Programmed ageing: the theory of maximal metabolic scope. How does the biological clock tick?
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Aging↗
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Age breakers. Rupturing the body's sugar-protein bonds might turn back the clock.
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Aging↗
Worm genes imply a master clock.
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Aging↗
Gompertzian mortality originates in the winding-down of the mitotic clock.
UNLABELLED: Gompertz' age-related exponential increase in mortality rate and the obdurately flat mortality trajectory of Drosophila are paradoxical notions for metazoan aging theory. A multiclonal model of Gompertzian organisms provides a resolution by assuming that (a) conception initiates a stochastic process producing a train of replications of fixed length (the Hayflick limit); (b) unique stem cells arise early on to generate multiple vital clones; (c) life continues until one such clone critically depletes its replicative potential. Lifespan is thus governed by the time it takes to reach the terminal branches of the mitotic tree. Although these times are not independent, asymptotic independence can be justified. This clears the way for asymptotic extreme-value theory to guarantee: (1) a non-increasing failure rate, under unlimited replicability; (2) an exponentially increasing failure rate, under limited replicability. However, to obtain an exact fit to the human force-of-mortality function also requires the inclusion of the phenomenon of mitotic deceleration (implemented with a lognormal model of replication). CONCLUSION: the sine qua non of Gompertzian mortality is cellular aging, expressed through these two mitotic phenomena. Conversely, those metazoa with unlimited cellular replicability, by staving off clonal failure would succumb only to catastrophic, age-independent events, yielding a constant mortality rate, the signature of a mitotic clock that does not run down.
Animals↗
Amide molecular clocks in drosophila proteins: potential regulators of aging and other processes.
After synthesis and folding, peptides and proteins undergo changes in charge and conformation through nonenzymatic deamidation of asparaginyl and glutaminyl residues. Each amide has a specific deamidation rate that is genetically determined by the sequence of residues immediately adjacent in the peptide chain and by secondary, tertiary, and quaternary structure. By means of experimentally verified computations, we have determined the deamidation rates of 49 Drosophila peptides and proteins. These rates demonstrate that deamidation provides molecular clocks that are suitable for the regulation of Drosophila aging, development, and other biochemical processes. We have also determined the rates of deamidation for 17,886 other proteins from a wide variety of organisms. The distribution function of these deamidation rates demonstrates the suitability of amide residues as biomolecular clocks.
Aging↗
Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes.
With about 24,000 extant species, teleosts are the largest group of vertebrates. They constitute more than 99% of the ray-finned fishes (Actinopterygii) that diverged from the lobe-finned fish lineage (Sarcopterygii) about 450 MYA. Although the role of genome duplication in the evolution of vertebrates is now established, its role in structuring the teleost genomes has been controversial. At least two hypotheses have been proposed: a whole-genome duplication in an ancient ray-finned fish and independent gene duplications in different lineages. These hypotheses are, however, based on small data sets and lack adequate statistical and phylogenetic support. In this study, we have made a systematic comparison of the draft genome sequences of Fugu and humans to identify paralogous chromosomal regions ("paralogons") in the Fugu that arose in the ray-finned fish lineage ("fish-specific"). We identified duplicate genes in the Fugu by phylogenetic analyses of the Fugu, human, and invertebrate sequences. Our analyses provide evidence for 425 fish-specific duplicate genes in the Fugu and show that at least 6.6% of the genome is represented by fish-specific paralogons. We estimated the ages of Fugu duplicate genes and paralogons using the molecular clock. Remarkably, the ages of duplicate genes and paralogons are clustered, with a peak around 350 MYA. These data strongly suggest a whole-genome duplication event early during the evolution of ray-finned fishes, probably before the origin of teleosts.
Animals↗
The effect of old age on the free-running period of circadian rhythms in rat.
The free-running period is regarded to be an exclusive feature of the endogenous circadian clock. Changes during aging in the free-running period may therefore reflect age-related changes in the internal organization of this clock. However, the literature on alterations in the free-running period in aging is not unequivocal. In the present study, with various confounding factors kept to a minimum, it was found that the free-running periods for active wakefulness, body temperature, and drinking behavior were significantly shorter (by 12-17 min) in old than in young rats. In addition, it was found that the day-to-day stability of the different sleep states was reduced in old rats, whereas that of the drinking rhythm was enhanced. Transient cycles were not observed, nor were there any age-related differences in daily totals of the various sleep-wake states. The amplitudes of the circadian rhythms of active wakefulness, quiet sleep, and temperature were reduced, whereas those of paradoxical sleep and quiet wakefulness remained unchanged.
