Arctic charr exposed to acute thermal stress
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PROVIDER: PRJNA136745 | ENA |
REPOSITORIES: ENA
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Project description:Arctic charr is an especially attractive aquaculture species given that it features the desirable tissue traits of other salmonids, but can be bred and grown at inland freshwater tank farms year round. It is therefore of interest to develop upper temperature tolerant (UTT) strains of Arctic charr to increase the robustness of the species in the face of climate change, as well as to enable production in more southern regions. We conducted an acute temperature trial to identify temperature tolerant and intolerant Arctic charr individuals. Specifically, approximately 200 fish were transferred to an experimental tank (diameter: 1.86 m, depth 50 cm) and left to acclimate for 48 h at ambient temperature. After acclimation, 10 fish were removed to act as a control group, then water that had been diverted through a heat exchanger was added to the flow-through system to increase the water temperature in the tank by 6°C/h until it reached 22°C, then 0.5°C every 30 min until the water reached 25°C, the observed lethal temperature for these fish. When the water temperature reached 25°C, the temperature was held constant and the fish were closely monitored for signs of stress. The first and last 10 individuals to show loss of balance were quickly removed from the tank for sampling, thus representing the 5% least and most temperature tolerant fish, respectively. A reference design microarray study was then performed with the cGRASP 32K microarray using six samples from each group (Intolerant, Tolerant, Control) to identify genes differentially expressed between groups. The results of this study will feed into an ongoing Arctic charr marker-assisted selection based broodstock development program, and may contribute to population-based conservation initiatives for salmonids in general.
2011-06-01 | GSE26306 | GEO
Project description:Arctic charr is an especially attractive aquaculture species given that it features the desirable tissue traits of other salmonids, but can be bred and grown at inland freshwater tank farms year round. It is therefore of interest to develop upper temperature tolerant (UTT) strains of Arctic charr to increase the robustness of the species in the face of climate change, as well as to enable production in more southern regions. We conducted an acute temperature trial to identify temperature tolerant and intolerant Arctic charr individuals. Specifically, approximately 200 fish were transferred to an experimental tank (diameter: 1.86 m, depth 50 cm) and left to acclimate for 48 h at ambient temperature. After acclimation, 10 fish were removed to act as a control group, then water that had been diverted through a heat exchanger was added to the flow-through system to increase the water temperature in the tank by 6°C/h until it reached 22°C, then 0.5°C every 30 min until the water reached 25°C, the observed lethal temperature for these fish. When the water temperature reached 25°C, the temperature was held constant and the fish were closely monitored for signs of stress. The first and last 10 individuals to show loss of balance were quickly removed from the tank for sampling, thus representing the 5% least and most temperature tolerant fish, respectively. A reference design microarray study was then performed with the cGRASP 32K microarray using six samples from each group (Intolerant, Tolerant, Control) to identify genes differentially expressed between groups. The results of this study will feed into an ongoing Arctic charr marker-assisted selection based broodstock development program, and may contribute to population-based conservation initiatives for salmonids in general. 18 microarray slides representing 6 individuals from 3 treatment groups (Intolerant, Tolerant and Control). One test cDNA labeled with cy5 and the common reference aRNA labeled with Cy3 was hybridized to each slide Reference design: 18 slides (6 x Tolerant fish, 6x Intolerant fish, 6x Control fish) were used.
2011-06-01 | E-GEOD-26306 | biostudies-arrayexpress
Project description:Arctic charr thrive at high densities and can live in freshwater year round, making this species especially suitable for inland, closed containment aquaculture. However, it is a cold water salmonid, which both limits where the species can be farmed and places wild populations at particular risk to climate change. Previously, we identified genes associated with tolerance and intolerance to acute, lethal temperature stress in Arctic charr. However, there remained a need to examine the genes involved in the stress response to more realistic temperatures that could be experienced during a summer heat wave in grow-out tanks that are not artificially cooled, or under natural conditions. Here, we exposed Arctic charr to moderate heat stress of 15–18ºC for 72 hours, and gill tissues extracted before, during (i.e., at 72 hrs), immediately after cooling and after 72 hours of recovery at ambient temperature (6ºC) were used for gene expression profiling by microarray and qPCR analyses. The results revealed an expected pattern for heat shock protein (Hsp) expression, which was highest during heat exposure, with significantly reduced expression (approaching control levels) quickly thereafter. We also found that the expression of numerous ribosomal proteins was significantly elevated immediately and 72 hrs after cooling, suggesting that the gill tissues were undergoing ribosomal biogenesis while recovering from damage caused by heat stress. We suggest that these are candidate gene targets for the future development of genetic markers for broodstock development or for monitoring temperature stress and recovery in wild or cultured conditions.
