Network theory of aging

Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with challenges to proteostasis

Chromatin instability and protein homeostasis (proteostasis) stress are two well-established hallmarks of aging, which have been considered largely independent of each other. Using microfluidics and single-cell imaging approaches, we observed that, during the replicative aging of Saccharomyces cerevisiae, a challenge to proteostasis occurs specifically in the fraction of cells with decreased stability within the ribosomal DNA (rDNA). A screen of 170 yeast RNA-binding proteins identified ribosomal RNA (rRNA)-binding proteins as the most enriched group that aggregate upon a decrease in rDNA stability induced by inhibition of a conserved lysine deacetylase Sir2. Further, loss of rDNA stability induces age-dependent aggregation of rRNA-binding proteins through aberrant overproduction of rRNAs. These aggregates contribute to age-induced proteostasis decline and limit cellular lifespan. Our findings reveal a mechanism underlying the interconnection between chromatin instability and proteostasis stress and highlight the importance of cell-to-cell variability in aging processes.

The role of nutrition in inflammaging

BACKGROUND

Old age is characterized by a peculiar low-grade, chronic, and "sterile" inflammatory state, which has been termed "inflammaging." This is believed to substantially contribute to the pathogenesis of many age-related diseases and to the progression of the ageing process. An adequate nutritional status is of great importance for maintaining proper immune system functionality and preventing frailty in the elderly.

METHODS

The purpose of this narrative review is to synthesize what is known about the interaction between inflammaging and nutrition, focusing on the role of the Mediterranean diet, gut microbiota and calorie restriction (CR) in reducing systemic inflammation and improving clinical outcomes.

CONCLUSIONS

Dietary components may affect inflammation directly, counteracting the low grade age-related inflammation. In this regard, healthy diets, including the Mediterranean diet, are associated with lower concentrations of inflammatory mediators, like C-reactive protein (CRP) and Tumor Necrosis Factor-α (TNF-α), that are hallmarks of inflammaging. Among the components of a healthy diet, a higher intake of whole grains, vegetables and fruits, nuts and fish are all associated with lower inflammation. One area of promising research is the microbiome-ageing interaction. Indeed, dysbiosis plays a role in sub-optimal metabolism, immune function and brain function and contributes to the poor health and impaired well-being associated with ageing. Modulation of the gut microbiota has shown promising results in some disorders. Additionally, the discovery of several molecular pathways associated with ageing, and the characterization of the beneficial effects of calorie restriction (CR) in modulating metabolic pathways and preventing inflammation, should encourage research on CR mimetics, drugs able to promote lifespan and extend healthspan.

Protein interaction potential landscapes for yeast replicative aging

We proposed a novel interaction potential landscape approach to map the systems-level profile changes of gene networks during replicative aging in Saccharomyces cerevisiae. This approach enabled us to apply quasi-potentials, the negative logarithm of the probabilities, to calibrate the elevation of the interaction landscapes with young cells as a reference state. Our approach detected opposite landscape changes based on protein abundances from transcript levels, especially for intra-essential gene interactions. We showed that essential proteins play different roles from hub proteins on the age-dependent interaction potential landscapes. We verified that hub proteins tend to avoid other hub proteins, but essential proteins prefer to interact with other essential proteins. Overall, we showed that the interaction potential landscape is promising for inferring network profile change during aging and that the essential hub proteins may play an important role in the uncoupling between protein and transcript levels during replicative aging.

Nutrition-Based Management of Inflammaging in CKD and Renal Replacement Therapies

Access to renal transplantation guarantees a substantial improvement in the clinical condition and quality of life (QoL) for end-stage renal disease (ESRD) patients. In recent years, a greater number of older patients starting renal replacement therapies (RRT) have shown the long-term impact of conservative therapies for advanced CKD and the consequences of the uremic milieu, with a frail clinical condition that impacts not only their survival but also limits their access to transplantation. This process, referred to as “inflammaging,” might be reversible with a tailored approach, such as RRT accompanied by specific nutritional support. In this review, we summarize the evidence demonstrating the presence of several proinflammatory substances in the Western diet (WD) and the positive effect of unprocessed food consumption and increased fruit and vegetable intake, suggesting a new approach to reduce inflammaging with the improvement of ESRD clinical status. We conclude that the Mediterranean diet (MD), because of its modulative effects on microbiota and its anti-inflammaging properties, may be a cornerstone in a more precise nutritional support for patients on the waiting list for kidney transplantation.