Aging↗
A SuperLearner-based pipeline for the development of DNA methylation-derived predictors of phenotypic traits.
BACKGROUND: DNA methylation (DNAm) provides a window to characterize the impacts of environmental exposures and the biological aging process. Epigenetic clocks are often trained on DNAm using penalized regression of CpG sites, but recent evidence suggests potential benefits of training epigenetic predictors on principal components. METHODOLOGY/FINDINGS: We developed a pipeline to simultaneously train three epigenetic predictors; a traditional CpG Clock, a PCA Clock, and a SuperLearner PCA Clock (SL PCA). We gathered publicly available DNAm datasets to generate i) a novel childhood epigenetic clock, ii) a reconstructed Hannum adult blood clock, and iii) as a proof of concept, a predictor of polybrominated biphenyl exposure using the three developmental methodologies. We used correlation coefficients and median absolute error to assess fit between predicted and observed measures, as well as agreement between duplicates. The SL PCA clocks improved fit with observed phenotypes relative to the PCA clocks or CpG clocks across several datasets. We found evidence for higher agreement between duplicate samples run on alternate DNAm arrays when using SL PCA clocks relative to traditional methods. Analyses examining associations between relevant exposures and epigenetic age acceleration (EAA) produced more precise effect estimates when using predictions derived from SL PCA clocks. CONCLUSIONS: We introduce a novel method for the development of DNAm-based predictors that combines the improved reliability conferred by training on principal components with advanced ensemble-based machine learning. Coupling SuperLearner with PCA in the predictor development process may be especially relevant for studies with longitudinal designs utilizing multiple array types, as well as for the development of predictors of more complex phenotypic traits.
DNA Methylation↗
[Research Advances on Mechanisms and Interventions of DNA Methylation-Regulated Aging-Related Imbalance in Bone Metabolism].
Aging can induce age-related bone diseases such as osteoporosis. DNA methylation, a core epigenetic regulatory mechanism, participate in the pathological process of aging-induced bone metabolism imbalance by modulating gene expression at the epigenetic level. Using S-adenosylmethionine as a methyl donor, it exhibits characteristics of hypomethylation in genomic repetitive regions and abnormal methylation in CpG islands of promoters of key bone metabolism genes with advancing age. The "epigenetic clock" constructed based on these features can accurately predict an individual's biological age. In bone metabolism, DNA methylation disrupts the osteoblast-osteoclast balance by targeting key factors. Such abnormalities are driven by aging-related inflammation and oxidative stress, while bone loss feedback exacerbates epigenetic disorders, forming a vicious cycle. Targeted intervention strategies have demonstrated significant potential in addressing bone metabolism-related issues. Low-dose DNA methyltransferase inhibitors can improve bone metabolism; nutrients such as folate and cobalamin maintain methylation homeostasis by optimizing one-carbon metabolism pathways; while CRISPR/dCas technology enables precise regulation in the cellular and animal levels, thereby affecting bone metabolism. However, existing strategies still face challenges such as off-target effects and low delivery efficiency. Future research needs to deepen mechanistic studies, optimize intervention methods, and promote their translation into clinical prevention and treatment of osteoporosis.
DNA Methylation↗
Age-related changes in the immune system of mice of eight medium and long-lived strains and hybrids. I. Organ, cellular, and activity changes.
