Scharf, A. et al. (2017) International Worm Meeting "How does aging influence C. elegans population dynamics?"

Jin, H., Kornfeld, K., Scharf, A., Mitteldorf, J.

[International Worm Meeting, 2017]

Aging research primarily concentrates on how individuals age in order to develop strategies to prolong life or retard age-related changes. Another dimension of aging that has received less attention is the effects of individual aging on whole populations and the emergent property of population dynamics. In this context, aging is one life-history trait and has the potential to affect the number of individuals and the age-structure in a population. To analyze the role of aging in the context of population dynamics, we developed an artificial ecosystem with the nematode C. elegans so that we can directly measure population dynamics. Worms are cultured in liquid medium with a controlled nutrient influx of E. coli, a predefined predation-rate, and automated worm counters are used to monitor population size. In parallel we developed a computational simulation that mirrors the laboratory ecosystem and allows us to systematically analyze the relationship of aging and other life history traits on population dynamics in high throughput. Using this approach, we observed that wild type populations grew to a maximum population size of 1 million animals and declined rapidly to 300,000 animals in the first month. Finally, the population recovered and fluctuated constantly between 300,000 and 600,000 animals over the next 2 months. The first high inflection point followed by a crash of the population is typical for starting populations and is often observed during repopulations in the wild. In the starting population the number of animals is low and, therefore, food or prey accumulates until the population reaches a maximum. Food or prey is now the limiting capacity and the population decreases until it reaches an equilibrium between size of the population and availability of food. While this population is stable, the number of animals fluctuates over time. The specific population dynamics can be characterized by measuring the mean number of animals, the average minimum and maximum, the time between population peaks, and thence by calculating the amplitude and period of the fluctuations. Next, we are exploring the population dynamics of long- and short-lived mutants in the laboratory and with the computational simulation to systematically analyze how aging in combination with other life history traits such as reproduction, metabolism, or dauer formation affects the stability of populations. We compare the respective population dynamic characteristics to wild type worm populations and estimate the relative risk of each population to become extinct. The presented data will address the impact of aging in the context of systems biology.

Scharf A et al. (2021) Front Cell Dev Biol "Reproductive Aging in Caenorhabditis elegans: From Molecules to Ecology."

Pohl F, Egan BM, Kornfeld K, Scharf A, Kocsisova Z

[Front Cell Dev Biol, 2021]

Aging animals display a broad range of progressive degenerative changes, and one of the most fascinating is the decline of female reproductive function. In the model organism Caenorhabditis elegans, hermaphrodites reach a peak of progeny production on day 2 of adulthood and then display a rapid decline; progeny production typically ends by day 8 of adulthood. Since animals typically survive until day 15 of adulthood, there is a substantial post reproductive lifespan. Here we review the molecular and cellular changes that occur during reproductive aging, including reductions in stem cell number and activity, slowing meiotic progression, diminished Notch signaling, and deterioration of germ line and oocyte morphology. Several interventions have been identified that delay reproductive aging, including mutations, drugs and environmental factors such as temperature. The detailed description of reproductive aging coupled with interventions that delay this process have made C. elegans a leading model system to understand the mechanisms that drive reproductive aging. While reproductive aging has dramatic consequences for individual fertility, it also has consequences for the ecology of the population. Population dynamics are driven by birth and death, and reproductive aging is one important factor that influences birth rate. A variety of theories have been advanced to explain why reproductive aging occurs and how it has been sculpted during evolution. Here we summarize these theories and discuss the utility of C. elegans for testing mechanistic and evolutionary models of reproductive aging.

