Short-lived Fish Research Articles

Development of the Thymus and Kidney and Effects of Resveratrol on Their Aging in a Short-LivedFish.

Annual fishes of the genus Nothobranchius have been widely used in cognitive, behavioral, and genetic studies, and have become an excellent animal model for studying aging. However, the development and degeneration of immune organs in annual fishes and the antagonistic effects of resveratrol remain unclear. In the present study, the development of thymus and kidney was investigated systematically using Nothobranchius guentheri from larvae, juveniles, and young and old fish with hematoxylin and eosin staining. We found that thymus primordium was observed first in the larvae at 2days after hatching (dah). After the lymphoid cells became evident at 5 dah, the thymus acquired an irregular shape at 7 dah. Then it formed a wedge shape at 15 dah. Thymus looked as homogeneous distribution of lymphocytes at 1month old, and it differentiated into cortex and medulla approximately in 2-month-old fish. Combined with TUNEL and senescence-associated β-galactosidase (SA-β-gal) staining, it showed the degeneration of the thymus appeared in 4-month-old fish. Kidney primordium appeared on 1 dah, and the glomerulus was visible at 7 dah. The nephrogenic activity was most apparent in 1-month-old fish. Alarge hematopoietic tissue was arranged in the renal interstitium in 2- and 3-month-old fish. In 6-month-old fish, the kidney structure became less dense. By 12months, the kidney exhibited the most pronounced histological characteristics of aging. Feeding resveratrol ameliorated renal fibrosis and SA-β-gal staining with age, increased SIRT1 and SIRT3 expression, and decreased the levels of NF-κB and inflammatory factors in thymus and kidney of the fish. We provided basic data for the development and degeneration of immune organs and resveratrol's anti-aging effects in short-lived fish.

Lessons learnt on the management of short-lived fish from the Bay of Biscay anchovy case study: Satisfying fishery needs and sustainability under recruitment uncertainty

This paper summarizes the lessons learnt for the management of small pelagic fish from the case study of managing the international fishery on the Bay of Biscay anchovy. A constant catch regime ended up with a fishery crash and closure (2005–2009) after a series of recruitment failures. Precautionary advices had been disregarded due to their inability to predict the size of the population during the first half of the year when the major fishery takes place. The crash triggered the EU to develop a long-term management plan in 2008. In the absence of a recruitment indicator, biological risk was minimized through a close coupling between assessment, advice and management, changing the management year to start just after the spring surveys on adults. A major improvement arrived in 2014 by the incorporation of an early recruitment indicator from an autumn acoustic survey on juveniles. This allowed additional exploitation of the resource at similar risk levels. Accordingly, TACs are nowadays set after the recruit survey on a management calendar basis. The interactive collaboration between fishers, scientists, and managers allowed inclusion of the stakeholders’ preferences for a biomass-based catch bounded harvest strategy suitable for these valuable fisheries. This strategy allows catches between a minimum and maximum TAC level, to account for an economically viable minimum activity when approaching a minimum biomass threshold level, and for the limited market absorption capacity when exceeding an upper biomass threshold level, respectively. Such strategy was adopted by consensus and supposed a successful participatory process in fishery management.

Resveratrol Alleviates Inflammation and ER Stress Through SIRT1/NRF2 to Delay Ovarian Aging in a Short-Lived Fish.

