with much higher amplitude in ventral tanycytes compared to more dorsal ependymocytes and that adult, tanycyte-specific knockout of core clock gene Bmal1 reduces diet-associated weight gain and fat mass in female mice. Fate mapping studies show that female mice have higher baseline tanycyte-derived neurogenesis than males, with many of the resulting neurons localizing to the feeding-relevant arcuate nucleus. Female but not male mice show reduced tanycyte-derived arcuate neurogenesis after adult Bmal1 deletion, with an increased proportion of newborn neurons acquiring a feeding-suppressing POMC neuropeptidergic fate. Together, our data support a role for tanycyte BMAL1 as a sex-specific regulator of body composition and hypothalamic adult neurogenesis.