Towards a network theory of ageing: a model combining the free radical theory and the protein error theory

Towards AI-driven longevity research: An overview

While in the past technology has mostly been utilized to store information about the structural configuration of proteins and molecules for research and medical purposes, Artificial Intelligence is nowadays able to learn from the existing data how to predict and model properties and interactions, revealing important knowledge about complex biological processes, such as aging. Modern technologies, moreover, can rely on a broader set of information, including those derived from the next-generation sequencing (e.g., proteomics, lipidomics, and other omics), to understand the interactions between human body and the external environment. This is especially relevant as external factors have been shown to have a key role in aging. As the field of computational systems biology keeps improving and new biomarkers of aging are being developed, artificial intelligence promises to become a major ally of aging research.

Human ageing, longevity and evolution: can ageing be programmed?

Understanding the proximate and ultimate causes of ageing is one of the key challenges in current biology and medicine. These problems are so important that they are sometimes referred to as the Holy Grail of biology and the Great Conundrum in biogerontology. From an evolutionary perspective, ageing is due to a failure of selection that is caused either by declining strength of selection after the onset of sexual reproduction (Medawar’s theory and Charlesworth’s model) or pleiotropic constraints (Williams’ theory). According to the disposable soma theory, which was proposed by Kirkwood and Holliday, ageing is driven by the accumulation of damage during life and failures of defensive and repair mechanisms as the more an animal expends on sexual reproduction, the less it can expend on bodily maintenance, and vice versa. Although these standard models rule out the possibility that ageing is programmed, there is no consensus about the nature of ageing within the life history in current biogerontology. Interestingly, empirical studies show that there are molecular instructions for ageing and evolutionarily conserved mechanisms for ageing, which seems inconsistent with the idea that ageing is a matter of neglect or a consequence of a failure of selection due to pleiotropic constraints. Here, selected arguments for programmed (i.e. either determined and adaptive or prearranged but non-adaptive) and non-programmed ageing are discussed. Recent advances in biogerontology that cast new light on these problems are outlined here in the context of the idea that the pace of ageing can act as an adaptation in nature, even though ageing is non-programmed and non-adaptive.

Network analysis of frailty and aging: Empirical data from the Mexican Health and Aging Study

BACKGROUND

Frailty remains a challenge in the aging research area with a number of gaps in knowledge still to be filled. Frailty seems to behave as a network, and in silico evidence is available on this matter. Having in vivo evidence that frailty behaves as a complex network was the main purpose of our study.

METHODS

Data from the Mexican Health and Aging Study (main data 2012, mortality 2015) was used. Frailty was operationalized with a 35-deficit frailty index (FI). Analyzed nodes were the deficits plus death. The edges, linking those nodes were obtained through structural learning, and an undirected graph associated with a discrete probabilistic graphical model (Markov network) was derived. Two algorithms, hill-climbing (hc) and Peter and Clark (PC), were used to derive the graph structure. Analyses were performed for the whole population and tertiles of the total FI score.

RESULTS

From the total sample of 10,983 adults aged 50 or older, 43.8% were women, and the mean age was 64.6 years (SD = 9.3). The number of connections increased according to the tertile level of the FI score. As the FI score raised, groups of interconnected deficits increased and how the nodes are connected changed.

CONCLUSIONS

Frailty phenomenon can be modeled using a Bayesian network. Using the full sample, the most central nodes were self-report of health (most connected node) and difficulty walking a block, and all deficits related to mobility were very interconnected. When frailty levels are considered, the most connected nodes differ, but are related with vitality, mainly at lower frailty levels. We derived that not all deficits are equally related since clusters of very related deficits and non-connected deficits were obtained, which might be considered in the construction of the FI score. Further research should aim to identify the nature of all observed interactions, which might allow the development of specific interventions to mitigate the consequences of frailty in older adults.

Recent Advances in the Systems Biology of Aging

SIGNIFICANCE

Reductionist studies have contributed greatly to our understanding of the basic biology of aging in recent years but we still do not understand fundamental mechanisms for many identified drugs and pathways. Use of systems approaches will help us move forward in our understanding of aging. Recent Advances: Recent work described here has illustrated the power of systems biology to inform our understanding of aging through the study of (i) diet restriction, (ii) neurodegenerative disease, and (iii) biomarkers of aging.

CRITICAL ISSUES

Although we do not understand all of the individual genes and pathways that affect aging, as we continue to uncover more of them, we have now also begun to synthesize existing data using systems-level approaches, often to great effect. The three examples noted here all benefit from computational approaches that were unknown a few years ago, and from biological insights gleaned from multiple model systems, from aging laboratories as well as many other areas of biology.

FUTURE DIRECTIONS

Many new technologies, such as single-cell sequencing, advances in epigenetics beyond the methylome (specifically, assay for transposase-accessible chromatin with high throughput sequencing ), and multiomic network studies, will increase the reach of systems biologists. This suggests that approaches similar to those described here will continue to lead to striking findings, and to interventions that may allow us to delay some of the many age-associated diseases in humans; perhaps sooner that we expect. Antioxid. Redox Signal. 29, 973-984.