Fifty-three organ, cellular and activity indices were assessed in aging mice of 8 strains and hybrids (5 inbred strains, 1 random bred strain and 2 hybrids of inbred strains) in an attempt to determine which aspects of immunologic aging are characteristic of the species. The results indicate that thymic weight, cellular, and activity indices exhibit a statistically significant negative correlation with age for mice of all 8 strains and hybrids; and B cell cellular indices show a statistically significant positive correlation with age for all mice, while the B cell activity index, lipopolysaccharide response, is dependent on the strain or hybrid. This correlation study supports the view that the T cell component of the immune system deteriorates with age while the B cell component remains relatively intact. Further, the results suggest that thymic aging is a characteristic of the mouse species and that the intrinsic "clock" for immunologic aging resides in the thymus, because most splenic and lymph node T cell activity and cellular indices are associated with thymic weight and cellular indices. Finally, the findings that indices which correlate best with age show the same trend for all strains and hybrids examined suggest that (a) if randomly occurring somatic mutation does play a role in immunologic aging, its influence is limited, and (b) genetic factors not easily influenced by environmental factors regulate immunologic aging.
Aging↗
Human skeletal muscle satellite cells: aging, oxidative stress and the mitotic clock.
Normal satellite cell cultures, isolated from human skeletal muscle, have a limited proliferative capacity and inevitably reach replicative senescence. In this study, we have focused on the consequences of a single oxidative stress by hydrogen peroxide (H(2)O(2)) on both proliferative capacity and myogenic characteristics. Treatment with 1mM H(2)O(2) for 30 min causes a small decrease in the viability and lifespan while the number of cells which are able to proliferate, decreases dramatically. This premature arrest of the cells in a non-proliferative state was not due to spontaneous differentiation since there was no increase in the number of myogenin positive cells. This stress did not affect the myogenicity of the cells or their ability to differentiate and fuse to form multinucleated myotubes. In addition, the mitotic clock does not seem to be modified by oxidative stress treatment since the rate of telomere shortening was similar in H(2)O(2)-treated and control cells. This could be the consequence of the high level of oxygen consumption with an even higher level of ROS being produced in skeletal muscle than in other tissues which would be counteracted by an increase in the antioxidant defense system.
Cell Division↗
Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age.
The bacterium Helicobacter pylori colonizes the gastric mucosa of half of the human population, resulting in chronic gastritis, ulcers, and cancer. We sequenced ten gene fragments from pairs of strains isolated sequentially at a mean interval of 1.8 years from 26 individuals. Several isolates had acquired small mosaic segments from other H. pylori or point mutations. The maximal mutation rate, the import size, and the frequency of recombination were calculated by using a Bayesian model. The calculations indicate that the last common ancestor of H. pylori existed at least 2,500-11,000 years ago. Imported mosaics have a median size of 417 bp, much smaller than for other bacteria, and recombination occurs frequently (60 imports spanning 25,000 bp per genome per year). Thus, the panmictic population structure of H. pylori results from very frequent recombination during mixed colonization by unrelated strains.
Bayes Theorem↗
Can the clock be turned back on ovarian aging?
A basic tenet of reproductive biology is that female mammals are born with a set number of germ cells (oocytes). A new study by Johnson et al. challenges these beliefs by demonstrating that the postnatal mouse ovary contains actively dividing germ cells. These findings have implications for prolonging the reproductive life span of women.
Aging↗
Tempo of hybrid inviability in centrarchid fishes (Teleostei: Centrarchidae).
Hybrid viability decreases with divergence time, a pattern consistent with a so-called speciation clock. However, the actual rate at which this clock ticks is poorly known. Most speciation-clock studies have used genetic divergence as a proxy for time, adopting a molecular clock and often far-distant calibration points to convert genetic distances into age. Because molecular clock assumptions are violated for most genetic datasets and distant calibrations are of questionable utility, the actual rate at which reproductive isolation evolves may be substantially different than current estimates suggest. We provide a robust measure of the tempo at which hybrid viability declines with divergence time in a clade of freshwater fishes (Centrarchidae). This incompatibility clock is distinct from a speciation clock because speciation events in centrarchids appear to be driven largely by prezygotic isolation. Our analyses used divergence times estimated with penalized likelihood applied to a phylogeny derived from seven gene regions and calibrated with six centrarchid fossils. We found that hybrid embryo viability declined at mean rate of 3.13% per million years, slower than in most other taxa investigated to date. Despite measurement error in both molecular estimated ages and hatching success of hybrid crosses, divergence time explained between 73% and 90% of the variation in hybrid viability among nodes. This high correlation is consistent with the gradual accumulation of many genetic incompatibilities of small effect. Hybrid viability declined with the square of time, consistent with an increasing rate of accumulation of incompatibilities between divergent genomes (the snowball effect). However, the quadratic slope is due to a lag phase resulting from heterosis among young species pairs, a phenomenon rarely considered in predictions of hybrid fitness. Finally, we found that reciprocal crosses often show asymmetrical hybrid viabilities. We discuss several alternative explanations for this result including possible deleterious cytonuclear interactions. Speciation-clock studies have been a small cottage industry recently, but there are still novel insights to be gained from analyses of more taxonomic groups. However, between-group comparisons require more careful molecular-clock calibration than has been the norm.
