An automated feeding system for the African killifish reveals the impact of diet on lifespan and allows scalable assessment of associative learning

Skeletal Muscle Aging: Lessons From Teleosts

Aging is the greatest risk factor for a multitude of age-related diseases including sarcopenia-the loss of skeletal muscle mass and strength-which occurs at remarkable rates each year. There is an unmet need not only to understand the mechanisms that drive sarcopenia but also to identify novel therapeutic strategies. Given the ease and affordability of husbandry, along with advances in genomics, genome editing technologies, and imaging capabilities, teleost models are increasingly used for aging and sarcopenia research. Here, we explain how teleost species such as zebrafish, African turquoise killifish, and medaka recapitulate many of the classical hallmarks of sarcopenia, and discuss the various dietary, pharmacological, and genetic approaches that have been used in teleosts to understand the mechanistic basis of sarcopenia.

Surviving on Limited Resources: Effects of Caloric Restriction on Growth, Gene Expression and Gut Microbiota in a Species With Male Pregnancy (Hippocampus erectus)

Caloric restriction (CR) studies have traditionally focused on species with conventional reproductive roles, emphasising female's greater investment in costly gametes and parental care. While the divergent impact of CR on males and females is evident across species, the factors driving this variation, that is, resource allocation to reproductive elements as part of distinct life history strategies, remain unclear. To address this, we investigated the effects of CR on development, gene expression and intestinal microbiota in the lined seahorse Hippocampus erectus, a species with male pregnancy, where fathers invest in offspring through gestation. Juvenile seahorses were subjected to ad libitum (AL) or CR feeding for 5 months. CR stunted male growth and brood pouch development, reflecting the energy demands of this crucial parental care trait. However, condition index declined in CR females but not males, while ovarian weight remained unchanged. Transcriptome analysis demonstrated organ- and sex-specific responses to CR with distinct lipid and energy-related pathways activated in male and female livers, indicative of survival enhancement strategies. CR had minimal impact on genes associated with spermatogenesis, but downregulated lipid metabolic and inflammatory genes in ovaries, emphasising the importance of pre-copulatory resource allocation in female gametes. CR strongly shaped gut microbial composition, creating distinct communities from AL seahorses while also driving sex-specific taxonomic differences. Our research indicates that nutrient limitation's impact on males and females is influenced by their allocation of resources to reproduction and parental investment. We underscore the significance of studying species with diverse reproductive strategies, sex roles and life-history strategies.

Life in Extreme Conditions: Diet and Condition of the Extremophile Fish Aphanius almiriensis (Teleostei: Cyprinodontiformes) in a Thermal Rheocrene Spring

This study aims to understand the bioecological traits of an extremophile fish, Aphanius almiriensis, in order to explore how it survives and colonizes extreme habitat conditions. To achieve this, the bioecological characteristics-condition, diet, and feeding strategy-of A. almiriensis inhabiting the Tuzla thermal spring, which is characterized by extreme habitat conditions in terms of physicochemical water parameters, were studied. Among the physicochemical parameters measured, salinity and temperature were remarkably high, ranging from 23.7°C (in winter) to 42.7°C (in summer) and from 47.7 ppt (in autumn) to 60.7 ppt (in winter). A total of 248 fish individuals were collected from the thermal spring, and the diet analyzed seasonally consisted of 17 different food items, and their importance values (MI% and IRI%) varied seasonally. According to the F%, IRI%, and MI% values, the population fed mainly on Diatom, Cyanobacteria, and Diptera, resulting in niche breadth with low values ranging from 0.25 to 0.54. The extreme conditions of the thermal spring indicated that the environment was poor in terms of macroinvertebrate diversity (six taxa), and fish showed food selectivity (E) for Chironomidae and Ceratopogonidae in winter, spring, and summer and for Ephydridae in autumn (E > 0; positive selectivity). Seasonally influenced fish condition was represented by high values in summer (K = 1.43 ± 0.14) and was positively correlated with both water temperature and the increasing importance of the genus Phormidium in its diet. This study provides the first comprehensive insight into the seasonal diet and condition of A. almiriensis, shedding light on its survival strategies in harsh ecological conditions.

