Specific age-related signatures in Drosophila body parts transcriptome

The influence of skeletal muscle on systemic aging and lifespan

Epidemiological studies in humans suggest that skeletal muscle aging is a risk factor for the development of several age-related diseases such as metabolic syndrome, cancer, Alzheimer's and Parkinson's disease. Here, we review recent studies in mammals and Drosophila highlighting how nutrient- and stress-sensing in skeletal muscle can influence lifespan and overall aging of the organism. In addition to exercise and indirect effects of muscle metabolism, growing evidence suggests that muscle-derived growth factors and cytokines, known as myokines, modulate systemic physiology. Myokines may influence the progression of age-related diseases and contribute to the intertissue communication that underlies systemic aging.

Analysis of nonlinear gene expression progression reveals extensive pathway and age-specific transitions in aging human brains

Several recent gene expression studies identified hundreds of genes that are correlated with age in brain and other tissues in human. However, these studies used linear models of age correlation, which are not well equipped to model abrupt changes associated with particular ages. We developed a computational algorithm for age estimation in which the expression of each gene is treated as a dichotomized biomarker for whether the subject is older or younger than a particular age. In addition, for each age-informative gene our algorithm identifies the age threshold with the most drastic change in expression level, which allows us to associate genes with particular age periods. Analysis of human aging brain expression datasets from three frontal cortex regions showed that different pathways undergo transitions at different ages, and the distribution of pathways and age thresholds varies across brain regions. Our study reveals age-correlated expression changes at particular age points and allows one to estimate the age of an individual with better accuracy than previously published methods.

Mechanisms of skeletal muscle aging: insights from Drosophila and mammalian models

A characteristic feature of aged humans and other mammals is the debilitating, progressive loss of skeletal muscle function and mass that is known as sarcopenia. Age-related muscle dysfunction occurs to an even greater extent during the relatively short lifespan of the fruit fly Drosophila melanogaster. Studies in model organisms indicate that sarcopenia is driven by a combination of muscle tissue extrinsic and intrinsic factors, and that it fundamentally differs from the rapid atrophy of muscles observed following disuse and fasting. Extrinsic changes in innervation, stem cell function and endocrine regulation of muscle homeostasis contribute to muscle aging. In addition, organelle dysfunction and compromised protein homeostasis are among the primary intrinsic causes. Some of these age-related changes can in turn contribute to the induction of compensatory stress responses that have a protective role during muscle aging. In this Review, we outline how studies in Drosophila and mammalian model organisms can each provide distinct advantages to facilitate the understanding of this complex multifactorial condition and how they can be used to identify suitable therapies.

BACH2: a marker of DNA damage and ageing

DNA damage and ageing share expression changes involving alterations in many aspects of metabolism, suppression of growth and upregulation of defence and genome maintenance systems. "Omics" technologies have permitted large-scale parallel measurements covering global cellular constituents and aided the identification of specific response pathways that change during ageing and after DNA damage. We have set out to identify genes with highly conserved response patterns through meta-analysis of mRNA expression datasets collected during natural ageing and accelerated ageing caused by a Transcription-Coupled Nucleotide Excision Repair (TC-NER) defect in a diverse set of organs and tissues in mice, and from in vitro UV-induced DNA damage in a variety of murine cells. The identified set of genes that show similar expression patterns in response to organ ageing (accelerated and normal), and endogenously and exogenously induced DNA damage, consists of genes involved in anti-oxidant systems and includes the transcription factor Bach2 as one of the most consistent markers. BACH2 was originally identified as a partner of the small Maf proteins and antagonist of the NRF2 anti-oxidant defence pathway and has been implicated in B-cell differentiation and immune system homeostasis. Although BACH2 has never before been associated with UV-induced damage or ageing, it shows a strong downregulation in both conditions. We have characterized the dynamics of Bach2 expression in response to DNA damage and show that it is a highly sensitive responder to transcription-blocking DNA lesions. Gene expression profiling using Affymetrix microarray analysis after siRNA-mediated silencing of Bach2 identified cell cycle and transcription regulation as the most significantly altered processes consistent with a function as transcription factor affecting proliferation.

Effect of temperature on the rate of ageing: an experimental study of the blowfly Calliphora stygia

All organisms age, the rate of which can be measured by demographic analysis of mortality rates. The rate of ageing is thermally sensitive in ectothermic invertebrates and we examined the effects of temperature on both demographic rates of ageing and on cellular senescence in the blowfly, Calliphora stygia. The short lifespan of these flies is advantageous for demographic measurements while their large body size permits individual-based biochemical characterisation. Blowflies maintained at temperatures from 12°C to 34°C had a five to six-fold decrease in maximum and average longevity, respectively. Mortality rates were best described by a two-phase Gompertz relation, which revealed the first-phase of ageing to be much more temperature sensitive than the second stage. Flies held at low temperatures had both a slower first-phase rate of ageing and a delayed onset of second-phase ageing, which significantly extended their longevity compared with those at high temperatures. Blowflies that were transferred from 29°C to 15°C had higher first-phase mortality rates than those of flies held at constant 15°C, but their onset of second-phase ageing was deferred beyond that of flies held constantly at this temperature. The accumulation of fluorescent AGE pigment, a measure of cellular oxidative damage, increased steadily over time in all blowflies, irrespective of the temporal pattern of mortality. Pigment accumulated steadily during periods of 'negligible senescence', as measured by minimal rate of mortality, and the rate of accumulation was significantly affected by temperature. Thus accumulation of AGE pigment is more representative of chronological age than a reflection of biological age or a cause of mortality.

