Epigenetic stratification: the role of individual change in the biological aging process

A role for cell polarity in lifespan and mitochondrial quality control in the budding yeast Saccharomyces cerevisiae

Babies are born young, largely independent of the age of their mothers. Mother-daughter age asymmetry in yeast is achieved, in part, by inheritance of higher-functioning mitochondria by buds and retention of some high-functioning mitochondria in mother cells. The mitochondrial F box protein, Mfb1p, tethers mitochondria at both poles in a cell cycle-regulated manner: it localizes to and anchors mitochondria at the mother cell tip throughout the cell cycle and at the bud tip before cytokinesis. Here, we report that cell polarity and polarized localization of Mfb1p decline with age in Saccharomyces cerevisiae. Moreover, deletion of genes (BUD1, BUD2, and BUD5) that mediate symmetry breaking during establishment of cell polarity and asymmetric yeast cell division cause depolarized Mfb1p localization and defects in mitochondrial distribution and quality control. Our results support a role for the polarity machinery in lifespan through modulating Mfb1 function in asymmetric inheritance of mitochondria during yeast cell division.

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Budding polarity declines with age

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Polarization of a mitochondrial tether, Mfb1p, within mother cells declines with age

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Defects in budding polarity disrupt Mfb1p polarization and mitochondrial distribution

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Polarity defects affect Mfb1p-mediated mitochondrial quality and lifespan control

Upregulation of the Cdc42 GTPase limits the replicative lifespan of budding yeast

Cdc42, a conserved Rho GTPase, plays a central role in polarity establishment in yeast and animals. Cell polarity is critical for asymmetric cell division, and asymmetric cell division underlies replicative aging of budding yeast. Yet how Cdc42 and other polarity factors impact life span is largely unknown. Here we show by live-cell imaging that the active Cdc42 level is sporadically elevated in wild type during repeated cell divisions but rarely in the long-lived bud8 deletion cells. We find a novel Bud8 localization with cytokinesis remnants, which also recruit Rga1, a Cdc42 GTPase activating protein. Genetic analyses and live-cell imaging suggest that Rga1 and Bud8 oppositely impact life span likely by modulating active Cdc42 levels. An rga1 mutant, which has a shorter life span, dies at the unbudded state with a defect in polarity establishment. Remarkably, Cdc42 accumulates in old cells, and its mild overexpression accelerates aging with frequent symmetric cell divisions, despite no harmful effects on young cells. Our findings implicate that the interplay among these positive and negative polarity factors limits the life span of budding yeast.

Modeling aging and its impact on cellular function and organismal behavior

Aging is a complex phenomenon of functional decay in a biological organism. Although the effects of aging are readily recognizable in a wide range of organisms, the cause(s) of aging are ill defined and poorly understood. Experimental methods on model organisms have driven significant insight into aging as a process, but have not provided a complete model of aging. Computational biology offers a unique opportunity to resolve this gap in our knowledge by generating extensive and testable models that can help us understand the fundamental nature of aging, identify the presence and characteristics of unaccounted aging factor(s), demonstrate the mechanics of particular factor(s) in driving aging, and understand the secondary effects of aging on biological function. In this review, we will address each of the above roles for computational biology in aging research. Concurrently, we will explore the different applications of computational biology to aging in single-celled versus multicellular organisms. Given the long history of computational biogerontological research on lower eukaryotes, we emphasize the key future goals of gradually integrating prior models into a holistic map of aging and translating successful models to higher-complexity organisms.

Rethinking mortality deceleration

The evolution of mortality shows a marked deceleration at older ages. This phenomenon is generally thought to be an effect of selection: mortality decelerates because it progressively selects the most robust individuals in the cohort. Other processes, however, may contribute to mortality deceleration as well. People may not be passive in the face of ageing and may try to counter it by modifying their behaviours and lifestyles. In this paper, I propose a method to test whether selection is to be considered the unique mechanism responsible for mortality deceleration. I applied this method to the life tables of selected female cohorts drawn from the Human Mortality Database. The results indicate mortality decelerates more rapidly than predicted by the selection theory.

A modeling study of budding yeast colony formation and its relationship to budding pattern and aging

Budding yeast, which undergoes polarized growth during budding and mating, has been a useful model system to study cell polarization. Bud sites are selected differently in haploid and diploid yeast cells: haploid cells bud in an axial manner, while diploid cells bud in a bipolar manner. While previous studies have been focused on the molecular details of the bud site selection and polarity establishment, not much is known about how different budding patterns give rise to different functions at the population level. In this paper, we develop a two-dimensional agent-based model to study budding yeast colonies with cell-type specific biological processes, such as budding, mating, mating type switch, consumption of nutrients, and cell death. The model demonstrates that the axial budding pattern enhances mating probability at an early stage and the bipolar budding pattern improves colony development under nutrient limitation. Our results suggest that the frequency of mating type switch might control the trade-off between diploidization and inbreeding. The effect of cellular aging is also studied through our model. Based on the simulations, colonies initiated by an aged haploid cell show declined mating probability at an early stage and recover as the rejuvenated offsprings become the majority. Colonies initiated with aged diploid cells do not show disadvantage in colony expansion possibly due to the fact that young cells contribute the most to colony expansion.