Reduction in Chronic Disease Risk and Burden in a 70-Individual Cohort Through Modification of Health Behaviors

Introduction

Health risk factors, including lifestyle risks and health literacy, are known to contribute to the chronic disease epidemic. According to the Centers for Disease Control and Prevention (CDC), chronic diseases account for 90% of healthcare costs, morbidity, and mortality. In the United States, healthcare providers attempt to modulate a limited set of risks. However, chronic diseases continue to proliferate despite expansion of wellness programs and drugs to manage and prevent chronic conditions. Pandemics, exemplified by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), show that people in good health suffer mortality rates at 10% the rate compared to those with pre-existing chronic conditions. Healthcare costs and morbidity rates often parallel mortality rates. New root-cause risk and health tools that accommodate low health literacy and are linked to personalized health improvement care plans are needed to reverse the chronic disease epidemic. Reported here is a study on 70 manufacturing employees in the Midwest US using a personalized and group approach to chronic disease reversal and prevention which may also find utility in pandemic severity and policy decisions.

Methods

Health, lifestyle, behavior, and motivation data were collected on 70 individuals at the beginning of a nine-month disease reversal and prevention program. The data were updated every two to six months over the period. Inputs included information from a novel health risk assessment, serum biomarkers specific for chronic disease, and traditional medical information. Using all these data we generated robust, personalized, and modifiable care plans that were implemented by the participant and guided by a care team including health coaches and medical providers. Periodic renewal of profile data and biomarkers facilitated adjustment of care plans to optimize the path toward health goals set mutually by the participant and the care team.

Results

Ninety percent of participants experienced a favorable reduction in chronic disease biomarkers. The reduction in serum biomarkers coincided with a reduction in disease and risk attributes based on medical chart data and before and after interviews. Hemoglobin A1C, for example, lowered in all but one participant concomitant with reported improved energy and reduced need for medications in the majority of participants. Markers of inflammation lowered across the population. Most importantly each individual reported improvement in their overall health.

Conclusions

This simple, inexpensive, root-cause based risk and health approach generates a “do no harm” action plan that guides a care team, including the participant, on a path to improved health. The data demonstrate that changes in a novel risk calculator score coincide with changes in sensitive biomarkers for chronic disease. When the risks of an individual are reduced, the biomarkers reflect that change with self-reported wellbeing also improved. This program and process may be of value to society plagued with escalating levels of chronic disease and merits further study and implementation.

Age-Related Epigenetic Derangement upon Reprogramming and Differentiation of Cells from the Elderly

Aging is a complex multi-layered phenomenon. The study of aging in humans is based on the use of biological material from hard-to-gather tissues and highly specific cohorts. The introduction of cell reprogramming techniques posed promising features for medical practice and basic research. Recently, a growing number of studies have been describing the generation of induced pluripotent stem cells (iPSCs) from old or centenarian biologic material. Nonetheless, Reprogramming techniques determine a profound remodelling on cell epigenetic architecture whose extent is still largely debated. Given that cell epigenetic profile changes with age, the study of cell-fate manipulation approaches on cells deriving from old donors or centenarians may provide new insights not only on regenerative features and physiology of these cells, but also on reprogramming-associated and age-related epigenetic derangement.

Biomarkers of Aging: From Function to Molecular Biology

Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a single biomarker or gold standard tool that can monitor successful or healthy aging. Within this short review the current knowledge of putative biomarkers is presented, focusing on their application to the major physiological mechanisms affected by the aging process including physical capability, nutritional status, body composition, endocrine and immune function. This review emphasizes molecular and DNA-based biomarkers, as well as recent advances in other biomarkers such as microRNAs, bilirubin or advanced glycation end products.