Aging is a complex process in which the structure and function of various tissues and organs gradually decline with age, and ovarian aging affects the reproductive capacity of females and induces age-related diseases. Resveratrol, a natural polyphenol compound, extends the life span and has a protective effect on the ovaries of vertebrates. However, the effects and underlying mechanisms of resveratrol delaying ovarian aging are unclear. In this study, using an annual fish Nothobranchius guentheri, we demonstrated that senescence-associated-beta-galactosidase (SA-β-gal) activity and lipofuscin accumulation increased with age in the ovaries, and resveratrol reversed this phenomenon. Resveratrol increased proliferating cell nuclear antigen (PCNA) expression and the oocyte proportions of the primary growth stage, cortical alveolus stage and vitellogenesis stage, and decreased the number of atretic follicles in the ovaries of 6-, 9-, and 12-month-old fish. Moreover, the expression of SIRT1 and NRF2 decreased and the levels of NF-κB, pro-inflammatory cytokines IL-1β, TNF-α, and IL-8 and endoplasmic reticulum (ER) stress markers GRP78 and CHOP increased with aging, while resveratrol up-regulated SIRT1 and NRF2 expression and down-regulated NF-κB, IL-1β, TNF-α, IL-8, GRP78, and CHOP levels in the ovaries of 6- and 9-month-old fish. In HEK293T cells, knockdown SIRT1 decreased NRF2 and increased NF-κB p65, pro-inflammatory cytokines (IL-1β and TNF-α), and ER stress marker GRP78 expression markedly. Silencing SIRT1 and then treating the cells with resveratrol significantly reversed the phenomenon. Collectively, resveratrol might activate SIRT1/NRF2 to reduce inflammation and ER stress, and finally delay ovarian aging in a short-lived fish. This study highlights the protective effect and mechanism of resveratrol on ovarian aging.

The Capacity of Freshwater Ecosystems to Recover from Exceedences of Aquatic Life Criteria.

In the United States, national chemical water quality criteria for the protection of aquatic life assume that aquatic ecosystems have sufficient resiliency to recover from criteria exceedences occurring up to once every 3 years. This resiliency assumption was critically reviewed through two approaches: (1) synthesis of case studies, and (2) population modeling. The population modeling examined differences in recovery of species with widely different life histories. One invertebrate (Hyalella azteca) and four fish species were modeled (fathead minnow, brook trout, lake trout, and shortnose sturgeon) with various disturbance magnitudes and intervals. The synthesis of ecosystem case studies showed generally faster recoveries for insect communities rather than fish, and recoveries from pulse (acute) disturbances were often faster than recoveries from press (chronic) disturbances. When the recovery dataset excluded severe disturbances that seemed unrepresentative of common facility discharge upsets that might cause criteria exceedences, the median recovery time was 1 year, 81% of the cases were considered recovered within 3 years, and 95% were considered recovered within 10 years. The modeling projected that short-lived fish species with high recovery times could thrive despite enduring 50% mortality disturbances every other year. However, long-lived fish species had longer recovery times and declined under the one disturbance every 3 years scenario. Overall, the analyses did not refute the long-standing judgements that 3 years is generally sufficient for recovery from nonrepetitive, moderate intensity disturbances of a magnitude up to 2× the chronic criteria in waters without other pollution sources or stresses. However, these constraints may not always be met and if long-lived fish species are a concern, longer return intervals such as 5-10 years could be indicated. Environ Toxicol Chem 2022;41:2887-2910. Published 2022. This article is a U.S. Government work and is in the public domain in the USA.

An assessment of sampling approaches for estimating growth from fishery-dependent biological samples

Abstract Accuracy of fish growth estimates depends greatly on how samples are collected. A total of three common sampling strategies are random, fixed otolith sampling (FOS), and proportional otolith sampling (POS). Random sampling is inefficient and rarely random. While POS has been shown to produce more accurate estimates of growth compared to FOS under ideal conditions, it is unclear how variables such as sample size, fishery selectivity, and fishing mortality influence sampling bias. Simulated age-at-length observations from two tropical deepwater species were used to evaluate the accuracy of von Bertalanffy growth parameter estimates comparing FOS and POS for a fast-growing, short-lived fish (Prisitipomoides auricilla) and a slow-growing, long-lived fish (Etelis coruscans). A total of 24 scenarios were tested to examine the influence of sample size, minimum size selected in the fishery, fishery exploitation rates, and supplemental sampling on growth parameter estimates. Furthermore, tests were applied to real fishery age–length observations for P. auricilla. POS consistently performed better than FOS, especially when the catch was representative of the population. However, FOS performed better when catch was not representative. This research demonstrates the importance of considering effects of fishery selectivity, fishing mortality, and sample size on sampling strategy and provides a tool to select an appropriate approach.