2011-07-05 | GSE29610 | GEO
Project description:Arctic charr thrive at high densities and can live in freshwater year round, making this species especially suitable for inland, closed containment aquaculture. However, it is a cold water salmonid, which both limits where the species can be farmed and places wild populations at particular risk to climate change. Previously, we identified genes associated with tolerance and intolerance to acute, lethal temperature stress in Arctic charr. However, there remained a need to examine the genes involved in the stress response to more realistic temperatures that could be experienced during a summer heat wave in grow-out tanks that are not artificially cooled, or under natural conditions. Here, we exposed Arctic charr to moderate heat stress of 15–18ºC for 72 hours, and gill tissues extracted before, during (i.e., at 72 hrs), immediately after cooling and after 72 hours of recovery at ambient temperature (6ºC) were used for gene expression profiling by microarray and qPCR analyses. The results revealed an expected pattern for heat shock protein (Hsp) expression, which was highest during heat exposure, with significantly reduced expression (approaching control levels) quickly thereafter. We also found that the expression of numerous ribosomal proteins was significantly elevated immediately and 72 hrs after cooling, suggesting that the gill tissues were undergoing ribosomal biogenesis while recovering from damage caused by heat stress. We suggest that these are candidate gene targets for the future development of genetic markers for broodstock development or for monitoring temperature stress and recovery in wild or cultured conditions. 24 microarray slides representing 6 individuals from 4 treatment groups (Control, During, After and Recovery). One test cDNA labeled with Cy5 and the common reference aRNA labeled with Cy3 was hybridized to each slide. Reference design: 6x control fish, 6x group D fish, 6x group A fish, 6x group R fish.
2011-07-05 | E-GEOD-29610 | biostudies-arrayexpress
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:We report here the release of a multi organ transcriptome developped for the Arctic char Salvelinus alpinus. This reference set was obtained using the 454 GS FLX+ technology. A pool of one-year-old, immature offspring of wild, anadromous Arctic charr originating from Lake Varflusjoen, Svalbard (79oN), including both lean and fat individuals, and three-years-old mature offspring of charr originating from Lake Vårflusjøen, North-Norway (70oN) was sampled. In order to maximize the diversity of expressed transcripts, we sampled a variety of organs and tissues; the whole brain, gill and head kidney and pieces of the liver, gonad, abdominal fat and muscle.
2016-08-18 | E-MTAB-3522 | biostudies-arrayexpress
Project description:Cold water coral exposed to thermal stress Raw sequence reads
| PRJNA648865 | ENA
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:Background: Geographic variation in the thermal environment impacts a broad range of biochemical and physiological processes and can be a major selective force leading to local population adaptation. In the intertidal copepod Tigriopus californicus, populations along the coast of California show differences in thermal tolerance that are consistent with adaptation, i.e., southern populations withstand thermal stresses that are lethal to northern populations. To understand the genetic basis of these physiological differences, we use an RNA-seq approach to compare genome-wide patterns of gene expression in two populations known to differ in thermal tolerance. Results: Observed differences in gene expression between the southern (San Diego) and the northern (Santa Cruz) populations included both the number of affected loci as well as the identity of these loci. However, the most pronounced differences concerned the amplitude of up-regulation of genes producing heat shock proteins (Hsps) and genes involved in ubiquitination and proteolysis. Cuticle genes were up-regulated in SD but down-regulated in SC, and mitochondrial genes were downregulated in both populations. Among the hsp genes, orthologous pairs show markedly different thermal responses as the amplitude of hsp response was greatly elevated in the San Diego population, most notably in members of the hsp70 gene family. There was no evidence of accelerated evolution at the sequence level for hsp genes. Conclusions: Marked changes in gene expression were observed in response to acute sublethal thermal stress in the copepod T. californicus. Although some qualitative differences were observed between populations (e.g., cuticle gene regulation), the most pronounced differences involved the magnitude of induction of numerous hsp and ubiquitin genes. These differences in gene expression suggest that evolutionary divergence in the regulatory pathway(s) involved in acute temperature stress may offer at least a partial explanation of latitudinal trends in thermal tolerance observed in Tigriopus.
2012-09-11 | GSE38546 | GEO
Project description:Background: Geographic variation in the thermal environment impacts a broad range of biochemical and physiological processes and can be a major selective force leading to local population adaptation. In the intertidal copepod Tigriopus californicus, populations along the coast of California show differences in thermal tolerance that are consistent with adaptation, i.e., southern populations withstand thermal stresses that are lethal to northern populations. To understand the genetic basis of these physiological differences, we use an RNA-seq approach to compare genome-wide patterns of gene expression in two populations known to differ in thermal tolerance. Results: Observed differences in gene expression between the southern (San Diego) and the northern (Santa Cruz) populations included both the number of affected loci as well as the identity of these loci. However, the most pronounced differences concerned the amplitude of up-regulation of genes producing heat shock proteins (Hsps) and genes involved in ubiquitination and proteolysis. Cuticle genes were up-regulated in SD but down-regulated in SC, and mitochondrial genes were downregulated in both populations. Among the hsp genes, orthologous pairs show markedly different thermal responses as the amplitude of hsp response was greatly elevated in the San Diego population, most notably in members of the hsp70 gene family. There was no evidence of accelerated evolution at the sequence level for hsp genes. Conclusions: Marked changes in gene expression were observed in response to acute sublethal thermal stress in the copepod T. californicus. Although some qualitative differences were observed between populations (e.g., cuticle gene regulation), the most pronounced differences involved the magnitude of induction of numerous hsp and ubiquitin genes. These differences in gene expression suggest that evolutionary divergence in the regulatory pathway(s) involved in acute temperature stress may offer at least a partial explanation of latitudinal trends in thermal tolerance observed in Tigriopus. For each population, ~600 copepods were split into two equal samples, one for control and one for treatment. Each sample was placed in a 50 mL Falcon tube containing 30 mL filtered seawater. After equilibrating samples to 20 degrees C, each tube was immersed in water bath at its target temperature (control: 20 C; treatment: 35 C) for one hour, and then immersed at 20 C for one hour for recovery. Copepods were then collected in a net mesh and quickly transferred to a tube containing 5 mL Tri-reagent for standard RNA extraction.
2012-09-11 | E-GEOD-38546 | biostudies-arrayexpress