Gene expression changes in response to aging compared to heat stress, oxidative stress and ionizing radiation in Drosophila melanogaster

Gene expression changes in response to aging, heat stress, hyperoxia, hydrogen peroxide, and ionizing radiation were compared using microarrays. A set of 18 genes were up-regulated across all conditions, indicating a general stress response shared with aging, including the heat shock protein (Hsp) genes Hsp70, Hsp83 and l(2)efl, the glutathione-S-transferase gene GstD2, and the mitochondrial unfolded protein response (mUPR) gene ref(2)P. Selected gene expression changes were confirmed using quantitative PCR, Northern analysis and GstD-GFP reporter constructs. Certain genes were altered in only a subset of the conditions, for example, up-regulation of numerous developmental pathway and signaling genes in response to hydrogen peroxide. While aging shared features with each stress, aging was more similar to the stresses most associated with oxidative stress (hyperoxia, hydrogen peroxide, ionizing radiation) than to heat stress. Aging is associated with down-regulation of numerous mitochondrial genes, including electron-transport-chain (ETC) genes and mitochondrial metabolism genes, and a sub-set of these changes was also observed upon hydrogen peroxide stress and ionizing radiation stress. Aging shared the largest number of gene expression changes with hyperoxia. The extensive down-regulation of mitochondrial and ETC genes during aging is consistent with an aging-associated failure in mitochondrial maintenance, which may underlie the oxidative stress-like and proteotoxic stress-like responses observed during aging.

Differential regulation of proteasome functionality in reproductive vs. somatic tissues of Drosophila during aging or oxidative stress

Proteasome is central to proteostasis maintenance, as it degrades both normal and damaged proteins. Herein, we undertook a detailed analysis of proteasome regulation in the in vivo setting of Drosophila melanogaster. We report that a major hallmark of somatic tissues of aging flies is the gradual accumulation of ubiquitinated and carbonylated proteins; these effects correlated with a ~50% reduction of proteasome expression and catalytic activities. In contrast, gonads of aging flies were relatively free of proteome oxidative damage and maintained substantial proteasome expression levels and highly active proteasomes. Moreover, gonads of young flies were found to possess more abundant and more active proteasomes than somatic tissues. Exposure of flies to oxidants induced higher proteasome activities specifically in the gonads, which were, independently of age, more resistant than soma to oxidative challenge and, as analyses in reporter transgenic flies showed, retained functional antioxidant responses. Finally, inducible Nrf2 activation in transgenic flies promoted youthful proteasome expression levels in the aged soma, suggesting that age-dependent Nrf2 dysfunction is causative of decreasing somatic proteasome expression during aging. The higher investment in proteostasis maintenance in the gonads plausibly facilitates proteome stability across generations; it also provides evidence in support of the trade-off theories of aging.

Differential regulation of proteasome functionality in reproductive vs. somatic tissues of Drosophila during aging or oxidative stress

Proteasome is central to proteostasis maintenance, as it degrades both normal and damaged proteins. Herein, we undertook a detailed analysis of proteasome regulation in the in vivo setting of Drosophila melanogaster. We report that a major hallmark of somatic tissues of aging flies is the gradual accumulation of ubiquitinated and carbonylated proteins; these effects correlated with a ~50% reduction of proteasome expression and catalytic activities. In contrast, gonads of aging flies were relatively free of proteome oxidative damage and maintained substantial proteasome expression levels and highly active proteasomes. Moreover, gonads of young flies were found to possess more abundant and more active proteasomes than somatic tissues. Exposure of flies to oxidants induced higher proteasome activities specifically in the gonads, which were, independently of age, more resistant than soma to oxidative challenge and, as analyses in reporter transgenic flies showed, retained functional antioxidant responses. Finally, inducible Nrf2 activation in transgenic flies promoted youthful proteasome expression levels in the aged soma, suggesting that age-dependent Nrf2 dysfunction is causative of decreasing somatic proteasome expression during aging. The higher investment in proteostasis maintenance in the gonads plausibly facilitates proteome stability across generations; it also provides evidence in support of the trade-off theories of aging.