Population and sex-specific survival estimates for Atlantic sturgeon: addressing detection probability and tag loss

Survival estimates of animal populations provide managers with critical information on productivity, population stability, and demography. Telemetry-based survival estimates can be obtained remotely. The Atlantic sturgeon Acipenser oxyrinchus oxyrinchus is a wide-ranging species whose populations overlap along the East Coast of North America, complicating survival estimation. The objective of this study was to estimate apparent annual survival of the York River population using a Cormack-Jolly-Seber model. In this study, 36 males and 24 females were telemetered and monitored between 2013 and 2019. We considered the fit of a variety of models, selecting the best fit using Akaike’s information criterion. The optimal model estimated survival in seasonal increments and detection probability by sex in monthly increments. Five transmitters failed to leave the river and another 3 stopped being detected within 21 mo, but of those, recapturing fish confirmed 2 had been lost and 3 were technological failures (12.8% of 39 recaptured). Apparent adult annual survival was estimated to be 99.2% (95% CL: 97.9-99.7%). Addressing sex-specific detection probability and failed transmitters while including a length covariate for each individual produced higher survival estimates than previously reported studies of Atlantic sturgeon. Four males and one female appear to have died, with the location of last detection for 4 of the suspected mortalities in shipping channels near the mouth of the Chesapeake Bay, suggesting managers should focus on this area of increased risk. Such high survival estimates of the adult stage suggest Atlantic sturgeon survival may be more similar to other long-lived, late-maturing animal species than to most other short-lived fish species.

Population dynamic regulators in an empirical predator-prey system

Capelin (Mallotus villosus) is a short-lived (1–4 years) fish species, that plays a crucial role by dominating the intermediate trophic level in the Barents Sea. Several episodes of extreme biomass decline (collapse) have been observed during the last three decades. We postulate that these collapses might be regulated by food availability (bottom-up effect) and/or by time discrepancy between capelin feeding and abundance of its prey (match-mismatch hypothesis). This paper investigates our postulate using a model consisting of a set of coupled differential equations to describe the predator-prey system, with a single delay term, τ, in description of the predator dynamics. We derive theoretical conditions on τ, as well as determine how changes in these conditions define different stability regimes of the system. Unconstrained optimization is used to calculate optimal model parameters by fitting the predator-prey model to empirical data. The optimization results are combined with those from the theoretical analysis, to make inference about the empirical system stability. Our results show that Hopf bifurcation occurs in the predatory-prey system when τ exceeds a theoretically derived value τ∗>0. This value represents the critical time for prey availability in advance of the optimal predator growth period.Set into an ecological context, our findings provide mathematical evidence for validity of the match-mismatch hypothesis and a bottom-up effect for capelin.

Adapting Simple Index-Based Catch Rules for Data-Limited Stocks to Short-Lived Fish Stocks’ Characteristics

Most of the methods developed for managing data-limited stocks have been designed for long-lived species and result in a poor performance when applied to short-lived fish due to their high interannual variability of stock size (IAV). We evaluate the performance of several catch rules in managing two typical short-lived fish (anchovy-like: characterized by high natural mortality, and hence, IAV, and full maturity at age 1; and sprat/sardine-like: with medium natural mortality and IAV, being fully mature at age 2). We followed the management strategy evaluation approach implemented in FLBEIA software to test several model-free harvest control rules, where the Total Allowable Catch (TAC) is yearly modified according to the recent trends in an abundance index (n-over-m rules: means of the most recent n values over the precedent m ones). The performance of these rules was assessed across a range of settings, such as time-lags between the index availability and management implementation, and alternative restrictions on TACs’ interannual variability (the uncertainty caps, UC). Moreover, we evaluated the sensitivity of the rule performance to the operating model assumptions (stock type, productivity, recruitment variability and initial depletion level) and to the observation error of the index. In general, the shorter the lag between observations, advice and management, the bigger the catches and the smaller the biological risks. For in-year management, 1-over-m rules are reactive enough to stock fluctuations as to gradually reduce risks. The 1-over-2 rule with symmetric 80% UCs reduces catches and risks toward precautionary levels in about 10 years, faster than if applied unconstrained (i.e., without UC), whilst the ICES default 2-over-3 rule with symmetric 20% UC is not precautionary. We prove that unconstrained rules gradually reduce the fishing opportunities, with amplified effects with increasing IAV. This property explains the stronger reductions of catches and risks achieved for the anchovy compared to the sprat/sardine-like stocks for any rule and the balance between catches and risks as the index CV increases. However, to avoid unnecessary long-term losses of catches from such reduction properties, it is suggested that the rules should be applied provisionally until a better assessment and management system is set up.

