Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv

OASIS portable: User-friendly offline suite for secure survival analysis

Online application for survival analysis (OASIS) and its update, OASIS 2, have been widely used for survival analysis in biological and medical sciences. Here, we provide a portable version of OASIS, an all-in-one offline suite, to facilitate secure survival analysis without uploading the data to online servers. OASIS portable provides a virtualized and isolated instance of the OASIS 2 webserver, operating on the users' personal computers, and enables user-friendly survival analysis without internet connection and security issues.

Protective Role of Hsp27 in the Nonylphenol-Induced Locomotory and Longevity Toxicity

Background Gut health is directly proportional to an organism's fitness. Our recent study showed a functional link between oxidative stress and heat shock protein 27 (Hsp27, a stress protein) in the Drosophila larval gut, which coordinates the nonylphenol (an endocrine disruptor) allied sub-cellular and developmental adversities.

Objective In continuation with the prior study, the present study aimed to explore the association of Hsp27 with locomotory and survival against nonylphenol-induced toxicity in the Drosophila gut.

Methods and Methodology The freshly emerged adult flies were exposed to nonylphenol (5.0 µg/mL) for 10 to 40 days, and their locomotory performance (climbing activity) and survivability were assessed. ANOVA was used to evaluate the statistical significance of the mean values in control and treated flies.

Results Nonylphenol exposure markedly influenced locomotory activity and survivability after 30 to 40 days. For instance, ∼76% (40 days) declined locomotor behavior, and ∼35% (40 days) reduced survivability was observed. While the overexpression of Hsp27 in the organism's gut showed improvement in locomotory performance and survivability after 30 to 40 days. No significant alteration in locomotory performance and survivability was observed after 10 to 20 days of nonylphenol exposure.

Conclusion The present study illustrates that Hsp27 overexpression in the Drosophila gut improves the locomotory performance and survivability in the nonylphenol exposed Drosophila. This also indicates the possible connection between the gut and organismal fitness.

Relationship between lifespan and somatic mutation in D. melanogaster after treatment with chlorophyllin

Sodium copper chlorophyllin (SCC) has a genetic damage inhibitory capacity due to its antioxidant action. For this reason, it was considered to investigate its role in the life span of Drosophila melanogaster and its relationship with the frequency of somatic mutation induced by gamma rays. Results indicated that SCC alone prolonged the lifespan only in females, but in combination with 20 Gy of gamma rays, the aging delay in both sexes was significant. In addition to confirming that the porphyrin reduces the frequency of mutation, the individuals with the highest mutation load are the individuals who die more quickly, and once they are eliminated, the survivor individuals treated with 20 Gy or with SCC + 20 Gy, died at the same rate. The results together indicate that SCC not only inhibits induced genetic damage, but it also has beneficial effects that probably cause an aging delay of the treated population that need to be investigated.

Impact of Dietary Potassium Nitrate on the Life Span of Drosophila melanogaster

The recently defined and yet rather new topic of healthy aging is attracting more attention worldwide. As the world population is getting older, it is rapidly becoming essential to develop and maintain functional abilities at older age and develop mechanisms to protect the senior population from chronic diseases. One of the most effective components, as well as processes associated with aging, is the recently discovered and Nobel prize-awarded—nitric oxide (NO) (as a signaling molecule), which, followed by later discoveries, showed to have a positive metabolic, immunological, and anti-inflammatory effect. Nitrates are one of the most debated topics of the last decade in the scientific community due to their pathways involved in the production of nitric oxide. Thus, the objective of this study is to evaluate the effect of different potassium nitrate concentrate supplementation on Drosophila melanogaster longevity imitating a human carbohydrate-based diet with relationship to possible cause of oxidative stress. Influence of 0.5–3% potassium nitrate medium on the lifespan and motor function in different groups consisting of 100 fruit fly females in each was analyzed. In this assay, female fly species supplemented with potassium nitrate diet showed life span increase by 18.6% and 5.1% with 1% and 2% KNO3, respectively, with a positive impact on locomotor function. In conclusion, we found that low concentration of potassium nitrate medium increased lifespan and locomotor function in Drosophila melanogaster.

Calorie restriction is the most reasonable anti-ageing intervention: a meta-analysis of survival curves

Despite technological advances, the survival records from longevity experiments remain the most indispensable tool in ageing-related research. A variety of interventions, including medications, genetic manipulations and calorie restriction (CR), have been demonstrated to extend the lifespan of several species. Surprisingly, few systematic studies have investigated the differences among these anti-ageing strategies using survival data. Here, we conduct a comprehensive and comparative meta-analysis of numerous published studies on Caenorhabditis elegans and Drosophila. We found that CR and genetic manipulations are generally more effective than medications at extending the total lifespan in both models, and CR can improve the ageing pattern of C. elegans. We further analysed the survival variation for different anti-ageing medications and determined that hypoglycaemic agents and antioxidants are advantageous despite only moderately increasing the overall lifespan; therefore, these two types of medications are promising CR mimetics. Analysis of genetic manipulations also indicated that the genes or pathways that extend lifespan in a healthier pattern are associated with CR. These results suggest that CR or CR mimetics may be the most reasonable and potentially beneficial anti-ageing strategy.