Effects of Flight on Gene Expression and Aging in the Honey Bee Brain and Flight Muscle

Honey bees move through a series of in-hive tasks (e.g., “nursing”) to outside tasks (e.g., “foraging”) that are coincident with physiological changes and higher levels of metabolic activity. Social context can cause worker bees to speed up or slow down this process, and foragers may revert back to their earlier in-hive tasks accompanied by reversion to earlier physiological states. To investigate the effects of flight, behavioral state and age on gene expression, we used whole-genome microarrays and real-time PCR. Brain tissue and flight muscle exhibited different patterns of expression during behavioral transitions, with expression patterns in the brain reflecting both age and behavior, and expression patterns in flight muscle being primarily determined by age. Our data suggest that the transition from behaviors requiring little to no flight (nursing) to those requiring prolonged flight bouts (foraging), rather than the amount of previous flight per se, has a major effect on gene expression. Following behavioral reversion there was a partial reversion in gene expression but some aspects of forager expression patterns, such as those for genes involved in immune function, remained. Combined with our real-time PCR data, these data suggest an epigenetic control and energy balance role in honey bee functional senescence.

dJun and Vri/dNFIL3 are major regulators of cardiac aging in Drosophila

Cardiac aging is a complex process, which is influenced by both environmental and genetic factors. Deciphering the mechanisms involved in heart senescence therefore requires identifying the molecular pathways that are affected by age in controlled environmental and genetic conditions. We describe a functional genomic investigation of the genetic control of cardiac senescence in Drosophila. Molecular signatures of heart aging were identified by differential transcriptome analysis followed by a detailed bio-informatic analysis. This approach implicated the JNK/dJun pathway and the transcription factor Vri/dNFIL3 in the transcription regulatory network involved in cardiac senescence and suggested the possible involvement of oxidative stress (OS) in the aging process. To validate these predictions, we developed a new in vivo assay to analyze heart performance in various contexts of adult heart-specific gene overexpression and inactivation. We demonstrate that, as in mammals, OS plays a central role in cardiac senescence, and we show that pharmacological interventions impinging on OS slow heart senescence. These observations strengthen the idea that cardiac aging is controlled by evolutionarily conserved mechanisms, further validating Drosophila as a model to study cardiac senescence. In addition, we demonstrate that Vri, the ortholog of the vertebrate NFIL3/E4B4 transcription factor, is a major genetic regulator of cardiac aging. Vri overexpression leads to major heart dysfunctions, but its loss of function significantly reduces age-related cardiac dysfunctions. Furthermore, we unambiguously show that the JNK/AP1 pathway, the role of which in cardiac aging in mammals is controversial, is activated during cardiac aging and has a detrimental effect on cardiac senescence. This data-driven functional genomic analysis therefore led to the identification of key components of the Gene Regulatory Network of cardiac aging in Drosophila and may prompt to investigate the involvement of their counterparts in the cardiac aging process in mammals.

Age-associated changes in cardiac structure and function have been implicated in the markedly increased risk of cardiovascular disease, but the molecular basis of these processes is ill-defined. It is difficult to study the genetics of heart aging in mammalian models because of their long life spans and their complexity, involving notably genetic redundancy. Here, we address this issue through identification of molecular signatures of cardiac aging in Drosophila, a model organism in which heart senescence occurs within 2 months. Tissue-specific transcriptome comparison of young and aging fly hearts were performed followed by in silico predictions of the regulatory networks involved. This analysis implicated oxidative stress (OS), the JNK/dJun pathway, and Vri/dNFIL3 in the gene regulatory network that drives cardiac senescence. Measuring heart variables in vivo following heart-specific genetic and pharmacological manipulations confirmed these predictions. We show that OS has a central role in the aging of the fly heart. Moreover, heart-specific partial knockdown of dJun and Vri prevented cardiac senescence, demonstrating that they are essential regulators of cardiac aging. Thus, our results uncover two major genetic determinants of Drosophila cardiac aging whose activities enhance heart senescence. It may therefore be valuable to investigate their involvement in the cardiac aging process in mammals.

Age-dependent changes in the transcription profile of long-lived Drosophila over-expressing glutamate cysteine ligase

In our prior studies (Orr et al., 2005) we achieved a 30-50% increase in the life span of Drosophila by manipulating glutathione (GSH) production in neuronal tissues, through over-expression of glutamate-cysteine ligase (GCL), a key enzyme in glutathione biosynthesis. In the present study, we identified gene response patterns from which plausible mechanisms responsible for the observed effects on life span might be inferred. Functional clustering analysis of the transcriptome data revealed that biological processes affected by GCLc in young flies (10 days) were generally related to cell morphogenesis and differentiation, while those in older flies were associated with nucleosome organization and detoxification processes. Notably, in older flies there was considerable reduction in the expression of genes related to humoral immunity in the GCLc over-expressors and this was observed in flies of the same chronological age (∼40 days old flies) and in flies of equivalent physiological age (10% dead for both experimentals and controls). Our study demonstrates that most of the GSH-mediated processes and targets are relatively distinct in young and old flies. Nevertheless there exists a restricted number of related processes affected by GCLc in both young and old flies and prominent among them are those associated with proteolysis and metabolism.

Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension

Background

While studying long-lived mutants has advanced our understanding of the processes involved in ageing, the mechanisms underlying natural variation in lifespan and ageing rate remain largely unknown. Here, we characterise genome-wide expression patterns of a long-lived, natural variant of Drosophila melanogaster resulting from selection for starvation resistance (SR) and compare it with normal-lived control flies (C). We do this at two time points representing middle age (90% survival) and old age (10% survival) respectively, in three adult diets (malnutrition, optimal food, and overfeeding).

Results

We found profound differences between Drosophila lines in their age-related expression. Most of the age-associated changes in normal-lived flies were abrogated in long-lived Drosophila. The stress-related genes, including those involved in proteolysis and cytochrome P450, were generally higher expressed in SR flies and showed a smaller increase in expression with age compared to C flies. The genes involved in reproduction showed a lower expression in middle-aged SR than in C flies and, unlike C flies, a lack of their downregulation with age. Further, we found that malnutrition strongly affected age-associated transcript patterns overriding the differences between the lines. However, under less stressful dietary conditions, line and diet affected age-dependent expression similarly. Finally, we present lists of candidate markers of ageing and lifespan extension.

Conclusions

Our study unveils transcriptional changes associated with lifespan extension in SR Drosophila. The results suggest that natural genetic variation for SR and lifespan can operate through similar transcriptional mechanisms as those of dietary restriction and life-extending mutations.

Lipid profiles as indicators of functional senescence in the medfly

Changes associated with the age-related decline of physiological functions, and their relation with mortality rates, are thoroughly being investigated in the aging research field. We used the Mediterranean fruit fly Ceratitis capitata, largely studied by biodemographers, as a model for functional senescence studies. The aim of our work was to find novel combinatorial indicators able to reflect the functional state of adult insects, regardless of chronological age. We studied the profiles of neutral and polar lipids of head, thorax and abdomen of standard populations kept at 23 °C, at different ages. Lipid classes were separated by thin layer chromatography, and the quantitative values were used to find patterns of change using a multivariate principal component analysis approach. The lipid-dependent principal components obtained correlated with age, and differences between sexes were consistent with differences in the shape of the survival curves and the mortality parameters. These same components were able to discriminate populations with a behavioral decline due to a mild 28 °C thermal stress. Thus, young populations at 28 °C showed similar lipid profiles than old populations at 23 °C. The results indicated that the lipid-dependent components reflect the functional state of the flies, and so were named functional state components (FSCs). It is proposed that FSCs may be used as functional senescence indicators.

Ferritin overexpression in Drosophila glia leads to iron deposition in the optic lobes and late-onset behavioral defects

Cellular and organismal iron storage depends on the function of the ferritin protein complex in insects and mammals alike. In the central nervous system of insects, the distribution and relevance of ferritin remain unclear, though ferritin has been implicated in Drosophila models of Alzheimers' and Parkinsons' disease and in Aluminum-induced neurodegeneration. Here we show that transgene-derived expression of ferritin subunits in glial cells of Drosophila melanogaster causes a late-onset behavioral decline, characterized by loss of circadian rhythms in constant darkness and impairment of elicited locomotor responses. Anatomical analysis of the affected brains revealed crystalline inclusions of iron-loaded ferritin in a subpopulation of glial cells but not significant neurodegeneration. Although transgene-induced glial ferritin expression was well tolerated throughout development and in young flies, it turned disadvantageous at older age. The flies we characterize in this report contribute to the study of ferritin in the Drosophila brain and can be used to assess the contribution of glial iron metabolism in neurodegenerative models of disease.

Computational biology for ageing

High-throughput genomic and proteomic technologies have generated a wealth of publicly available data on ageing. Easy access to these data, and their computational analysis, is of great importance in order to pinpoint the causes and effects of ageing. Here, we provide a description of the existing databases and computational tools on ageing that are available for researchers. We also describe the computational approaches to data interpretation in the field of ageing including gene expression, comparative and pathway analyses, and highlight the challenges for future developments. We review recent biological insights gained from applying bioinformatics methods to analyse and interpret ageing data in different organisms, tissues and conditions.

Flies selected for longevity retain a young gene expression profile

We investigated correlated responses in the transcriptomes of longevity-selected lines of Drosophila melanogaster to identify pathways that affect life span in metazoan systems. We evaluated the gene expression profile in young, middle-aged, and old male flies, finding that 530 genes were differentially expressed between selected and control flies when measured at the same chronological age. The longevity-selected flies consistently showed expression profiles more similar to control flies one age class younger than control flies of the same age. This finding is in accordance with a younger gene expression profile in longevity-selected lines. Among the genes down-regulated in longevity-selected lines, we found a clear over-representation of genes involved in immune functions, supporting the hypothesis of a life-shortening effect of an overactive immune system, known as inflammaging. We judged the physiological age as the level of cumulative mortality. Eighty-four genes were differentially expressed between the control and longevity-selected lines at the same physiological age, and the overlap between the same chronological and physiological age gene lists included 40 candidate genes for increased longevity. Among these candidates were genes with roles in starvation resistance, immune response regulation, and several that have not yet been linked to longevity. Investigating these genes would provide new knowledge of the pathways that affect life span in invertebrates and, potentially, mammals.

