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Small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages), embryonic samples of N. furzeri and 6 other killifish species

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

OTHER RELATED OMICS DATASETS IN: PRJNA358711PRJNA414505PRJNA412694

ORGANISM(S): Nothobranchius rachovii Nothobranchius pienaari Iconisemion striatum Nothobranchius kuhntae Nothobranchius furzeri Nothobranchius korthausae Nothobranchius kadleci

PROVIDER: GSE92854 | GEO | 2017/02/01

SECONDARY ACCESSION(S): PRJNA358711

REPOSITORIES: GEO

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small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages) and Brain samples of 6 other killifish species

Project description:The RNA-seq data contain 3 tissues (brain, liver, skin) of N. furzeri strains MZM-0410 and GRZ plus 2 biological replicates of brain of 6 other killifish species. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

2017-09-29 | GSE104321 | GEO

small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages), embryonic samples of N. furzeri and 6 other killifish species

Project description:small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages), embryonic samples of N. furzeri and 6 other killifish species

| PRJNA358711 | ENA

small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages) and Brain samples of 6 other killifish species

Project description:small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages) and Brain samples of 6 other killifish species

| PRJNA412694 | ENA

Sperm cryopreservation and in vitro fertilization techniques for the African turquoise killifish Nothobranchius furzeri.

Project description:Over the last decade, the African turquoise killifish, Nothobranchius furzeri, has emerged as an important model system for the study of vertebrate biology and ageing. Propagation of laboratory inbred strains of Nothobranchius furzeri, such as GRZ, however, can pose challenges due to the short window of fertility, the efforts and space requirements involved in continuous strain maintenance, and the risks of further inbreeding. The current method for long term strain preservation relies on arrest of embryos in diapause. To create an alternative for long term maintenance, we developed a robust protocol to cryopreserve and revive sperm for in vitro fertilization (IVF). We tested a variety of extender and activator buffers for sperm IVF, as well as cryoprotectants to achieve practical long-term storage and fertilization conditions tailored to this species. Our protocol enabled sperm to be preserved in a cryogenic condition for months and to be revived with an average of 40% viability upon thawing. Thawed sperm were able to fertilize nearly the same number of eggs as natural fertilization, with an average of ~ 25% and peaks of ~ 55% fertilization. This technical advance will greatly facilitate the use of N. furzeri as a model organism.

| S-EPMC8387425 | biostudies-literature

Good performance of turquoise killifish (Nothobranchius furzeri) on pelleted diet as a step towards husbandry standardization.

Project description:Dietary alteration is one of the most universally effective aging interventions, making its standardization a fundamental need for model organisms in aging. In this dietetic study we address the current lack of standardized formulated diet for turquoise killifish Nothobranchius furzeri - a promising model organism. We first demonstrated that N. furzeri can be fully weaned at the onset of puberty onto a commercially available pelleted diet as the sole nutrition when kept in social tanks. We then compared nine somatic and six reproductive parameters between fish fed a typical laboratory diet - frozen chironomid larvae (bloodworms) and fish weaned from bloodworms to BioMar pellets. Both dietary groups had comparable somatic and reproductive performance. There was no difference between diet groups in adult body size, specific growth rate, condition or extent of hepatocellular vacuolation. Fish fed a pelleted diet had higher juvenile body mass and more visceral fat. Pellet-fed males had lower liver mass and possessed a lipid type of hepatocellular vacuolation instead of the prevailing glycogen-like vacuolation in the bloodworm-fed group. No considerable effect was found on reproductive parameters. The negligible differences between dietary groups and good acceptance of pellets indicate their suitability as a useful starting point for the development of standardized diet for Nothobranchius furzeri.

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Quantification of noradrenergic-, dopaminergic-, and tectal-neurons during aging in the short-lived killifish Nothobranchius furzeri.