Budding yeast is a model organism in understanding fundamental aspects of eukaryotic cells, such as cell polarization and cell aging. Previously, extensive research has focused on the molecular mechanisms of biological processes in yeast, but many questions regarding yeast budding remain unsolved. For example, how do different budding patterns affect yeast colony growth? How does declined spatial order due to aging impact the colony at the population level? To address these questions, we developed a computational agent-based model, which incorporates key biological processes, the effect of aging, as well as cell-environment interaction. We performed and analyzed a large number of simulations for a variety of situations, and obtained insightful results. We found that axial budding pattern enhances the percentage of diploid cells at early stage and bipolar budding pattern improves colony development under nutrient limitation; the frequency of mating type switch might control the trade-off between diploidization and inbreeding; aging affects the percentage of diploid cells in colonies initiated by a single haploid cell, but does not have much influence in the expansion of colonies initiated by diploid cells. The framework of the model can be extended to study other important systems, such as tissue with stem cell lineage.

The aging feline kidney: A model mortality antagonist?

Traditional thinking views apparently non-programmed disruptions of aging, which medical science calls geriatric diseases, as separate from ‘less harmful’ morphological and physiological aging phenotypes that are more universally expected with passage of time (loss of skin elasticity, graying of hair coat, weight gain, increased sleep time, behavioral changes, etc). Late-life disease phenotypes, especially those involving chronic processes, frequently are complex and very energy-expensive. A non-programmed process of homeostatic disruption leading into a death trajectory seems inconsistent with energy intensive processes. That is, evolutionary mechanisms do not favor complex and prolonged energy investment in death. Taking a different view, the naturally occurring feline ( Felis silvestris catus) renal model suggests that at least some diseases of late life represent only the point of failure in essentially survival-driven adaptive processes. In the feline renal model, individuals that succumbed to failure most frequently displayed progressive tubular deletion and peritubular interstitial fibrosis, but had longer mean life span than cats that died from other causes. Additionally, among cats that died from non-renal causes, those that had degrees of renal tubular deletion and peritubular interstitial fibrosis also had longer mean life span than those cats with no changes, even though causes of death differed minimally between these latter two groups. The data indicate that selective tubular deletion very frequently begins early in adult life, without a clear initiating phase or event. The observations support a hypothesis that this prolonged process may be intrinsic and protective prior to an ultimate point of failure. Moreover, given the genetic complexity and the interplay with associated risk factors, existing data also do not support the ideas that these changes are simple compensatory responses and that breed- or strain-based ‘default’ diseases are inevitable results of increasing individual longevity. Emerging molecular technology offers the future potential to further evaluate and refine these observations. At present, the existence of plastic and adaptive aging programming is suggested by these findings.

Evidence for the hallmarks of human aging in replicatively aging yeast

Recently, efforts have been made to characterize the hallmarks that accompany and contribute to the phenomenon of aging, as most relevant for humans 1. Remarkably, studying the finite lifespan of the single cell eukaryote budding yeast (recently reviewed in 2 and 3) has been paramount for our understanding of aging. Here, we compile observations from literature over the past decades of research on replicatively aging yeast to highlight how the hallmarks of aging in humans are present in yeast. We find strong evidence for the majority of these, and summarize how yeast aging is especially characterized by the hallmarks of genomic instability, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, and mitochondrial dysfunction.

Budding yeast as a model organism to study the effects of age

Although a budding yeast culture can be propagated eternally, individual yeast cells age and eventually die. The detailed knowledge of this unicellular eukaryotic species as well as the powerful tools developed to study its physiology makes budding yeast an ideal model organism to study the mechanisms involved in aging. Considering both detrimental and positive aspects of age, we review changes occurring during aging both at the whole-cell level and at the intracellular level. The possible mechanisms allowing old cells to produce rejuvenated progeny are described in terms of accumulation and inheritance of aging factors. Based on the dynamic changes associated with age, we distinguish different stages of age: early age, during which changes do not impair cell growth; intermediate age, during which aging factors start to accumulate; and late age, which corresponds to the last divisions before death. For each aging factor, we examine its asymmetric segregation and whether it plays a causal role in aging. Using the example of caloric restriction, we describe how the aging process can be modulated at different levels and how changes in different organelles might interplay with each other. Finally, we discuss the beneficial aspects that might be associated with age.