OASIS 2: online application for survival analysis 2 with features for the analysis of maximal lifespan and healthspan in aging research

Online application for survival analysis (OASIS) has served as a popular and convenient platform for the statistical analysis of various survival data, particularly in the field of aging research. With the recent advances in the fields of aging research that deal with complex survival data, we noticed a need for updates to the current version of OASIS. Here, we report OASIS 2 (http://sbi.postech.ac.kr/oasis2), which provides extended statistical tools for survival data and an enhanced user interface. In particular, OASIS 2 enables the statistical comparison of maximal lifespans, which is potentially useful for determining key factors that limit the lifespan of a population. Furthermore, OASIS 2 provides statistical and graphical tools that compare values in different conditions and times. That feature is useful for comparing age-associated changes in physiological activities, which can be used as indicators of “healthspan.” We believe that OASIS 2 will serve as a standard platform for survival analysis with advanced and user-friendly statistical tools for experimental biologists in the field of aging research.

Drosophila as a model for ageing

Drosophila melanogaster has been a key model in developing our current understanding of the molecular mechanisms of ageing. Of particular note is its role in establishing the evolutionary conservation of reduced insulin and IGF-1-like signaling in promoting healthy ageing. Capitalizing on its many advantages for experimentation, more recent work has revealed how precise nutritional and genetic interventions can improve fly lifespan without obvious detrimental side effects. We give a brief summary of these recent findings as well as examples of how they may modify ageing via actions in the gut and muscle. These discoveries highlight how expanding our understanding of metabolic and signaling interconnections will provide even greater insight into how these benefits may be harnessed for anti-ageing interventions.

Meta-Analysis of 29 Experiments Evaluating the Effects of Rapamycin on Life Span in the Laboratory Mouse

Rapamycin has favorable effects on aging in mice and may eventually be applied to encourage "healthy aging" in humans. This study analyzed raw data from 29 survival studies of rapamycin- and control-treated mice, with the goals of estimating summary statistics and identifying factors associated with effect size heterogeneity. Meta-analysis demonstrated significant heterogeneity across studies, with hazard ratio (HR) estimates ranging from 0.22 (95% confidence interval [CI]: 0.06-0.82) to 0.92 (95% CI: 0.65-1.28). Sex was the major factor accounting for effect size variation, and mortality was decreased more in females (HR = 0.41; 95% CI: 0.35-0.48) as compared with males (HR = 0.63; 95% CI: 0.55-0.71). Rapamycin effects were also genotype dependent, however, with stronger survivorship increases in hybrid mice (14.4%; 95% CI: 12.5-16.3%) relative to pure inbred strains (8.8%; 95% CI: 6.2-11.6%). Number needed to treat was applied as an effect size metric, which consistently identified early senescence as the age of peak treatment benefit. These results provide synthesis of existing data to support the potential translation of findings from mouse to primate species. Because rapamycin's effect on survival depends on sex and genotype, further work is justified to understand how these factors shape treatment response.

Computational Analysis of Lifespan Experiment Reproducibility

Independent reproducibility is essential to the generation of scientific knowledge. Optimizing experimental protocols to ensure reproducibility is an important aspect of scientific work. Genetic or pharmacological lifespan extensions are generally small compared to the inherent variability in mean lifespan even in isogenic populations housed under identical conditions. This variability makes reproducible detection of small but real effects experimentally challenging. In this study, we aimed to determine the reproducibility of C. elegans lifespan measurements under ideal conditions, in the absence of methodological errors or environmental or genetic background influences. To accomplish this, we generated a parametric model of C. elegans lifespan based on data collected from 5,026 wild-type N2 animals. We use this model to predict how different experimental practices, effect sizes, number of animals, and how different "shapes" of survival curves affect the ability to reproduce real longevity effects. We find that the chances of reproducing real but small effects are exceedingly low and would require substantially more animals than are commonly used. Our results indicate that many lifespan studies are underpowered to detect reported changes and that, as a consequence, stochastic variation alone can account for many failures to reproduce longevity results. As a remedy, we provide power of detection tables that can be used as guidelines to plan experiments with statistical power to reliably detect real changes in lifespan and limit spurious false positive results. These considerations will improve best-practices in designing lifespan experiment to increase reproducibility.