Project description:Parkinson's disease (PD) is characterized by phosphorylation and aggregation of the protein α-Synuclein and ensuing neuronal death progressing from the noradrenergic locus coeruleus to midbrain dopaminergic neurons. In 2019, Matsui and colleagues reported a spontaneous age-dependent degeneration of dopaminergic neurons and an even greater neurodegeneration of the noradrenergic neurons in the short-lived killifish Nothobranchius furzeri. Given the great possible relevance of a spontaneous model for PD, we assessed neurodegeneration of noradrenergic and dopaminergic neurons in two further laboratory strains of N. furzeri. We implemented, for the first time in N. furzeri, a whole-brain clarification technique and proceeded to entire 3D nuclei reconstruction to quantify total cell numbers in two different stains of N. furzeri. In both strains, we observed that age-dependent neurodegeneration is limited to the locus coeruleus and does not involve the posterior tuberculum. We also applied 3D counting to the optic tectum, an area of active adult neurogenesis, and detected an increase of neurons with age. Our results confirm age-dependent neurodegeneration of noradrenergic neurons, a condition reminiscent of the presymptomatic stage of PD indicating that N. furzeri could be used in the future to identify modifying factors for age-dependent neurodegeneration and open the intriguing possibility that natural genetic variation may influence the susceptibility of dopaminergic neurons.

| S-EPMC9470901 | biostudies-literature

Phylogenetic analysis and expression profiling of the Klotho gene family in the short-lived African killifish Nothobranchius furzeri.

Project description:Members of the Klotho gene family have been identified as modulators of the aging process. Deletion of αklotho in the mouse results in a syndrome resembling rapid human aging. Conversely, overexpression of αklotho extends mammalian lifespan. Here, we identify klotho orthologs in the vertebrate aging model Nothobranchius furzeri and provide a detailed spatio-temporal expression profile of both paralogs, α and βklotho, from embryogenesis until old age spanning the entire life cycle of the organism. Specifically, we observe low levels of expression of both paralogs during embryogenesis followed by a significant transcriptional induction as development proceeds. In adult killifish, αklotho is predominantly expressed in the liver, the kidney, and the developing pharyngeal teeth. Particularly high levels of αKlotho protein were identified in the kidney tubules, closely resembling mammalian expression patterns. Prominent βklotho expression was detected in the killifish intestine and liver. Overall, qRT-PCR analysis of Klotho members as a function of age revealed steady transcript levels, except for βklotho expression in the liver which was significantly downregulated with age. This spatio-temporal expression profiling may serve as a useful starting point to further investigate the distinct physiological roles of Klotho members during the aging process.

| S-EPMC6267267 | biostudies-literature

RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at age of 12 weeks)

Project description:The RNA-seq data contain 3 tissues (brain, liver, skin) of N.furzeri GRZ Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

2015-12-03 | GSE69122 | GEO

Aging impairs the essential contributions of non-glial progenitors to neurorepair in the dorsal telencephalon of the Killifish Nothobranchius furzeri.

Project description:The aging central nervous system (CNS) of mammals displays progressive limited regenerative abilities. Recovery after loss of neurons is extremely restricted in the aged brain. Many research models fall short in recapitulating mammalian aging hallmarks or have an impractically long lifespan. We established a traumatic brain injury model in the African turquoise killifish (Nothobranchius furzeri), a regeneration-competent vertebrate that evolved to naturally age extremely fast. Stab-wound injury of the aged killifish dorsal telencephalon unveils an impaired and incomplete regeneration response when compared to young individuals. In the young adult killifish, brain regeneration is mainly supported by atypical non-glial progenitors, yet their proliferation capacity clearly declines with age. We identified a high inflammatory response and glial scarring to also underlie the hampered generation of new neurons in aged fish. These primary results will pave the way to unravel the factor age in relation to neurorepair, and to improve therapeutic strategies to restore the injured and/or diseased aged mammalian CNS.

| S-EPMC8441397 | biostudies-literature

RNA-seq of the killifish Nothobranchius furzeri strain MZM-0410

Project description:The study consists of 12 samples of 39-week-old N. furzeri (skin and brain). Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

2015-12-03 | GSE72584 | GEO

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