Protein quality control in time and space - links to cellular aging

The evolutionary theory of aging regards aging as an evolved characteristic of the soma, and proponents of the theory state that selection does not allow the evolution of aging in unicellular species lacking a soma-germ demarcation. However, the life history of some microorganisms, reproducing vegetatively by either budding or binary fission, has been demonstrated to encompass an ordered, polar-dependent, segregation of damage leading to an aging cell lineage within the clonal population. In the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, such segregation is under genetic control and includes an asymmetrical inheritance of protein aggregates and inclusions. Herein, the ultimate and proximate causation for such an asymmetrical inheritance, with special emphasis on damaged/aggregated proteins in budding yeast, is reviewed.

Microfluidics device for single cell gene expression analysis in Saccharomyces cerevisiae

We have measured single-cell gene expression over time using a microfluidics-based flow cell which physically traps individual yeast using microm-sized structures (yeast jails). Our goal was to determine variability of gene expression within a cell over time, as well as variability between individual cells. In our flow cell system, yeast jails are fabricated out of PDMS and gene expression is visualized using fluorescently-tagged proteins of interest. Previously, single-cell yeast work has been done using micromanipulation on agar, or FACS. In the present device agar is eliminated, resulting in a superior optical system. The flow of media through the flow cell washes daughter cells away, eliminating the need for micromanipulation. Unlike FACS, the described device can track individual yeast over a time course of many hours. The flow cells are compatible with the needs of quantitative fluorescence microscopy, and allow simultaneous measurements to be done on a large number of individual yeast. We used these flow cells to determine the expression of HSP104-GFPand RAS2-YFP, genes known to affect yeast life span. The results demonstrate inter-cell variation in expression of both genes that could not have been detected without this single-cell analysis.

Accumulation of health disorders as a systemic measure of aging: Findings from the NLTCS data

BACKGROUND

An index of age-associated health/well-being disorders (deficits), called the "frailty index" (FI), appears to be a promising characteristic to capture dynamic variability in aging manifestations among age-peers. In this study we provide further support toward this view focusing on the analysis of the FI age patterns in the participants of the National Long Term Care Survey (NLTCS).

METHODS

The NLTCS assessed health and functioning of the U.S. elderly in 1982, 1984, 1989, 1994, and 1999. Detailed information for our sample was assessed from about 26,700 interviews. The individual FI is defined as a proportion of health deficits for a given person.

RESULTS

The FI in the NLTCS exhibits accelerated age patterns. The acceleration is larger for elderly who, at younger ages, had a lower FI (low FI group) than for those who showed a higher FI at younger ages (high FI group). Age-patterns for low and high FI groups tend to converge at advanced ages. The rate of deficit accumulation is sex-sensitive.

CONCLUSIONS

The accelerated FI age patterns suggest that FI can be considered as a systemic measure of aging process. Convergence of the (sex-specific) FI age patterns for low and high FI groups by extreme ages might reflect the limit of the FI-specific (or systemic) age as well as the limit of adaptation capacity in aging individuals.

Myocardial aging

This review questions the old paradigm that describes the heart as a post-mitotic organ and introduces the notion of the heart as a self-renewing organ regulated by a compartment of multipotent cardiac stem cells (CSCs) capable of regenerating myocytes and coronary vessels throughout life. Because of this dramatic change in cardiac biology, the objective is to provide an alternative perspective of the aging process of the heart and stimulate research in an area that pertains to all of us without exception. The recent explosion of the field of stem cell biology, with the recognition that the possibility exists for extrinsic and intrinsic regeneration of myocytes and coronary vessels, necessitates reevaluation of cardiac homeostasis and myocardial aging. From birth to senescence, the mammalian heart is composed of non-dividing and dividing cells. Loss of telomeric DNA is minimal in fetal and neonatal myocardium but rather significant in the senescent heart. Aging affects the growth and differentiation potential of CSCs interfering not only with their ability to sustain physiological cell turnover but also with their capacity to adapt to increases in pressure and volume loads. The recognition of factors enhancing the activation of the CSC pool, their mobilization, and translocation, however, suggests that the detrimental effects of aging on the heart might be prevented or reversed by local stimulation of CSCs or the intramyocardial delivery of CSCs following their expansion and rejuvenation in vitro. CSC therapy may become, perhaps, a novel strategy for the devastating problem of heart failure in the old population.