System-wide assembly of pathways and modules hierarchically reveal metabolic mechanism of cerebral ischemia

The relationship between cerebral ischemia and metabolic disorders is poorly understood, which is partly due to the lack of comparative fusing data for larger complete systems and to the complexity of metabolic cascade reactions. Based on the fusing maps of comprehensive serum metabolome, fatty acid and amino acid profiling, we identified 35 potential metabolic biomarkers for ischemic stroke. Our analyses revealed 8 significantly altered pathways by MetPA (Metabolomics Pathway Analysis, impact score >0.10) and 15 significantly rewired modules in a complex ischemic network using the Markov clustering (MCL) method; all of these pathways became more homologous as the number of overlapping nodes was increased. We then detected 24 extensive pathways based on the total modular nodes from the network analysis, 12 of which were new discovery pathways. We provided a new perspective from the viewpoint of abnormal metabolites for the overall study of ischemic stroke as well as a new method to simplify the network analysis by selecting the more closely connected edges and nodes to build a module map of stroke.

An Integrative Thrombosis Network: Visualization and Topological Analysis

A comprehensive understanding of the integrative nature of the molecular network in thrombosis would be very helpful to develop multicomponent and multitarget antithrombosis drugs for use in traditional Chinese medicine (TCM). This paper attempts to comprehensively map the molecular network in thrombosis by combining platelet signaling, the coagulation cascade, and natural clot dissolution systems and to analyze the topological characteristics of the network, including the centralities of nodes, network modules, and network robustness. The results in this research advance understanding of functions of proteins in the thrombosis network and provide a reference for predicting potential therapeutic antithrombotic targets and evaluating their influence on the network.

Systemic impact molds mesenchymal stromal/stem cell aging

Aging is associated with an accruing emergence of non-functional tissues. Mesenchymal stem cells (MSC) bring forth progenitors with multi-lineage differentiation potential, yet, they also exhibit anti-inflammatory and tissue-protective properties. Due to aging, altered tissue microenvironments constrict controlled stem cell proliferation and progenitor differentiation, thus diminishing the fitness of MSC. Therefore, deepening our understanding of metabolic, molecular and environmental factors impacting on MSC during human aging as well as providing new vistas on their role in promoting healthy aging and preventing age-associated disease is pivot. It is anticipated that integrative quantification of systemic parameters dominantly impacting on MSC will also enable effective personalized prognosis and provision of effective early medical interventions. Working along this line, it can be envisaged that standards in medical therapies can be individually adjusted by accounting not solely for the patient's chronological age or other physical parameters rather than specific physiological parameters which are believed to functionally shape stem cell niches within the bone marrow.

Darwin-Wallace Demons: survival of the fastest in populations of duckweeds and the evolutionary history of an enigmatic group of angiosperms

In evolutionary biology, the term 'Darwinian fitness' refers to the lifetime reproductive success of an individual within a population of conspecifics. The idea of a 'Darwinian Demon' emerged from this concept and is defined here as an organism that commences reproduction almost immediately after birth, has a maximum fitness, and lives forever. It has been argued that duckweeds (sub-family Lemnoideae, order Alismatales), a group containing five genera and 34 species of small aquatic monocotyledonous plants with a reduced body plan, can be interpreted as examples of 'Darwinian Demons'. Here we focus on the species Spirodela polyrhiza (Great duckweed) and show that these miniaturised aquatic angiosperms display features that fit the definition of the hypothetical organism that we will call a 'Darwin-Wallace Demon' in recognition of the duel proponents of evolution by natural selection. A quantitative analysis (log-log bivariate plot of annual growth in dry biomass versus standing dry body mass of various green algae and land plants) revealed that duckweeds are thus far the most rapidly growing angiosperms in proportion to their body mass. In light of this finding, we discuss the disposable soma and metabolic optimising theories, summarise evidence for and against the proposition that the Lemnoideae (family Araceae) reflect an example of reductive evolution, and argue that, under real-world conditions (environmental constraints and other limitations), 'Darwin-Wallace Demons' cannot exist, although the concept remains useful in much the same way that the Hardy-Weinberg law does.

