Ontology highlight
ABSTRACT:
PROVIDER: PRJNA477413 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7410700.fastq.gz | Fastqsanger.gz | |||
| SRR7410710.fastq.gz | Fastqsanger.gz | |||
| SRR7410720.fastq.gz | Fastqsanger.gz | |||
| SRR7410730.fastq.gz | Fastqsanger.gz | |||
| SRR7410740.fastq.gz | Fastqsanger.gz |
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Project description:RNAseq used to examine gene expression in thermal challenged redband rainbow trout
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Project description:RNAseq used to examine gene expression in thermal challenged redband rainbow trout RNAseq data obtained from libraries prepared from Gill RNA
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Project description:In this project, effects of chronic temperature changes on the transcriptome of the rainbow trout heart (Oncorhynchus mykiss) were examined. Ectothermic animals of north-temperate latitudes experience large seasonal changes in temperature which strongly affect the rate of body functions. To compensate for the effects of temperature changes ectotherms can respond to chronic temperature changes by increasing the quantity of tissue or enzyme needed for different physiological tasks, or by expressing proteins isoforms which are more appropriate for the new thermal conditions. On the other hand, proteins which are needed in lesser amounts in the new thermal regime could be depressed or down-regulated. Although expression of proteins can be changed by multiple mechanisms during synthesis and degradation, temperature dependent changes in transcription of genes is probably the most important factor in modifying the proteome of the tissues. Rainbow trout are active throughout their thermal tolerance range (0-25°C). Maintenance of adequate cardiac function at different thermal conditions requires a thorough change of the cardiac phenotype which appears as compensatory changes in relative heart mass, energy metabolism, nervous and humoral control of cardiac contractility and in electrical and mechanical properties of the trout heart. Such an extensive structural and functional remodeling of the heart probably necessitates both qualitative and quantitative changes among the numerous macromolecules which constitute the cardiac phenotype and cannot, therefore, be solely based on posttranslational modification of proteins but is expected to require differential gene expression. As a power supply of the circulatory system, the heart is in the focal point of physiological plasticity and sets limits for the activity level of the animal in different thermal conditions. Although several aspects of heart function have been studied in thermally acclimated fish and a number of structural changes have been noticed on exposure to different temperatures, the cellular and molecular mechanisms involved in chronic thermal stress of the fish heart are only partially elucidated. An interesting and poorly examined feature of the cold-acclimated phenotype of the trout heart is the increased heart mass which attenuates the depressive effect of low temperature on cardiac pump function. The heart is a complex organ composed of multiple tissues which together provide the system all necessary qualifications for cardiac pump function. In addition to the contractile and metabolic machinery of the cardiac myocytes, the amount and quality of the extracellular matrix also contribute to the properties of the heart as a muscular pump. Due to the complexity of the heart an enormous amounts of research efforts are needed to find out and examine all crucial aspects of cardiac plasticity required for thermal acclimation. In this regard the screening of gene expression by cDNA micro arrays might provide a broader view to genomic basis of cardiac remodeling under changing temperatures and aid to reveal the candidate genes which are important for thermal acclimation and which might remain unnoticed by traditional biochemical and physiological methods. In the present study we the steady-state effects of temperature acclimation on gene expression of the rainbow trout heart were screened by micro array analysis.
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Project description:In this project, effects of chronic temperature changes on the transcriptome of the rainbow trout heart (Oncorhynchus mykiss) were examined. Ectothermic animals of north-temperate latitudes experience large seasonal changes in temperature which strongly affect the rate of body functions. To compensate for the effects of temperature changes ectotherms can respond to chronic temperature changes by increasing the quantity of tissue or enzyme needed for different physiological tasks, or by expressing proteins isoforms which are more appropriate for the new thermal conditions. On the other hand, proteins which are needed in lesser amounts in the new thermal regime could be depressed or down-regulated. Although expression of proteins can be changed by multiple mechanisms during synthesis and degradation, temperature dependent changes in transcription of genes is probably the most important factor in modifying the proteome of the tissues. Rainbow trout are active throughout their thermal tolerance range (0-25°C). Maintenance of adequate cardiac function at different thermal conditions requires a thorough change of the cardiac phenotype which appears as compensatory changes in relative heart mass, energy metabolism, nervous and humoral control of cardiac contractility and in electrical and mechanical properties of the trout heart. Such an extensive structural and functional remodeling of the heart probably necessitates both qualitative and quantitative changes among the numerous macromolecules which constitute the cardiac phenotype and cannot, therefore, be solely based on posttranslational modification of proteins but is expected to require differential gene expression. As a power supply of the circulatory system, the heart is in the focal point of physiological plasticity and sets limits for the activity level of the animal in different thermal conditions. Although several aspects of heart function have been studied in thermally acclimated fish and a number of structural changes have been noticed on exposure to different temperatures, the cellular and molecular mechanisms involved in chronic thermal stress of the fish heart are only partially elucidated. An interesting and poorly examined feature of the cold-acclimated phenotype of the trout heart is the increased heart mass which attenuates the depressive effect of low temperature on cardiac pump function. The heart is a complex organ composed of multiple tissues which together provide the system all necessary qualifications for cardiac pump function. In addition to the contractile and metabolic machinery of the cardiac myocytes, the amount and quality of the extracellular matrix also contribute to the properties of the heart as a muscular pump. Due to the complexity of the heart an enormous amounts of research efforts are needed to find out and examine all crucial aspects of cardiac plasticity required for thermal acclimation. In this regard the screening of gene expression by cDNA micro arrays might provide a broader view to genomic basis of cardiac remodeling under changing temperatures and aid to reveal the candidate genes which are important for thermal acclimation and which might remain unnoticed by traditional biochemical and physiological methods. In the present study we the steady-state effects of temperature acclimation on gene expression of the rainbow trout heart were screened by micro array analysis. Keywords: parallel sample
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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.
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