Scharf A et al. (2013) ACS Nano "Effect of nanoparticles on the biochemical and behavioral aging phenotype of the nematode Caenorhabditis elegans."

von Mikecz A, Piechulek A, Scharf A

[ACS Nano, 2013]

Invertebrate animal models such as the nematode Caenorhabditis elegans (C. elegans) are increasingly used in nanotechnological applications. Research in this area covers a wide range from remote control of worm behavior by nanoparticles (NPs) to evaluation of organismal nanomaterial safety. Despite of the broad spectrum of investigated NP-bio interactions, little is known about the role of nanomaterials with respect to aging processes in C. elegans. We trace NPs in single cells of adult C. elegans and correlate particle distribution with the worm's metabolism and organ function. By confocal microscopy analysis of fluorescently labeled NPs in living worms, we identify two entry portals for the uptake of nanomaterials via the pharynx to the intestinal system and via the vulva to the reproductive system. NPs are localized throughout the cytoplasm and the cell nucleus in single intestinal, and vulval B and D cells. Silica NPs induce an untimely accumulation of insoluble ubiquitinated proteins, nuclear amyloid and reduction of pharyngeal pumping that taken together constitute a premature aging phenotype of C. elegans on the molecular and behavioral level, respectively. Screening of different nanomaterials for their effects on protein solubility shows that polystyrene or silver NPs do not induce accumulation of ubiquitinated proteins suggesting that alteration of protein homeostasis is a unique property of silica NPs. The nematode C. elegans represents an excellent model to investigate the effect of different types of nanomaterials on aging at the molecule, cell, and whole organism level.

Scharf, Andrea et al. (2015) International Worm Meeting "Amyloid formation controls worm behavior."

Piechulek, Annette, Scharf, Andrea, von Mikecz, Anna

[International Worm Meeting, 2015]

The accumulation of amyloid-like structures and protein aggregation are hallmarks of aging and neurodegenerative diseases, but the role of impaired protein homeostasis in the aging process and in pathogenesis is still controversial. To analyze the role of protein fibrillation we use nanoparticles to induce proteostatic stress in Caenorhabditis elegans. Filter-trap assays show that stressed young worms accumulate SDS-insoluble, ubiquitinated proteins that are normally a feature of old adult C. elegans. The premature biochemical phenotype concurs with concentrated amyloid in the nucleoli of intestinal cells that can be detected after 24h nanoparticle exposition. Single cell imaging and light sheet microscopy reveal that nanoparticles enter cells and nuclei of the worm and accumulate in organs such as pharynx, intestine, spermathecae and vulva. The nanoparticle exposition results in a premature decline of the respective organ function such as egg laying and pharyngeal pumping (Scharf et al., 2013). In addition, nanoparticle-stressed worms show locomotion defects including locomotory senescence and reduced ability to reach food compared to untreated worms. We follow the idea that the observed changes in worm behavior are the results of nanoparticle-induced protein fibrillation. The affected behavior is driven by well described neural circuits which allows for correlation between protein fibrillation and neural function in organismal aging. The presented data will address interactions between amyloid formation, altered neural behavior phenotypes and neurotoxicity of protein aggregation in premature aging of C. elegans.

Scharf A et al. (2011) Nucleic Acids Res "Distant positioning of proteasomal proteolysis relative to actively transcribed genes."

Kubitscheck U, Meier UT, von Mikecz A, Veith R, Scharf A, Grozdanov PN

[Nucleic Acids Res, 2011]

While it is widely acknowledged that the ubiquitin-proteasome system plays an important role in transcription, little is known concerning the mechanistic basis, in particular the spatial organization of proteasome-dependent proteolysis at the transcription site. Here, we show that proteasomal activity and tetraubiquitinated proteins concentrate to nucleoplasmic microenvironments in the euchromatin. Such proteolytic domains are immobile and distinctly positioned in relation to transcriptional processes. Analysis of gene arrays and early genes in Caenorhabditis elegans embryos reveals that proteasomes and proteasomal activity are distantly located relative to transcriptionally active genes. In contrast, transcriptional inhibition generally induces local overlap of proteolytic microdomains with components of the transcription machinery and degradation of RNA polymerase II. The results establish that spatial organization of proteasomal activity differs with respect to distinct phases of the transcription cycle in at least some genes, and thus might contribute to the plasticity of gene expression in response to environmental stimuli.