Yeast longevity and aging—the mitochondrial connection

Studies of the yeast Saccharomyces cerevisiae reveal four processes determining life span: metabolism, stress resistance, chromatin-dependent gene regulation, and genome stability. The retrograde response, which signals mitochondrial dysfunction resulting in changes in nuclear gene expression, extends yeast life span and is induced during normal aging. This response involves extensive metabolic adaptations. The retrograde response links metabolism and genome stability during yeast aging. A reduction in the availability of nutrients also extends yeast life span. This metabolic mechanism operates by pathways distinct from the retrograde response, although it shares with the latter some longevity effectors. Life extension by calorie restriction entails re-modeling of mitochondrial function. The retrograde response appears to compensate for age changes, while calorie restriction may be a preventive mechanism. The maintenance of age asymmetry between the mother and daughter yeast cells also depends on mitochondrial function. Loss of this age asymmetry occurs during normal yeast aging and may be a paradigm for stem cell aging. The importance of mitochondrial integrity in yeast longevity is emphasized by the role of prohibition function in attenuating oxidative damage. Our studies point to the central role of mitochondria in yeast aging. They highlight the importance of the maintenance of mitochondrial membrane potential, which drives the transport of biosynthetic precursors derived from the Krebs cycle. Common threads weave their way through the studies of aging in yeast and in other model organisms. This suggests conserved features of aging across phyla.

Cross-life stage and cross-generational effects of ? irradiations at the egg stage on Drosophila melanogaster life histories

The long-term effects of X-irradiation with 0.25, 0.5, 0.75 and 1 Gy of 1 h eggs on the fitness-related life history traits in adult Drosophila melanogaster fruit flies and their offspring were investigated. Following irradiation with 0.25, 0.5 and 0.75 Gy, both F0 and F1 flies have decreased adult body weight and increased locomotor (photo- and geotactic) activity, whereas metabolic rate measured as the rate of CO2 production was unchanged or even increased, and female fecundity was slightly reduced compared to appropriate controls. In some cases, irradiation resulted in hormetic effects increased resistance to both starvation and heat shock stresses as well as life extension. An explanation of the beneficial long lasting effects induced by early irradiation is offered, which suggests that these effects are due to cross-life stage and cross-generational adaptive phenotypic plasticity.

Biodemographic trajectories of age-specific reproliferation from stationary phase in the yeast Saccharomyces cerevisiae seem multiphasic

Ageing is usually seen as a monotonic decline of functions and survival. However, recent studies reported that age-specific mortality rates increased and then leveled off or even declined at later ages in several species including humans. Preliminary data using the yeast, Saccharomyces cerevisiae, demonstrated an even more complicated, non-monotonic pattern of reproliferation after stationary phase (i.e. the ability of a cell to exit stationary phase and form a colony). In the present article, we conducted a study of the age-specific reproliferation rates of yeast populations. Stationary phase yeast cells were maintained in water and the reproliferation rates were estimated by the number of yeast able to exit stationary phase on rich growth media. We showed that the age-specific reproliferation rates in yeast seem to rise, fall and rise again. Furthermore, we observed this pattern in different experiments and in different genotypes and established that this pattern was not due to genetic heterogeneity of the populations.

Myocardial aging and senescence: where have the stem cells gone?

Heart failure remains a leading cause of hospital admissions and mortality in the elderly, and current interventional approaches often fail to treat the underlying cause of pathogenesis. Preservation of structure and function in the aging myocardium is most likely to be successful via ongoing cellular repair and replacement, as well as survival of existing cardiomyocytes that generate contractile force. Research has led to a paradigm shift driven by application of stem cells to generate cardiovascular cell lineages. Early controversial findings of pluripotent precursors adopting cardiac phenotypes are now widely accepted, and current debate centers upon the efficiency of progenitor cell incorporation into the myocardium. Much work remains to be done in determining the relevant progenitor cell population and optimizing conditions for efficient differentiation and integration. Significant implications exist for treatment of pathologically damaged or aging myocardium since future interventional approaches will capitalize upon the use of cardiac stem cells as therapeutic reagents.

The transcriptome of prematurely aging yeast cells is similar to that of telomerase-deficient cells

To help define the pathologies associated with yeast cells as they age, we analyzed the transcriptome of young and old cells isolated by elutriation, which allows isolation of biochemical quantities of old cells much further advanced in their life span than old cells prepared by the biotin-streptavidin method. Both 18-generation-old wild-type yeast and 8-generation-old cells from a prematurely aging mutant (dna2-1), with a defect in DNA replication, were evaluated. Genes involved in gluconeogenesis, the glyoxylate cycle, lipid metabolism, and glycogen production are induced in old cells, signifying a shift toward energy storage. We observed a much more extensive generalized stress response known as the environmental stress response (ESR), than observed previously in biotin-streptavidin-isolated cells, perhaps because the elutriated cells were further advanced in their life span. In addition, there was induction of DNA repair genes that fall in the so-called DNA damage "signature" set. In the dna2-1 mutant, energy production genes were also induced. The response in the dna2-1 strain is similar to the telomerase delete response, genes whose expression changes during cellular senescence in telomerase-deficient cells. We propose that these results suggest, albeit indirectly, that old cells are responding to genome instability.

