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

Biochemical integration of blood redox state in captive zebra finches (Taeniopygia guttata)

Integration is a property of biological systems that refers to the extent to which their components are correlated through functional, structural, developmental or evolutionary interdependency. This study examined patterns of functional integration among different molecular components of the blood redox system (both plasma and red blood cells) in zebra finches (Taeniopygia guttata). Our results show a two cluster organization of the six measured variables: one cluster includes glutathione peroxidase in both red blood cells and plasma, thiol concentration in red blood cells and plasma hydroperoxides; the other cluster comprises a measure of the non-enzymatic antioxidant capacity in red blood cells and plasma. The interaction network amongst these variables shows (i) a strong positive connectivity among hydroperoxides, glutathione peroxidase and thiols, and (ii) negative connectivity between non-enzymatic and enzymatic antioxidants. Overall, our results also suggest strong and significant integration between the oxidative state of red blood cells and plasma.

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.

Correlation analysis confirms differences in antioxidant defence in the blood of types I and II schizophrenic male patients treated with anti-psychotic medication

The activities of antioxidant defence enzymes were determined in erythrocytes isolated from types I and II schizophrenic male patients and from healthy controls. Significant differences in superoxide dismutase (SOD) activity (type I: 3284+/-577; type II: 2959+/-697 compared with controls: 3778+/-577; analysis of variance (ANOVA) P<0.001), catalase (CAT) activity (type I: 17.8+/-1.8 compared to type II: 19.2+/-1.5 and both compared with controls: 19.2+/-1.5; ANOVA P<0.05), glutathione peroxidase (GSH-Px) activity (controls: 17.8+/-2.3; type I: 13.9+/-2.9 and type II: 11.6+/-1.9; ANOVA P<0.001) as well as in glutathione reductase (GR) activity (controls: 5,0+/-0.8; type I: 4.3+/-0.9 and type II: 4.5+/-0.8; ANOVA P<0.01) were apparent. Correlation analysis of antioxidant defence enzymes showed significant negative correlation between GSH-Px and CAT activities (P<0.01) in type I patients. In type II patients, GSH-Px activity was significantly positively correlated with GR (P<0.01). Canonical discriminant analysis separated type I and type II patients from controls (and among each other) with a high degree of certainty according to the overall group composition of antioxidant defence enzymes. Our results indicate differences in the composition of antioxidant defence between controls and anti-psychotic treated type I and type II patients with a possible negative feedback influence on the pathological process, which could provide a rationale for applying antioxidants during schizophrenic therapy.

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.

Network strategies to understand the aging process and help age-related drug design

Recent studies have demonstrated that network approaches are highly appropriate tools for understanding the extreme complexity of the aging process. Moreover, the generality of the network concept helps to define and study the aging of technological and social networks and ecosystems, which may generate novel concepts for curing age-related diseases. The current review focuses on the role of protein-protein interaction networks (inter-actomes) in aging. Hubs and inter-modular elements of both interactomes and signaling networks are key regulators of the aging process. Aging induces an increase in the permeability of several cellular compartments, such as the cell nucleus, introducing gross changes in the representation of network structures. The large overlap between aging genes and genes of age-related major diseases makes drugs that aid healthy aging promising candidates for the prevention and treatment of age-related diseases, such as cancer, atherosclerosis, diabetes and neurodegenerative disorders. We also discuss a number of possible research options to further explore the potential of the network concept in this important field, and show that multi-target drugs (representing 'magic-buckshots' instead of the traditional 'magic bullets') may become an especially useful class of age-related drugs in the future.

Disease-aging network reveals significant roles of aging genes in connecting genetic diseases

One of the challenging problems in biology and medicine is exploring the underlying mechanisms of genetic diseases. Recent studies suggest that the relationship between genetic diseases and the aging process is important in understanding the molecular mechanisms of complex diseases. Although some intricate associations have been investigated for a long time, the studies are still in their early stages. In this paper, we construct a human disease-aging network to study the relationship among aging genes and genetic disease genes. Specifically, we integrate human protein-protein interactions (PPIs), disease-gene associations, aging-gene associations, and physiological system-based genetic disease classification information in a single graph-theoretic framework and find that (1) human disease genes are much closer to aging genes than expected by chance; and (2) diseases can be categorized into two types according to their relationships with aging. Type I diseases have their genes significantly close to aging genes, while type II diseases do not. Furthermore, we examine the topological characters of the disease-aging network from a systems perspective. Theoretical results reveal that the genes of type I diseases are in a central position of a PPI network while type II are not; (3) more importantly, we define an asymmetric closeness based on the PPI network to describe relationships between diseases, and find that aging genes make a significant contribution to associations among diseases, especially among type I diseases. In conclusion, the network-based study provides not only evidence for the intricate relationship between the aging process and genetic diseases, but also biological implications for prying into the nature of human diseases.

Toward a systems biology framework for understanding aging and health span

It is argued that aging research is at a stage where it could benefit greatly from a more intense engagement with the perspectives emphasized by systems biology and complexity science. A more integrated, systematic approach is needed if we are ever to have a fully developed, fundamental understanding of aging, longevity, and their relationship to health. A broader, deeper, more quantitative, and predictive conceptual framework can lead to theoretical approaches and realistic models that can be quantitatively confronted with data and, perhaps more importantly, stimulate novel questions and novel experiments. Integral to this is the search for underlying causal multilevel mechanisms and principles that can be quantified and developed into a serious predictive theoretical framework, providing a point of departure for framing a more integrated research agenda.