Nonhuman primate calorie restriction

Calorie restriction (CR) is the only dietary intervention that repeatedly extends both median and maximal lifespan in a broad range of species. Although there has been considerable interest in CR and its ability to retard aging, the mechanism has remained elusive. In contrast to studies in rodent and nonmammalian systems that are now beginning to provide mechanistic insights into how CR promotes longevity, the efficacy of CR in delaying primate aging has yet to be fully demonstrated. Here we review some of the insights from CR studies in short-lived species. We describe the advantages of using the rhesus monkey as a model for human aging and detail how CR can be successfully implemented in this species. We discuss the findings from our ongoing longitudinal study and outline the effects to date of CR on rhesus monkey health. Finally, we highlight the importance of primate studies in the context of aging research and its potential to advance our understanding of human aging and health.

Transcriptomic underpinning of toxicant-mediated physiological function alterations in three terrestrial invertebrate taxa: a review

Diverse anthropogenic activities often lead to the accumulation of inorganic and organic residues in topsoils. Biota living in close contact with contaminated soils may experience stress at different levels of biological organisation throughout the continuum from the molecular-genetic to ecological and community levels. To date, the relationship between changes at the molecular (mRNA expression) and biochemical/physiological levels evoked by exposures to chemical compounds has been partially established in a limited number of terrestrial invertebrate species. Recently, the advent of a family of transcriptomic tools (e.g. Real-time PCR, Subtractive Suppressive Hybridization, Expressed Sequence Tag sequencing, pyro-sequencing technologies, Microarray chips), together with supporting informatic and statistical procedures, have permitted the robust analyses of global gene expression changes within an ecotoxicological context. This review focuses on how transcriptomics is enlightening our understanding of the molecular-genetic responses of three contrasting terrestrial macroinvertebrate taxa (nematodes, earthworms, and springtails) to inorganics, organics, and agrochemicals.

Gene expression profiling implicates OXPHOS complexes in lifespan extension of flies over-expressing a small mitochondrial chaperone, Hsp22

Aging is a complex process accompanied by a decreased capacity to tolerate and respond to various stresses. Heat shock proteins as part of cell defense mechanisms are up-regulated following stress. In Drosophila, the mitochondrial Hsp22 is preferentially up-regulated in aged flies. Its over-expression results in an extension of lifespan and an increased resistance to stress. Hsp22 has chaperone-like activity in vitro, but the mechanism(s) by which it increases lifespan in flies are unknown. Genome-wide analysis was performed on long-lived Hsp22+ and control flies to unveil transcriptional changes brought by Hsp22. Transcriptomes obtained at 45days, 90% and 50% survival were then compared between them to focus more on genes up- or down-regulated in presence of higher levels of hsp22 mRNA. Hsp22+ flies display an up-regulation of genes mainly related to mitochondrial energy production and protein biosynthesis, two functions normally down-regulated during aging. Interestingly, among the 26 genes up-regulated in Hsp22+ flies, 7 genes encode for mitochondrial proteins, 5 of which being involved in OXPHOS complexes. Other genes that could influence aging such as CG5002, dGCC185 and GstS1 also displayed a regulation linked to Hsp22 expression. The up-regulation of genes of the OXPHOS system in Hsp22+ flies suggest that mitochondrial homeostasis is at the center of Hsp22 beneficial effects on lifespan.

Modifiers of Prat, a de novo purine synthesis gene, in Drosophila melanogaster

Drosophila melanogaster was used to identify genes with a potential role in genetic regulation of purine biosynthesis. In this study we examine two dominant genetic modifiers of the essential gene Prat, which encodes amidophosphoribosyltransferase (EC 2.4.2.14). We found that Mod(Prat:bw)3-1 enhances Prat expression only in female heads, whereas Mod(Prat:bw)3-5 suppresses Prat in all stages and tissues examined for both sexes. For Mod-3-5, gene expression microarrays were used to identify other genes that are affected by the modifier. Three mapping approaches were used to localize these modifiers. Deficiency and meiotic mapping showed that the complex lethal complementation group previously associated with Mod-3-1 and Mod-3-5 is actually due to shared second-site lethal mutations. Using male recombination mapping, Mod-3-1 was localized to a 21 kilobase region containing nine genes, and Mod-3-5 was localized to a 53 kilobase region containing eight genes.