Early programming of adult longevity: demographic and experimental studies

It is supposed that longevity might be programmed by early life exposures. We had carried out demographic and experimental researches for the examination of the possibility of longevity programming. In demographic study, the recorded deaths in Kiev (Ukraine) between 1990 and 2000 (51,503 men and 50,131 women) were used. Age at death was strongly associated with month of birth. Subjects born in the middle of year (April-July) had the lowest longevity. Increasing longevity was observed with each successive birth-month in the second half of the year, with a peak longevity for births in December. To research of the mechanisms responsible for longevity programming, study of adult D. melanogaster DNA repair capacity after irradiation at the egg stage was carried out, using marker such as DNA strand breaks. Insects irradiated in low doses (0.50 and 0.75 Gy) had extended life span and increased stability to S1 nuclease treatment. The probable explanation of observed postponed effects might be the long-term modulation of certain (possibly repair) genes activity. We hypothesize that life-extending effects of different anti-aging treatments might be a consequence of their unspecific (hormetic) action, rather then specific (geroprotector) action on the some aging-related processes, and induction an "transcriptional reprogramming" may be a key mechanism of the longevity programming and artificial life extension.

Senescence and death of primitive cells and myocytes lead to premature cardiac aging and heart failure

Chronological myocardial aging is viewed as the inevitable effect of time on the functional reserve of the heart. Cardiac failure in elderly patients is commonly interpreted as an idiopathic or secondary myopathy superimposed on the old heart independently from the aging process. Thus, aged diseased hearts were studied to determine whether cell regeneration was disproportionate to the accumulation of old dying cells, leading to cardiac decompensation. Endomyocardial biopsies from 19 old patients with a dilated myopathy were compared with specimens from 7 individuals of similar age and normal ventricular function. Ten patients with idiopathic dilated cardiomyopathy were also analyzed to detect differences with aged diseased hearts. Senescent cells were identified by the expression of the cell cycle inhibitor p16INK4a and cell death by hairpin 1 and 2. Replication of primitive cells and myocytes was assessed by MCM5 labeling, myocyte mitotic index, and telomerase function. Aged diseased hearts had moderate hypertrophy and dilation, accumulation of p16INK4a positive primitive cells and myocytes, and no structural damage. Cell death markedly increased and occurred only in cells expressing p16INK4a that had significant telomeric shortening. Cell multiplication, mitotic index and telomerase increased but did not compensate for cell death or prevented telomeric shortening. Idiopathic dilated cardiomyopathy had severe hypertrophy and dilation, tissue injury, and minimal level of p16INK4a labeling. In conclusion, telomere erosion, cellular senescence, and death characterize aged diseased hearts and the development of cardiac failure in humans.

Growing old: metabolic control and yeast aging

The metabolic characteristics of a yeast cell determine its life span. Depending on conditions, stress resistance can have either a salutary or a deleterious effect on longevity. Gene dysregulation increases with age, and countering it increases life span. These three determinants of yeast longevity may be interrelated, and they are joined by a potential fourth, genetic stability. These factors can also operate in phylogenetically diverse species. Adult longevity seems to borrow features from the genetic programs of dormancy to provide the metabolic and stress resistance resources necessary for extended survival. Both compensatory and preventive mechanisms determine life span, while epigenetic factors and the element of chance contribute to the role that genes and environment play in aging.

Biological aging research today: potential, peeves, and problems

Aging research has benefited immensely from the application of genetics during the past decade. This success frequently obscures some of the latent difficulties associated with this method. Interpretations of many experiments are overly optimistic. The emerging functional methods spawned by the knowledge of the genome promise a new window on the biological aging process. However, conceptual approaches have not quite caught up with the technology. An integrative approach to aging is needed, based on systems biology, to tap into this technology and to provide a deeper understanding of the operation of this complex process. The profound quantitative changes inherent in such phenomena as caloric restriction may actually result in stark qualitative changes in metabolism and aging. The ultimate goal is to understand the aging of the individual, and not simply to describe the mortality trajectories of the population. However, this will require the development of indices of frailty and of healthy aging. In the end, we may be able to 'cure' aging, but only in a statistical sense which is measured at the level of the population.

