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An automated feeding system for the African killifish reveals effects of dietary restriction on lifespan and allows scalable assessment of associative learning

ABSTRACT: To study the effect of dietary restriction on killifish, we generated transcriptomes (RNA-seq) for the livers and brains of male and female killifish that had been subjected to different dietary treatements.

ORGANISM(S): Nothobranchius furzeri

PROVIDER: GSE216369 | GEO | 2022/10/29

REPOSITORIES: GEO

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Circular RNAs in the ageing African turquoise killifish

Project description:In this work we took 9 samples from brain and 6 samples from muscle of the African turquoise killifish (Nothobranchius furzeri) at 3.5, 8.5 and 14 weeks. Total RNA was sequenced and circRNAs were detected.

2019-07-31 | GSE134065 | GEO

RNA Seq of the ventricular region from young and aged killifish

Project description:In order to understand molecular basis of cardiac ageing in killifish, we have performed RNA Seq on the ventricular regions of young and aged killifish. Experiment was performed in biological triplicates.

2019-03-22 | E-MTAB-7582 | biostudies-arrayexpress

Circular RNAs in the ageing African turquoise killifish

Project description:Circular RNAs in the ageing African turquoise killifish

| PRJNA553674 | ENA

MicroRNA profiling in Atlantic killifish (Fundulus heteroclitus)

Project description:The Atlantic killifish (Fundulus heteroclitus) is an ideal model species to study physiological and toxicological adaptations to stressors. Killifish inhabiting the PCB-contaminated Superfund site in New Bedford Harbor, MA (NBH) have evolved resistance to toxicity and activation of the aryl hydrocarbon receptor (AHR) signaling pathway after exposure to PCBs and other AHR agonists. Until recently, a lack of genomic information has limited efforts to understand the molecular mechanisms underlying environmental adaptation to stressors. The advent of high throughput sequencing has facilitated an unbiased assessment of coding as well as non-coding RNAs in any species of interest. Among non-coding RNAs, microRNAs (miRNAs) are important regulators of gene expression and play crucial roles in development and physiology. The objective of this study is to catalog the miRNAs in killifish and determine their expression patterns in the embryos from contaminated (NBH) and pristine (Scorton Creek, MA (SC)) sites. Embryos from NBH and SC were collected daily from 1 to 15 days post-fertilization and RNA from pooled samples from each site was sequenced using SOLiD sequencing. We obtained 7.5 and 11 million raw reads from pooled SC and NBH samples, respectively. Analysis of the sequencing data identified 216 conserved mature miRNA sequences that are expressed during development. Using the draft killifish genome, we retrieved the miRNA precursor sequences. Based on the capacity of these putative precursor sequences to form the characteristic hairpin loop (assessed using RNAfold), we identified 197 conserved miRNA sequences in the genome.

2015-07-20 | GSE70953 | GEO

The heat shock response of killifish (Fundulus heteroclitus): candidate gene and heterologous microarray approaches.

Project description:Subspecies of the Atlantic killifish, Fundulus heteroclitus, differ in their maximum thermal tolerance. To determine whether there is a link between the heat shock response (HSR) and maximum thermal tolerance, we exposed 20ÂºC acclimated killifish from these subspecies to a 2hr heat shock at 34ÂºC and examined gene expression during heat shock and recovery using real time quantitative PCR and a heterologous cDNA microarray designed for salmonid fishes. Keywords: Expression profiling by array Microarray analyses were performed on four individual fish per subspecies of killifish (northern and southern) prior to heat shock (control) and after 60 minutes of heat shock, hybridized (one slide per individual) against a common reference RNA pool composed of an equal amount of RNA from all samples in the analysis.

2010-06-20 | E-GEOD-18792 | biostudies-arrayexpress

Chromosome conformation capture (Hi-C) of the turquoise killifish

Project description:This approach was used to increase the continuity of the killifish genome, and assess the relative distance of specific genes from the sex locus.

2024-03-06 | GSE218971 | GEO

Profiling microRNA expression in Atlantic killifish (Fundulus heteroclitus) gill and responses to arsenic and hyperosmotic stress

Project description:The Atlantic killifish (Fundulus heteroclitus), native to estuarine areas of the Atlantic coast of the United States, has become a valuable ecotoxicological model due to its ability to acclimate to rapid environmental changes and adapt to polluted habitats. Killifish respond to rapid increases in salinity with an immediate change in gene expression, as well as long-term remodeling of the gills. Arsenic, a major environmental toxicant, was previously shown to inhibit the ability of killifish gill to respond to a rapid increase in salinity. We characterized miRNA expression in killifish gill under salinity acclimation with and without arsenic and identified a small group of highly expressed, well-conserved miRNAs as well as 16 novel miRNAs not yet identified in other organisms.

2018-12-26 | GSE118062 | GEO

The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan.

Project description: Not available

| S-EPMC4684691 | biostudies-literature

The heat shock response of killifish (Fundulus heteroclitus): candidate gene and heterologous microarray approaches.

2009-10-30 | GSE18792 | GEO

Evolution of diapause in the African killifish by remodeling ancient gene regulatory landscape

Project description:Suspended animation (e.g. hibernation, diapause) allows organisms to survive extreme environments. But the mechanisms underlying the evolution of suspended animation states are unknown. The African turquoise killifish has evolved diapause as a form of suspended development to survive the complete drought that occurs every summer. Here, we show that gene duplicates – paralogs – exhibit specialized expression in diapause compared to normal development in the African turquoise killifish. Surprisingly, paralogs with specialized expression in diapause are evolutionarily very ancient and are present even in vertebrates that do not exhibit diapause. To determine if evolution of diapause is due to the regulatory landscape rewiring at ancient paralogs, we assessed chromatin accessibility genome-wide in fish species with or without diapause. This analysis revealed an evolutionary recent increase in chromatin accessibility at very ancient paralogs in African turquoise killifish. The increase in chromatin accessibility is linked to the presence of new binding sites for transcription factors, likely due to de novo mutations and transposable element (TE) insertion. Interestingly, accessible chromatin regions in diapause are enriched for lipid metabolism genes, and our lipidomics studies uncover a striking difference in lipid species in African turquoise killifish diapause, which could be critical for long-term survival. Together, our results show that diapause likely originated by repurposing pre-existing gene programs via recent changes in the regulatory landscape. This work raises the possibility that suspended animation programs could be reactivated in other species for long-term preservation via transcription factor remodeling and suggests a mechanism for how complex adaptations evolve in nature.

2021-08-05 | ST001898 | MetabolomicsWorkbench

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