Divergent immunity and energetic programs in the gills of migratory and resident Oncorhynchus mykiss
Ontology highlight
ABSTRACT:
ORGANISM(S): Salmo salar Oncorhynchus mykiss
PROVIDER: GSE48844 | GEO | 2014/03/04
SECONDARY ACCESSION(S): PRJNA211922
REPOSITORIES: GEO
Similar Datasets
Project description:To identify gene expression differences between Oncorhynchus mykiss that migrate and those that reside in freshwater, we compared gill transcriptomes of fish prior to release from a hatchery with those of fish recaptured eight days post-release while all fish were still in freshwater, but some were captured next to the hatchery (non-migrants) and others were captured moving toward the ocean (migrants). The in-hatchery sampling method represents a highly similar environment for all the fish, and allows for the determination of activated genes predictive of smolting programs prior to release into streams. Morphological (e.g. color) and physiological (gill NaCl-ATPase activity) data were also obtained and correlated to gene expression differences to aid in predictions. Gill tissue was sampled for transcriptome profiling 13 days prior to two different releases from the hatchery (total sampled within hatchery n = 19). Samples were also taken eight days after the two releases near-hatchery (total in-creek n = 20) or migrating towards the ocean but still in freshwater (second release only n = 20). Finally, 48 days after the second release a final set of resident fish were sampled near the hatchery (n =10). In terms of time after release, the most parallel comparison is the second 8 day post release sample in-creek and migrating. Although all samples were obtained in freshwater, the samples with the most similar local environment are the pre-release samples.
2014-03-04 | E-GEOD-48844 | biostudies-arrayexpress
Project description:Amoebic gill disease (AGD) is an ectoparasitic condition of some farm-reared marine fish and is caused by Neoparamoeba perurans. Tanks housing Atlantic salmon (Salmo salar) were inoculated with Neoparamoeba perurans and fish were sampled at 36 days postinoculation (pi.). AGD-affected gill tissue was dissected from N. perurans infected fish, and a DNA microarray was used to compare global gene expression against tissues from AGD-naive fish. To determine whether the changes in gene expression were restricted to AGD-lesions, lesion tissue from AGD-affected fish was also compared with non-lesion gill tissue dissected from the same gill arch. Samples were assessed using a DNA microarray. Keywords: comparative gene expression, parasite-induced lesion, Neoparamoeba perurans, amoebic gill disease
2007-11-15 | GSE9595 | GEO
Project description:Fish gills represent a complex organ that perform multiple physiological functions and is composed of several cell types. Among these cells, ionocytes are implicated in the maintenance of ion homeostasis. However, because the ionocyte represents only a small percent of whole gill tissue, its specific transcriptome can be overlooked among the numerous cell types included in the gill. The objective of this study is to better understand ionocyte functions by comparing the RNA expression of this cell type in freshwater and seawater adapted rainbow trout. To realize this objective, ionocytes were captured from gill cryosections using laser capture microdissection after immunohistochemistry. Then, transcriptome analyses were performed on an Agilent trout oligonucleotide microarray. Gene expression analysis identified 108 unique annotated genes differentially expressed between freshwater and seawater ionocytes, with a gene fold higher than 3. Most of these genes were up regulated in freshwater cells. Interestingly, several genes implicated in ion transport, extracellular matrix and structural cellular proteins appeared up regulated in freshwater ionocytes. Among them, several ion transporters, such as CIC2, SLC26A6, and NBC, were validated by qPCR and/or in situ hybridization. The latter technique allowed us to localize the transcripts of these ion transporters in only ionocytes and more particularly in the freshwater cells. Genes involved in metabolism and also several genes implicated in transcriptional regulation, cell signaling and the cell cycle were also over-expressed in freshwater ionocytes. In conclusion, laser capture microdissection combined with microarray analysis allowed for the determination of the cell signature of scarce cells in fish gills, such as ionocytes, and aided characterization of the transcriptome of these cells in freshwater and seawater adapted trout.
2015-10-08 | GSE69409 | GEO
Project description:Amoebic gill disease (AGD) is an ectoparasitic condition of some farm-reared marine fish and is caused by Neoparamoeba perurans. Tanks housing Atlantic salmon (Salmo salar) were inoculated with Neoparamoeba perurans and fish were sampled at 36 days postinoculation (pi.). AGD-affected gill tissue was dissected from N. perurans infected fish, and a DNA microarray was used to compare global gene expression against tissues from AGD-naive fish. To determine whether the changes in gene expression were restricted to AGD-lesions, lesion tissue from AGD-affected fish was also compared with non-lesion gill tissue dissected from the same gill arch. Samples were assessed using a DNA microarray. mRNA from lesion and non-lesion gill tissue was amplified and labeled. Six biological and two technical replicates were utilised to hybridise to 12 arrays using amplified RNA from AGD-affected lesion gill tissue with AGD-naive fish as a control. Four biological and two technical replicates were utilised to hybridise to 8 arrays using amplified RNA from AGD-affected lesion gill tissue with non-lesion tissue from the same gill arch as a control. The assignment of microarrays to treatment groups for hybridization was randomised by using a random number generator.