The genetics of ageing: insight from genome-wide approaches in invertebrate model organisms

Intense effort has been directed at understanding pathways modulating ageing in invertebrate model organisms. Prior to this decade, several longevity genes had been identified in flies, worms and yeast. More recently, with the development of RNAi libraries in worms and the yeast open reading frame (ORF) deletion collection, it has become routine to perform genome-wide screens for phenotypes of interest. A number of worm screens have now been performed to identify genes whose reduced expression leads to longer lifespan, and two ORF deletion longevity screens have been performed in yeast. Interestingly, these screens have linked previously unidentified cellular pathways to invertebrate ageing. More surprising, however, is the sheer number of longevity genes in worms and yeast. In this review, I discuss data from genome-wide screens in the context of evolutionary theories of ageing and raise issues regarding the increasing complexity associated with the genetics of longevity.

Systems approaches to the networks of aging

The aging of an organism is the result of complex changes in structure and function of molecules, cells, tissues, and whole body systems. To increase our understanding of how aging works, we have to analyze and integrate quantitative evidence from multiple levels of biological organization. Here, we define a broader conceptual framework for a quantitative, computational systems biology approach to aging. Initially, we consider fractal supply networks that give rise to scaling laws relating body mass, metabolism and lifespan. This approach provides a top-down view of constrained cellular processes. Concomitantly, multi-omics data generation build such a framework from the bottom-up, using modeling strategies to identify key pathways and their physiological capacity. Multiscale spatio-temporal representations finally connect molecular processes with structural organization. As aging manifests on a systems level, it emerges as a highly networked process regulated through feedback loops between levels of biological organization.

Oxidative stress, accumulation of biological 'garbage', and aging

Normal metabolism is associated with unavoidable mild oxidative stress resulting in biomolecular damage that cannot be totally repaired or removed by cellular degradative systems, including lysosomes, proteasomes, and cytosolic and mitochondrial proteases. Consequently, irreversibly damaged and functionally defective structures (biological 'garbage') accumulate within long-lived postmitotic cells, such as cardiac myocytes and neurons, leading to progressive loss of adaptability and increased probability of death and characterizing a process called aging, or senescence. Intralysosomal 'garbage' is represented by lipofuscin (age pigment), an undegradable autophagocytosed material, while extralysosomal 'garbage' involves oxidatively modified cytosolic proteins, altered biomembranes, defective mitochondria and other organelles. In aged postmitotic cells, heavily lipofuscin-loaded lysosomes perform poorly, resulting in the enhanced accumulation of defective mitochondria, which in turn produce more reactive oxygen species causing additional damage (the mitochondrial-lysosomal axis theory). Potential anti-aging strategies may involve not only overall reduction of oxidative stress, but also the use of intralysosomal iron chelators hampering Fenton-type chemistry as well as the stimulation of cellular degradative systems.

A life-history perspective on short- and long-term consequences of compensatory growth

Compensatory or catch-up growth (CG) is widely observed following periods of resource deprivation. Because of this commonness, it is generally assumed that compensatory growth is adaptive, but most theory to date has explicitly ignored considerations of fitness. Following a period of deprivation, when resources become plentiful again, individuals may not respond at all and continue on a "normal" trajectory from a smaller size at age, may exhibit faster-than-normal growth immediately following the end of the period, or may adopt a growth strategy that involves faster-than-normal growth at some later time. Compensating individuals may also overtake control individuals who have been growing normally throughout. We hypothesize that the key to understanding CG is that growth leads to the accumulation of damage at the cellular level that is expressed (and thus must be modeled) at the level of the organism. We show that a life-history model incorporating the mortality consequences of both size and damage provides a framework for understanding compensatory growth. We use the theory to classify physiological and life-history characteristics for which CG is predicted to be the optimal response to deprivation.

Understanding and modulating ageing

Ageing is characterized by a progressive accumulation of molecular damage in nucleic acids, proteins and lipids. The inefficiency and failure of maintenance, repair and turnover pathways is the main cause of age-related accumulation of damage. Research in molecular gerontology is aimed at understanding the genetic and epigenetic regulation of survival and maintenance mechanisms at the levels of transcription, post-transcriptional processing, post-translational modifications, and interactions among various gene products. Concurrently, several approaches are being tried and tested to modulate ageing in a wide variety of organisms. The ultimate aim of such studies is to improve the quality of human life in old age and prolong the health-span. Various gerontomodulatory approaches include gene therapy, hormonal supplementation, nutritional modulation and intervention by free radical scavengers and other molecules. A recent approach is that of applying hormesis in ageing research and therapy, which is based on the principle of stimulation of maintenance and repair pathways by repeated exposure to mild stress. A combination of molecular, physiological and psychological modulatory approaches can realize "healthy ageing" as an achievable goal in the not-so-distant future.