Novel putative mechanisms to link circadian clocks to healthy aging

The circadian clock coordinates the internal physiology to increase the homeostatic capacity thereby providing both a survival advantage to the system and an optimization of energy budgeting. Multiple-oscillator circadian mechanisms are likely to play a role in regulating human health and may contribute to the aging process. Our aim is to give an overview of how the central clock in the hypothalamus and peripheral clocks relate to aging and metabolic disorders, including hyperlipidemia and hyperglycemia. In particular, we unravel novel putative mechanisms to link circadian clocks to healthy aging. This review may lead to the design of large-scale interventions to help people stay healthy as they age by adjusting daily activities, such as feeding behavior, and or adaptation to age-related changes in individual circadian rhythms.

Melatonin and the theories of aging: a critical appraisal of melatonin's role in antiaging mechanisms

The classic theories of aging such as the free radical theory, including its mitochondria-related versions, have largely focused on a few specific processes of senescence. Meanwhile, numerous interconnections have become apparent between age-dependent changes previously thought to proceed more or less independently. Increased damage by free radicals is not only linked to impairments of mitochondrial function, but also to inflammaging as it occurs during immune remodeling and by release of proinflammatory cytokines from mitotically arrested, DNA-damaged cells that exhibit the senescence-associated secretory phenotype (SASP). Among other effects, SASP can cause mutations in stem cells that reduce the capacity for tissue regeneration or, in worst case, lead to cancer stem cells. Oxidative stress has also been shown to promote telomere attrition. Moreover, damage by free radicals is connected to impaired circadian rhythmicity. Another nexus exists between cellular oscillators and metabolic sensing, in particular to the aging-suppressor SIRT1, which acts as an accessory clock protein. Melatonin, being a highly pleiotropic regulator molecule, interacts directly or indirectly with all the processes mentioned. These influences are critically reviewed, with emphasis on data from aged organisms and senescence-accelerated animals. The sometimes-controversial findings obtained either in a nongerontological context or in comparisons of tumor with nontumor cells are discussed in light of evidence obtained in senescent organisms. Although, in mammals, lifetime extension by melatonin has been rarely documented in a fully conclusive way, a support of healthy aging has been observed in rodents and is highly likely in humans.

Distinctive topology of age-associated epigenetic drift in the human interactome

Recently, it has been demonstrated that DNA methylation, a covalent modification of DNA that can regulate gene expression, is modified as a function of age. However, the biological and clinical significance of this age-associated epigenetic drift is unclear. To shed light on the potential biological significance, we here adopt a systems approach and study the genes undergoing age-associated changes in DNA methylation in the context of a protein interaction network, focusing on their topological properties. In contrast to what has been observed for other age-related gene classes, including longevity- and disease-associated genes, as well as genes undergoing age-associated changes in gene expression, we here demonstrate that age-associated epigenetic drift occurs preferentially in genes that occupy peripheral network positions of exceptionally low connectivity. In addition, we show that these genes synergize topologically with disease and longevity genes, forming unexpectedly large network communities. Thus, these results point toward a potentially distinct mechanistic and biological role of DNA methylation in dictating the complex aging and disease phenotypes.

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review

Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of drug development costs. Network description and analysis not only give a systems-level understanding of drug action and disease complexity, but can also help to improve the efficiency of drug design. We give a comprehensive assessment of the analytical tools of network topology and dynamics. The state-of-the-art use of chemical similarity, protein structure, protein-protein interaction, signaling, genetic interaction and metabolic networks in the discovery of drug targets is summarized. We propose that network targeting follows two basic strategies. The "central hit strategy" selectively targets central nodes/edges of the flexible networks of infectious agents or cancer cells to kill them. The "network influence strategy" works against other diseases, where an efficient reconfiguration of rigid networks needs to be achieved by targeting the neighbors of central nodes/edges. It is shown how network techniques can help in the identification of single-target, edgetic, multi-target and allo-network drug target candidates. We review the recent boom in network methods helping hit identification, lead selection optimizing drug efficacy, as well as minimizing side-effects and drug toxicity. Successful network-based drug development strategies are shown through the examples of infections, cancer, metabolic diseases, neurodegenerative diseases and aging. Summarizing >1200 references we suggest an optimized protocol of network-aided drug development, and provide a list of systems-level hallmarks of drug quality. Finally, we highlight network-related drug development trends helping to achieve these hallmarks by a cohesive, global approach.