Invertebrate models of age-related muscle degeneration

Functional and structural deterioration of muscles is an inevitable consequence of ageing in a wide variety of animal species. What underlies these changes is a complex network of interactions between the muscle-intrinsic and muscle-extrinsic factors, making it very difficult to distinguish between the cause and the consequence. Many of the genes, structures, and processes implicated in mammalian skeletal muscle ageing are preserved in invertebrate species Drosophila melanogaster and Caenorhabditis elegans. The absence in these organisms of mechanisms that promote muscle regeneration, and substantially different hormonal environment, warrant caution when extrapolating experimental data from studies conducted in invertebrates to mammalian species. The simplicity and accessibility of these models, however, offer ample opportunities for studying age-related myopathologies as well as investigating drugs and therapies to alleviate them.

Expression of hsp22 and hsp70 transgenes is partially predictive of drosophila survival under normal and stress conditions

Drosophila Hsp70 is a highly conserved molecular chaperone with numerous cytoplasmic targets. Hsp22 is an alpha-crystallin-related chaperone (small hsp) that localizes to the mitochondrial matrix. The hsp70 and hsp22 genes are induced in response to acute heat and oxidative stress and are also upregulated during normal aging. Here the hsp22 promoter (-314 to +10) and the hsp70 promoter (-194 to +10) were used to drive expression of the fluorescent reporter proteins green fluorescent protein (GFP) and Discosoma sp. red fluorescent protein (DsRED) in transgenic flies. Multiple transgenic lines were analyzed under normal culture conditions and under oxidative stress and heat stress conditions that significantly shorten life span. Flies were individually housed, and GFP (or DsRED) was quantified at young-age time points using the fluorescence stereomicroscope and image analysis software. Expression of the hsp reporters in young flies was partially predictive of remaining life span: Young flies with high expression tended to die sooner under both control and stress conditions.

Heterochromatin-mediated gene silencing is not affected by Drosophila CBP activity

Cyclic AMP Response Element Binding protein (CREB)-binding protein (CBP) is an acetyltransferase important for modifying histones and chromatin-associated proteins and thus affecting transcription and other DNA metabolic processes. We found that the Drosophila CBP (dCBP) is associated with the NAD(+)-dependent deacetylase, SIR2, which was originally identified as a silencing information regulator in yeast that models silenced and repeated sequence chromatin such as centric heterochromatin, telomeres, and the repeated rDNA sequences. As in yeast, Drosophila sir2 (dsir2) affects the formation and/or function of centric heterochromatin. The fact that we found dCBP in immunecomplexes with dSIR2 in vivo and found that dCBP can interact with dSIR2 directly in vitro suggested that dCBP might affect the packaging of silencing heterochromatin as well. A careful study of the dCBP mutations provides evidence that dCBP does not affect the formation and/or function of centric heterochromatin and thus may affect other dSIR2 functions.

Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue

The fruitfly Drosophila melanogaster is increasingly used as a model organism for studying acute hypoxia tolerance and for studying aging, but the interactions between these two factors are not well known. Here we show that hypoxia tolerance degrades with age in post-hypoxic recovery of whole-body movement, heart rate and ATP content. We previously used (1)H NMR metabolomics and a constraint-based model of ATP-generating metabolism to discover the end products of hypoxic metabolism in flies and generate hypotheses for the biological mechanisms. We expand the reactions in the model using tissue- and age-specific microarray data from the literature, and then examine metabolomic profiles of thoraxes after 4 h at 0.5% O(2) and after 5 min of recovery in 40- versus 3-day-old flies. Model simulations were constrained to fluxes calculated from these data. Simulations suggest that the decreased ATP production during reoxygenation seen in aging flies can be attributed to reduced recovery of mitochondrial respiration pathways and concomitant overdependence on the acetate production pathway as an energy source.

Mitochondria and ageing in Drosophila

Studies in different organisms have revealed that ageing is a complex process involving a tight regulation of gene expression. Among other features, ageing organisms generally display an increased oxidative stress and a decreased mitochondrial function. The increase in oxidative stress can be attributable to reactive oxygen species, which are mainly produced by mitochondria as a by-product of energy metabolism. Consistent with these data, mitochondria have been suggested to play a significant role in lifespan determination. The fruitfly Drosophila melanogaster is a well-suited organism to study ageing as it is relatively short-lived, mainly composed of post-mitotic cells, has sequenced nuclear and mitochondrial genomes, and multiple genetic tools are available. It has been used in genome-wide studies to unveil the molecular signature of ageing, in different feeding and dietary restriction protocols and in overexpression and down-regulation studies to examine the effect of specific compounds or genes/proteins on lifespan. Here we review the various features linking mitochondria and ageing in Drosophila melanogaster.