Understanding the odd science of aging

Evolutionary considerations suggest aging is caused not by active gene programming but by evolved limitations in somatic maintenance, resulting in a build-up of damage. Ecological factors such as hazard rates and food availability influence the trade-offs between investing in growth, reproduction, and somatic survival, explaining why species evolved different life spans and why aging rate can sometimes be altered, for example, by dietary restriction. To understand the cell and molecular basis of aging is to unravel the multiplicity of mechanisms causing damage to accumulate and the complex array of systems working to keep damage at bay.

Imminent approaches towards molecular interventions in ageing

Ageing is an innate feature of living organisms. Sensational progress in its molecular understanding in the last decade has culminated into a highly complex picture. Emerging from this complexity are the distinctive roles of some of the tumor suppressor pathways including p53 and pRB in maintenance of senescence phenotype, and telomere maintaining pathways in its escape. We discuss here the current scenario of molecular ageing and the use of modern approaches for its intervention in culture system, at least. Many of the tools we describe here are the newly emergent functional RNA tools that are proved to be fruitful in decoding the human genome. These post-genomic technologies will help us in the discovery of gene targets for interventions aiming to improve the quality at later years of life beyond their mere algebraic extension.

Aging as a catabolic malfunction

Cellular degradative processes, which include lysosomal (autophagic) and proteasomal degradation, as well as catabolism of proteins by cytosolic and mitochondrial proteases, provide for a continuous turnover of cellular components, such as damaged or obsolete biomolecules and organelles. Inherent insufficiency of these degradative processes results in progressive accumulation within long-lived postmitotic cells of biological 'garbage' (waste material), such as various oxidized proteins, functionally effete mitochondria, and lipofuscin (age pigment), an intralysosomal, polymeric, undegradable material. There is increasing evidence that lipofuscin hampers lysosomal degradative capacity, thus promoting the aggravation of accumulated damage at old age. Being rich in redox-active iron, lipofuscin granules also may exacerbate oxidative stress levels in senescent cells. Thus, increasing the efficiency of cellular degradative pathways and preventing involvement of iron in oxidant-induced lysosomal and cellular damage may be potential strategies for anti-aging interventions.

Protein networks, pleiotropy and the evolution of senescence

The number of interactions, or connectivity, among proteins in the yeast protein interaction network follows a power law. I compare patterns of connectivity for subsets of yeast proteins associated with senescence and with five other traits. I find that proteins associated with ageing have significantly higher connectivity than expected by chance, a pattern not seen for most other datasets. The pattern holds even when controlling for other factors also associated with connectivity, such as localization of protein expression within the cell. I suggest that these observations are consistent with the antagonistic pleiotropy theory for the evolution of senescence. In further support of this argument, I find that a protein's connectivity is positively correlated with the number of traits it influences or its degree of pleiotropy, and further show that the average degree of pleiotropy is greatest for proteins associated with senescence. I explain these results with a simple mathematical model combining assumptions of the antagonistic pleiotropy theory for the evolution of senescence with data on network topology. These findings integrate molecular and evolutionary models of senescence, and should aid in the search for new ageing genes.

The shape of things to come: using models with physiological structure to predict mortality trajectories

If mortality rate is viewed as the outcome of processes of behavior, growth and reproduction, then it should be possible to predict mortality rate as a result of those processes. We provide two examples of how this may be done. In the first, we use the method of linear chains to treat mortality that is the result of multiple physiological processes, some of which may have delays. In the second, we assume that mortality is the result of damage associated with growth and metabolism. Both approaches lead to a rich diversity of predicted mortality trajectories. Although many of these look Gompertzian at young ages, the behavior at older ages depends upon the details of the physiological models.

To age or not to age

According to the antagonistic pleiotropy theory of ageing, natural selection has favoured genes conferring short-term benefits to the organism at the cost of deterioration in later life. The 'disposable soma' theory expresses this as a life-history strategy in which somatic maintenance is below the level required to prevent ageing, thus enabling higher immediate fertility. It has been argued that a non-ageing strategy will always be bettered by a low but non-zero rate of ageing, because the costs of such ageing will be felt only in the distant future when they are of negligible importance. Here, we examine this argument critically. We find that a non-ageing strategy will be locally optimal if, in the presence of ageing, the onset of deterioration is sufficiently rapid or early. Conversely, ageing will be optimal if deterioration is sufficiently slow or late. As the temporal profile of ageing changes from one of steady deterioration to one involving a sudden loss of vitality after a period of little or no decline, the conditions for a non-ageing strategy to be locally optimal become progressively more stringent. But for all forms of profile considered, conditions can be found for which a strategy involving no ageing is locally optimal.

Germ-line versus somatic cells. I. Stereological study of differentiating embryonic tissues of Tetrodontophora bielanensis (Hexapoda, Collembola)

We examined five different somatic tissues and compared them with germ-line cells to verify the "disposable soma" theory. Two embryonic stages and second-stage juveniles of Tetrodontophora bielanensis Waga, 1842 (Hexapoda, Collembola) were studied. Our results show that changes in relative volume of mitochondria during differentiation of cells correlate well with transformations of cell morphology. During morphological transformation of differentiating somatic cells, the relative volume of mitochondria in their cytoplasm is high, whereas in the differentiated tissues, this parameter is much lower. Surprisingly, the highest value of relative volume density of mitochondria is found in the cytoplasm of germ-line cells. If we accept that this parameter indicates the cell metabolism rate, then our results should be taken as supporting the "disposable soma" theory. It is also conceivable that the higher volume of mitochondria in the germ-line cells have nothing to do with energy production but, for instance, with the production or function of nuage material (germ-cell determinant) in the germ-line cells. These two possibilities are discussed.