Genome-scale studies of aging: challenges and opportunities

Whole-genome studies involving a phenotype of interest are increasingly prevalent, in part due to a dramatic increase in speed at which many high throughput technologies can be performed coupled to simultaneous decreases in cost. This type of genome-scale methodology has been applied to the phenotype of lifespan, as well as to whole-transcriptome changes during the aging process or in mutants affecting aging. The value of high throughput discovery-based science in this field is clearly evident, but will it yield a true systems-level understanding of the aging process? Here we review some of this work to date, focusing on recent findings and the unanswered puzzles to which they point. In this context, we also discuss recent technological advances and some of the likely future directions that they portend.

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.

Dynamic energy budget approaches for modelling organismal ageing

Ageing is a complex multifactorial process involving a progressive physiological decline that, ultimately, leads to the death of an organism. It involves multiple changes in many components that play fundamental roles under healthy and pathological conditions. Simultaneously, every organism undergoes accumulative 'wear and tear' during its lifespan, which confounds the effects of the ageing process. The scenario is complicated even further by the presence of both age-dependent and age-independent competing causes of death. Various manipulations have been shown to interfere with the ageing process. Calorie restriction, for example, has been reported to increase the lifespan of a wide range of organisms, which suggests a strong relation between energy metabolism and ageing. Such a link is also supported within the main theories for ageing: the free radical hypothesis, for instance, links oxidative damage production directly to energy metabolism. The Dynamic Energy Budgets (DEB) theory, which characterizes the uptake and use of energy by living organisms, therefore constitutes a useful tool for gaining insight into the ageing process. Here we compare the existing DEB-based modelling approaches and, then, discuss how new biological evidence could be incorporated within a DEB framework.

Pathological aspects of lipid peroxidation

Lipid peroxidation (LPO) product accumulation in human tissues is a major cause of tissular and cellular dysfunction that plays a major role in ageing and most age-related and oxidative stress-related diseases. The current evidence for the implication of LPO in pathological processes is discussed in this review. New data and literature review are provided evaluating the role of LPO in the pathophysiology of ageing and classically oxidative stress-linked diseases, such as neurodegenerative diseases, diabetes and atherosclerosis (the main cause of cardiovascular complications). Striking evidences implicating LPO in foetal vascular dysfunction occurring in pre-eclampsia, in renal and liver diseases, as well as their role as cause and consequence to cancer development are addressed.

Inverse correlation of protein oxidation and proteasome activity in liver and lung

Several studies have demonstrated that proteasome activity decreases whereas protein oxidation increases with aging in various tissues. However, no studies are available correlating both parameters directly comparing different tissues of one organism. Therefore, we determined whether there is an age-related change in proteasome activity and protein oxidation in heart, lung, liver, kidney and skeletal muscle samples of 6-, 10-, 18- and 26-month-old rats. There was a significant age-related increase in protein carbonyls at 18 and 26 months compared to young rats. Thereby, protein carbonyl formation was rather due to a general than a specific protein carbonylation as shown by immunblot studies. The highest increase in protein carbonyl formation was found in liver, lung and kidney samples. Proteasome activity decreased significantly with age in lung and liver samples. Proteasome activity in liver and lung decreased by factor five compared to young rats. Strong correlations between proteasome activity and protein oxidation were found in liver and lung, whereas in other tissues only a trend was found. These results demonstrate that the increase in protein oxidation and the decline in proteasome activity are correlating. Further studies are needed to determine the mechanisms which cause organ-specific aging-rates and their consequences.

Mosaic aging

Although all multicellular organisms undergo structural and functional deterioration with age, senescence is not a uniform process. Rather, each organism experiences a constellation of changes that reflect the heterogeneous effects of age on molecules, cells, organs and systems, an idiosyncratic pattern that we refer to as mosaic aging. Varying genetic, epigenetic and environmental factors (local and extrinsic) contribute to the aging phenotype in a given individual, and these agents influence the type and rate of functional decline, as well as the likelihood of developing age-associated afflictions such as cardiovascular disease, arthritis, cancer, and neurodegenerative disorders. Identifying key factors that drive aging, clarifying their activities in different systems, and in particular understanding how they interact will enhance our comprehension of the aging process, and could yield insights into the permissive role that senescence plays in the emergence of acute and chronic diseases of the elderly.

