Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Salmon Spawning Migration: Metabolic Shifts and Environmental Triggers

ABSTRACT: A large-scale functional genomics study revealed shifting energy generating processes in white muscle during the final 1,300 km migration of wild sockeye salmon to their spawning grounds in the Fraser River, British Columbia. In 2006, Lower Adams stock sockeye salmon ceased feeding after passing the Queen Charlotte Islands, 850 km from the Fraser River. Enhanced protein turnover and reduced transcription of actin, muscle contractile and heme-related proteins were early starvation responses in saltwater. Arrival to the estuarine environment triggered massive protein turnover through induction of proteasoma and lysosomal proteolysis and protein biosynthesis, and a shift from anaerobic glycolysis to oxidative phosphorylation. Response to entry into freshwater was modest, with up-regulation of heat shock proteins and nitric oxide biosynthesis. High river temperatures resulted in a strong defense/immune response and high mortalities in 50% of fish. Arrival to the spawning grounds triggered further up-regulation of oxidative phosphorylation and proteolysis, down-regulation of protein biosynthesis and helicase activity, and continued down-regulation of muscle proteins and most glycolytic enzymes. However, sharp up-regulation of PFK-I indicated induction of glycolytic potential at the spawning grounds. The identification of potential environmental cues triggering genome-wide transcriptional shifts in white muscle associated with migration and the strong activation of proteasomal proteolysis were both novel findings. Keywords: Functional genomics study on wild-caught fish The experiment was based on expression profiles of white muscle tissue collected from wild migrating adult sockeye salmon during their return spawning migration back to the Fraser River. Fish were collected from seven sites along the final 1,300 km migration path, and white muscle samples were quickly frozen in liquid nitrogen upon capture. Marine sampling sites included (from north to south) the Queen Charlotte Islands (QCI), Johnstone Strait (JS), Juan de Fuca Strait (JDFS), and the Strait of Georgia (SOG). Freshwater sampling sites included Whonnock (W), Savona (SV) and the Lower Adams Spawning Grounds. Genetically-based stock ID was used to identify the natal sites of fish collected from the wild. The experiment was designed to profile the transcriptional shifts associated with migration of the Adams River stock complex. The total experiment included 80 microarray slides, with a minimum biological replicate size per site of 6 (SV), and maximum of 18 (JS) (see supplemental table for details). Additional intra-site variables, which could only be addressed in some sites, included sex (female biased) and river entry timing (for JS, JDFS and W sites; identified through radio-tracking of marine collected fish). Total RNA was amplified (1 round) with MessageAmpTMII-96 kit (Ambion, TX, USA), and reverse transcribed to cDNA before labelling with ALEXA dyes using the Invitrogen Indirect Labelling Kit. The experiment was based on a reference design, with the reference containing the combined aRNA of all individuals used in the experiment. Individual samples were labelled with Alexa 555 and the reference control with Alexa 647, with no dye flips included. A single technical replicate of one SV fish (replicate 5) was included in the experimental design. This experiment is part of a larger white muscle experiment containing additional sockeye salmon stocks.

ORGANISM(S): Oncorhynchus nerka

SUBMITTER: David Patterson

PROVIDER: E-GEOD-13657 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The transcriptional response of Atlantic salmon (Salmo salar) to infectious hematopoietic necrosis (IHN) virus was elucidated using 16,008 gene GRASP cDNA microarrays. S. salar were exposed to the IHN virus in a waterborne challenge, and kidney samples from five fish sampled on each of days 0, 1, 5 and 9 were analysed in the microarray study. Validation of nine of the significant genes was conducted on fish sampled on alternate days from 1 to 13 and compared to the unchallenged control sampled on day 0. The key pathways up-regulated in response to the virus included endosomal transport, type I and II interferon responses, the alternative complement pathway, apoptosis, phagocytosis and phagocytic cell oxidation, natural killer cell activity, antiviral replication via iron sequestering, virally-induced disruption of the cell cycle, retroviral DNA integration, T-cell activation and cellular immunity. Fish that did not contain viral titer on days 5 and 9 responded in a similar manner to those with titer, but further induced a number of genes involved in anti-viral replication (Glutathione peroxidase 1 and ferritin H), anti-proliferation (PTEN and B-cell receptor associated protein 32), lysosomal response (CD63 antigen), pro-inflammatory response (lipopolysaccharide binding protein, stress activated JNK1, thiol peroxidase), and T-cell activation (T-cell activation Rho-GTPase activating protein) that may increase resistance to the virus. Three genes that were potentially co-opted by the virus to enhance infectivity were also identified, including uPAR (angiogenesis), CypA (viral replication and infectivity), and BAF1 (viral protein biosynthesis). Perhaps the most notable finding was the up-regulation of uPAR which can function to increase the density of fibronectin, the receptor of the IHN virus, on the cell surface, hence facilitate viral entry into the cell. Keywords: Immunlogical response to IHN virus challenge A preliminary microarray experiment was run on the waterborne-challenged S. salar whereby the five individuals sampled on a given day were combined and run on a single slide, and we compared the expression profiles from each day (days 0 (unchallenged control) through 11). From this experiment, we noted that the most profound changes were occurring around days 1, 5, and 9, so we performed subsequent experiments at these time points, with five fish per day and 5 control fish analysed in total.

Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish at the Weaver creek spawning grounds, and were observed for pre-spawning mortality or successful spawning. Weaver creek sockeye salmon (a late-run stock) spawn in an artificial spawning channel which has a controlled entrance and no exit, situated 100 km from the ocan. Females were dip-netted out of the entrance of the spawning channel, and placed into a sampling trough with flowing ambient water for the gill biopsy procedure and tagged with Petersen discs and returned to the spawning channel. Moribund fish were recovered daily and their gonads examined to assess whether they had spawned or not. Gene expression was assayed on the GRASP salmonid 32K cDNA microarray.

Project description:Although studies have established that exogenous growth hormone (GH) treatment stimulates growth in fish, its effects on target tissue gene expression are not well characterized. We assessed the effects PosilacÂ® (Monsanto Co., St. Louis, MO), a recombinant bovine somatotropin, on tissue transcript levels. Transcript abundance was measure in liver and muscle using the GRASP 16 K cDNA microarray. A selection of the genes identified as altered with the microarray, and also transcripts for insulin-like growth factors, growth hormone receptors (GHR) and myostatins were measured by realtime PCR in the liver, muscle, brain, kidney, intestine, stomach, gill and heart. In general, transcripts identified as differentially regulated in the muscle on the microarray showed similar direction of expression in the other non-hepatic tissues. Rainbow trout were selected from two high growth rate and two low growth rate families. A total of 113 and 67 transcripts were identified by microarray as differentially expressed with GH treatment across growth rate for muscle and liver respectively. The largest proportion of the transcripts represented novel transcripts, followed by immune and metabolism related genes. The immune related genes were primarily modulated in the liver and indicate activation of a non-specific immune response. The metabolic genes include lipid metabolism, oxidative phosphorylation and one carbon metabolism pathway transcripts. Most notable among the growth axis genes measured by realtime PCR were increases in GHR1 and-2 transcript in liver and muscle. Our results indicate that short-term GH treatment activates the immune system, shifts the metabolic sectors and modulates growth regulating genes. Keywords: Growth Hormone Injection Muscle and Liver Gene Expression Rainbow trout (hatched March 2005) selected for extreme growth rate were obtained from NCCCWA brood stock. Families were selected based on body weight at 7 months of age and thermal growth coefficient for the final month of growth. The two high growth families used in the study were in the top 2% in terms of growth rate, and the low growth families were in the lowest 10% for growth rate. Fish acclimated to the new tanks for two weeks prior to initiation of the treatments. Fish from each family were randomly selected to receive one of three treatments: 1) PosilacÂ® injection (120 mg/kg BW, n = 4 per family); 2) vehicle injection (n = 4 per family); or 3) untouched controls (n = 2 per family). We had determined there was no effect to growth or the GH/IGF-I axis in the vehicle treated fish, and therefore, all of the microarray hybridizations were made between the GH and vehicle injected groups. This study included a total of 16 two-channel arrays designed for the direct comparison of GH treatment levels. That is, for each of the four groups, 1) High Growth Rate Liver; 2) Low Growth Rate Liver; 3) High Growth Rate Muscle; and 4) Low Growth Rate Muscle, four slide were hybridizes using individual RNA samples from individual fish. RNA isolation from each tissue/organ sample was handled separately (without pooling) with the purpose of using biological replications. We hybridized two slides with the GH cDNA labeled with Alexa 555 and vehicle cDNA labeled with Alexa 647; and two slides, using unique RNA samples, for the with GH cDNA labeled with Alexa 647 and tissue from the vehicle injected group labeled with Alexa 647 within each tissue and growth rate. Sixteen slides were used in the current study representing 32 individual tissue samples, meaning a total of four biological replicates for each treatment group.

Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish sampled and tagged in the lower river and tracked as they swam towards the spawning grounds. Fish were caught in seine nets, gastrically implanted with radio transmitters, and biopsy sampled for blood, gill, muscle, and fin. Individual fish were tracked by receivers placed throughout the Fraser River watershed to identify and fate (i.e. the location of the receiver that last detected the fish). Targeted stocks of interest were genetically identified. Gene expression was profiled in gill tissue, a critical respiratory and ionoregulatory organ that is highly responsive to stress, chemical exposure and disease. Gene expression was assayed on the GRASP salmonid 16K cDNA microarray.

Project description:The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues. Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster. A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested. At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish. Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus. These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series is of gill expression profiles from the study of fish sampled and tagged in the ocean and tracked as they entered the river system and swam towards the spawning grounds. Fish were caught in seine nets, gastrically implanted with radio transmitters, and biopsy sampled for blood, gill, muscle, and fin. Individual fish were tracked by receivers placed throughout the Fraser River watershed to identify and fate (i.e. the location of the receiver that last detected the fish). Targeted stocks of interest were genetically identified. Gene expression was profiled in gill tissue, a critical respiratory and ionoregulatory organ that is highly responsive to stress, chemical exposure and disease. Gene expression was assayed on the GRASP salmonid 16K cDNA microarray.

Project description:Heterosis is the phenomenon whereby the progeny of particular inbred lines have enhanced agronomic performance relative to both parents. Although several hypotheses have been proposed to explain this fundamental biological phenomenon, the responsible molecular mechanisms have not been determined. The maize inbred lines B73 and Mo17 produce a heterotic F1 hybrid. Global patterns of gene expression were compared in seedlings of these three genotypes using a microarray that contains 13,999 cDNAs. Using an estimated 15% false discovery rate as a cut-off, 1,367 ESTs (9.8%) were identified as being significantly differentially expressed among genotypes. All possible modes of gene action were observed, including additivity, high- and low-parent dominance, under-dominance, and over-dominance. The largest proportion of the ESTs (78%, 1,062/1,367) exhibited expression patterns that are not statistically distinguishable from additivity. Even so, 22% of the differentially regulated genes exhibited non-additive modes of gene expression. Classified on the basis of significant pair-wise comparisons of genotype means, 181 of these 305 genes exhibited high-parent dominance and 23 exhibited low-parent dominance. In addition, 44 genes exhibited under- or over-dominant gene action. These findings are consistent with the hypothesis that multiple molecular mechanisms contribute to heterosis, including over-dominance Keywords: Genotype Comparison The inbreds B73 (Schnable Lab Accession #660) and Mo17 (Schnable Lab Accession #2618) used in this study were derived by self-pollination from stocks originally obtained from Don Robertson (Iowa State University) and Mike Lee (Iowa State University), respectively. Mo17 was crossed as a female by B73 to generate the F1. Kernels from three different seed sources (ears) per genotype were used in the experimental design. Prior to microarray analyses genotypes were confirmed by genotyping DNA extracted from each seed source using co-dominant IDP genetic markers that distinguish B73 from Mo17 (Fu et al., in preparation). Ten biological replications of B73, Mo17, and their F1 (Mo17xB73) were grown under highly controlled conditions in a randomized complete block design. For each replication, the B73, Mo17, and F1 samples were hybridized to three two-color cDNA microarrays using a loop design such that each loop included all pairwise comparisons between genotypes. RNA pools for each genotype were alternately labeled providing dye balance within each loop. After hybridization, one biological replicate was removed due to poor quality. The final analysis incorporated 27 microarray slides (3 slides for each of nine high-quality biological replicates).

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Salmon Spawning Migration: Metabolic Shifts and Environmental Triggers

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