Chronic feeding exposure to virgin and spiked microplastics disrupts essential biological functions in teleost fish

Toxicity of polyethylene (PE) and polyvinyl chloride (PVC) microplastics (MPs), either virgin or spiked with chemicals, was evaluated in two short-lived fish using a freshwater species, zebrafish, and a marine species, marine medaka. Exposures were performed through diet using environmentally relevant concentrations of MPs over 4 months. No modification of classical biomarkers, lipid peroxidation, genotoxicity or F0 behaviour was observed. A significant decrease in growth was reported after at least two months of exposure. This decrease was similar between species, independent from the type of MPs polymer and the presence or not of spiked chemicals, but was much stronger in females. The reproduction was evaluated and it revealed a significant decrease in the reproductive output for both species and in far more serious numbers in medaka. PVC appeared more reprotoxic than PE as were MPs spiked with PFOS and benzophenone-3 compared to MPs spiked with benzo[a]pyrene. Further, PVC-benzophenone-3 produced behavioural disruption in offspring larvae. These results obtained with two species representing different aquatic environments suggest that microplastics exert toxic effects, slightly different according to polymers and the presence or not of sorbed chemicals, which may lead in all cases to serious ecological disruptions.

NETO2 Is Deregulated in Breast, Prostate, and Colorectal Cancer and Participates in Cellular Signaling.

The NETO2 gene (neuropilin and tolloid-like 2) encodes a protein that acts as an accessory subunit of kainate receptors and is predominantly expressed in the brain. Upregulation of NETO2 has been observed in several tumors; however, its role in tumorigenesis remains unclear. In this study, we investigated NETO2 expression in breast, prostate, and colorectal cancer using quantitative PCR (qPCR), as well as the effect of shRNA-mediated NETO2 silencing on transcriptome changes in colorectal cancer cells. In the investigated tumors, we observed both increased and decreased NETO2 mRNA levels, presenting no correlation with the main clinicopathological characteristics. In HCT116 cells, NETO2 knockdown resulted in the differential expression of 17 genes and 2 long non-coding RNAs (lncRNAs), associated with the upregulation of circadian rhythm and downregulation of several cancer-associated pathways, including Wnt, transforming growth factor (TGF)-β, Janus kinase (JAK)-signal transducer and activator of transcription (STAT), mitogen-activated protein kinase (MAPK), and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) pathways. Furthermore, we demonstrated the possibility to utilize a novel model organism, short-lived fish Nothobranchius furzeri, for evaluating NETO2 functions. The ortholog neto2b in N. furzeri demonstrated a high similarity in nucleotide and amino acid sequences with human NETO2, as well as was characterized by stable expression in various fish tissues. Collectively, our findings demonstrate the deregulation of NETO2 in the breast, prostate, and colorectal cancer and its participation in the tumor development primarily through cellular signaling.

Cholinergic System and NGF Receptors: Insights from the Brain of the Short-Lived Fish Nothobranchius furzeri.