A unifying view of ageing and disease: the double-agent theory

The quest for therapies based on molecular genetics (pharmacogenomics, DNA microarrays, etc.) drives pharmaceutical research into individual diseases of old age, but has failed to deliver an unequivocal clinical breakthrough. Attempts to treat most age-related diseases using antioxidant supplements have been equally disappointing, despite the clear benefits of a healthy diet. The double-agent theory is a new, unifying synthesis that draws on flaws in three leading theories of ageing. It argues that there is a tradeoff between oxidative stress as a critical redox signal that marshals genetic defences against physiological stress (such as infection) and oxidative stress as a cause of ageing and age-related disease. The stress response and ageing are linked by redox-sensitive transcription factors, such as NFkappaB. Ageing is a function of rising intracellular oxidative stress, rather than chronological time, but this relationship is obscured because free-radical leakage from mitochondria also tends to rise with age. Mitochondrial leakage produces a genetic response which mirrors that following infection, but because mitochondrial leakage is continuous the shift in gene expression is persistent, leading to the chronic inflammation characteristic of old age. Age-related diseases are thus the price we pay for redox control of stress-gene expression. Because the selective pressure favouring the stress response in youth is stronger than that penalising degenerative diseases after reproductive decline, we may be homeostatically refractory to antioxidant supplements that 'swamp' the redox switch. Furthermore, because genetic selection takes place predominantly in the reductive homeostatic environment of youth, alleles associated with age-related diseases are not inherently damaging (they do not inevitably express a negative effect over time), but are simply less effective in the oxidising conditions of old age. Gene therapies for age-related diseases are unlikely to succeed unless oxidative stress can be controlled physiologically, thereby altering the activity and function of potentially hundreds of genes.

Invited review: Theories of aging

Several factors (the lengthening of the average and, to a lesser extent, of the maximum human life span; the increase in percentage of elderly in the population and in the proportion of the national expenditure utilized by the elderly) have stimulated and continue to expand the study of aging. Recently, the view of aging as an extremely complex multifactorial process has replaced the earlier search for a distinct cause such as a single gene or the decline of a key body system. This minireview keeps in mind the multiplicity of mechanisms regulating aging; examines them at the molecular, cellular, and systemic levels; and explores the possibility of interactions at these three levels. The heterogeneity of the aging phenotype among individuals of the same species and differences in longevity among species underline the contribution of both genetic and environmental factors in shaping the life span. Thus, the presence of several trajectories of the life span, from incidence of disease and disability to absence of pathology and persistence of function, suggest that it is possible to experimentally (e.g., by calorie restriction) prolong functional plasticity and life span. In this minireview, several theories are identified only briefly; a few (evolutionary, gene regulation, cellular senescence, free radical, and neuro-endocrineimmuno theories) are discussed in more detail, at molecular, cellular, and systemic levels.

Age-dependent generation of reactive oxygen species in the skin of live hairless rats exposed to UVA light

Aging proceeds by highly complicated biochemical processes, in which the involvement of the reactive oxygen species (ROS) and free radicals has been implicated. Although the relationship between UV-induced photoaging and ROS generation has been proposed, it has been difficult to establish direct proof of the generation of ROS in the skin under UV exposure. Recently, we reported finding endogenously generated ROS in the skin of live mice after UVA light exposure by a method of in vivo chemiluminescent detection, in which superoxide anion radical (*O2-) and singlet oxygen species (1O2) are contributed. In light of the results, we tried to understand the age-dependent changes in ROS generation in the skin of hairless rats under UVA exposure. Chemiluminescent levels due to ROS in the untreated and UVA-exposed skin decreased age dependently, and the signal intensities in old rats were significantly lower than those in young rats. However, the ratios of chemiluminescent intensities in the UVA-exposed skin to those in the untreated skin were significantly enhanced in an age-dependent manner. These results suggest that the antioxidative ability against ROS generation in the skin, possessed by antioxidant enzymes and low molecular weight antioxidants, is lowered age dependently.

Respiratory oscillations in yeast: mitochondrial reactive oxygen species, apoptosis and time; a hypothesis

Oscillatory metabolic activities occur more widely than is generally realised; detectability requires observation over extended times of single yeast cells or synchrony of individuals to provide a coherent population. Where oscillations in intracellular metabolite concentrations are observed, the phenomenon has been ascribed to sloppy control, energetic optimisation, signalling, temporal compartmentation of incompatible reactions, or timekeeping functions. Here we emphasise the consequences of respiratory oscillations as a source of mitochondrially generated reactive O(2) metabolites. Temporal co-ordination of intracellular activities necessitates a time base. This is provided by an ultradian clock, and one result of its long-term operation is cyclic energisation of mitochondria, and thereby the generation of deleterious free radical species. Our hypothesis is that unrepaired cellular constituents and components (especially mitochondria) eventually lead to cellular senescence and apoptosis when a finite number of respiratory cycles has occurred.