Hydrogen peroxide induced loss of heterozygosity correlates with replicative lifespan and mitotic asymmetry in Saccharomyces cerevisiae

Cellular aging in Saccharomyces cerevisiae can lead to genomic instability and impaired mitotic asymmetry. To investigate the role of oxidative stress in cellular aging, we examined the effect of exogenous hydrogen peroxide on genomic instability and mitotic asymmetry in a collection of yeast strains with diverse backgrounds. We treated yeast cells with hydrogen peroxide and monitored the changes of viability and the frequencies of loss of heterozygosity (LOH) in response to hydrogen peroxide doses. The mid-transition points of viability and LOH were quantified using sigmoid mathematical functions. We found that the increase of hydrogen peroxide dependent genomic instability often occurs before a drop in viability. We previously observed that elevation of genomic instability generally lags behind the drop in viability during chronological aging. Hence, onset of genomic instability induced by exogenous hydrogen peroxide treatment is opposite to that induced by endogenous oxidative stress during chronological aging, with regards to the midpoint of viability. This contrast argues that the effect of endogenous oxidative stress on genome integrity is well suppressed up to the dying-off phase during chronological aging. We found that the leadoff of exogenous hydrogen peroxide induced genomic instability to viability significantly correlated with replicative lifespan (RLS), indicating that yeast cells' ability to counter oxidative stress contributes to their replicative longevity. Surprisingly, this leadoff is positively correlated with an inverse measure of endogenous mitotic asymmetry, indicating a trade-off between mitotic asymmetry and cell's ability to fend off hydrogen peroxide induced oxidative stress. Overall, our results demonstrate strong associations of oxidative stress to genomic instability and mitotic asymmetry at the population level of budding yeast.

Aging and computational systems biology

Aging research is undergoing a paradigm shift, which has led to new and innovative methods of exploring this complex phenomenon. The systems biology approach endeavors to understand biological systems in a holistic manner, by taking account of intrinsic interactions, while also attempting to account for the impact of external inputs, such as diet. A key technique employed in systems biology is computational modeling, which involves mathematically describing and simulating the dynamics of biological systems. Although a large number of computational models have been developed in recent years, these models have focused on various discrete components of the aging process, and to date no model has succeeded in completely representing the full scope of aging. Combining existing models or developing new models may help to address this need and in so doing could help achieve an improved understanding of the intrinsic mechanisms which underpin aging.

Analysis of the behavior of mitochondria in the ovaries of the earthworm Dendrobaena veneta Rosa 1839

We examined six types of cells that form the ovary of the earthworm Dendrobena veneta ogonia, prooocytes, vitellogenic oocytes, trophocytes, fully grown postvitellogenic oocytes and somatic cells of the gonad. The quantitative stereological method revealed a much higher "volume density" of mitochondria in all of the types of germ-line cells except for the somatic cells. Fluorescent vital stain JC-1, however, showed a much higher oxidative activity of mitochondria in the somatic cells than in the germ-line cells. The distribution of active and inactive mitochondria within the studied cells was assessed using the computer program ImageJ. The analysis showed a higher luminosity of inactive mitochondria in all of the types of germ-line cells and a higher luminosity of active mitochondria in somatic cells. The OXPHOS activity was found in somatic cells mitochondria and in the peripheral mitochondria of the vitellogenic oocytes. The detection of reactive oxygen species (ROS) revealed a differentiated distribution of ROS in the different cell types. The amount of ROS substances was lower in somatic cells than in younger germ-line cells. The ROS level was also low in the cytoplasm of fully grown postwitellogenic oocytes. The distribution of the MnSOD enzyme that protects mitochondria against destructive role of ROS substances was high in the oogonia and in prooocytes and it was very high in vitellogenic and postvitellogenic oocytes. However, a much lower level of this protective enzyme was observed in the trophocytes and the lowest level was found in the cytoplasm of somatic cells. The lower mitochondrial activity and higher level of MnSOD activity in germ-line cells when compared to somatic cells testifies to the necessity of the organisms to protect the mitochondria of oocytes against the destructive role of the ROS that are produced during oxidative phosphorylation. The protection of the mitochondria in oocytes is essential for the transfer of healthy organelles to the next generation.

Achieving the balance between ROS and antioxidants: when to use the synthetic antioxidants

Free radical damage is linked to formation of many degenerative diseases, including cancer, cardiovascular disease, cataracts, and aging. Excessive reactive oxygen species (ROS) formation can induce oxidative stress, leading to cell damage that can culminate in cell death. Therefore, cells have antioxidant networks to scavenge excessively produced ROS. The balance between the production and scavenging of ROS leads to homeostasis in general; however, the balance is somehow shifted towards the formation of free radicals, which results in accumulated cell damage in time. Antioxidants can attenuate the damaging effects of ROS in vitro and delay many events that contribute to cellular aging. The use of multivitamin/mineral supplements (MVMs) has grown rapidly over the past decades. Some recent studies demonstrated no effect of antioxidant therapy; sometimes the intake of antioxidants even increased mortality. Oxidative stress is damaging and beneficial for the organism, as some ROS are signaling molecules in cellular signaling pathways. Lowering the levels of oxidative stress by antioxidant supplements is not beneficial in such cases. The balance between ROS and antioxidants is optimal, as both extremes, oxidative and antioxidative stress, are damaging. Therefore, there is a need for accurate determination of individual's oxidative stress levels before prescribing the supplement antioxidants.