Nerve growth factor (NGF) receptors are evolutionary conserved molecules, and in mammals are considered necessary for ensuring the survival of cholinergic neurons. The age-dependent regulation of NTRK1/NTRKA and p75/NGFR in mammalian brain results in a reduced response of the cholinergic neurons to neurotrophic factors and is thought to play a role in the pathogenesis of neurodegenerative diseases. Here, we study the age-dependent expression of NGF receptors (NTRK1/NTRKA and p75/NGFR) in the brain of the short-lived teleost fish Nothobranchius furzeri. We observed that NTRK1/NTRKA is more expressed than p75/NGFR in young and old animals, although both receptors do not show a significant age-dependent change. We then study the neuroanatomical organization of the cholinergic system, observing that cholinergic fibers project over the entire neuroaxis while cholinergic neurons appear restricted to few nuclei situated in the equivalent of mammalian subpallium, preoptic area and rostral reticular formation. Finally, our experiments do not confirm that NTRK1/NTRKA and p75/NGFR are expressed in cholinergic neuronal populations in the adult brain of N. furzeri. To our knowledge, this is the first study where NGF receptors have been analyzed in relation to the cholinergic system in a fish species along with their age-dependent modulation. We observed differences between mammals and fish, which make the African turquoise killifish an attractive model to further investigate the fish specific NGF receptors regulation.

Effects of Metformin on Life Span, Cognitive Ability, and Inflammatory Response in a Short-Lived Fish.

Metformin, an oral antidiabetic drug, prolongs the life span in nematode, silkworm, and other transgenic rodents, but its effects on longevity and aging-related cognitive ability using natural aging vertebrate models remain poorly understood. The genus of annual fish Nothobranchius show accelerated growth and expression of aging biomarkers. Here, using the short-lived fish Nothobranchius guentheri, we investigated effects of metformin on life span and aging-related cognitive ability and inflammation. Total of 145 fish, 72 fish were fed with metformin in the concentration of 2 mg/g food and 73 fish without metformin from 16 weeks of age until the end of their lives. The chronic feeding with metformin prolonged the life span of the fish and delayed aging with retarded accumulation of lipofuscin in liver, senescence-associated beta-galactosidase (SA-β-gal) activity in skin and serum levels of cholesterol and triglyceride significantly in the 10-month-old fish. Furthermore, metformin improved motor, learning, and memory skills by behavior tests accompanying with reduction of SA-β-gal activity and neurofibrillary degeneration and inhibition of inflammatory response including downregulated NF-κB and proinflammatory cytokines IL-8, TNF-α, and IL-1β expression and enhanced anti-inflammatory cytokine IL-10 level in brain. These findings demonstrate that metformin prolongs the life span and exerts neuroprotective and anti-inflammation function to improve cognitive ability in annual fish. It might be an effective strategy by using metformin to raise the possibility of promoting healthy aging of old population in aging process.

Spatio-temporal expression profile of sirtuins during aging of the annual fish Nothobranchius furzeri

The founding member of the sirtuin family, yeast Sir2, was the first evolutionarily conserved gene to be identified as a regulator of longevity. Sirtuins constitute a protein family of metabolic sensors, translating changes in NAD + levels into adaptive responses, thereby acting as crucial regulators of the network that controls energy homeostasis and as such determines healthspan. In mammals the sirtuin family comprises seven proteins, SIRT1-SIRT7, which vary in tissue specificity, subcellular localization, enzymatic activity and targets. Here, we report the identification and a detailed spatio-temporal expression profile of sirtuin genes in the short-lived fish Nothobranchius furzeri, from embryogenesis to late adulthood, mapping its entire life cycle. Database exploration of the recently published N. furzeri genome revealed eight orthologues corresponding to the seven known mammalian sirtuins, including two copies of the sirt5 gene. Phylogenetic analysis showed high cross species similarity of individual sirtuins in both their overall amino acid sequence and catalytic domain, suggesting a high degree of functional conservation. Moreover, we show that N. furzeri sirtuins exhibit ubiquitous and wide tissue distribution with a unique spatial expression pattern for each individual member of this enzyme family. Specifically, we observed a transcriptional down-regulation of several sirtuin genes with age, most significantly sirt1, sirt5a, sirt6 and sirt7 in a wide range of functionally distinct tissues. Overall, this spatio-temporal expression analysis provides the foundation for future research, both into genetic and pharmacological manipulation of this important group of enzymes in Nothobranchius furzeri, an emerging model organism for aging research.

Identification and Expression of Neurotrophin-6 in the Brain of Nothobranchius furzeri: One More Piece in Neurotrophin Research.