Mutations in DNA replication genes reduce yeast life span

Surprisingly, the contribution of defects in DNA replication to the determination of yeast life span has never been directly investigated. We show that a replicative yeast helicase/nuclease, encoded by DNA2 and a member of the same helicase subfamily as the RecQ helicases, is required for normal life span. All of the phenotypes of old wild-type cells, for example, extended cell cycle time, age-related transcriptional silencing defects, and nucleolar reorganization, occur after fewer generations in dna2 mutants than in the wild type. In addition, the life span of dna2 mutants is extended by expression of an additional copy of SIR2 or by deletion of FOB1, which also increase wild-type life span. The ribosomal DNA locus and the nucleolus seem to be particularly sensitive to defects in dna2 mutants, although in dna2 mutants extrachromosomal ribosomal circles do not accumulate during the aging of a mother cell. Several other replication mutations, such as rad27 Delta, encoding the FEN-1 nuclease involved in several aspects of genomic stability, also show premature aging. We propose that replication fork failure due to spontaneous, endogenous DNA damage and attendant genomic instability may contribute to replicative senescence. This may imply that the genomic instability, segmental premature aging symptoms, and cancer predisposition associated with the human RecQ helicase diseases, such as Werner, Bloom, and Rothmund-Thomson syndromes, are also related to replicative stress.

Profiles of random change during aging contain hidden information about longevity and the aging process

Many different morphological and physiological changes occur during the yeast replicative lifespan. It has been proposed that change is a cause rather than an effect of aging. It is difficult to ascribe causality to processes that manifest themselves at the level of the entire organism, because of their global nature. Although causal connections can be established for processes that occur at the molecular level, their exact contributions are obscured, because they are immersed in a highly interactive network of processes. A top-down approach that can isolate crucial features of aging processes for further study may be a productive avenue. We have mathematically depicted the complicated and random changes that occur in cellular spatial organization during the lifespan of individual yeast cells. We call them budding profiles. This has allowed us to demonstrate that budding profiles are a highly individual characteristic, and that they are correlated with an individual cell's longevity. Additional information can be extracted from our model, indicating that random budding is associated with longevity. This expectation was confirmed, providing new avenues for exploring causal factors in yeast aging. The methodology described here can be readily applied to other aspects of aging in yeast and in higher organisms.

Explaining mortality rate plateaus

We propose a stochastic model of aging to explain deviations from exponential growth in mortality rates commonly observed in empirical studies. Mortality rate plateaus are explained as a generic consequence of considering death in terms of first passage times for processes undergoing a random walk with drift. Simulations of populations with age-dependent distributions of viabilities agree with a wide array of experimental results. The influence of cohort size is well accounted for by the stochastic nature of the model.

Ageing and survival after different doses of heat shock: the results of analysis of data from stress experiments with the nematode worm Caenorhabditis elegans

Stress experiments performed on a population of sterilised nematode worms (Caenorhabditis elegans) show a clear hormesis effect after short exposure and clear debilitation effects after long exposure to heat shock. An intermediate duration of exposure results in a mixture of these two effects. In this latter case the survival curves for populations in the stress and control groups intersect. In this paper we develop an adaptation model of stress and apply it to the analysis of survival data from three such stress experiments. We show that the model can be used to explain empirical age-patterns of mortality and survival observed in these experiments. We discuss possible biological mechanisms involved in stress response and directions for further research.

Applying hormesis in aging research and therapy

Biology of aging is well understood at a descriptive level. Based on these data, biogerontological research is now able to develop various possibilities for intervention. A promising approach for the identification of gerontogenes and gerontogenic processes is through the hormetic effects of mild stress on slowing down aging. Although there are several issues remaining to be resolved, specially with regard to the notion of mild stress, application of hormesis in aging research and therapy is a powerful new approach.

An intervention resembling caloric restriction prolongs life span and retards aging in yeast

The yeast Saccharomyces cerevisiae has a finite life span that is measured by the number of daughter cells an individual produces. The 20 genes known to determine yeast life span appear to function in more than one pathway, implicating a variety of physiological processes in yeast longevity. Less attention has been focused on environmental effects on yeast aging. We have examined the role that nutritional status plays in determining yeast life span. Reduction of the glucose concentration in the medium led to an increase in life span and to a delay in appearance of an aging phenotype. The increase in life span was the more extensive the lower the glucose levels. Life extension was also elicited by decreasing the amino acids content of the medium. This suggests that it is the decline in calories and not a particular nutrient that is responsible, in striking similarity to the effect on aging of caloric restriction in mammals. The caloric restriction effect did not require the induction of the retrograde response pathway, which signals the functional status of the mitochondrion and determines longevity. Furthermore, deletion of RTG3, a downstream mediator in this pathway, and caloric restriction had an additive effect, resulting in the largest increase (123%) in longevity described thus far in yeast. Thus, retrograde response and caloric restriction operate along distinct pathways in determining yeast longevity. These pathways may be exclusive, at least in part. This provides evidence for multiple mechanisms of metabolic control in yeast aging. Inasmuch as caloric restriction lowers blood glucose levels, this study raises the possibility that reduced glucose alters aging at the cellular level in mammals.