Cellular senescence: unravelling complexity

Cellular senescence might be a tumour suppressing mechanism as well as a contributor to age-related loss of tissue function. It has been characterised classically as the result of the loss of DNA sequences called telomeres at the end of chromosomes. However, recent studies have revealed that senescence is in fact an intricate process, involving the sequential activation of multiple cellular processes, which have proven necessary for the establishment and maintenance of the phenotype. Here, we review some of these processes, namely, the role of mitochondrial function and reactive oxygen species, senescence-associated secreted proteins and chromatin remodelling. Finally, we illustrate the use of systems biology to address the mechanistic, functional and biochemical complexity of senescence.

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.

The szilard hypothesis on the nature of aging revisited

This year marks the 50th anniversary of a nearly forgotten hypothesis on aging by Leo Szilard, best known for his pioneering work in nuclear physics, his participation in the Manhattan Project during World War II, his opposition to the nuclear arms race in the postwar era, and his pioneering ideas in biology. Given a specific set of assumptions, Szilard hypothesized that the major reason for the phenomenon of aging was aging hits, e.g., by ionizing radiation, to the gene-bearing chromosomes and presented a mathematical target-hit model enabling the calculation of the average and maximum life span of a species, as well as the influence of increased exposure to DNA-damaging factors on life expectancy. While many new findings have cast doubt on the specific features of the model, this was the first serious effort to posit accumulated genetic damage as a cause of senescence. Here, we review Szilard's assumptions in the light of current knowledge on aging and reassess his mathematical model in an attempt to reach a conclusion on the relevance of Szilard's aging hypothesis today.

Protein aggregation as a paradigm of aging

The process of physiological decline leading to death of the individual is driven by the deteriorating capacity to withstand extrinsic and intrinsic hazards, resulting in damage accumulation with age. The dynamic changes with time of the network governing the outcome of misfolded proteins, exemplifying as intrinsic hazards, is considered here as a paradigm of aging. The main features of the network, namely, the non-linear increase of damage and the presence of amplifying feedback loops within the system are presented through a survey of the different components of the network and related cellular processes in aging and disease.

Age-related changes of NADPH-diaphorase-positive neurons in the rat inferior colliculus and auditory cortex

Nitric oxide (NO) has been implied in age-related changes of the central nervous system (CNS) and the central auditory pathway. The present study was conducted to investigate whether the number of NO-producing cells and their morphometric characteristics in the inferior colliculus (IC) and the auditory cortex (AC) are changed with the increasing age of the subjects. IC and AC sections of adult and senile Wistar rats were studied using the histochemical detection of NADPH-diaphorase activity (NADPH-d), a marker for neurons containing nitric oxide synthase (NOS). Our results showed a decreased area of the somas of NADPH-d-positive neurons in the dorsal cortex (DC) of the IC and a diffuse loss of NADPH-d-positive neurons in the senile IC and primary cortical auditory area (Te1). However, an increased number of NO-producing cells have been shown by other authors in different parts of the ageing auditory pathway and CNS. It seems that age-related changes in NADPH-d-positive cells may follow a region-specific route. These changes may be related to hearing impairments with increasing age.

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.

Longevity network: Construction and implications

The vast majority of studies on longevity have focused on individual genes/proteins, without adequately addressing the possible role of interactions between them. This study is the first attempt towards constructing a "longevity network" via analysis of human protein-protein interactions (PPIs). For this purpose, we (i) compiled a complete list of established longevity genes from different species, including those that most probably affect the longevity in humans, (ii) defined the human orthologs of the longevity genes, and (iii) determined whether the encoded proteins could be organized as a network. The longevity gene-encoded proteins together with their interacting proteins form a continuous network, which fits the criteria for a scale-free network with an extremely high contribution of hubs to the network connectivity. Most of them have never been annotated before in connection with longevity. Remarkably, almost all of the hubs of the "longevity network" were reported to be involved in at least one age-related disease (ARD), with many being involved in several ARDs. This may be one of the ways by which the proteins with multiple interactions affect the longevity. The hubs offer the potential of being primary targets for longevity-promoting interventions.