2010-05-25 | E-GEOD-9595 | biostudies-arrayexpress
Project description:Background: Rainbow trout (Oncorhynchus mykiss) is a salmonid species with a complex life-history. Wild populations are naturally divided into freshwater residents and sea-run migrants. Migrants undergo an energy-demanding adaptation for life in seawater, known as smoltification, while freshwater residents display these changes in an attenuated magnitude and rate. Despite this, in seawater rainbow trout farming all animals are transferred to seawater. Under these circumstances, weeks after seawater transfer, a significant portion of the fish die (around 10%) or experience growth stunting (GS; around 10%), which represents an important profitability and welfare issue. The underlying causes leading to GS in seawater-transferred rainbow trout remain unknown. In this study, we aimed at characterising the GS phenotype in seawater-transferred rainbow trout using untargeted and targeted approaches. To this end, the liver proteome (LC-MS/MS) and lipidome (LC-MS) of GS and fast-growing phenotypes were profiled to identify molecules and processes that are characteristic of the GS phenotype. Moreover, the transcription, abundance or activity of key proteins and hormones related to osmoregulation (Gill Na+, K+–ATPase activity), growth (plasma IGF-I, and liver igf1, igfbp1b, ghr1 and ctsl) and stress (plasma cortisol) were measured using targeted approaches. Results: No differences in Gill Na+, K+–ATPase activity and plasma cortisol were detected between the two groups. However, a significant downregulation in plasma IGF-I and liver igf1 transcription pointed at this growth factor as an important pathomechanism for GS. Changes in the liver proteome revealed reactive-oxygen-species-mediated endoplasmic reticulum stress as a key mechanism underlying the GS phenotype. From the lipidomic analysis, key observations include a reduction in triacylglycerols and elevated amounts of cardiolipins, a characteristic lipid class associated with oxidative stress, in GS phenotype. Conclusion: While the triggers to the activation of endoplasmic reticulum stress are still unknown, data from this study point towards either an unresolved infection or a nutritional deficiency as underlying drivers of this phenotype.
2022-02-17 | PXD026897 | Pride
Project description:Alkalinity stress is considered to be one of the major stressors for fish in saline-alkali water. Thus, it is of great significance from both aquaculture and physiological viewpoint to understand the molecular genetic response of aquatic organisms to alkalinity stress. The objective of this study is to determine genome-wide gene expression profiles to better understand the physiology response of medaka (Oryzias latipes) to high carbonate alkalinity stress. In lab-based cultures, adult fish were exposed to freshwater and high carbonate alkalinity water .We designed a microarray containing 26429 oligonucleotides and describe our experimental results for measuring gene expression changes in the gill of carbonate alkalinity stress exposed fish. The fish were exposed to freshwater (FW) and high carbonate alkalinity water (AW) for 96h, each with three replicates.
2014-01-24 | E-GEOD-27298 | biostudies-arrayexpress
Project description:Experiments and fish acclimations were performed in the laboratory of Prof. Avner Cnaani at the Agricultural Research Organization (ARO) Volcani Center (Israel). Proteomics sample preparation and biological mass spectrometry analyses (DDA) were performed in the laboratory of Prof. Dietmar Kueltz at UC Davis (CA). Samples represent protein extracts from gill epithelium of individual fish. Proteins were extracted, digested, and prepared for online LCMS2 as described previously (Kultz et al., 2013, Molecular & Cellular Proteomics 12/12, 3962-3975). Each sample represents a different biological replicate obtained from a separate fish.
2020-06-27 | MSV000085639 | MassIVE
Project description:Dietary zinc is routinely supplemented to promote growth, boost the immune system, protect against diabetes or aid recovery from diarrhoea. We exploited the zebrafish (Danio rerio) gill as a unique vertebrate ion transporting epithelium model to study the time-dependent regulatory networks of gene-expression leading to homeostatic control during zinc supplementation. This organ forms a conduit for zinc uptake whilst exhibiting conservation of zinc trafficking components. Fish were maintained with zinc supplemented water (4.0 uM) and diet (2023 mg zinc kg-1) or in un-amended water and diet, containing Zn2+ at 0.25 µM and 233 mg zinc kg-1 respectively. Gill tissues were harvested at five time points (8 hours to 14 days) and transcriptome changes analysed in quintuplicate using a 16K microarray.
2010-05-20 | GSE21907 | GEO
Project description:Zinc deficiency is detrimental to organisms highlighting its role as an essential micronutrient contributing to numerous biological processes. To investigate the underlying molecular events invoked by zinc depletion we performed a temporal analysis of transcriptome changes observed within zebrafish gill. This tissue represents a model system for studying ion absorption across polarised cells as it provides a major pathway for fish to acquire zinc directly from water whilst sharing a conserved zinc transporting system with mammals. Zebrafish were treated with either zinc-depleted (water = 2.61 μg L-1; diet = 26 mg kg-1) or zinc-adequate (water = 16.3 μg L-1; diet = 233 mg kg-1) conditions for two weeks. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array.
2010-05-20 | GSE21894 | GEO
Project description:Zinc deficiency is detrimental to organisms highlighting its role as an essential micronutrient contributing to numerous biological processes. To investigate the underlying molecular events invoked by zinc depletion we performed a temporal analysis of transcriptome changes observed within zebrafish gill. This tissue represents a model system for studying ion absorption across polarised cells as it provides a major pathway for fish to acquire zinc directly from water whilst sharing a conserved zinc transporting system with mammals. Zebrafish were treated with either zinc-depleted (water = 2.61 μg L-1; diet = 26 mg kg-1) or zinc-adequate (water = 16.3 μg L-1; diet = 233 mg kg-1) conditions for two weeks. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array. Global transcript levels were measured in zebrafish gills using a oligonucleotide array either zinc-depleted or zinc-adequate diet. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array
2010-05-20 | E-GEOD-21894 | biostudies-arrayexpress