Metabolic control and ageing

There appear to be multiple processes that are limiting for longevity and the associated mechanisms of ageing. Among these processes, metabolic control is coming to the forefront, because it has surfaced in studies in several model systems and because of its relevance to mammalian ageing. The genetic and molecular dissection of ageing in yeast points to mechanisms involving three aspects of metabolism. First, dysfunctional mitochondria signal many changes in nuclear gene expression that result in metabolic adjustments that extend life span. Second, manipulation of nutritional status can also increase longevity in a separate caloric-restriction pathway. Finally, protein synthesis is a third aspect, which depends on the transcriptional state of chromatin and the histone deacetylases that modulate it.

Coordination of metabolic activity and stress resistance in yeast longevity

The genetic analysis of longevity in yeast has revealed the importance of metabolic control and resistance to stress in aging. It has also shown that these two physiological processes are interwoven. Molecular mechanisms underlying the longevity effects of metabolic control and stress resistance, as well as genetic stability, are emerging. The yeast RAS genes play a substantial role in coordinating at least the first two of these processes. Numerous correlates can be found between the physiological processes involved in yeast aging and aging in Caenorhabditis elegans and in Drosophila, and the dietary restriction paradigm in mammals.

Metabolic mechanisms of yeast ageing

The genetic analysis of ageing of the yeast Saccharomyces cerevisiae points to several processes important in determining life span. Among these, metabolic control plays a leading role. An examination of the molecular mechanisms underlying metabolic control of longevity has revealed two separate pathways. The retrograde response signals mitochondrial dysfunction to the nucleus resulting in gene regulatory changes that compensate. Nutritional status also modulates life span, adjusting metabolism to efficiently utilize energy resources, in a response that closely resembles the caloric restriction paradigm described in rodents. Although the retrograde response and caloric restriction are distinct pathways of life span extension, there appears to be some overlap of the longevity effectors under their control.

Biogerontology: the next step

After a long period of collecting empirical data describing the changes in organisms, organs, tissues, cells, and macromolecules, biogerontological research is now able to develop various possibilities for intervention. Because aging is a stochastic and nondeterministic process characterized by a progressive failure of maintenance and repair, it is reasoned that gene involved in homeodynamic repair pathways are the most likely candidate gerontogenes. A promising approach for the identification of critical gerontogenic processes is through the hormesis-like positive effects of mild stress. Stimulation of various repair pathways by mild stress has significant effects on delaying the onset of various age-associated alterations in cells, tissues, and organisms.

Metabolic control and gene dysregulation in yeast aging

Life span in the yeast Saccharomyces cerevisiae is usually measured by the number of divisions individual cells complete. Four broad physiologic processes that determine yeast life span have been identified: metabolic control, resistance to stress, chromatin-dependent gene regulation, and genetic stability. A pathway of interorganelle communication involving mitochondria, the nucleus, and peroxisomes has provided a molecular mechanism of aging based on metabolic control. This pathway functions continuously, rather than as an on-off switch, in determining life span. The longevity gene RAS2 modulates this pathway. RAS2 also modulates a variety of other cellular processes, including stress responses and chromatin-dependent gene regulation. An optimal level of Ras2p activity is required for maximum longevity. This may be due to the integration of life maintenance processes by RAS2, which functions as a homeostatic device in yeast longevity. Loss of transcriptional silencing of heterochromatic regions of the genome is a mark of yeast aging. It is now clear that the functional status of chromatin plays an important role in aging. Changes in this functional status result in gene dysregulation, which can be altered by manipulation of the histone deacetylase genes. Silencing of ribosomal DNA appears to be of particular importance. Extrachromosomal ribosomal DNA circles are neither sufficient nor necessary for yeast aging.

Empirical laws of survival and evolution: their universality and implications

Presented analysis of human and fly life tables proves that with the specified accuracy their entire survival and mortality curves are uniquely determined by a single point (e.g., by the birth mortality q(0)), according to the law, which is universal for species as remote as humans and flies. Mortality at any age decreases with the birth mortality q(0). According to life tables, in the narrow vicinity of a certain q(0) value (which is the same for all animals of a given species, independent of their living conditions), the curves change very rapidly and nearly simultaneously for an entire population of different ages. The change is the largest in old age. Because probability to survive to the mean reproductive age quantifies biological fitness and evolution, its universal rapid change with q(0) (which changes with living conditions) manifests a new kind of an evolutionary spurt of an entire population. Agreement between theoretical and life table data is explicitly seen in the figures. Analysis of the data on basic metabolism reduces it to the maximal mean lifespan (for animals from invertebrates to mammals), or to the maximal mean fission time (for bacteria), and universally scales them with the total number of body atoms only. Phenomenological origin of this unification and universality of metabolism, survival, and evolution is suggested. Their implications and challenges are discussed.

Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae has a limited life-span, which is measured by the number of divisions that individual cells complete. Among the many changes that occur as yeasts age are alterations in chromatin-dependent transcriptional silencing. We have genetically manipulated histone deacetylases to modify chromatin, and we have examined the effect on yeast longevity. Deletion of the histone deacetylase gene RPD3 extended life-span. Its effects on chromatin functional state were evidenced by enhanced silencing at the three known heterochromatic regions of the genome, the silent mating type (HM), subtelomeric, and rDNA loci, which occurred even in the absence of SIR3. Similarly, the effect of the rpd3Delta on life-span did not depend on an intact Sir silencing complex. In fact, deletion of SIR3 itself had little effect on life-span, although it markedly accelerated the increase in cell generation time that is observed during yeast aging. Deletion of HDA1, another histone deacetylase gene, did not result in life-span extension, unless it was combined with deletion of SIR3. The hda1Delta sir3Delta resulted in an increase in silencing, but only at the rDNA locus. Deletion of RPD3 suppressed the loss of silencing in rDNA in a sir2 mutant; however, the silencing did not reach the level found in the rpd3Delta single mutant, and RPD3 deletion did not overcome the life-span shortening seen in the sir2 mutant. Deletion of both RPD3 and HDA1 caused a decrease in life-span, which resulted from a substantial increase in initial mortality of the population. The expression of both of these genes declines with age, providing one possible explanation for the increase in mortality during the life-span. Our results are consistent with the loss of rDNA silencing leading to aging in yeast. The functions of RPD3 and HDA1 do not overlap entirely. RPD3 exerts its effect on chromatin at additional sites in the genome, raising the possibility that events at loci other than rDNA play a role in the aging process.

The RAS genes: a homeostatic device in Saccharomyces cerevisiae longevity

The genetic analysis of the yeast replicative life span has revealed the importance of metabolic control and resistance to stress. It has also illuminated the pivotal role in determining longevity that the RAS genes play by the maintenance of homeostasis. This role appears to be performed by the coordination of a variety of cellular processes. Metabolic control seems to occupy a central position among these cellular processes that include stress resistance. Some of the features of metabolic control in yeast resemble the effects of the daf pathway for adult longevity in Caenorhabditis elegans and the metabolic consequences of selection for extended longevity in Drosophila melanogaster, as well as some of the features of caloric restriction in mammals. The distinction between dividing and nondividing cells is proposed to be less important for the aging process than generally believed because these cell types are part of a metabolic continuum in which the total metabolic capacity determines life span. As a consequence, the study of yeast aging may be helpful in understanding processes occurring in the aging brain.

Phenomenological theory of mortality evolution: its singularities, universality, and superuniversality

The probability to survive to the age x universally increases with the mean lifespan x(bar). For species as remote as humans and flies, for a given x the rate of its evolution with x is constant, except for the narrow vicinity of a certain x(bar) = x* (which equals 75 years for humans and 32 days for flies and which is independent of age, population, and living conditions). At x(bar) approximately x* the evolution rate jumps to a different value. Its next jump is predicted at x(bar) approximately 87 years for humans and approximately 59 days for flies. Such singularities are well known in physics and mathematics as phase transitions. In the considered case different population "phases" have significantly different survival evolution rates. The evolution is rapid-life expectancy may double within a lifespan of a single generation. Survival probability depends on age x and mean longevity x(bar) only (for instance, survival curves of 1896 Swedes and 1947 Japanese with approximately equal x(bar) are very close, although they are related to different races in different countries at different periods in their different history.) With no adjustable parameters, its presented universal law quantitatively agrees with all lifetable data. According to this law, the impact of all factors but age reduces to the mean lifespan only. In advanced and old age, this law is superuniversal--it is approximately the same for species as remote as humans and flies. It yields survival probability that linearly depends on the mean lifespan x(bar). As a result, when human x(bar) almost doubles (from 35.5 to 69.3 years), life expectancy at 70 years increases from 8 to 9.5 years only. Other implications of the universal law are also considered.

Longevity, genes, and aging: a view provided by a genetic model system

The genetic analysis of aging in the yeast Saccharomyces cerevisiae has revealed the importance of metabolic capacity, resistance to stress, integrity of gene regulation, and genetic stability for longevity. A balance between these life maintenance processes is sustained by the RAS2 gene, which channels cellular resources among them. This gene cooperates with mitochondria and PHB1 in metabolic adjustments important for longevity. It also modulates stress responses. Transcriptional silencing of heterochromatic regions of the genome is lost during aging, suggesting that gene dysregulation accompanies the aging process. There is evidence that this age change plays a causal role. Aging possesses features of a nonlinear process, and it is likely that application of nonlinear system methodology to aging will be productive.