Augmented discounting: interaction between ageing and time-preference behaviour

Discounting occurs when an immediate benefit is systematically valued more highly than a delayed benefit of the same magnitude. It is manifested in physiological and behavioural strategies of organisms. This study brings together life-history theory and time-preference theory within a single modelling framework. We consider an animal encountering reproductive opportunities as a random process. Under an external hazard, optimal life-history strategy typically prioritizes immediate reproduction at the cost of declining fertility and increasing mortality with age. Given such ageing, an immediate reproductive reward should be preferred to a delayed reward because of both the risk of death and declining fertility. By this analysis, ageing is both a consequence of discounting by the body and a cause of behavioural discounting. A series of models is developed, making different assumptions about external hazards and biological ageing. With realistic ageing assumptions (increasing mortality and an accelerating rate of fertility decline) the time-preference rate increases in old age. Under an uncertain external hazard rate, young adults should also have relatively high time-preference rates because their (Bayesian) estimate of the external hazard is high. Middle-aged animals may therefore be the most long term in their outlook.

Age, diet and injury affect the survival of facial motoneurons

Using the model of facial nerve avulsion, we have compared the effects of injury, age and diet on motoneuronal survival. One to four weeks after nerve avulsion, 50-75% motoneuron loss was quantified in ad libitum-fed rats aged 7 days (neonate), 6 months (adult) and 24 months (aging) at the time of injury. Evidence of apoptosis was found for neonatal rats at 3 days post-injury, but not for neonates examined 7 days or adult or aging rats examined 1 month after injury. Non-operated, ad libitum-fed rats showed no significant loss of facial motoneurons by 24 months. Surprisingly, non-operated rats whose food intake was restricted to 15 g standard rat chow per day from the age of 6 months lost 50% of their motoneurons by 24 months. Facial nerve avulsion of 24-month-old rats raised on this restricted diet did not result in any additional loss of motoneurons one month after injury. These results challenge the common view that aging results in neuronal loss and that dietary restriction is universally beneficial.

Towards an e-biology of ageing: integrating theory and data

Ageing is a highly complex process; it involves interactions between numerous biochemical and cellular mechanisms that affect many tissues in an organism. Although work on the biology of ageing is now advancing quickly, this inherent complexity means that information remains highly fragmented. We describe how a new web-based modelling initiative is seeking to integrate data and hypotheses from diverse biological sources.

Somatic mutations and ageing in silico

Considerable evidence points to an accumulation of somatic mutations in older cells and organisms but the causal role of mutations in the ageing process is still unclear. In addition to demonstrating that mutations accumulate, it is important to address the question of whether they do so at a sufficient rate and with a dynamic profile that is consistent with them playing a causative role. We describe the development of in silico models that can be used to explore the role of somatic mutations in ageing and which form a part of a growing effort to build predictive mathematical and computer models that can help unravel the complexity of the functional genomics of ageing. Our models address, in particular, how mutations affect populations of dividing cells like human fibroblasts, in which the challenge to the somatic mutation theory is greatest, since selection at the cellular level will tend to suppress the accumulation of mutations.

Iron as the malignant spirit in successful ageing

Iron enhances the production of the highly reactive and toxic hydroxyl radical, thus stimulating oxidative damage. Iron has been associated with a number of oxidative injury-dependent, age-related conditions and diseases. Indeed, oxidative injury is a major factor of (accelerated) ageing. This commentary reviews part of the existing literature on iron's deleterious effects, particularly in the context of ischemia-reperfusion injury and cardiovascular, brain and muscle diseases as well as skin ageing. Furthermore, the advantages of iron chelation are presented. Indeed, iron chelation or deprivation has been shown to act as a potent anti-oxidant in a variety of animal models of human diseases, preventing oxidative stress to tissues and organs. Iron chelators favor successful ageing in general, and when applied topically, successful skin ageing. It has also been proposed that gender-related differences in iron status are responsible for the increased longevity of women as compared to men. Despite this evidence, the role of iron in ageing and the possibilities of pharmacologically targeting iron have remained essentially unexplored. Iron thus appears as the "malignant spirit" in successful ageing.

Association of the longevity-associated mitochondrial DNA 5178 A/C polymorphism with serum protein fraction levels in healthy Japanese women

Mitochondrial DNA 5178 adenine/cytosine (mt5178 A/C) polymorphism was reported to be associated with longevity and susceptibility to adult-onset diseases in Japanese. To examine whether mt5178 A/C genotypes are associated with serum protein fraction profiles, we genotyped 461 healthy Japanese individuals, and studied the relationship of mt5178 A/C genotypes to both proportion and levels of serum protein fraction. The mt5178 A/C was genotyped using polymerase chain reaction-restriction fragment length polymorphism method. The alpha-1, alpha-2, and beta globulin proportions in females carrying mt5178A were significantly higher than those in females carrying mt5178C (P=0.002, 0.006, and 0.008, respectively). Moreover, the alpha-1, alpha-2, and beta globulin levels in females carrying mt5178A were significantly higher than those in females carrying mt5178C (P=0.001, 0.002, 0.018, respectively). This difference in globulin fraction level between the two genotypes was more evident in premenopausal females than in postmenopausal females. However, no such difference was found in males. These results provide the first evidence that the mt5178 A/C polymorphism may influence the serum protein fraction levels of the healthy Japanese women.