Genomic studies in ageing research: the need to integrate genetic and gene expression approaches

Genome-wide and hypothesis-based approaches to the study of ageing and longevity have been dominated by genetic investigations. To identify essential mechanisms of a complex trait such as ageing in higher species, a holistic understanding of interacting pathways is required. More information on such interactions is expected to be obtained from global gene expression analysis if combined with genetic studies. Genetic sequence variation often provides a functional gene marker for the trait, whereas a gene expression profile may provide a quantitative biomarker representing complex cellular pathway interactions contributing to the trait. Thus far, gene expression studies have associated multiple pathways to ageing including mitochondrial electron transport and the oxidative stress response. However, most of the studies are underpowered to detect small age-changes. A systematic survey of gene expression changes as a function of age in human individuals and animal models is lacking. Well designed gene expression studies, especially at the level of biological processes, will provide hypotheses on gene-environmental interactions determining biological ageing rate. Cross-sectional studies monitoring the profile as a chronological marker of ageing must be integrated with prospective studies indicating which profiles represent biomarkers preceding and predicting physiological decline and mortality. New study designs such as the Leiden Longevity Study, including two generations of subjects from longevity families, aim to achieve these combined approaches.

Separating cause from effect: how does insulin/IGF signalling control lifespan in worms, flies and mice?

Ageing research has been revolutionized by the use of model organisms to discover genetic alterations that can extend lifespan. In the last 5 years alone, it has become apparent that single gene mutations in the insulin and insulin-like growth-factor signalling pathways can lengthen lifespan in worms, flies and mice, implying evolutionary conservation of mechanisms. Importantly, this research has also shown that these mutations can keep the animals healthy and disease-free for longer and can alleviate specific ageing-related pathologies. These findings are striking in view of the negative effects that disruption of these signalling pathways can also produce. Here, we summarize the body of work that has lead to these discoveries and point out areas of interest for future work in characterizing the genetic, molecular and biochemical details of the mechanisms to achieving a longer and healthier life.

Integrating metabolomics and phenomics with systems models of cardiac hypoxia

Hypoxia is the major cause of necrotic cell death in myocardial infarction. Cellular energy supply and demand under hypoxic conditions is regulated by many interacting signaling and transcriptional networks, which complicates studies on individual proteins and pathways. We apply an integrated systems approach to understand the metabolic and functional response to hypoxia in muscle cells of the fruit fly Drosophila melanogaster. In addition to its utility as a hypoxia-tolerant model organism, Drosophila also offers advantages due to its small size, fecundity, and short life cycle. These traits, along with a large library of single-gene mutations, motivated us to develop new, computer-automated technology for gathering in vivo measurements of heart function under hypoxia for a large number of mutant strains. Phenotype data can be integrated with in silico cellular networks, metabolomic data, and microarrays to form qualitative and quantitative network models for prediction and hypothesis generation. Here we present a framework for a systems approach to hypoxia in the cardiac myocyte, starting from nuclear magnetic resonance (NMR) metabolomics, a constraint-based metabolic model, and phenotypic profiles.

The salivary glands and saliva of Anopheles gambiae as an essential step in the Plasmodium life cycle: a global proteomic study

Proteins synthesized in the salivary glands of the Anopheles gambiae mosquito are thought to be important in the life cycle of the malaria parasite Plasmodium. To describe A. gambiae salivary gland and saliva contents, we combined several techniques: 1-DE, 2-DE and LC MS/MS. This study has identified five saliva proteins and 122 more proteins from the salivary glands, including the first proteomic description for 89 of these salivary gland proteins. Since the invasion and sporozoite maturation take place during the process of salivary glands ageing, the effect of salivary gland age on salivary component composition was examined. LC MS/MS profiling of young versus old salivary gland proteomes suggests that there is an over-representation of proteins involved in signaling and proteins related to the immune response in the proteins from older mosquitoes. The iTRAQ labeling was used for a comparative proteomic analysis of salivary gland samples from infected or Plasmodium berghei-free mosquitoes. The expression levels of five secreted proteins were altered when the parasite was present. These observations will serve as a basis for future work concerning the possible role of these proteins in the interaction between A. gambiae, Plasmodium and the mammalian host.

Systems biology of aging in four species

Using DNA microarrays to generate transcriptional profiles of the aging process is a powerful tool for identifying biomarkers of aging. In Caenorhabditis elegans, a number of whole-genome profiling studies identified genes that change expression levels with age. High-throughput RNAi screens in worms determined a number of genes that modulate lifespan when silenced. Transcriptional profiling of the fly head identified a molecular pathway, the 'response to light' gene set, that increases expression with age and could be directly related to the tendency for a reduction in light levels to extend fly's lifespan. In mouse, comparing the gene expression profiles of several drugs to the gene expression profile of caloric restriction identified metformin as a drug whose action could potentially mimic caloric restriction in vivo. Finally, genes in the mitochondrial electron transport chain group decrease expression with age in the human, mouse, fly, and worm.

