Gene expression profiling of juvenile salmon in Pacific Northwest urban streams
Ontology highlight
ABSTRACT:
ORGANISM(S): Oncorhynchus kisutch
PROVIDER: GSE115688 | GEO | 2018/06/13
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression profiling of juvenile salmon in Pacific Northwest urban streams
| PRJNA475767 | ENA
Project description:Freshwater salinization poses global challenges for aquatic organisms inhabiting urban streams, impacting their physiology and ecology. However, current salinization research predominantly focuses on mortality endpoints in limited model species, overlooking the sublethal effects on a broader spectrum of organisms and the exploration of adaptive mechanisms and pathways under natural field conditions. To address these gaps, we conducted high-throughput sequencing transcriptomic analysis on the gill tissue of the euryhaline fish Gasterosteus aculeatus, investigating its molecular response to salinity stress in the highly urbanized river Boye, Germany. We found that in stream sections with sublethal concentrations of chloride costly osmoregulatory systems were activated, evidenced by the differential expression of genes related to osmoregulation. Our enrichment analysis revealed differentially expressed genes (DEGs) related to transmembrane transport and regulation of transport and other osmoregulation pathways, which aligns with the crucial role of these pathways in maintaining biological homeostasis. Notably, we identified candidate genes involved in increased osmoregulatory activity under salinity stress, including those responsible for moving ions across membranes: ion channels, ion pumps, and ion transporters. Particularly, genes from the solute carrier family SLC, aquaporin AQP1, chloride channel CLC7, ATP-binding cassette transporter ABCE1, and ATPases member ATAD2 exhibited prominent differential expression. These findings provide insights into the potential molecular mechanisms underlying the adaptive response of euryhaline fish to salinity stress and have implications for their conservation and management in the face of freshwater salinization.
2024-03-14 | GSE254383 | GEO
Project description:Stream biofilms from four Swiss streams Metagenome
| PRJNA414706 | ENA
Project description:The goal of this study was to use global gene expression as a diagnostic tool to compare hepatic gene expression patterns in both male and female FHM in streams with the lowest and highest reproductive success, and potentially identify a suite of mRNA transcripts indicative of reproduction in a population The goal of this study was to compare differences in hepatic mRNA expression between gender at high and low egg-producing streams, not differences between individual streams. A k-means cluster analysis was performed using eggs/pair/day on the original 17 streams to delineate 3 clusters: high, medium and low. From that analysis, FHM from 6 of the original 17-streams used in Crago et al. (2010) were chosen for the microarray experiment (Fig. 1, Table 1). In this study the experimental condition is reproductive success; High versus Low reproductive success. The streams grouped into High Reproductive Success were Oak Creek-2007 (2313 eggs), Point Creek (1277 eggs), Meeme Creek (1164 eggs) and Baird Creek (967 eggs). The streams grouped into Low Reproductive Success were: Ashwaubenon Creek (0 eggs), Devils Creek (541 eggs) and Oak Creek-2006 (642 eggs). Multiple regression analysis using the 22 sediment and water quality characteristics measured in the 6 streams with the highest (n = 4 and lowest (n = 3) streams demonstrated that there were no differences amongst the streams in regards to measure sediment and water variables. .5 One array was run for each gender from each stream. So that Males from Point Creek were pooled and run on one array, males from Ashwaubenon Creek were run on a separate array, and so forth. There were 14 arrays used in this study, 7 for males, 7 for females from individual rivers. So that Males from Point Creek were pooled and run on one array, males from Ashwaubenon Creek were run on a separate array, and so forth. In the case of Oak Creek, which was sampled in both years, there was a large difference in egg production between two years. Therefore separate arrays were run for Oak Creek 2006 and Oak Creek 2007. All streams chosen had overall survival rates of at least 80% through the 21-day sampling period, except Devils River. The survival rate for Devils River was at 100% until four days prior to the end of the experiment when six fish died or escaped.
2014-04-09 | E-GEOD-56604 | biostudies-arrayexpress
Project description:Prolific heterotrophic biofilm growth is a common occurrence in airport receiving streams containing deicer and anti-icer runoff. This study investigated relations of heterotrophic biofilm prevalence and community composition to environmental conditions at stream sites upstream and downstream of Milwaukee Mitchell International Airport in Milwaukee, WI, during two deicing seasons (2009–2010 and 2010–2011). Modern genetic tools (such as microarray) have not previously been applied to biofilm communities in this type of setting. We used microarray results to characterize biofilm community composition as well as the response of the biofilm community to environmental factors (i.e., organic content (using chemical oxygen demand concentration) and temperature).
2019-05-13 | GSE129990 | GEO
Project description:This study investigates host-specific gene expression of the Pacific salmon lice, Lepeophtheirus salmonis oncorhynchii, while parasitizing a resistant host (Coho salmon), two susceptible hosts (Atlantic salmon, Sockeye salmon), and a population with-held hosts (starved), over 48 hrs.
2017-01-25 | GSE80220 | GEO
Project description:The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals.
2014-12-22 | GSE64286 | GEO
Project description:The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals. Microbial community structure was determined using PhyoChio (G3)
2014-12-22 | GSE64368 | GEO
Project description:Coho Salmon GH Transgenic Study Keywords: other
2005-05-01 | GSE2388 | GEO
Project description:To assess the effect of rapid individual growth on trace element concentrations in fish, we measured concentrations of seven trace elements (As, Cd, Cs, Hg, Pb, Se, Zn) in stream-dwelling Atlantic salmon (Salmo salar) from 15 sites encompassing a 10-fold range in salmon growth. All salmon were hatched under uniform conditions, released into streams, and sampled approximately 120 days later for trace element analysis. For most elements, element concentrations in salmon tracked those in their prey. Fast-growing salmon had lower concentrations of all elements than slow growers, after accounting for prey concentrations. This pattern held for essential and nonessential elements, as well as elements that accumulate from food and those that can accumulate from water. At the sites with the fastest salmon growth, trace element concentrations in salmon were 37% (Cs) to 86% (Pb) lower than at sites where growth was suppressed. Given that concentrations were generally below levels harmful to salmon and that the pattern was consistent across all elements, we suggest that dilution of elements in larger biomass led to lower concentrations in fast-growing fish. Streams that foster rapid, efficient fish growth may produce fish with lower concentrations of elements potentially toxic for human and wildlife consumers.
| S-EPMC2861850 | biostudies-literature