The Institute for Ageing and Health, University of Newcastle, UK

The Institute For Ageing And Health (IAH) is the largest cross-disciplinary research grouping within Newcastle University's Faculty of Medicine, which recently obtained the highest 5 or 5* ratings in all fields evaluated in the UK Research Assessment Exercise 2001. The IAH was set up in 1994 to bring together clinical, basic and social scientists in partnership with colleagues in the National Health Service. It builds upon a long tradition of outstanding clinical research on age-related disorders, particularly in the field of dementia where the pioneering studies of Tomlinson and Roth in the 1960s first showed Alzheimer's disease to be the commonest cause of cognitive decline in later life. The clinical research of the IAH now extends to both neurodegenerative and vascular dementia in a joint Medical Research Council-University Development for Clinical Brain Ageing, and to studies in many other areas including depression in later life, falls and neurovascular instability, stroke and ischaemic brain disease, and health services research on the medical and social care of older people. These diverse areas of clinical investigation are now complemented by strong research on the basic biology of ageing within the new Department of Gerontology with its programmes on the genetics of ageing and longevity; molecular mechanisms of cellular ageing, including oxidative stress, DNA damage and genomic instability, telomere reduction and regulation, mitochondrial DNA mutations, and accumulation of aberrant proteins; and theoretical models of the ageing process. An ambitious strategy for future research on ageing and age-related disorders is based on the synergy between these complementary approaches.

Molecular gerontology

Evolutionary theory and empirical evidence from many lines of research suggest that ageing is a process of gradual accumulation of damage in cells and tissues of the body, leading eventually to frailty and increased risk from a spectrum of age-associated diseases. There are multiple kinds of damage that affect cells, ranging from mutations in DNA to oxidative attack on proteins by chemical by-products of normal cellular metabolism. In some ways the surprising thing is not that we age, but that we live as long as we do. The key to understanding longevity lies in the network of cell maintenance systems that cooperate to slow the accumulation of damage. Research has shown that long-lived species carry out cellular maintenance better than short-lived species, suggesting that enhancement of the body's natural maintenance systems may postpone aspects of ageing. Recognition that ageing results from accumulation of damage also points to a role for lifestyle interventions (e.g. nutrition and exercise) to help prevent damage or promote repair.

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.

A stochastic model of cell replicative senescence based on telomere shortening, oxidative stress, and somatic mutations in nuclear and mitochondrial DNA

Human diploid fibroblast cells can divide for only a limited number of times in vitro, a phenomenon known as replicative senescence or the Hayflick limit. Variability in doubling potential is observed within a clone of cells, and between two sister cells arising from a single mitotic division. This strongly suggests that the process by which cells become senescent is intrinsically stochastic. Among the various biochemical mechanisms that have been proposed to explain replicative senescence, particular interest has been focussed on the role of telomere reduction. In the absence of telomerase--an enzyme switched off in normal diploid fibro-blasts-cells lose telomeric DNA at each cell division. According to the telomere hypothesis of cell senescence, cells eventually reach a critically short telomere length and cell cycle arrest follows. In support of this concept, forced expression of telomerase in normal fibroblasts appears to prevent cell senescence. Nevertheless, the telomere hypothesis in its basic form has some difficulty in explaining the marked stochastic variations seen in the replicative lifespans of individual cells within a culture, and there is strong empirical and theoretical support for the concept that other kinds of damage may contribute to cellular ageing. We describe a stochastic network model of cell senescence in which a primary role is played by telomere reduction but in which other mechanisms (oxidative stress linked particularly to mitochondrial damage, and nuclear somatic mutations) also contribute. The model gives simulation results that are in good agreement with published data on intra-clonal variability in cell doubling potential and permits an analysis of how the various elements of the stochastic network interact. Such integrative models may aid in developing new experimental approaches aimed at unravelling the intrinsic complexity of the mechanisms contributing to human cell ageing.

Garbage catastrophe theory of aging: imperfect removal of oxidative damage?

Increasing evidence suggests an important role of oxidant-induced damage in the progress of senescent changes, providing support for the free radical theory of aging proposed by Harman in 1956. However, considering that biological organisms continuously renew their structures, it is not clear why oxidative damage should accumulate with age. No strong evidence has been provided in favor of the concept of aging as an accumulation of synthetic errors (e.g. Orgel's 'error-catastrophe' theory and the somatic mutation theory). Rather, we believe that the process of aging may derive from imperfect clearance of oxidatively damaged, relatively indigestible material, the accumulation of which further hinders cellular catabolic and anabolic functions. From this perspective, it might be predicted that: (i) suppression of oxidative damage would enhance longevity; (ii) accumulation of incompletely digested material (e.g. lipofuscin pigment) would interfere with cellular functions and increase probability of death; (iii) rejuvenation during reproduction is mainly provided by dilution of undigested material associated with intensive growth of the developing organism; and (iv) age-related damage starts to accumulate substantially when development is complete, and mainly affects postmitotic, cells and extracellular matrix, not proliferating cells. There is abundant support for all these predictions.