Zinc and diabetic retinopathy

Zinc (Zn) is an important nutrient that is involved in various physiological metabolisms. Zn dyshomeostasis is often associated with various pathogeneses of chronic diseases, such as metabolic syndrome, diabetes, and related complications. Zn is present in ocular tissue in high concentrations, particularly in the retina and choroid. Zn deficiencies have been shown to affect ocular development, cataracts, age-related macular degeneration, and even diabetic retinopathy. However, the mechanism by which Zn deficiency increases the prevalence of diabetic retinopathy remains unclear. In addition, due to the negative effect of Zn deficiency on the eye, Zn supplementation should prevent diabetic retinopathy; however, limited available data do not always support this notion. Therefore, the goal of this paper was to summarize these pieces of available information regarding Zn prevention of diabetic retinopathy. Current theories and possible mechanisms underlying the role of Zn in the eye-related diseases are discussed. The possible factors that affect the preventive effect of Zn supplementation on diabetic retinopathy were also discussed.

Lithocholic acid extends longevity of chronologically aging yeast only if added at certain critical periods of their lifespan

Our studies revealed that LCA (lithocholic bile acid) extends yeast chronological lifespan if added to growth medium at the time of cell inoculation. We also demonstrated that longevity in chronologically aging yeast is programmed by the level of metabolic capacity and organelle organization that they developed before entering a quiescent state and, thus, that chronological aging in yeast is likely to be the final step of a developmental program progressing through at least one checkpoint prior to entry into quiescence. Here, we investigate how LCA influences longevity and several longevity-defining cellular processes in chronologically aging yeast if added to growth medium at different periods of the lifespan. We found that LCA can extend longevity of yeast under CR (caloric restriction) conditions only if added at either of two lifespan periods. One of them includes logarithmic and diauxic growth phases, whereas the other period exists in early stationary phase. Our findings suggest a mechanism linking the ability of LCA to increase the lifespan of CR yeast only if added at either of the two periods to its differential effects on various longevity-defining processes. In this mechanism, LCA controls these processes at three checkpoints that exist in logarithmic/diauxic, post-diauxic and early stationary phases. We therefore hypothesize that a biomolecular longevity network progresses through a series of checkpoints, at each of which (1) genetic, dietary and pharmacological anti-aging interventions modulate a distinct set of longevity-defining processes comprising the network; and (2) checkpoint-specific master regulators monitor and govern the functional states of these processes.

Reproductive benefit of oxidative damage: an oxidative stress "malevolence"?

High levels of reactive oxygen species (ROS) compared to antioxidant defenses are considered to play a major role in diverse chronic age-related diseases and aging. Here we present an attempt to synthesize information about proximate oxidative processes in aging (relevant to free radical or oxidative damage hypotheses of aging) with an evolutionary scenario (credited here to Dawkins hypotheses) involving tradeoffs between the costs and benefits of oxidative stress to reproducing organisms. Oxidative stress may be considered a biological imperfection; therefore, the Dawkins' theory of imperfect adaptation of beings to environment was applied to the role of oxidative stress in processes like famine and infectious diseases and their consequences at the molecular level such as mutations and cell signaling. Arguments are presented that oxidative damage is not necessarily an evolutionary mistake but may be beneficial for reproduction; this may prevail over its harmfulness to health and longevity in evolution. Thus, Dawkins' principle of biological “malevolence” may be an additional biological paradigm for explaining the consequences of oxidative stress.

Systems biology of ageing and longevity

Ageing is intrinsically complex, being driven by multiple causal mechanisms. Each mechanism tends to be partially supported by data indicating that it has a role in the overall cellular and molecular pathways underlying the ageing process. However, the magnitude of this role is usually modest. The systems biology approach combines (i) data-driven modelling, often using the large volumes of data generated by functional genomics technologies, and (ii) hypothesis-driven experimental studies to investigate causal pathways and identify their parameter values in an unusually quantitative manner, which enables the contributions of individual mechanisms and their interactions to be better understood, and allows for the design of experiments explicitly to test the complex predictions arising from such models. A clear example of the success of the systems biology approach in unravelling the complexity of ageing can be seen in recent studies on cell replicative senescence, revealing interactions between mitochondrial dysfunction, telomere erosion and DNA damage. An important challenge also exists in connecting the network of (random) damage-driven proximate mechanisms of ageing with the higher level (genetically specified) signalling pathways that influence longevity. This connection is informed by actions of natural selection on the determinants of ageing and longevity.