Neurotrophins contribute to the complexity of vertebrate nervous system, being involved in cognition and memory. Abnormalities associated with neurotrophin synthesis may lead to neuropathies, neurodegenerative disorders and age-associated cognitive decline. The genome of teleost fishes contains homologs of some mammalian neurotrophins as well as a gene coding for an additional neurotrophin (NT-6). In this study, we characterized this specific neurotrophin in the short-lived fish Nothobranchius furzeri, a relatively new model for aging studies. Thus, we report herein for the first time the age-related expression of a neurotrophin in a non-mammalian vertebrate. Interestingly, we found comparable expression levels of NT-6 in the brain of both young and old animals. More in detail, we used a locked nucleic acid probe and a riboprobe to investigate the neuroanatomical distribution of NT-6 mRNA revealing a significant expression of the neurotrophin in neurons of the forebrain (olfactory bulbs, dorsal and ventral telencephalon, and several diencephalic nuclei), midbrain (optic tectum, longitudinal tori, and semicircular tori), and hindbrain (valvula and body of cerebellum, reticular formation and octavolateral area of medulla oblongata). By combining in situ hybridization and immunohistochemistry, we showed that NT-6 mRNA is synthesized in mature neurons. These results contribute to better understanding the evolutionary history of neurotrophins in vertebrates, and their role in the adult brain.

Estimating the Size Selectivity of Fishing Trawls for a Short-Lived Fish Species

Long-term fish survey monitoring programs use a variety of fishing gears to catch fish, and the resulting catches are the basis for status and trends reports on the condition of different fish stocks. These catches can also be part of the data used to set stock assessment models, which establish harvest regulations, and to fit population dynamics models, which are used to analyze population viability. However, most fishing gears are size-selective, and fish size — among other possible covariates, such as environmental conditions — affects the probability that a fish will be caught in the path the gear sweeps. Failing to properly account for selectivity can adversely affect the ability to interpret and use status and trends measures, stock-assessment models, and population-dynamics models. Our side-by-side gear comparison study evaluated the selectivity of multiple open-water trawl surveys that have provided decades worth of information on the imperiled fish species Delta Smelt (Hypomesus transpacificus). We used data from the study to estimate gear selectivity curves for multiple trawls using two methods. The first method examines the total number of fish-at-length caught across all gears, and does not directly use or estimate fish length distribution in the population. The second method examines the total number of fish caught by each gear separately, and explicitly estimates fish length distribution in the population. The results from the two methods were similar, and we found that one trawl was highly efficient at catching larger Delta Smelt. This is the first formal multi-gear evaluation of the relative selectivity of how well survey gear used to monitor Delta Smelt in the San Francisco Estuary selects fish by size, and we plan to incorporate the results into Delta Smelt population models.

Limited scope for reproductive senescence in wild populations of a short-lived fish.

Senescence in wild populations was long considered negligible but current evidence suggests that it is widespread in natural populations of mammals and birds, affecting the survival and reproductive output of older individuals. In contrast, little is known about reproductive senescence in species with asymptotic growth that can keep increasing their reproductive output as they grow older and larger. Using a cross-sectional study, we tested age-related decline in fecundity and relative allocation to reproduction in five wild populations of an annual killifish, Nothobranchius furzeri (Cyprinodontiformes). We did not detect any decline in absolute female egg production over their short lifespan in the wild. Relative fecundity (egg production controlled for female body mass) tended to decrease with age. This effect was driven primarily by a single population that survived 17weeks, almost twice as long as the median persistence of the other four study populations. There was no decrease in relative ovary mass while in males, relative testes mass actually increased with age. Intra-population variation in relative ovary mass increased in older females suggesting heterogeneity in individual trajectories of female reproductive allocation. Overall, we demonstrate that annual killifish do not experience significant age-related decline in reproductive functions during their very short lifespan in the wild despite the marked deterioration of gonad tissue detected in captivity.

Impact of a shift work-like lighting schedule on the functioning of the circadian system in the short-lived fish Nothobranchius furzeri.