HCSGD: An integrated database of human cellular senescence genes

Cellular senescence is an irreversible cell cycle arrest program in response to various exogenous and endogenous stimuli like telomere dysfunction and DNA damage. It has been widely accepted as an anti-tumor program and is also found closely related to embryo development, tissue repair, organismal aging and age-related degenerative diseases. In the past decades, numerous efforts have been made to uncover the gene regulatory mechanisms of cellular senescence. There is a strong demand to integrate these data from various resources into one open platform. To facilitate researchers on cellular senescence, we have developed Human Cellular Senescence Gene Database (HCSGD) by integrating multiple online published data sources into a comprehensive senescence gene annotation platform (http://bioinfo.au.tsinghua.edu.cn/member/xwwang/HCSGD). Potential Human Cellular Senescence Genes (HCSGS) were collected by combining information from published literatures, gene expression profiling data and Protein-Protein Interaction networks. Additionally, genes are annotated with gene ontology annotation and microRNA/drug/compound target information. HCSGD provides a valuable resource to visualize cellular senescence gene networks, browse annotated functional information, and retrieve senescence-associated genes with a user-friendly web interface.

Protocols to Study Aging in Drosophila

The fruit fly Drosophila melanogaster offers a host of advantages for studying the biology of aging: a well-understood biology, a wide range of genetic reagents, well-defined dietary requirements, and a relatively short life span, with a median of ~80 days and maximum ~100 days. Several phenotypes can be used to assess the aging process, but the simplest and most widely used metric is length of life. Here we describe a standard life span assay for Drosophila housed on a simple sugar/yeast diet.

SurvCurv database and online survival analysis platform update

Understanding the biology of ageing is an important and complex challenge. Survival experiments are one of the primary approaches for measuring changes in ageing. Here, we present a major update to SurvCurv, a database and online resource for survival data in animals. As well as a substantial increase in data and additions to existing graphical and statistical survival analysis features, SurvCurv now includes extended mathematical mortality modelling functions and survival density plots for more advanced representation of groups of survival cohorts.

AVAILABILITY AND IMPLEMENTATION

The database is freely available at https://www.ebi.ac.uk/thornton-srv/databases/SurvCurv/. All data are published under the Creative Commons Attribution License.

CONTACT

matthias.ziehm@ebi.ac.uk.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

MDL-1, a growth- and tumor-suppressor, slows aging and prevents germline hyperplasia and hypertrophy in C. elegans

In C. elegans, increased lifespan in daf-2 insulin/IGF-1 receptor mutants is accompanied by up-regulation of the MDL-1 Mad basic helix-loop-helix leucine zipper transcription factor. Here we describe the role of mdl-1 in C. elegans germline proliferation and aging. The deletion allele mdl-1(tm311) shortened lifespan, and did so significantly more so in long-lived daf-2 mutants implying that mdl-1(+) contributes to effects of daf-2 on lifespan. mdl-1 mutant hermaphrodites also lay increased numbers of unfertilized oocytes. During aging, unfertilized oocytes in the uterus develop into tumors, whose development was accelerated by mdl-1(tm311). Opposite phenotypes were seen in daf-2 mutants, i.e. mdl-1 and daf-2 mutant germlines are hyperplastic and hypoplastic, respectively. Thus, MDL-1, like its mammalian orthologs, is an inhibitor of cell proliferation and growth that slows progression of an age-related pathology in C. elegans (uterine tumors). In addition, intestine-limited rescue of mdl-1 increased lifespan but not to wild type levels. Thus, mdl-1 likely acts both in the intestine and the germline to influence age-related mortality.

The C. elegans lifespan assay toolkit

Since the discovery of single gene mutations that double its lifespan, the nematode Caenorhabditis elegans has provided remarkable insights into the biology of aging. The precisely measurable lifespan of worms has proven to be an efficient tool to assess the impact of various genetic, physiological and environmental factors on organismal aging. In this article, we describe methods to set up and monitor experiments to determine worm lifespan. We include procedures used for classical, small-scale lifespan assays that are generally performed on solid media, and review recent advances in high-throughput, automated longevity experiments conducted in liquid culture and microfluidic devices. In addition, tools that help analyze this data to obtain survival statistics are summarized, and C. elegans strains that offer particular advantages for lifespan studies are listed.

Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data

Survival records of longevity experiments are a key component in research on aging. However, surprisingly there have been very few cross-study analyses, besides comparisons of median lifespans or similar summary information. Here, we use a large set of full survival data from various studies to address questions in aging, which are beyond the scope of individual studies. We characterize survival differences between female and male flies of different genetic Drosophila strains, showing significant differences between strains. We further analyse the variation in survival of control cohorts recorded under highly similar conditions within different Drosophila strains. We found that overall transgenic constructs of the UAS/GAL4 expression system which should have no effect (e.g. a GAL4 construct alone) extend lifespan significantly in the w1118 strain. Using a large data set comprised of various studies, we found no evidence for larger lifespan extensions being associated with shorter lifespans of the control in Drosophila. This demonstrates that lifespan extending treatments are not purely rescuing weak backgrounds.