Computational systems biology of aging

Computational systems biology is expected to make major contributions to unravel the complex molecular mechanisms underlying the progression of aging in cells, tissues, and organisms. The development of computational approaches is, however, challenged by a wide spectrum of aging mechanisms participating on different levels of biological organization. The tight connectivity between the molecular constituents, functions, and cell states requires frameworks and strategies that extend beyond current practice to model, simulate, and predict the progression of aging and the emerging aging phenotypes. We provide a general overview of the specific computational tasks and opportunities in aging research, and discuss some illustrative systems level concepts in more detail. One example provided here is the assembly of a conceptual whole cell model that considers the temporal dynamics of the aging process grounded on molecular mechanisms. Another application is the assembly of interactomes, such as protein networks that allow us to analyze changes in network topology and interaction of proteins that have been implicated in aging with other cellular constituents and processes. We introduce the necessary key steps to build these applications and discuss their merits and future extensions for aging research. WIREs Syst Biol Med 2011 3 414-428 DOI: 10.1002/wsbm.126

Rule-based cell systems model of aging using feedback loop motifs mediated by stress responses

Investigating the complex systems dynamics of the aging process requires integration of a broad range of cellular processes describing damage and functional decline co-existing with adaptive and protective regulatory mechanisms. We evolve an integrated generic cell network to represent the connectivity of key cellular mechanisms structured into positive and negative feedback loop motifs centrally important for aging. The conceptual network is casted into a fuzzy-logic, hybrid-intelligent framework based on interaction rules assembled from a priori knowledge. Based upon a classical homeostatic representation of cellular energy metabolism, we first demonstrate how positive-feedback loops accelerate damage and decline consistent with a vicious cycle. This model is iteratively extended towards an adaptive response model by incorporating protective negative-feedback loop circuits. Time-lapse simulations of the adaptive response model uncover how transcriptional and translational changes, mediated by stress sensors NF-κB and mTOR, counteract accumulating damage and dysfunction by modulating mitochondrial respiration, metabolic fluxes, biosynthesis, and autophagy, crucial for cellular survival. The model allows consideration of lifespan optimization scenarios with respect to fitness criteria using a sensitivity analysis. Our work establishes a novel extendable and scalable computational approach capable to connect tractable molecular mechanisms with cellular network dynamics underlying the emerging aging phenotype.

The global process of aging disturbs a broad range of cellular mechanisms in a complex fashion and is not well understood. One important goal of computational approaches in aging is to develop integrated models in terms of a unifying aging theory, predicting progression of aging phenotypes grounded on molecular mechanisms. However, current experimental data incoherently reflects many isolated processes from a large diversity of approaches, biological model systems, and species, which makes such integration a challenging task. In an attempt to close this gap, we iteratively develop a fuzzy-logic cell systems model considering the interplay of damage, metabolism, and signaling by positive and negative feedback-loop motifs using relationships drawn from literature data. Because cellular biodynamics may be considered a complex control system, this approach seems particularly suitable. Here, we demonstrate that rule-based fuzzy-logic models provide semi-quantitative predictions that enhance our understanding of complex and interlocked molecular mechanisms and their implications on the aging physiome.

Comparative analyses of time-course gene expression profiles of the long-lived sch9Delta mutant

In an attempt to elucidate the underlying longevity-promoting mechanisms of mutants lacking SCH9, which live three times as long as wild type chronologically, we measured their time-course gene expression profiles. We interpreted their expression time differences by statistical inferences based on prior biological knowledge, and identified the following significant changes: (i) between 12 and 24 h, stress response genes were up-regulated by larger fold changes and ribosomal RNA (rRNA) processing genes were down-regulated more dramatically; (ii) mitochondrial ribosomal protein genes were not up-regulated between 12 and 60 h as wild type were; (iii) electron transport, oxidative phosphorylation and TCA genes were down-regulated early; (iv) the up-regulation of TCA and electron transport was accompanied by deep down-regulation of rRNA processing over time; and (v) rRNA processing genes were more volatile over time, and three associated cis-regulatory elements [rRNA processing element (rRPE), polymerase A and C (PAC) and glucose response element (GRE)] were identified. Deletion of AZF1, which encodes the transcriptional factor that binds to the GRE element, reversed the lifespan extension of sch9Δ. The significant alterations in these time-dependent expression profiles imply that the lack of SCH9 turns on the longevity programme that extends the lifespan through changes in metabolic pathways and protection mechanisms, particularly, the regulation of aerobic respiration and rRNA processing.

Stochastic modelling for quantitative description of heterogeneous biological systems

Two related developments are currently changing traditional approaches to computational systems biology modelling. First, stochastic models are being used increasingly in preference to deterministic models to describe biochemical network dynamics at the single-cell level. Second, sophisticated statistical methods and algorithms are being used to fit both deterministic and stochastic models to time course and other experimental data. Both frameworks are needed to adequately describe observed noise, variability and heterogeneity of biological systems over a range of scales of biological organization.

Stress and ageing interactions: A paradox in the context of shared etiological and physiopathological processes

Gerontology has made considerable progress in the understanding of the mechanisms underlying the ageing process and age-related neurodegenerative disorders. However, ways to improve quality of life in the elderly remain to be elucidated. It is now clear that stress and the ageing process share a number of underlying mechanisms bound in a very close, if not indissociable, relationship. The ageing process is regulated by the factors underlying the ability to adjust to stress, whilst stress has an influence on the life span and the quality of ageing. In addition, the ability to cope with stress in adulthood predicts life expectancy and quality of life at senescence. The ageing process and stress also share several common mechanisms, particularly in relation to the energy factor. Stress consumes energy and ageing may be considered as a cost of the energy expended to deal with the stressors to which the body is exposed throughout its lifetime. This suggests that the ageing process is associated with and/or a consequence of a long-lasting activation of the major stress responsive systems. However, despite common features, the interaction between stress and the ageing process gives rise to some paradoxes. Stress can either diminish or exacerbate the ageing process just as the ageing process can worsen or counter the effects of stress. There has been little attempt to understand how ageing and stress might interact to promote "successful" or pathological ageing. A key factor in this respect is the individual's ability to adapt to stress. Viewed from this angle, the quality of life of aged subjects may be improved through therapy designed to improve the tolerance to stress.