Temporal and spatial transcriptional profiles of aging in Drosophila melanogaster

Temporal and tissue-specific alterations in gene expression have profound effects on aging of multicellular organisms. However, much remains unknown about the patterns of molecular changes in different tissues and how different tissues interact with each other during aging. Previous genomic studies on invertebrate aging mostly utilized the whole body or body parts and limited age-points, and failed to address tissue-specific aging. Here we measured genome-wide expression profiles of aging in Drosophila melanogaster for seven tissues representing nervous, muscular, digestive, renal, reproductive, and storage systems at six adult ages. In each tissue, we identified hundreds of age-related genes exhibiting significant changes of transcript levels with age. The age-related genes showed clear tissue-specific patterns: <10% of them in each tissue were in common with any other tissue; <20% of the biological processes enriched with the age-related genes were in common between any two tissues. A significant portion of the age-related genes were those involved in physiological functions regulated by the corresponding tissue. Nevertheless, we identified some overlaps of the age-related functional groups among tissues, suggesting certain common molecular mechanisms that regulate aging in different tissues. This study is one of the first that defined global, temporal, and spatial changes associated with aging from multiple tissues at multiple ages, showing that different tissues age in different patterns in an organism. The spatial and temporal transcriptome data presented in this study provide a basis and a valuable resource for further genetic and genomic investigation of tissue-specific regulation of aging.

Aging perturbs 26S proteasome assembly in Drosophila melanogaster

Aging is associated with loss of quality control in protein turnover. The ubiquitin-proteasome pathway is critical to this quality control process as it degrades mutated and damaged proteins. We identified a unique aging-dependent mechanism that contributes to proteasome dysfunction in Drosophila melanogaster. Our studies are the first to show that the major proteasome form in old (43-47 days old) female and male flies is the weakly active 20S core particle, while in younger (1-32 days old) flies highly active 26S proteasomes are preponderant. Old (43-47 days) flies of both genders also exhibit a decline (approximately 50%) in ATP levels, which is relevant to 26S proteasomes, as their assembly is ATP-dependent. The steep declines in 26S proteasome and ATP levels were observed at an age (43-47 days) when the flies exhibited a marked drop in locomotor performance, attesting that these are "old age" events. Remarkably, treatment with a proteasome inhibitor increases ubiquitinated protein levels and shortens the life span of old but not young flies. In conclusion, our data reveal a previously unknown mechanism that perturbs proteasome activity in "old-age" female and male Drosophila most likely depriving them of the ability to effectively cope with proteotoxic damages caused by environmental and/or genetic factors.

Aging impact on biochemical activities and gene expression of Drosophila melanogaster mitochondria

The consequences of aging are characterized by a decline in the main cellular functions, including those of the mitochondria. Although these consequences have been much studied, efforts have often focused solely on a few parameters used to assess the "state" of mitochondrial function during aging. We performed comparative measurements of several parameters in young (a few days) and old (8 and 12 weeks) adult male Drosophila melanogaster: respiratory complex activities, mitochondrial respiration, ATP synthesis, lipid composition of the inner membrane, concentrations of respiratory complex subunits, expression of genes (nuclear and mitochondrial) coding for mitochondrial proteins. Our results show that, in the mitochondria of "old" flies, the activities of three respiratory complexes (I, III, IV) are greatly diminished, ATP synthesis is decreased, and the lipid composition of the inner membrane (fatty acids, cardiolipin) is modified. However, the respiration rate and subunit concentrations measured by Western blot are unaffected. Although cellular mitochondrial DNA (mtDNA) content remains constant, there is a decrease in concentrations of nuclear and mitochondrial transcripts apparently coordinated. The expression of nuclear genes encoding the transcription factors TFAM, TFB1, TFB2, and DmTTF, which are essential for the maintenance and expression of mtDNA are also decreased. The decrease in nuclear and mitochondrial transcript concentrations may be one of the principal effects of aging on mitochondria, and could explain observed decreases in mitochondrial efficiency.

Application of advanced technologies in ageing research

Several technologies that emerged in the post-genomic era have been particularly useful in dissecting the molecular mechanisms of complex biological processes through the systems approach. Here, we review how three of these technologies, namely transcriptional profiling, large-scale RNA interference (RNAi) and genome-wide location analysis of protein-DNA interactions, have been used in the study of ageing in metazoans. We also highlight recent developments of these three technologies and how these developments are applicable to ageing research.

Age-dependent usage of double-strand-break repair pathways

A DNA double-strand break (DSB) can be repaired by any of several alternative and competing mechanisms. The repaired sequences often differ from the original depending on which mechanism was used so that the cell's "choice" of repair mechanism can have profound genetic consequences. DSBs can accumulate with age , and human diseases that mimic some of the effects of aging, such as increased susceptibility to cancer, are associated with certain defects in DSB repair . The premeiotic germ cells of Drosophila provide a useful model for exploration of the connection between aging and DNA repair because these cells are subject to mortality and other age-related changes , and their DNA repair process is easily quantified. We used Rr3, a repair reporter system in Drosophila, to show that the relative usage of DSB repair mechanisms can change substantially as an organism ages. Homologous repair increased linearly in the male germline from 14% in young individuals to more than 60% in old ones, whereas two other pathways showed a corresponding decrease. Furthermore, the proportion of longer conversion tracts (>156 bp) also increased nearly 2-fold as the flies aged. These findings are relevant to the more general question of how DNA damage and repair are related to aging.