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.

Cellular networks and the aging process

The most important interactions between cellular molecules have a high affinity, are unique and specific, and require a network approach for a detailed description. After a brief introduction to cellular networks (protein--protein interaction networks, metabolic networks, gene regulatory networks, signalling networks and membrane--organelle networks) an overview is given on the network aspects of the theories on aging. The most important part of the review summarizes our knowledge on the aging of networks. The effects of aging on the general network models are described, as well as the initial findings on the effects of aging on the cellular networks. Finally we suggest a 'weak link theory of aging' linking the random damage of the network constituents to the overwhelming majority of the low affinity, transient interactions (weak links) in the cellular networks. We show that random damage of weak links may lead to an increase of noise and an increased vulnerability of cellular networks, and make a comparison between these predictions and the observed behaviour of the emergent properties of cellular networks in aged organisms.

Biomarkers of aging: combinatorial or systems model?

Systemwide functional and structural changes caused by the aging process encourage the implementation of new bioinformatics search strategies for markers of aging. Combinatorial biomarkers should be particularly favored, as they can quantify processes on multiple levels of biological organization and overcome an otherwise limited ability to access heterogeneities in populations. An even more challenging but rational approach is the development of systems biology models to describe molecular pathways and key networks mechanistically as they relate to age. Such reverse engineered models not only indicate critical and diagnostic components (that is, potential biomarkers) but also should be able to predict the progression of aging through computer simulation.

Decrease in the relative heterogeneity of health with age: A cross-national comparison

Using data from seven studies from Canada, Australia and the United States we were able to evaluate the heterogeneity of health status for 34,095 people aged 60 years and older. We found that relative heterogeneity (measured by the coefficient of variation) decreased with age. The coefficient of variation also decreased as a function of deficit accumulation (i.e. was lower when people demonstrated more deficits) displaying a power-law relationship. The exponent was close to 0.5, and therefore belongs to the dynamic universality class, which is typical for complex dynamical networks. We interpret this as showing that decline in relative heterogeneity is a robust finding, and represents, at the group level, increased vulnerability amongst elderly people.

Is the rate of biological aging, as measured by age at diagnosis of cancer, socioeconomically patterned?

STUDY OBJECTIVE

To investigate the hypothesis that biological aging, as measured by age at diagnosis of some common cancers, is socioeconomically patterned.

DESIGN

A cross sectional analysis of the association between an area based measure of material deprivation and age at diagnosis of four common cancers (breast, prostate, colorectal, and lung cancers). A further analysis, restricted to breast and colorectal cancer, adjusted for stage and grade of cancer at diagnosis.

SETTING

The Northern and Yorkshire cancer registry and information service, Northern and Yorkshire region, UK.

PARTICIPANTS

All people living in the Northern and Yorkshire region diagnosed with breast, prostate, colorectal, or lung cancer in 1986-1995. All people living in the Northern and Yorkshire region diagnosed with breast or colorectal cancer in 1998-2000 with data on stage and grade of cancer at diagnosis.

MAIN RESULTS

There was evidence that greater material deprivation was associated with younger age at diagnosis of cancer in prostate (beta coefficient -0.073), colorectal (women: -0.042; men: -0.063), and lung cancer (women: -0.214; men: -0.161). The opposite association was found in women with breast cancer (0.149). Adjusting for stage and grade at incidence, where possible, had little effect on the magnitude of the beta coefficients.

CONCLUSIONS

Age at diagnosis of some common cancers seems to be socioeconomically patterned with people from more deprived areas being diagnosed with prostate, colorectal, and lung cancers earlier in life. The opposite was seen in women with breast cancer. Further work is required to investigate the socioeconomic distribution of more accurate measures of biological aging.