The Evolving Role of Structural and Functional Imaging in Assessment of Age-Related Changes in the Body

Aging is an extremely complex, multifactorial, and inevitable process that varies in rate from person to person and that is not fully understood at its most basic levels. Despite this complexity, knowledge of age-related changes and normal variation in organ structure and function is essential to differentiate them from alterations that are associated with pathology. Combined structural and functional imaging, which increasingly is used to assess a multitude of disorders, including cancer, cardiovascular disease, and central nervous system abnormalities, can be applied to study changes in structure and function related to aging. This article reviews the major theories of biological aging and presents our approach and rationale to study age-related changes through quantitative tomographic radiological and scintigraphic approaches. In the series of articles that follow, we have made an attempt to determine age-related changes in volume, attenuation, and function as measured by computed tomography, magnetic resonance imaging, and position emission tomography in the following organs and systems: central nervous system, head and neck, heart and major arteries, lungs, abdominal and pelvic parenchymal organs, gastrointestinal tract, genitourinary tract, breast, bone and bone marrow, joints, and skin. The population examined includes a large number of subjects in all decades of life. We have also made an effort to introduce some new concepts such as partial volume correction and measurements of global metabolic activity of the organs examined, and emphasize the importance of quantitative techniques in such applications. It is our hope that this new initiative will further enhance the role of novel imaging techniques in the management of patients with cancer and other disorders.

The essential mechanisms of aging: Irreparable damage accumulation of biochemical side-reactions

Explanations on aging mechanisms have now become unexpectedly complicated. However, it is gradually accepted that 'senescence is a collective consequence of both inheritance and environment'. Based on the achievements of biological and medical research in related fields, we pinpoint in this review that although aging is mainly considered a physiological (non-pathological) process, the biochemical structure of aged organisms is deranged, or 'sick' at the molecular level. The free radical/glycation induced carbonyl stress, the key culprit to form crosslinks, has been identified to cause stable cyclic conjugates of mainly protein-based aggregates implying entropy increase (the Second Law of Thermodynamics) during aging. When combining such key aging processes with age pigment biochemistry, a general picture of aging process can be figured out, as the main clues and results are available. In this review we also propose for the first time that by focusing on 'process' rather than on 'causes' (damages), we can then get a clear view of aging mechanisms. Through rational thinking and critical analysis, we conclude that the accumulation of irreparable damages and alternations caused by spontaneous biological side-reactions seems to be the essential and profound nature of higher animals' aging mechanisms.

Zinc might protect oxidative changes in the retina and pancreas at the early stage of diabetic rats

It is well documented that oxidative stress is a basic mechanism behind the development of diabetic retinopathy (DR). The current study was undertaken to elucidate the possible role of zinc as an antioxidant and a biological membrane stabilizer in the protection against (DR). Male Wistar rats weighing 250 +/- 50 g were made diabetic by injection with a single ip dose of alloxan (100 mg/kg). Another group of rats was simultaneously treated with alloxan (100 mg/kg) and a single ip dose of zinc chloride (ZnCl2) (5 mg/kg). Blood and tissue samples were collected at 24, 48, and 72 h post-treatment in both groups. Diabetic state was confirmed by the determination of plasma glucose levels (significantly elevated at any time of the experiment when compared with controls receiving vehicle). Plasma insulin was significantly increased 24 h after treatment in both alloxan and alloxan plus ZnCl2-treated groups, and then decreased markedly 48 and 72 h post treatment in both groups. Alloxan treatment depleted both retinal and liver glutathione contents. The decrease in retinal and liver GSH in alloxan-treated rats was accompanied with a sustained increase in their thiobarbituric acid (TBA) content. Simultaneous treatment of rats with alloxan and ZnCl2 blunted the sustained increment in plasma glucose induced by alloxan. The combined administration of alloxan and zinc reversed the depleting effect on retinal and hepatic GSH in alloxan-treated rats and reduced the elevations in TBA content of both retinas and livers. At variance with many other antioxidants the current results clearly indicate the beneficial effects of Zn in both controlling hyperglycemia and the protection of the retina against oxidative stress in diabetes which may help set a new direction toward the development of effective treatments of DR.

