Lambro River
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REPOSITORIES: ENA
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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.
2010-12-31 | GSE22177 | GEO
Project description:Soil Samples Collected from Along the DC-Metro Area of the Potomac River
2023-10-06 | E-MTAB-13365 | biostudies-arrayexpress
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.
2010-12-31 | GSE22171 | GEO
Project description:The zebra mussel is present in Spain since early 2000,s, when it was discovered in the lower part of the Ebro river. To study the gene expression pattern of different populations of zebra mussel a long the Ebro River we use a custom microarray developed in our laboratory, using 4057 publicly available DNA sequences from Dreissena polymorpha and other related genera. Also it was used an external sampling site located in Sitjar Dam, about 200km form the Ebro river. Transcriptome profiles were analysed using the gills of individuals collected in the same period (20-23 March) to diminish seasonal effects. A total of 755 transcripts changed significantly their mRNA levels among the sites of the study (ANOVA p<0.01, fc ±1.5). Genes encoding for xenobiotic, energetic and calcium metabolism and cell proliferation were those showing the highest differences among populations. Geographical origin appeared as the major driver of the differences among the studied populations, as the transcriptomic profiles from four populations collected within a radius of few km around the Flix factory clustered together and separated from those from other distant populations both upstream the Ebro River or in the Sitjar dam.
2012-10-10 | GSE41416 | GEO
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River.
2016-08-02 | GSE85064 | GEO
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.
2010-12-31 | E-GEOD-22177 | biostudies-arrayexpress
Project description:The zebra mussel is present in Spain since early 2000,s, when it was discovered in the lower part of the Ebro river. To study the gene expression pattern of different populations of zebra mussel a long the Ebro River we use a custom microarray developed in our laboratory, using 4057 publicly available DNA sequences from Dreissena polymorpha and other related genera. Also it was used an external sampling site located in Sitjar Dam, about 200km form the Ebro river. Transcriptome profiles were analysed using the gills of individuals collected in the same period (20-23 March) to diminish seasonal effects. A total of 755 transcripts changed significantly their mRNA levels among the sites of the study (ANOVA p<0.01, fc M-BM-11.5). Genes encoding for xenobiotic, energetic and calcium metabolism and cell proliferation were those showing the highest differences among populations. Geographical origin appeared as the major driver of the differences among the studied populations, as the transcriptomic profiles from four populations collected within a radius of few km around the Flix factory clustered together and separated from those from other distant populations both upstream the Ebro River or in the Sitjar dam. Differences on gene expression pattern were measure in gills of Dreissena polymorpha in different populations in five populations along the Ebro river and one population in Sitjar dam. The collection of samples were done during Srping (March). For the microarray it was used 2 replicates of each sites of the study.
2012-10-10 | E-GEOD-41416 | biostudies-arrayexpress
Project description:Whole Genome Metagenomic analysis of the Pampa river
| PRJNA849354 | ENA
Project description:The copper redhorse (Moxostoma hubbsi) is an endangered fish endemic to Quebec, Canada that is only known to spawn in two locations within the Richelieu River, a waterway draining a significant area of agricultural land. Accordingly, concerns have been raised over the impacts that agricultural pesticide contamination of spawning grounds and nursery habitats within the Richelieu River may have on early life stage copper redhorse. We assessed the effects of contaminants on early life stages of copper redhorse and river redhorse (Moxostoma carinatum), a closely related fish that shares the copper redhorse’s habitat and spawning grounds but is distributed more widely and is not yet listed as endangered. Copper and river redhorse embryos (1000 each) were exposed to either Richelieu River water in an in-situ flow-through system or to laboratory water used as a control. We assessed embryos hatching time, incidence of deformities and survival in copper and river redhorses. We then performed RNA sequencing on copper redhorse larvae to better understand changes due to river water exposure. We identified 341 compounds in the river water that were absent from lab water. Pesticide concentrations in the river peaked following rainfall during the spawning season. Embryos exposed to river water hatched prematurely at 63.0 and 59.2 cumulative degree days (CDD) compared to 65.4 and 69.9 CDD in laboratory water for river and copper redhorse, respectively. Copper redhorse exposed to river water also had a significantly lower survival rate than laboratory water (73% vs. 93%). RNA sequencing of copper redhorse revealed 18 differentially expressed genes (DEGs) following river water exposure. Eight of the upregulated DEGs (cd44, il1b, lamb3, lamc2, tgm5, orm1, saa, acod1) are linked to immune function and injury response and 7 of the downregulated DEGs (cpa2, ctrb, cela2a, ctrl, cpa1, prss1, cel) are involved with digestion and nutrient absorption. This study provided valuable data on the effects of anthropogenic contaminants present in the Richelieu River and increased our knowledge on the individual and mixture effects they have on an endangered fish.
2022-06-01 | GSE185175 | GEO