Ageing and maintenance of the interstitial fluid traffic: possible roles of initial lymphatics and circadian hormones

It is here proposed that the interstitial fluid traffic depends on the widespread system of initial lymphatics without valves. The filtered fluid forced by the interstitial hydrostatic pressure enters initial lymphatics through loose junctions in segments that are near arterial ends of blood capillaries. Loose junctions might also allow fluid to leave initial lymphatics in segments that are near the venous ends of blood capillaries. Thus, initial lymphatics help daily transfer of 24 L of interstitial fluid from points of filtration to the points of resorption. Muscle contractions compress initial lymphatics and force the intraluminal content to enter collecting lymphatics. Contractions are needed to re-establish initial lymphatics as interstitial fluid shortcuts. Even small differences in interstitial flow can become important and lead to uneven flow distribution that might damage tissue and accelerate ageing. The proposed model of interstitial traffic maintenance requires three separate effects: (a) Thyroid hormones and control of tissue metabolism. It directly affects the cell shape and size, synthesis or degradation of interstitial material. Thyroid hormones control metabolic rates and prevent accumulation of interstitial material, as can be seen in severe hypothyroidism. (b) Somatotropin anabolic effects. Somatotropin increases number and volumes of cells, synthesis of interstitial material. These actions increase interstitial flow resistance. (c) Cortisol catabolic action. A cortisol induced tissue catabolism reduces the interstitial flow resistance toward normal. The presented idea is that known rhythms of GH and cortisol (GH during night sleep and cortisol in the morning) separate anabolic and catabolic actions in time, or otherwise they would diminish each other. The model predicts that the maintenance would be best during growth, when GH surges are higher. GH and cortisol are secreted together in cases of trauma, stress or starvation. Since this would probably block the proposed mechanism, a possible speculation is that frequent repetitions of stressful conditions accelerate ageing. The same prediction can be made for the long term glucocorticoid administration.

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.

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.

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.

Mitochondrial involvement in brain function and dysfunction: relevance to aging, neurodegenerative disorders and longevity

It is becoming increasingly evident that the mitochondrial genome may play a key role in neurodegenerative diseases. Mitochondrial dysfunction is characteristic of several neurodegenerative disorders, and evidence for mitochondria being a site of damage in neurodegenerative disorders is partially based on decreases in respiratory chain complex activities in Parkinson's disease, Alzheimer's disease, and Huntington's disease. Such defects in respiratory complex activities, possibly associated with oxidant/antioxidant balance perturbation, are thought to underlie defects in energy metabolism and induce cellular degeneration. Efficient functioning of maintenance and repair process seems to be crucial for both survival and physical quality of life. This is accomplished by a complex network of the so-called longevity assurance processes, which are composed of genes termed vitagenes. A promising approach for the identification of critical gerontogenic processes is represented by the hormesis-like positive effect of stress. In the present review, we discuss the role of energy thresholds in brain mitochondria and their implications in neurodegeneration. We then review the evidence for the role of oxidative stress in modulating the effects of mitochondrial DNA mutations on brain age-related disorders and also discuss new approaches for investigating the mechanisms of lifetime survival and longevity.

NO synthase and NO-dependent signal pathways in brain aging and neurodegenerative disorders: the role of oxidant/antioxidant balance

Nitric oxide and other reactive nitrogen species appear to play several crucial roles in the brain. These include physiological processes such as neuromodulation, neurotransmission and synaptic plasticity, and pathological processes such as neurodegeneration and neuroinflammation. There is increasing evidence that glial cells in the central nervous system can produce nitric oxide in vivo in response to stimulation by cytokines and that this production is mediated by the inducible isoform of nitric oxide synthase. Although the etiology and pathogenesis of the major neurodegenerative and neuroinflammatory disorders (Alzheimer's disease, amyothrophic lateral sclerosis, Parkinson's disease, Huntington's disease and multiple sclerosis) are unknown, numerous recent studies strongly suggest that reactive nitrogen species play an important role. Furthermore, these species are probably involved in brain damage following ischemia and reperfusion, Down's syndrome and mitochondrial encephalopathies. Recent evidence also indicates the importance of cytoprotective proteins such as heat shock proteins (HSPs) which appear to be critically involved in protection from nitrosative and oxidative stress. In this review, evidence for the involvement of nitrosative stress in the pathogenesis of the major neurodegenerative/ neuroinflammatory diseases and the mechanisms operating in brain as a response to imbalance in the oxidant/antioxidant status are discussed.