Protective effects of antioxidants on age-related changes in the electrophoretic patterns of cardiac LDH, hepatic ALP and serum proteins in male golden hamster

Basal and antioxidant-induced changes in the isoenzyme and isoform patterns of cardiac lactate dehydrogenase (EC 1.1.1.27) and hepatic alkaline phosphatase (EC 3.1.3.1), respectively, as well as the electrophoretic patterns of serum proteins in different age groups of male golden hamster were compared. This is to test whether age-induced changes could be corrected by long-term administration of antioxidants. Data indicated that aging causes no remarkable change in the total activity of either cardiac LDH or hepatic ALP, however a significant increase in the fractional activity of some cardiac LDH isoenzymes and a significant reduction in the fractional activity of some hepatic ALP isoforms were induced by aging. On the other hand, long-term administration of antioxidants appeared to manifest a clear counteracting effect on the age-related changes in old age. This effect was indicated in the fractional activity of cardiac LDH isoenzymes and of hepatic ALP isoforms. The present study has also shown a wide-range variation in serum protein patterns due to aging and/or antioxidant administration, which indirectly reflect a parallel variation in the process of gene expression and/or proteolytic activity.

Modelling perspectives on aging: can mathematics help us stay young?

We survey several types of mathematical models that keep track of age distributions in a population, or follow some aspects of aging, such as loss of replicative potential of stem cells. The properties of a class of linear models of this type are discussed and compared. We illustrate the applicability of such models with a simple example based on hypothetical stem cell dynamics developed to address age-related telomere loss in the human granulocyte pool. We then describe the contrasting behaviour of nonlinear systems. Examples are drawn from the class of "dynamical diseases" to illustrate some of the aspects of nonlinear systems. Applications of these, and other models to the problems of aging and replicative aging are discussed.

Heumann-Hötzel model for aging revisited

Since its proposition in 1995, the Heumann-Hötzel model has remained as an obscure model of biological aging. The main arguments used against it were its apparent inability to describe populations with many age intervals and its failure to prevent a population extinction when only deleterious mutations are present. We find that with a simple and minor change in the model these difficulties can be surmounted. Our numerical simulations show a plethora of interesting features: the catastrophic senescence, the Gompertz law and that postponing the reproduction increases the survival probability, as has already been experimentally confirmed for the drosophila fly.

Quantitative aspects of metabolic organization: a discussion of concepts

Metabolic organization of individual organisms follows simple quantitative rules that can be understood from basic physical chemical principles. Dynamic energy budget (DEB) theory identifies these rules, which quantify how individuals acquire and use energy and nutrients. The theory provides constraints on the metabolic organization of subcellular processes. Together with rules for interaction between individuals, it also provides a basis to understand population and ecosystem dynamics. The theory, therefore, links various levels of biological organization. It applies to all species of organisms and offers explanations for body-size scaling relationships of natural history parameters that are otherwise difficult to understand. A considerable number of popular empirical models turn out to be special cases of the DEB model, or very close numerical approximations. Strong and weak homeostasis and the partitionability of reserve kinetics are cornerstones of the theory and essential for understanding the evolution of metabolic organization.

The network and the remodeling theories of aging: historical background and new perspectives

Two general theories, i.e. "the network theory of aging" (1989) and "the remodeling theory of aging" (1995), as well as their implications, new developments, and perspectives are reviewed and discussed. Particular attention has been paid to illustrate: (i) how the network theory of aging fits with recent data on aging and longevity in unicellular organisms (yeast), multicellular organisms (worms), and mammals (mice and humans); (ii) the evolutionary and experimental basis of the remodeling theory of aging (immunological, genetic, and metabolic data in healthy centenarians, and studies on the evolution of the immune response, stress and inflammation) and its recent development (the concepts of "immunological space" and "inflamm-aging"); (iii) the profound relationship between these two theories and the data which suggest that aging and longevity are related, in a complex way, to the capability to cope with a variety of stressors.

Molecular gerontology. Bridging the simple and the complex

It is clear, both empirically and theoretically, that the mechanisms of aging are multiple and complex. Nevertheless, single gene mutations and simple interventions such as calorie restriction have broad effects on the senescent phenotype. The major challenge is to unite highly reductionist analysis of molecular components with integrative model systems that can "put it all together." Two themes are developed. In the first, biochemical models are described that show how the network concept of cellular aging can be used to integrate multiple biochemical mechanisms that contribute to cellular instability. In the second theme, the role of intrinsic developmental chance is examined as a major factor contributing, in addition to genes and environment, to the divergence of the senescent phenotype. The implications of these themes for research strategies in molecular gerontology are discussed.

Time evolution of the Partridge-Barton model

The time evolution of the Partridge-Barton model in the presence of the pleiotropic constraint and deleterious somatic mutations is exactly solved for arbitrary fecundity in the context of a matricial formalism. Analytical expressions for the time dependence of the mean survival probabilities are derived. Using the fact that the asymptotic behavior for large time t is controlled by the largest matrix eigenvalue, we obtain the steady state values for the mean survival probabilities and the Malthusian growth exponent. The mean age of the population exhibits a t-1 power law decayment. Some Monte Carlo simulations were also performed and they corroborated our theoretical results.