Stress, DNA damage and ageing -- an integrative approach

Ageing is highly complex, involving multiple mechanisms at different levels. Nevertheless, recent evidence suggests that several of the most important mechanisms are linked via endogenous stress-induced DNA damage caused by reactive oxygen species (ROS). Understanding how such damage contributes to age-related changes requires that we explain how these different mechanisms relate to each other and potentially interact. In this article, we review the contributions of stress-induced damage to cellular DNA through (i) the role of damage to nuclear DNA and its repair mediated via the actions of poly(ADP-ribose) polymerase-1, (ii) the role of damage to telomeric DNA and its contribution to telomere-driven cell senescence, and (iii) the role of damage to and the accumulation of mutations in mitochondrial DNA. We describe how an integrative approach to studying these mechanisms, coupled with computational modelling, may be of considerable importance in resolving some of the complexity of cellular ageing.

Coenzymes Q9 and Q10, vitamin E and peroxidation in rat synaptic and non-synaptic occipital cerebral cortex mitochondria during ageing

Great attention has been devoted both to ageing phenomena at the mitochondrial level and to the antioxidant status of membrane structures. These kinds of investigations are difficult to perform in the brain because of its heterogeneity. It is known that synaptic heavy mitochondria (HM) may represent an aged mitochondrial population characterized by a partial impairment of their typical mitochondrial function. We arranged a novel system requiring no extraction procedure, very limited handling of the samples and their direct injection into the HPLC apparatus, to carry out, for the first time, a systematic and concomitant determination of vitamin E, Coenzyme Q9 (CoQ9) and Coenzyme Q10 (CoQ10) contents in rat brain mitochondria. The trends found for CoQ9 and CoQ10 levels in synaptic and non-synaptic occipital cerebral cortex mitochondria during rat ageing are consistent with previous data. Hydroperoxides (HP) differed with age and it was confirmed that in the HM fraction the summation of contributions results in an oxidatively jeopardized subpopulation. We found that vitamin E seems to increase with age, at least in non-synaptic free (FM) and synaptic light (LM) mitochondria, while it was inclined to remain substantially constant in HM.

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.

Free radical induced inactivation of creatine kinase: sites of interaction, protection, and recovery

The study aims at a clarification of the oxidative damage of creatine kinase isoenzymes by X-ray-induced water radiolysis. The radical species generated by this method (under appropriate conditions) are similar to those discussed in the context of mitochondrial energy metabolism. The decay of the enzyme activity is accompanied by a strong decrease of the number of accessible SH groups and by a reduction of the endogenous tryptophan fluorescence. Free radical effects are diminished if irradiation is carried out in the presence of 2-mercaptoethanol. Partial recovery of the activity (repair) is observed if 2-mercaptoethanol is added after irradiation. The experiments suggest a twofold importance of thiol reagents (RSH): to reduce the concentration of free radicals by scavenger reactions and to modify the inactivation mechanism in such a way that efficient repair of enzyme damage may be achieved. Cysteine 282 of MM-CK (Cys-278 in the case of Mi-CK) seems to play a crucial role in this respect. Blockage of the SH group of cysteine 282 by oxidized glutathione effectively protects the enzyme against inactivation by NO(*)(2) radicals. In the absence of nitrogen dioxide and of thiol reagents, however, inactivation seems to proceed via a less specific mechanism involving additional targets of the enzyme.

For debate: defective mitochondria, free radicals, cell death, aging-reality or myth-ochondria?

As both experimental evidence and theoretical considerations may suggest that free radicals and mitochondria might be associated as key factors in aging, these organelles have been implicated in various versions of the free radical theory of aging. However, except for a few cases, no evidence for a death process specifically activated in respiratory defective cells could be found in patients with a mitochondrial disorder, including those harboring high levels of mutant mtDNA associated with profound respiratory chain deficiencies. This and more recent evidence suggest that damages produced by free-radicals endogenously generated in the mitochondria result in a distinctive biochemical profile, only occur under exceptional conditions and that a dysfunction of the respiratory chain does not cause opening of the permeability transition pore and is not sufficient per se to trigger massive entrance of cells into death processes, neither apoptosis nor necrosis. Therefore, defective mitochondria and their particular genome, should not be considered as a major and primary source of free radicals either leading cells into a death cascade or resulting in an accelerated aging process.

Mutation frequency and specificity with age in liver, bladder and brain of lacI transgenic mice

Mutation frequency and specificity were determined as a function of age in nuclear DNA from liver, bladder, and brain of Big Blue lacI transgenic mice aged 1.5-25 months. Mutations accumulated with age in liver and accumulated more rapidly in bladder. In the brain a small initial increase in mutation frequency was observed in young animals; however, no further increase was observed in adult mice. To investigate the origin of mutations, the mutational spectra for each tissue and age were determined. DNA sequence analysis of mutant lacI transgenes revealed no significant changes in mutational specificity in any tissue at any age. The spectra of mutations found in aging animals were identical to those in younger animals, suggesting that they originated from a common set of DNA lesions manifested during DNA replication. The data also indicated that there were no significant age-related mutational changes due to oxidative damage, or errors resulting from either changes in the fidelity of DNA polymerase or the efficiency of DNA repair. Hence, no evidence was found to support hypotheses that predict that oxidative damage or accumulation of errors in nuclear DNA contributes significantly to the aging process, at least in these three somatic tissues.

