Notothenioidei
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA368682 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5210461.fastq.gz | Fastqsanger.gz | |||
| SRR5210372.fastq.gz | Fastqsanger.gz | |||
| SRR5210462.fastq.gz | Fastqsanger.gz | |||
| SRR5210373.fastq.gz | Fastqsanger.gz | |||
| SRR5210463_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Antarctic notothenioid fishes are noteworthy for their history of isolation and indications they lack the heat shock response. The mechanistic basis for stenothermy has not been fully elucidated, and some aspects of stenothermy could arise post-transcriptionally. Antarctic emerald rockcod (Trematomus bernacchii) were sampled after exposure to chronic and/or acute high temperatures, followed by assessment of proteomic responses in brain, gill, and kidney using tissue-specific DIA assay libraries. Few cellular stress response proteins were induced, and overall responses were modest in terms of numbers of differentially expressed proteins and their fold changes. Inconsistencies in protein induction across treatments and tissues are suggestive of dysregulation, rather than an adaptive response. Changes in regulation of translation in Antarctic notothenioids could explain these patterns. Some components of the “integrative stress response” that regulates translation are highly conserved (e.g., Ser-52 of eIF2α), but the eIF2α kinases GCN2 and PERK may have evolved along different trajectories in Antarctic fishes. Together, these observations suggest a novel hypothesis for stenothermy and the absence of a coordinated cellular stress response in Antarctic fishes.
2024-10-03 | PXD051983 | panorama
Project description:The goal of this study was to measure the effect of heat stress on the transcriptome of a cold-adapted fish species - Trematomus bernacchii - an Antarctic fish species. Keywords: Stress response
2007-12-14 | GSE9871 | GEO
Project description:We sequenced and assembled de novo the coding transcriptomes in four species of Notothenioid fish: Neopagetopsis ionah (Jonah’s ice fish), Pseudochaenichtys georgianus (South Georgia icefish), Harpagifer antarcticus (Antarctic spiny plunderfish) and Parachaenichthys charcoti (Charcot’s dragonfish). We sampled 1-4 individuals and 1-14 tissues (brain, white muscle, liver, head kidney, trunk kidney, skin, heart, red muscle, spleen, ovary, testis, whole blood, gill, red blood cells) in each species, depending on tissue availability.
2018-06-13 | E-MTAB-6759 | biostudies-arrayexpress
Project description:The Antarctic eelpout, Pachycara brachycephalum, is a member of the cosmopolitan fish family Zoarcidae, which comprises 284 species distributed all over the globe. Since the Antarctic realm is a highly constant habitat, the species P. brachycephalum was employed in a global approach to characterize thermal response mechanisms in terms of long-term cold- and warm acclimation. Specimen of P. brachycephalum were incubated for 2 months at six different temperatures: -1C, 0C (control), 3C, 5C, 7C, 9C. In each group 5 fish were selected for hybridization (except control: n=7). By comparing the features of control and treatment groups we addressed temperature dependent expression profiles in liver tissue.
2014-03-20 | E-MTAB-2252 | biostudies-arrayexpress
Project description:Antarctic notothenioid fish genomes project
| PRJEB53202 | ENA
Project description:Halohasta litchfieldiae and Halorubrum lacusprofundi are important members of Deep Lake in Antarctica, representing ~44% (the most abundance) and ~10% (the 3rd most abundance) of the lake population. Deep Lake is in the Vestfold Hills, East Antarctica (68°33’36.8S, 78°11’48.7E) and is 36 m deep, monomictic, and perennially cold (down to -20C) (DeMaere et al., 2013; Williams et al., 2014; Tschitschko et al., 2015; Tschitschko et al., 2016). In this project, using quantitative proteomics (8-plex iTRAQ labeling), proteins, pathways and cellular processes important for cold adaptation were determined for both Hht. litchfieldiae and Hrr. lacusprofundi. The data provided a new level of understanding about molecular mechanisms and regulatory networks involved in adaptation of the Antarctic haloarchaea to cold environment. DeMaere, M. Z., Williams, T. J., Allen, M. A., Brown, M. V., Gibson, J. A., Rich, J., et al. (2013) High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci USA 110: 16939-16944. Tschitschko, B., Williams, T. J., Allen, M. A., Páez-Espino, D., Kyrpides, N., Zhong, L., et al. (2015) Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. ISME J 9: 2094-2107. Tschitschko, B., Williams, T. J., Allen, M. A., Zhong, L., Raftery, M. J., and Cavicchioli, R. (2016) Ecophysiological distinctions of haloarchaea from a hypersaline Antarctic lake determined using metaproteomics. Appl Environ Microbiol 82: 3165 – 3173. Williams, T. J., Allen, M. A., DeMaere, M. Z., Kyrpides, N. C., Tringe, S. G., Woyke, T., and Cavicchioli, R. (2014) Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea. ISME J 8: 1645-1658.
2017-02-27 | PXD005076 | Pride
Project description:Changes in gene expression are thought to be required for maintaining tissue's proper function under cold stress, but little is known about the role of each tissue in setting the cold tolerance ability in fish. Oreochromis niloticus and Danio rerio are two tropical fishes; they differ in their abilities of cold tolerance. In this study, both fishes were exposed to graded cold temperatures, ranging from 28°C to 18°C and 10°C, and the transcriptomes of 8 tissues at each tempeature were sequenced and compared. By characterizing tissue-based gene expression variation between the two fishes we identified some key tissue specific biological processes, which provide a better understating of the typical biological functions of tissues in physiological fitness under cold stress.
2017-11-30 | GSE63727 | GEO
Project description:Transcriptome sequencing of three Antarctic notothenioid species
| PRJNA80115 | ENA
Project description:The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold-responsive transcriptional patterns have been determined in fishes, the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures, ranging from normal (28°C) to mild (18°C) and severe (10°C) cold, using RNA-seq. The tissues varied in the number of cold-responsive genes, of which the kidney appeared to be most sensitive, whereas the brain was the least. Fuzzy k-means clustering revealed 34 gene clusters of distinct expression patterns, demonstrating diverse tissue-specific responses in conjunction with multiple aspects of ubiquitous cross-tissue responses to cold. Thirty-one GO terms were over-represented upon cold treatment. These terms are involved in basic cellular processes, such as RNA splicing and proton transport, as well tissue-specific processes, such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis-regulatory elements governing the concerted cold responses, the promoters of the genes that demonstrated strong co-regulation were analyzed using an enriched motif discovery program, DREME. Eleven motifs, 6 known and 5 novel, were identified. These motifs belong to the genes corresponding to the 16 over-represented GO terms identified above. Some motifs, such as the AP-1 and STAT1 binding sites, are known to be stress responsive. By integrating comprehensive cold-induced transcriptional changes with a cis-motif identification tool, we identified genome-wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Examination of gene expression of 24 samples (eight tissues at three temperatures)
2015-08-06 | E-GEOD-62221 | biostudies-arrayexpress