Accumulation of defective mitochondria through delayed degradation of damaged organelles and its possible role in the ageing of post-mitotic and dividing cells

The mitochondrial theory of ageing proposes that an accumulation of defective mitochondria is a major contributor to the cellular deterioration that underlies the ageing process. The plausibility of the mitochondrial theory depends critically upon the population dynamics of intact and mutant mitochondria in different cell types. Earlier work suggested that mutant mitochondria might have a replication advantage but failed to account for the fact that mutants accumulate faster in post-mitotic than in dividing cells. We describe a new mathematical model that allows for damaged mitochondria to replicate more slowly, which accommodates experimental evidence of impaired energy generation and a reduced proton gradient in defective mitochondria. However, this is compensated for by a slower degradation rate of damaged mitochondria than intact ones, as suggested by de Grey (1997), which gives damaged mitochondria a selective advantage and leads to a clonal expansion of damaged mitochondria. This theoretical result is important because it agrees with evidence that, during ageing, single muscle fibres are taken over by one or only a few types of mtDNA mutants. The model also shows that cell division can rejuvenate and stabilize the mitochondrial population, consistent with data that post-mitotic tissues accumulate mitochondrial damage faster than mitotically active tissues.

Quantitative and ultrastructural changes in glia and pericytes in the parietal cortex of the aging rat

The frequency of astrocytes, microglia plus oligodendrocytes, and pericytes displaying nuclei was analyzed and quantified in 160-microm-wide strips of the parietal cortex (Par1 region) from young and aged Wistar rats. The study was performed on two groups of rats aged 3-4 and 32-36 months. Quantifications of the glial cell types and pericytes were made in 1-microm-thick sections stained with toluidine blue. Ultrathin sections were also made to analyze the ultrastructural features of these cells during aging. Astrocytes and pericytes increased in number by about 20% and 22%, respectively, with age. These increases were most significant in layers II-IV and V for both cellular types. Clusters of astrocytes were common in these layers of aging rats. The ultrastructural analysis also indicated changes in all cell types that stored inclusions and vacuoles with age, which were particularly abundant in microglial cells. End-feet astrocytes and pericytes surrounding the vascular wall also contained vacuoles and inclusions, and consequently the vascular wall increased in thickness. In conclusion, the aging process increased astrocyte and pericyte populations, but not microglia plus oligodendrocyte populations, in the rat parietal cortex. Although no significant change in nuclear size could be observed in any cell type, all glial cells as well as pericytes underwent morphological ultrastructural changes. These modifications may result from the need to correct possible homeostatic imbalances during aging.

Network theory of aging

Evolution theory indicates that investment in mechanisms of somatic maintenance and repair is likely to be limited, suggesting that aging may result from the accumulation of unrepaired somatic defects. An important corollary of this hypothesis is that multiple mechanisms of aging operate in parallel. We describe a recently developed "network theory of aging" that integrates the contributions of defective mitochondria, aberrant proteins, and free radicals in the aging process and that includes the protective effects of antioxidant enzymes and proteolytic scavengers. Possibilities for further extension of the theory and its role in prediction and simulation of experimental results are discussed.

Human senescence

Human life expectancy has increased dramatically through improvements in public health, housing, nutrition and general living standards. Lifespan is now limited chiefly by intrinsic senescence and its associated frailty and diseases. Understanding the biological basis of the ageing process is a major scientific challenge that will require integration of molecular, cellular, genetic and physiological approaches. This article reviews progress that has been made to date, particularly with regard to the genetic contribution to senescence and longevity, and assesses the scale of the task that remains.

Rapid development and a long life: an association expected under a stress theory of aging

Life span and development time are considered in the context of the abiotic stresses to which free-living organisms are normally exposed. Under these circumstances, long life span depends upon metabolically efficient stress-resistance genes, which tend to be heterozygous. Similarly, rapid development time tends to be a feature of heterozygous stress-resistant individuals. Therefore, individuals who have high inherited stress resistance should develop fastest and live longest; in addition, they should show high homeostasis in the fact of the energy costs of stress. In this way, the stress theory of aging can incorporate the developmental stage, based upon oxidative stress as an important major direct challenge.

A network theory of ageing: the interactions of defective mitochondria, aberrant proteins, free radicals and scavengers in the ageing process

Evolution theory indicates that ageing is caused by progressive accumulation of defects, since the evolutionary optimal level of maintenance is always below the minimum required for indefinite survival. Evolutionary theories also suggest that multiple processes are operating in parallel, but unfortunately they make no predictions about specific mechanisms. To understand and evaluate the many different mechanistic theories of ageing which have been proposed, it is therefore important to understand and study the network of maintenance processes which control cellular homeostasis. In this paper we describe a Network Theory of Ageing which integrates the contributions of defective mitochondria, aberrant proteins, and free radicals to the ageing process, and which includes the protective effects of antioxidant enzymes and proteolytic scavengers. The model simulations not only confirm and explain many experimental, age related findings like an increase in the fraction of inactive proteins, a significant rise in protein half-life, an increase in the amount of damaged mitochondria, and a drop in the energy generation per mitochondrion, but they also show interactions between the different theories which could not have been observed without the network approach. In some simulations, for example, the mechanism of the final breakdown seems to be a consequence of the cooperation of mitochondrial and cytoplasmic reactions, the mitochondria being responsible for a long term, gradual change which eventually triggers a short lived cytoplasmic error loop.