Cerebral oligaemia episode triggers free radical formation and late cognitive deficiencies

Sixty minutes of cerebral oligaemic hypoxia, induced by bilateral clamping of the carotid arteries (BCCA) in pentobarbital-anaesthetized normotensive rats, induces a late progressive cognitive decline when compared with sham-operated controls. Analysis at BCCA of hippocampal metabolism using microdialysis showed increased release of glutamate, aspartate and gamma-aminobutyric acid, followed by a progressive rise in the formation of hydroxyl free radicals measured as 2,3-dihydroxybenzoic acid (2,3-DHBA), their reaction product with salicylate, though only in the re-perfusion phase. In the striatum increased dopamine release occurred during BCCA, whereas glutamate and aspartate showed an increase only during the late re-perfusion phase. gamma-Aminobutyric acid (GABA) concentration increased during BCCA and early re-perfusion. An increase in 2,3-DHBA was seen during BCCA, and persisted over 2 h of re-perfusion. Six and 13 months after surgery, though not as early as 3 months, BCCA-treated rats perform worse than sham-operated controls in a water-maze, where decreased swimming speed reveals striatal dysfunction, while hippocampal dysfunction manifested as diminished spatial bias. These results show that cerebral oligaemia, similarly to cerebral ischaemia, leads to increased extracellular dopamine, aspartate and glutamate, and the production of hydroxyl radicals in structures associated with learning and memory processes. Unlike cerebral ischaemia, in cerebral oligaemia the appearance of spatial memory deficits is delayed.

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.

Altered levels of primary antioxidant enzymes in progeria skin fibroblasts

Free radicals are involved in the aging process. In this study, the profile of primary antioxidant enzymes that scavenge reactive oxygen species (ROS) was examined for the first time in human skin fibroblasts from progeria, a premature aging disease. Altered levels of antioxidant enzymes were found in progeria cells. Basal levels of MnSOD were decreased in progeria cells as well as a blunted induction in response to chronic stress. This change may contribute to the accelerated aging process in progeria cells. In contrast, the levels of CuZnSOD showed no progeria-related change. Two H2O2 removing enzymes demonstrated a significant reduction in progeria cells: only 50% of normal CAT activity and 30% of normal GPX activity can be detected in progeria cells. This diminished H2O2 removing capacity in progeria cells may lead to an imbalance of intracellular ROS and therefore may play an important role in the development of progeria.

Mitochondrial aging: open questions

Interest in the role of mitochondria in aging has intensified in recent years. This focus on mitochondria originated in part from the free radical theory of aging, which argues that oxidative damage plays a key role in degenerative senescence. Among the numerous mechanisms known to generate oxidants, leakage of the superoxide anion and hydrogen peroxide from the mitochondrial electron transport chain are of particular interest, due to the correlation between species-specific metabolic rate ("rate of living") and life span. Phenomenological studies of mitochondrial function long ago noted a decline in mitochondrial function with age, and on-going research continues to add to this body of knowledge. The extranuclear somatic mutation theory of aging proposes that the accumulation of mutations in the mitochondrial genome may be responsible in part for the mitochondrial phenomenology of aging. Recent studies of mitochondrial DNA (mtDNA) deletions have shown that they increase with age in humans and other mammals. Currently, there exist numerous important and fundamental questions surrounding mitochondria and aging. Among these are (1) How important are mitochondrial oxidants in determining overall cellular oxidative stress? (2) What are the mechanisms of mitochondrial oxidant generation? (3) How are lesions and mutations in mtDNA formed? (4) How important are mtDNA lesions and mutations in causing mitochondrial dysfunction? (5) How are mitochondria regulated, and how does this regulation change during aging? (6) What are the dynamics of mitochondrial turnover? (7) What is the relationship between mitochondrial damage and lipofuscinogenesis? (8) What are the relationships among mitochondria, apopotosis, and aging? and (9) How can mitochondrial function (ATP generation and the establishment of a membrane potential) and dysfunction (oxidant generation) be modulated and degenerative senescence thereby treated?

The free radical theory of aging matures

The free radical theory of aging, conceived in 1956, has turned 40 and is rapidly attracting the interest of the mainstream of biological research. From its origins in radiation biology, through a decade or so of dormancy and two decades of steady phenomenological research, it has attracted an increasing number of scientists from an expanding circle of fields. During the past decade, several lines of evidence have convinced a number of scientists that oxidants play an important role in aging. (For the sake of simplicity, we use the term oxidant to refer to all "reactive oxygen species," including O2-., H2O2, and .OH, even though the former often acts as a reductant and produces oxidants indirectly.) The pace and scope of research in the last few years have been particularly impressive and diverse. The only disadvantage of the current intellectual ferment is the difficulty in digesting the literature. Therefore, we have systematically reviewed the status of the free radical theory, by categorizing the literature in terms of the various types of experiments that have been performed. These include phenomenological measurements of age-associated oxidative stress, interspecies comparisons, dietary restriction, the manipulation of metabolic activity and oxygen tension, treatment with dietary and pharmacological antioxidants, in vitro senescence, classical and population genetics, molecular genetics, transgenic organisms, the study of human diseases of aging, epidemiological studies, and the ongoing elucidation of the role of active oxygen in biology.