Strategies for studying sex differences in brain aging

Studying sex effects and their underlying mechanisms is of major relevance to understanding brain health. Despite growing interests, experimentally studying sex differences, particularly in the context of aging, remains challenging. Since sex chromosomal content influences gonadal development, separating the effects of gonadal hormones and chromosomal factors requires specific model systems. Here, we highlight rodent and tractable models for examining sex dimorphism in brain and cognitive aging. In addition, we discuss multi-omic and bioinformatic approaches that yield biological insights from animal and human studies. This review provides a comprehensive overview of the diverse toolkit now available to advance our understanding of sex differences in brain aging.

Hallmarks of aging: A user's guide for comparative biologists

Since the first description of a set of characteristics of aging as so-called hallmarks or pillars in 2013/2014, these characteristics have served as guideposts for the research in aging biology. They have been examined in a range of contexts, across tissues, in response to disease conditions or environmental factors, and served as a benchmark for various anti-aging interventions. While the hallmarks of aging were intended to capture generalizable characteristics of aging, they are derived mostly from studies of rodents and humans. Comparative studies of aging including species from across the animal tree of life have great promise to reveal new insights into the mechanistic foundations of aging, as there is a great diversity in lifespan and age-associated physiological changes. However, it is unclear how well the defined hallmarks of aging apply across diverse species. Here, we review each of the twelve hallmarks of aging defined by Lopez-Otin in 2023 with respect to the availability of data from diverse species. We evaluate the current methods used to assess these hallmarks for their potential to be adapted for comparative studies. Not unexpectedly, we find that the data supporting the described hallmarks of aging are restricted mostly to humans and a few model systems and that no data are available for many animal clades. Similarly, not all hallmarks can be easily assessed in diverse species. However, for at least half of the hallmarks, there are methods available today that can be employed to fill this gap in knowledge, suggesting that these studies can be prioritized while methods are developed for comparative study of the remaining hallmarks.

Multi-tissue transcriptomic aging atlas reveals predictive aging biomarkers in the killifish

Aging is associated with progressive tissue dysfunction, leading to frailty and mortality. Characterizing aging features, such as changes in gene expression and dynamics, shared across tissues or specific to each tissue, is crucial for understanding systemic and local factors contributing to the aging process. We performed RNA-sequencing on 13 tissues at 6 different ages in the African turquoise killifish, the shortest-lived vertebrate that can be raised in captivity. This comprehensive, sex-balanced 'atlas' dataset reveals the varying strength of sex-age interactions across killifish tissues and identifies age-altered biological pathways that are evolutionarily conserved. Demonstrating the utility of this resource, we discovered that the killifish head kidney exhibits a myeloid bias during aging, a phenomenon more pronounced in females than in males. In addition, we developed tissue-specific 'transcriptomic clocks' and identified biomarkers predictive of chronological age. We show the importance of sex-specific clocks for selected tissues and use the tissue clocks to evaluate a dietary intervention in the killifish. Our work provides a comprehensive resource for studying aging dynamics across tissues in the killifish, a powerful vertebrate aging model.

Brain aging and rejuvenation at single-cell resolution

Brain aging leads to a decline in cognitive function and a concomitant increase in the susceptibility to neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. A key question is how changes within individual cells of the brain give rise to age-related dysfunction. Developments in single-cell "omics" technologies, such as single-cell transcriptomics, have facilitated high-dimensional profiling of individual cells. These technologies have led to new and comprehensive characterizations of brain aging at single-cell resolution. Here, we review insights gleaned from single-cell omics studies of brain aging, starting with a cell-type-centric overview of age-associated changes and followed by a discussion of cell-cell interactions during aging. We highlight how single-cell omics studies provide an unbiased view of different rejuvenation interventions and comment on the promise of combinatorial rejuvenation approaches for the brain. Finally, we propose new directions, including models of brain aging and neural stem cells as a focal point for rejuvenation.

