Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1035934 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Thermal stress is a serious and growing challenge facing Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and poses a threat to dwindling salmon populations. In order to better understand how acute thermal stress affects the biology of salmon, we performed a transcriptional analysis of gill tissue from unacclimated Chinook juveniles exposed to short periods at water temperatures ranging from ideal to potentially lethal. Reverse transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified.
2015-07-25 | GSE59756 | GEO
Project description:Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Populations return to freshwater for spawning at many different times of year, resulting in segregated populations that may use differing molecular pathways for these large behavioral and physiological differences. Using a population of Chinook from California’s Central Valley, we sought to generate novel expressed sequences using Long Serial Analysis of Gene Expression (LongSAGE). We constructed three LongSAGE libraries from brains of samples caught in the spring and fall in freshwater and from the ocean. Using cDNA libraries from Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), we were able to assign 59% of putatively differentially expressed tags to genes. Additionally, we tested the expression levels of seven genes, indicated by LongSAGE to be putatively differentially expressed between the fall and spring, and found none significantly differentially expressed. This study is the first to apply LongSAGE to salmon and provides a framework for conducting future research on gene expression differences between Chinook salmon of different populations, as well as underlying mechanisms of differing physiology and behavior. Keywords: seasonal difference
2007-10-10 | GSE6009 | GEO
Project description:Thermal stress is a serious and growing challenge facing Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and poses a threat to dwindling salmon populations. In order to better understand how acute thermal stress affects the biology of salmon, we performed a transcriptional analysis of gill tissue from unacclimated Chinook juveniles exposed to short periods at water temperatures ranging from ideal to potentially lethal. Reverse transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. Fifty-five fish were randomly assigned to one of five treatment groups and were allowed to acclimate at 12 degrees C in the experimental chambers overnight. Treatments consisted of a three-hour water bath at 15 degrees C, 18 degrees C, 21 degrees C or 25 degrees C degrees, followed by one hour of recovery at 12 degrees C. The experimental chambers were moved to water baths held at a constant temperature, facilitating very rapid change in the temperature experienced by the fish. Controls were handled identically to the other four treatment groups, but remained at 12 degrees C. Three replicates were performed on consecutive days. RNA from the 11 individuals in each treatment group were proportionally pooled and used to create 15 illumina libraries.
2015-07-25 | E-GEOD-59756 | biostudies-arrayexpress
Project description:Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Populations return to freshwater for spawning at many different times of year, resulting in segregated populations that may use differing molecular pathways for these large behavioral and physiological differences. Using a population of Chinook from California’s Central Valley, we sought to generate novel expressed sequences using Long Serial Analysis of Gene Expression (LongSAGE). We constructed three LongSAGE libraries from brains of samples caught in the spring and fall in freshwater and from the ocean. Using cDNA libraries from Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), we were able to assign 59% of putatively differentially expressed tags to genes. Additionally, we tested the expression levels of seven genes, indicated by LongSAGE to be putatively differentially expressed between the fall and spring, and found none significantly differentially expressed. This study is the first to apply LongSAGE to salmon and provides a framework for conducting future research on gene expression differences between Chinook salmon of different populations, as well as underlying mechanisms of differing physiology and behavior. Keywords: seasonal difference Single individuals were used to construct each LongSAGE library. The fall, spring and ocean samples were then compared between each other and examined for differences in the number of tags observed.
2007-10-09 | E-GEOD-6009 | biostudies-arrayexpress
Project description:Transciptional response to acute thermal stress in Chinook salmon
| PRJNA256138 | ENA
Project description:Understanding the molecular mechanisms of feed efficiency is an important step toward sustainability of salmonids aquaculture. In this study, the liver and white muscle proteomes of efficient (EFF) and inefficient (INEFF) Chinook salmon (Oncorhynchus tshawytscha) farmed in sea water were investigated by liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach. In total, 2,746 liver and 702 white muscle quantified proteins were compared between 21 EFF and 22 INEFF fish. Protein synthesis was enriched in both liver and white muscle of the EFF group while conversely, pathways related to protein degradation (amino acid catabolism and proteolysis, respectively) were the most affected processes in the liver and white muscle of INEFF fish. The SOM in the INEFF group was significantly higher than EFF fish showing INEFF fish probably was the dominant group. The INEFF group (dominant) suffered stress and shifted to consume energy through protein catabolism. As the first study, the results provide a preliminary picture of the fundamental molecular landscape of feed efficiency in Chinook salmon farmed in sea water
2023-04-27 | PXD028025 | Pride
Project description:Ovarian fluid was collected from 6 adult female Chinook salmon during their annual spawning run. Two replicates were analyzed for each ovarian fluid sample fraction using 80 and 100 minute gradients, respectively. Protein abundances were estimated using iTRAQ.
2021-04-17 | PXD014551 | Pride
Project description:Atlantic salmon production in Tasmania (Southern Australia) occurs near the upper limits of the species thermal tolerance. Summer water temperatures can average over 19°C over several weeks and have negative effects on performance and health. Liver tissue exerts important metabolic functions in thermal adaptation. With the aim of identifying the mechanisms underlying liver plasticity in response to chronic elevated temperature in Atlantic salmon, label-free quantitative shotgun proteomics was used to explore quantitative protein changes after 43 days of exposure to elevated temperature. A total of 277 proteins were differentially (adjusted p-value <0.05) expressed between the control (15°C) and elevated (21°C) temperature treatments. As predicted identified by Ingenuity pathway analysis (IPA), transcription and translation mechanisms, protein degradation via the proteasome, and cytoskeletal components were down-regulated at elevated temperature. In contrast, an up-regulated response was predicted identified for NRF2-mediated oxidative stress, endoplasmic reticulum stress, and amino acid degradation. The proteome response was paralleled by reduced fish condition factor and hepato-somatic index at elevated temperature . The present study provides further evidence of the interplay among different cellular machineries in a scenario of heat-induced energy deficit and oxidative stress, and refines present understanding of how Atlantic salmon cope with chronic exposure to temperature near the upper limits of thermal tolerance.
2018-03-01 | PXD004985 | Pride
Project description:Here, we investigate the genetic mechanisms that underlie thermal specialization of closely-related vibrios isolated from coastal water at the Beaufort Inlet (Beaufort, NC, USA). This location experiences large seasonal temperature fluctuations (annual range of ~20°C), and a clear seasonal shift in vibrio diversity has been observed (Yung et al. 2015). This previous study suggested that the mechanisms of thermal adaptation apparently differ based on evolutionary timescale: shifts in the temperature of maximal growth occur between deeply branching clades but the shape of the thermal performance curve changes on shorter time scales (Yung et al. 2015). The observed thermal specialization in vibrio populations over relatively short evolutionary time scales indicates that few genes or cellular processes may contribute to the differences in thermal performance between populations. In order to understand the molecular mechanisms that underlie adaptation to local thermal regimes in environmental vibrio populations, we employ genomic and transcriptomic approaches to examine transcriptomic changes that occur within strains grown at their thermal optima and under heat and cold stress. Moreover, we compare two closely-related strains with different laboratory thermal preferences to identify in situ evolutionary responses to different thermal environments in genome content and alleles as well as gene expression.
2018-07-31 | GSE83396 | GEO