Scharf A et al. (2022) iScience "Pollutants corrupt resilience pathways of aging in the nematode C. elegans"

Scharf A, von Mikecz A, Guehrs KH, Limke A

[iScience, 2022]

Delaying aging while prolonging health and lifespan is a major goal in aging research. One promising strategy is to focus on reducing negative interventions such as pollution and their accelerating effect on age-related degeneration and disease. Here, we used the short-lived model organism C. elegans to analyze whether two candidate pollutants corrupt general aging pathways. We show that the emergent pollutant silica nanoparticles (NPs) and the classic xenobiotic inorganic mercury reduce lifespan and cause a premature protein aggregation phenotype. Comparative mass spectrometry revealed that increased insolubility of proteins with important functions in proteostasis is a shared phenotype of intrinsic- and pollution-induced aging supporting the hypothesis that proteostasis is a central resilience pathway controlling lifespan and aging. The presented data demonstrate that pollutants corrupt intrinsic aging pathways. Reducing pollution is, therefore, an important step to increasing healthy aging and prolonging life expectancies on a population level in humans and animals.

Scharf, A. et al. (2019) International Worm Meeting "Stayin' alive in a worm population - a system biology approach to aging."

Mitteldorf, J., Jin, H., Scharf, A., Kornfeld, K.

[International Worm Meeting, 2019]

The quest for the fountain of youth is as old as humanity, but we still know little about how to defeat aging. If we take a step back from the human desire to prolong our lives, aging is a fascinating life-history trait that has the potential to influence population dynamics. In principle, if an organism lives briefly or forever, it will change the number of individuals and the age-structure in a population, with important implications for population stability. Although aging of individual organisms is frequently analyzed in laboratories, most wild populations don't support the survival of senior individuals. This raises ecological questions: (1) What are the characteristics of populations that support senior individuals? (2) Why are demographic trajectories so different if senior individuals rarely occur in nature? (3) How does the fine-tuned balance between lifespan and reproductive span prevent extinction? Aging of individual C. elegans in the laboratory is observed and described in detail, but the role of aging in natural populations is not well characterized. To fill this gap and to analyze the effects of organismal aging on the emergent property of population dynamics, we developed an artificial ecosystem that allows us to track and manipulate worm populations over months. Worms are cultured in liquid medium with a controlled nutrient influx of E. coli and a predefined predation-rate. Automated worm counters are used to monitor population size. To complement this experimental system, we developed a computational simulation that corresponds to the laboratory worm ecosystem and allows us to systematically change single worm traits to analyze the relationship of life-history traits on population dynamics in high throughput. We will highlight new conclusions from this integrated experimental system. In particular, the level and stage specificity of predation dramatically affects the number of animals that die of aging. We have defined conditions where very few animals die of old age and lifespan has little effect on population dynamics. By contrast, there are conditions where nearly all adults die of old age and lifespan significantly effects population dynamics. These conditions may be shared by wild populations that support senior individuals.

Scharf A et al. (2015) Nanotoxicology "Anti-amyloid compounds protect from silica nanoparticle-induced neurotoxicity in the nematode C. elegans."

Guhrs KH, von Mikecz A, Scharf A

[Nanotoxicology, 2015]

Identifying nanomaterial-bio-interactions are imperative due to the broad introduction of nanoparticle (NP) applications and their distribution. Here, we demonstrate that silica NPs effect widespread protein aggregation in the soil nematode Caenorhabditis elegans ranging from induction of amyloid in nucleoli of intestinal cells to facilitation of protein aggregation in body wall muscles and axons of neural cells. Proteomic screening revealed that exposure of adult C. elegans with silica NPs promotes segregation of proteins belonging to the gene ontology (GO) group of "protein folding, proteolysis and stress response" to an SDS-resistant aggregome network. Candidate proteins in this group include chaperones, heat shock proteins and subunits of the 26S proteasome which are all decisively involved in protein homeostasis. The pathway of protein homeostasis was validated as a major target of silica NPs by behavioral phenotyping, as inhibitors of amyloid formation rescued NP-induced defects of locomotory patterns and egg laying. The analysis of a reporter worm for serotonergic neural cells revealed that silica NP-induced protein aggregation likewise occurs in axons of HSN neurons, where presynaptic accumulation of serotonin, e.g. disturbed axonal transport reduces the capacity for neurotransmission and egg laying. The results suggest that in C. elegans silica NPs promote a cascade of events including disturbance of protein homeostasis, widespread protein aggregation and inhibition of serotonergic neurotransmission which can be interrupted by compounds preventing amyloid fibrillation.