Aging and oxidative stress: modulation by dietary restriction

Aging is an inevitable biological process that affects most living organisms. Despite the enormous consequences associated with the aging process, until recently, relatively little systematic effort has been expended on the scientific understanding of this important life process. Society, however, urged by an ever increasing older population, is challenging scientists from many disciplines to explore one of nature's most complex phenomena-biological aging. For the past two decades, research directed toward the basic understanding of biological aging mechanisms and possible aging interventions have given us new insights into the molecular bases and the biological events that contribute to age-related deterioration. To further investigate the aging processes, one probe uniquely suited to exploring the progression of aging in animal models is dietary restriction, currently the only antiaging intervention accepted by gerontologists and nutritionists. Recent research renders a better understanding of how reduced dietary intake extends the life span, supplying evidence that dietary restriction is a diverse and effective modulator of oxidative stress. It has been proposed that this antioxidative mechanism is the underlying anti-aging action of dietary restriction.

Kinetic modelling of in vitro lipid peroxidation experiments--'low level' validation of a model of in vivo lipid peroxidation

Kinetic modelling overcomes some of the drawbacks of purely intuitive thinking in integrating information accumulated on chemical reactions involved in oxidative stress. However, it is important to assess if current knowledge about the reactions that mediate lipid peroxidation already allows satisfactory modelling of this process in near-to-physiological conditions. In this paper, a set of increasingly complex in vitro experiments on antioxidants (alpha-tocopherol and ascorbate) and lipid peroxidation in heterogeneous systems is simulated. Quantitative to semiquantitative agreement is found between experimental and simulation results. In addition, this theoretical analysis provided useful insights, suggested new hypotheses and experiments and pointed out relevant aspects needing further research. The results encourage and serve as partial validation for the formulation of relatively detailed mathematical models of in vivo lipid peroxidation. Some important aspects of the formulation and analysis of such models are discussed.

Inherited stress resistance and longevity: a stress theory of ageing

Ageing is considered in the context of the abiotic stresses to which free-living organisms are normally exposed. Assuming that the primary target of selection of stress is at the level of energy carriers, trade-offs under the rate-of-living theory of ageing predict increased longevity from selection for stress resistance. Changes in longevity then become incidental to selection for stress resistance. I therefore suggest the reformulation of the rate-of-living theory to become a stress theory of ageing. This directly incorporates the characteristics of habitats in nature. Under this theory, the primary trait inherited is resistance to stress. Consequently, at extreme ages those with inherited resistance to abiotic stress should dominate. Furthermore, the reduction in homeostasis manifested by deteriorating ability to adapt to abiotic stress as ageing proceeds, should be slowest in those surviving longest.

Understanding the biology of aging: the key to prevention and therapy

OBJECTIVE

To review recent progress and consider future approaches for basic research on aging with clinical applicability.

DATA SOURCES

Peer-reviewed publications on experimental gerontology and geriatrics.

STUDY SELECTION AND DATA EXTRACTION

Studies were selected that described experimental approaches in gerontology and geriatrics, starting with the evolutionary basis of aging, through theories trying to explain its major causes, to novel experimental approaches, e.g., computer informatics, protein chemistry and genetics.

DATA SYNTHESIS

Our increased understanding of the evolutionary basis of aging has made it possible to consider a number of experimental strategies more rationally. Most theories on the causes of aging involve some kind of somatic damage that accumulates with age, the rate of which is determined by environmental, genetic, and behavioral factors. The recent emergence of more powerful methodology offers new possibilities for identifying basic mechanisms of aging, which would increase our understanding of biologically based susceptibility to age-related health problems.

CONCLUSIONS

There is a growing awareness that age-related deterioration will affect an ever growing number of people, in both absolute and relative terms. It can be expected that this will further increase the resources that will be made available for research on aging. Although ultimately unavoidable, aging is a process that appears to be experimentally accessible. Therefore, the mechanisms of senescence and death may eventually be more completely understood, with the promise of preventing and/or delaying many of the adverse effects associated with aging, including most of the common diseases, and possibly also of extending lifespan.

Comparative biochemical and stress analysis of genetically selected Drosophila strains with different longevities

We have performed a comparative analysis of the effects of age of reproduction on the biochemical (protein, lipid, and glycogen content) and stress resistance (ability to survive starvation, desiccation, and exogenous paraquat) parameters on 10 sister lines of five different Drosophila strains. Four pairs of these sister lines were selected under different regimens for either early or delayed reproduction; the fifth pair was maintained in a nonselected state and served as the baseline strain to which all others were compared. It is generally accepted that the early regimens give rise to short-lived phenotypes, whereas the delayed regimens give rise to long-lived phenotypes. Our results suggest that a mechanism involving lipid and starvation resistance is not operative in our long-lived strains. In addition, a mechanism involving glycogen content and desiccation resistance is only weakly supported. Finally, there is strong support for a mechanism that gives rise to enhanced paraquat resistance and therefore may involve regulatory changes in the pattern of ADS gene expression. In addition, the 15-day early age of reproduction regimen (M type) shows qualitatively similar responses to that of the late age at reproduction regimen (L type). These results suggest that correlations between biochemical traits and longevity must be interpreted with caution. We discuss possible reasons for these results, including the possibility of multiple mechanisms, each leading to a different extended longevity phenotype.