A framework for a low-cost system of automated gate control in assays of spatial cognition in fishes

Automation of experimental setups is a promising direction in behavioral research because it can facilitate the acquisition of data while increasing its repeatability and reliability. For example, research in spatial cognition can benefit from automated control by systematic manipulation of sensory cues and more efficient execution of training procedures. However, commercial solutions are often costly, restricted to specific platforms, and mainly focused on the automation of data acquisition, stimulus presentation, and reward delivery. Animal welfare considerations as well as experimental demands may require automating the access of an animal or animals to the experimental arena. Here, we provide and test a low-cost, versatile Raspberry Pi-based solution for such use cases. We provide four application scenarios of varying complexities, based on our research of spatial orientation and navigation in weakly electric fish, with step-by-step protocols for the control of gates in the experimental setups. This easy-to-implement, platform-independent approach can be adapted to various experimental needs, including closed-loop as well as field experiments. As such, it can contribute to the optimization and standardization of experiments in a variety of species, thereby enhancing the comparability of data.

Identification of protein aggregates in the aging vertebrate brain with prion-like and phase-separation properties

Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here, we use quantitative proteomics in the African turquoise killifish to identify protein aggregates that accumulate in old vertebrate brains. These aggregates are enriched for prion-like RNA-binding proteins, notably the ATP-dependent RNA helicase DDX5. We validate that DDX5 forms aggregate-like puncta in the brains of old killifish and mice. Interestingly, DDX5's prion-like domain allows these aggregates to propagate across many generations in yeast. In vitro, DDX5 phase separates into condensates. Mutations that abolish DDX5 prion propagation also impair the protein's ability to phase separate. DDX5 condensates exhibit enhanced enzymatic activity, but they can mature into inactive, solid aggregates. Our findings suggest that protein aggregates with prion-like properties form during normal brain aging, which could have implications for the age-dependency of cognitive decline.

Rearing and Experimental Uses of Daphnia: Controlling Animal Nutrition and Assessing Lifespan and Life-History Traits

Caloric restriction has been found to extend the lifespan of many organisms including mammals and other vertebrates. With lifespans exceeding months to years, age-related experiments involving fish and mammals can be overtly costly, both in terms of time and funding. The freshwater crustacean, Daphnia, has a relatively short lifespan (∼50 to 100 days), which makes it a cost-effective alternative animal model for longevity and aging studies. Besides age-specific mortality, there are a suite of physiological responses connected to "healthspan" that can be tracked as these animals age including growth, reproduction, and metabolic rates. These responses can be complemented by assessment of molecular and cellular processes connected to aging and health. Lifespan and metabolism of this model organism is responsive to long studied modulators of aging, such as rearing temperature and nutritional manipulation, but also pharmacological agents that target aging, e.g., rapamycin, which adds to its usefulness as a model organism. Here we describe how to culture Daphnia for aging experiments including maintaining laboratory populations of Daphnia mothers, growing algal food, and manipulating nutrition of these animals. In addition, we provide methods for tracking common physiological and longevity responses of Daphnia. This protocol provides researchers planning to use this model organism with methods to establish and maintain Daphnia populations and to standardize their experimental approaches. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Culturing algae for Daphnia food Basic Protocol 2: General methods for culturing Daphnia Basic Protocol 3: Standardizing and controlling nutrition for experimental Daphnia Basic Protocol 4: Monitoring Daphnia lifespan Basic Protocol 5: Evaluating Daphnia health: Heart rate and respiration, body mass and growth rates, and reproduction.