Scharf, Andrea et al. (2021) International Worm Meeting "A population state shift supports aging as a cause of adult death"

Tan, Chieh-Hsiang, Scharf, Andrea, Brady, Brian, Wilson, Andrea, Schneider, Daniel, DiAntonio, Gabe, Sanchez, Francesca, Ram, Natasha, Jin, He, Armstead, Brinda, Kocsisova, Zuzana, Kornfeld, Kerry

[International Worm Meeting, 2021]

Birth and death drive population dynamics and determine whether a population survives or is doomed for extinction. Individual traits that influence development, diapause, reproduction, aging and lifespan must impact the age structure and survival of a population. However, the relationships between individual traits and population dynamics are still a major challenge in the emerging field of ecology-development (eco-devo), because wild populations exist in complex ecosystems that are challenging to investigate and undesirable to manipulate. Here, we introduce a laboratory ecosystem based on the model organism C. elegans that can be used to measure and manipulate worm populations over hundreds of generations. To complement this experimental system, we developed a computational simulation that realistically models the ecosystem and makes it possible to monitor the life history of every single worm in the population. With this integrated systems approach, we investigated the role of aging in population dynamics. The first question we addressed was why some populations support old animals whereas, in other populations, all animals die young. We discovered that old age as a cause of death is influenced by three conditions: maximum lifespan, rate of adult culling, and progeny number/food stability. More specifically, the populations displayed an unexpected tipping point for aging as the primary cause of adult death. In populations with high progeny survival and regular starvation almost all adults died young. In contrast, a reduction of progeny survival over the tipping point caused a dramatic shift in the population with the consequence that nearly all adults died of old age. By defining these conditions, we establish a conceptual framework that explains why animals as different as mayflies and elephants die of old age in the wild. In conclusion, we created a powerful experimental platform to investigate the relationships between individual developmental processes, developmental plasticity, and population dynamics including extinction.

Scharf, Andrea et al. (2021) International Worm Meeting "Climate Change and Extinction - Lessons from C. elegans Population Dynamics"

Kornfeld, Kerry, Scharf, Andrea

[International Worm Meeting, 2021]

Biodiversity loss is one of the major challenges for the 21st century. Ecosystems suffer from our modern civilization through pollution, agriculture, overexploitation, industrialization, coastal disturbance, landscaping, and ultimately climate change. Humans have a track record of driving species extinct ranging from passenger pigeons over baiji dolphins to western black rhinoceros. In order to preserve biodiversity and minimize extinction, a deep understanding of population dynamics is necessary. To address this challenge, we are using our previously developed experimental platform comprised of a laboratory ecosystem with C. elegans and a complementary computational simulation. With this platform, we can model how overexploitation, habitat loss, and climate change destabilizes populations to extinction. We found that gradual changes in predation rates, habitat sizes, temperature, and food availability have little effect on population dynamics. In contrast, the populations collapsed if the environmental conditions reached a certain threshold (tipping point) and/or several environmental stressors accumulated. For example, C. elegans populations can only resist starvation for extended periods if predations rates are low and the temperature is optimal. We have defined the conditions for population collapse in wild type C. elegans in order to screen wild isolates, mutants, and in silico mutants for stabilizing traits. One future application is to modify the computational simulation to model different nematode species and to predict for example which plant-parasitic nematode populations are stabilized by increasing temperature due to climate change.