Adult Nothobranchius furzeri of the MZM-04/10 strain were individually kept and subjected to a "5 + 2" shifting lighting schedule (SHIFT) for 8 weeks in order to evaluate the desynchronizing effects of a simulated human-like shift-work schedule on the functioning of the circadian system (CS). With this aim, sixteen 21-week-old N. furzeri were placed into a Morning, Night and Evening schedule (lights on from 08:00 to 16:00, 00:00 to 08:00 and 16:00 to 00:00 h, respectively) and fed once a day in the middle of the corresponding photophase (12:00, 04:00 and 20:00 h, respectively). Then, in the weekends (2 days), fish were always returned to the Morning shift. As controls, 16 fish were maintained under a non-shifting LD cycle condition (CONTROL) throughout the whole experiment, with lights on from 08:00 to 16:00 h. Rest-activity rhythm (RAR) of fish subjected to SHIFT showed several symptoms of chronodisruption, such as a decrease in the percentage of diurnal activity and a reduction of the relative amplitude and the circadian function index with time. When a periodogram analysis was performed, RAR of N. furzeri under SHIFT conditions showed up to three separate circadian components: one longer than 24 h (26.5 h) that followed the weekly 8 h delays; a short-period component (~23 h) that was related to the weekend's phase advances, and finally, a 24 h component. The shifting LD schedule also affected fish CS at a molecular level, with several significant differences in the expression of core genes of the molecular clock (bmal1, clock, rorα, rev-erbα) between SHIFT and CONTROL animals. RAR impairment along with changes in clock gene expression could be associated with high stress and accelerated aging in these fish.

Corrigendum: Regulation of microRNA expression in the neuronal stem cell niches during aging of the short-lived annual fish Nothobranchius furzeri.

[This corrects the article DOI: 10.3389/fncel.2014.00051.].

Histone deacetylase 1 expression is inversely correlated with age in the short-lived fish Nothobranchius furzeri

Aging is associated with profound changes in the epigenome, resulting in alterations of gene expression, epigenetic landscape, and genome architecture. Class I Histone deacetylases (HDACs), consisting of HDAC1, HDAC2, HDAC3, and HDAC8, play a major role in epigenetic regulation of chromatin structure and transcriptional control, and have been implicated as key players in the pathogenesis of age-dependent diseases and disorders affecting health and longevity. Here, we report the identification of class I Hdac orthologs and their detailed spatio-temporal expression profile in the short-lived fish Nothobranchius furzeri from the onset of embryogenesis until old age covering the entire lifespan of the organism. Database search of the recently annotated N. furzeri genomes retrieved four distinct genes: two copies of hdac1 and one copy of each hdac3 and hdac8. However, no hdac2 ortholog could be identified. Phylogenetic analysis grouped the individual killifish class I Hdacs within the well-defined terminal clades. We find that upon aging, Hdac1 is significantly down-regulated in muscle, liver, and brain, and this age-dependent down-regulation in brain clearly correlates with increased mRNA levels of the cyclin-dependent kinase inhibitor cdkn1a (p21). Furthermore, this apparent reduction of class I HDACs in transcript and protein levels is mirrored in the mouse brain, highlighting an evolutionarily conserved role of class I HDACs during normal development and in the aging process.

A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri

BackgroundThe short-lived fish Nothobranchius furzeri is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especially miRNAs, are implicated in age dependent control of gene expression.ResultsHere, we present a comprehensive catalogue of miRNAs and several other non-coding RNA classes (ncRNAs) for Nothobranchius furzeri. Analyzing multiple small RNA-Seq libraries, we show most of these identified miRNAs are expressed in at least one of seven Nothobranchius species. Additionally, duplication and clustering of N. furzeri miRNAs was analyzed and compared to the four fish species Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Takifugu rubripes. A peculiar characteristic of N. furzeri, as compared to other teleosts, was a duplication of the miR-29 cluster.ConclusionThe completeness of the catalogue we provide is comparable to that of the zebrafish. This catalogue represents a basis to investigate the role of miRNAs in aging and development in this species.