Animals↗
Adult age and the rate of an internal clock.
Two experiments were conducted to determine whether young and old adults differ in the rate of a hypothetical internal clock. Clock rate was measured as the slope of the function relating actual duration to perceived duration. No age differences were apparent when subjects were asked to judge the duration of a flash of light in Exp. I, or to judge the duration of a dark interval between two light flashes in Exp. II. It was concluded that there is no evidence to support the hypothesis that perceptual and motor speed differences associated with increased age can be attributable to a slower rate of internal time.
Adolescent↗
Clonal haematopoiesis of indeterminate potential and epigenetic age acceleration: Systematic review and meta-analysis.
Clonal haematopoiesis of indeterminate potential (CHIP) represents somatic mutations in haematopoietic stem cells that drive clonal expansion. Epigenetic age acceleration (EAA), estimated from DNA methylation (DNAm) clocks, may capture age-related changes in haematopoiesis. This systematic review and meta-analysis was conducted to synthesise evidence on associations between CHIP and EAA and explore shared biological mechanisms that may underlie this relationship. Six databases were searched from January 1, 2011, to June 6, 2025, adhering to PRISMA 2020. Random-effects meta-analyses were performed. Five studies comprising 7483 individuals (ages 55-79, 67.1% female) assessing associations between CHIP and DNAm clocks were included. Across studies, CHIP individuals had higher EAA than no-CHIP individuals, and larger clones were associated with higher EAA. Meta-analysis of three cross-sectional studies (n = 6946) showed that CHIP had higher EAA versus no-CHIP for Horvath1Age IEAA (mean difference, MD=2.84 years, 95% confidence interval, CI: 1.49-4.19), HannumAge EEAA (MD=2.31 years, 95% CI: 1.14-3.49), PhenoAge (MD=1.84 years, 95% CI: 0.96-2.71), and GrimAge (MD=1.20 years, 95% CI: 0.80-1.61). Both DNMT3A- and TET2-mutated CHIP were associated with higher EAA with TET2-mutated CHIP showing larger effect sizes and more consistent associations than DNMT3A-mutated CHIP across DNAm clocks tested. Higher EAA may also act as an effect modifier for morbidity and mortality in CHIP. Larger longitudinal studies are needed to verify a temporal relationship and determine whether EAA provides incremental prognostic value for morbidity and mortality in CHIP.
Humans↗
A comparison of alternative approaches to the scoring of clock drawing.
Although a number of scoring procedures for clock drawing have emerged in the literature, no systematic comparison of the psychometric properties of various approaches has yet been conducted on a large sample of persons over 64 years of age diagnosed with dementia or deemed cognitively intact. The present study examined the reliability and validity of five scoring approaches (Doyon, Bouchard, Morin, Bourgeois, & Cote, 1991; Shulman, Shedletsky, & Silver, 1986; Tuokko, Hadjistavropoulos, Miller, & Beattie, 1992; Watson, Arfken, & Birge, 1993; Wolf-Klein, Silverstone, Levy, Brod, & Breuer, 1989) among the 493 participants of the Canadian Study of Health and Aging who completed clock drawing and who had a final diagnosis assigned at the conclusion of a comprehensive clinical examination. Inter- and intra-rater reliabilities were highest for the Tuokko et al. method. The Tuokko and Shulman scoring procedures had the highest sensitivities and relatively low specificities. The Wolf-Klein procedure had relatively low sensitivities and high specificities. Estimated areas under receiver operating curves were relatively high for all scoring methods. However, the area under the curve for the Watson procedure was significantly lower than the other procedures. All claims to the utility of clock drawing for differentiating between normal persons over 64 years of age and those with dementia appear validated.
Journal Article↗