The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes

The African turquoise killifish Nothobranchius furzeri is currently the shortest-lived vertebrate that can be bred in captivity. Because of its short life span of only 4-6 months, rapid generation time, high fecundity, and low cost of maintenance, the African turquoise killifish has emerged as an attractive model organism that combines the scalability of invertebrate models with the unique features of vertebrate organisms. A growing community of researchers is using the African turquoise killifish for studies in diverse fields, including aging, organ regeneration, development, "suspended animation," evolution, neuroscience, and disease. A wide range of techniques is now available for killifish research, from genetic manipulations and genomic tools to specialized assays for studying life span, organ biology, response to injury, etc. This protocol collection provides detailed descriptions of the methods that are generally applicable to all killifish laboratories and those that are limited to specific disciplines. Here, we give an overview of the features that render the African turquoise killifish a unique fast-track vertebrate model organism.

Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues

The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism for aging research. Here, we describe a multitissue, single-cell gene expression atlas of female and male blood, kidney, liver, and spleen. We annotate 22 cell types, define marker genes, and infer differentiation trajectories. We find pervasive sex-dimorphic gene expression across cell types. Sex-dimorphic genes tend to be linked to lipid metabolism, consistent with clear differences in lipid storage in female vs. male turquoise killifish livers. We use machine learning to predict sex using single-cell gene expression and identify potential markers for molecular sex identity. As a proof of principle, we show that our atlas can be used to deconvolute existing bulk RNA sequencing (RNA-seq) data to obtain accurate estimates of cell type proportions. This atlas can be a resource to the community that could be leveraged to develop cell-type-specific expression in transgenic animals.

Transcriptomes of aging brain, heart, muscle, and spleen from female and male African turquoise killifish

The African turquoise killifish is an emerging vertebrate model organism with great potential for aging research due to its naturally short lifespan. Thus far, turquoise killifish aging 'omic' studies have examined a single organ, single sex and/or evaluated samples from non-reference strains. Here, we describe a resource dataset of ribosomal RNA-depleted RNA-seq libraries generated from the brain, heart, muscle, and spleen from both sexes, as well as young and old animals, in the reference GRZ turquoise killifish strain. We provide basic quality control steps and demonstrate the utility of our dataset by performing differential gene expression and gene ontology analyses by age and sex. Importantly, we show that age has a greater impact than sex on transcriptional landscapes across probed tissues. Finally, we confirm transcription of transposable elements (TEs), which are highly abundant and increase in expression with age in brain tissue. This dataset will be a useful resource for exploring gene and TE expression as a function of both age and sex in a powerful naturally short-lived vertebrate model.

Rapid and precise genome engineering in a naturally short-lived vertebrate

The African turquoise killifish is a powerful vertebrate system to study complex phenotypes at scale, including aging and age-related disease. Here, we develop a rapid and precise CRISPR/Cas9-mediated knock-in approach in the killifish. We show its efficient application to precisely insert fluorescent reporters of different sizes at various genomic loci in order to drive cell-type- and tissue-specific expression. This knock-in method should allow the establishment of humanized disease models and the development of cell-type-specific molecular probes for studying complex vertebrate biology.

Widespread sex-dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues

The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism to study vertebrate aging. Here we describe the first multi-tissue, single-cell gene expression atlas of female and male turquoise killifish tissues comprising immune and metabolic cells from the blood, kidney, liver, and spleen. We were able to annotate 22 distinct cell types, define associated marker genes, and infer differentiation trajectories. Using this dataset, we found pervasive sex-dimorphic gene expression across cell types, especially in the liver. Sex-dimorphic genes tended to be involved in processes related to lipid metabolism, and indeed, we observed clear differences in lipid storage in female vs. male turquoise killifish livers. Importantly, we use machine-learning to predict sex using single-cell gene expression in our atlas and identify potential transcriptional markers for molecular sex identity in this species. As proof-of-principle, we show that our atlas can be used to deconvolute existing liver bulk RNA-seq data in this species to obtain accurate estimates of cell type proportions across biological conditions. We believe that this single-cell atlas can be a resource to the community that could notably be leveraged to identify cell type-specific genes for cell type-specific expression in transgenic animals.

The holy grail of longevity research

A new technology to study physiology and cognition elevates African turquoise killifish as a model organism for studies of aging in vertebrates.