Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1116796 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29188746_1.fastq.gz | Fastqsanger.gz | |||
| SRR29188746_2.fastq.gz | Fastqsanger.gz | |||
| SRR29188747_1.fastq.gz | Fastqsanger.gz | |||
| SRR29188747_2.fastq.gz | Fastqsanger.gz | |||
| SRR29188748_1.fastq.gz | Fastqsanger.gz |
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Project description:The salmon gill poxvirus (SGPV) is a large DNA virus that infects gill epithelial cells in Atlantic salmon and is associated with acute high mortality disease outbreaks in aquaculture. The pathological effects of SGPV infection include gill epithelial apoptosis in the acute phase of the disease and hyperplasia of gill epithelial cells in surviving fish, causing damage to the gill respiratory surface. Transcriptome responses to virus were assessed in gills at different stages of disease
2020-05-30 | GSE151463 | GEO
Project description:Fish gills are not only the respiratory organ, but also essential for ion-regulation, acid-base control, detoxification, waste excretion and host defense. Multifactorial gill diseases are common in farmed Atlantic salmon, and still poorly understood. Understanding gill pathophysiology is of paramount importance, but the sacrifice of large numbers of experimental animals for this purpose should be avoided. Therefore, in vitro models, such as cell lines, are urgently required to replace fish trials. An Atlantic salmon gill epithelial cell line, ASG-10, was established at the Norwegian Veterinary institute in 2018. This cell line forms a monolayer expressing cytokeratin, e-cadherin and desmosomes, hallmarks of a functional epithelial barrier. To determine the value of ASG-10 for comparative studies of gill functions, the characterization of ASG-10 was taken one step further by performing functional assays and comparing the cell proteome and transcriptome with those of gills from juvenile freshwater Atlantic salmon. The ASG-10 cell line appear to be a homogenous cell line consisting of epithelial cells, which express tight junction proteins. We demonstrated that ASG-10 forms a barrier, both alone and in co-culture with the Atlantic salmon gill fibroblast cell line ASG- 13. ASG-10 cells can phagocytose and express several ATP-binding cassette transport proteins. Additionally, ASG-10 expresses genes involved in biotransformation of xenobiotics and immune responses. Taken together, this study provides an overview of functions that can be studied using ASG-10, which will be an important contribution to in vitro gill epithelial research of Atlantic salmon.
2024-01-26 | PXD044533 | Pride
Project description:Climate change has resulted in record-breaking sea temperatures, posing significant challenges to the health, growth, and productivity of marine fish species, including farmed Atlantic salmon. As sea temperatures are projected to continue to rise, the impact of environmental changes requires significant attention. To devise effective climate adaptation strategies, there is a need to understand the response of salmon to sub-optimal temperatures alone and in-combination with other production-related stressors. Gills and skin were analyzed prior to and after temperature peaks, and before and after the varying simulated handling operations. The effects of the different operations upon macro level external injuries were also investigated. Results indicate that fluctuating and constant high temperatures induce macro- and micro-damages to tissues that may challenge salmon health and welfare, by having a negative effect upon scale loss and eye opacity, and reduced skin barrier integrity. This submission contains data of transcriptome analysis in skin.
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Project description:The six species of lungfish possess both lungs and gills and are the closest extant relatives of tetrapods. Here, we report a single-cell transcriptome atlas of the West African lungfish (Protopterus annectens). This species manifests the most extreme form of terrestrialization, a life history strategy to survive dry periods in five lungfish species that can last for years, characterized by dormancy and reversible adaptive changes of the gills and lungs. Our atlas highlights the cell type diversity of the West African lungfish, including gene expression consistent with phenotype changes of terrestrialization. Comparisons with terrestrial tetrapods and ray-finned fishes revealed broad homology between the swim bladder and lung cell types as well as shared and idiosyncratic changes of the external gills of the West African lungfish and the internal gills of Atlantic salmon. The single-cell atlas presented here provides a valuable resource for further exploring the evolution of the vertebrate respiratory system and the diversity of lungfish terrestrialization.
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Project description:Most Pacific salmonids undergo smoltification and transition from freshwater to saltwater. Saltwater acclimation requires salmonids to make various adjustments in color, shape, size, metabolism, catabolism, and osmotic and ion regulation. The molecular mechanisms underlying this transition are largely unknown. The present study acclimated coho salmon (Oncorhynchus kisutch) to four different salinities (<0.5, 8, 16, and 32 ppth) and assessed gene expression through microarray analysis of gill, liver and olfactory tissues. Gills are involved in osmotic regulation, liver plays a role in energetics, and olfactory tissues are involved in behavior. Between all salinity treatments, liver had the highest number of differentially expressed genes at 1,616. Gills had 1,074 differentially expressed genes and olfactory tissue had 924. The difference in the number of differentially expressed genes may be due to the higher responsiveness of liver to metabolic changes after salinity acclimation to provide energy to fuel other metabolic and osmoregulatory tissues like gills. Differentially expressed genes were tissue and salinity treatment dependent. There were no genes differentially expressed in all salinity treatments and all three tissues. Five genes were targeted for microarray confirmation by qPCR and included CCAAT/enhancer binding protein ? (CEBPB), calpain 1 (CAPN1), proto-oncogene, serine/threonine kinase (Pim1), aldolase B, fructose-bisphosphate (aldob), and complement component 3 (c3). qPCR expression profiles of these genes matched array outputs. Gene ontology term analysis revealed biological processes, molecular functions, and cellular components that were significant. Most terms were tissue dependent. For liver, oxygen binding and transport terms were highlighted, suggesting possible impacts on metabolism. For gills, muscle and cytoskeleton related terms were emphasized and for olfactory tissues, immune response related genes were accentuated. Interaction networks were examined in combination with GO terms and determined similarities between tissues for potential osmosenors and signal transduction cascades. Overall this study suggests that Pacific salmonids share many salinity acclimation molecular mechanisms with other species, with a few new genes identified, and that although the three tissues shared certain underlying mechanism, many of the differentially expressed genes were tissue-specific. To assess how salinity acclimation in coho salmon (Oncorhynchus kisutch) impacted gene expression in gills, liver, and olfactory tissues.
2016-03-22 | E-GEOD-67461 | biostudies-arrayexpress
Project description:Fish mucosal tissues lack the organized lymphoid structures present in mammals. Although this is also true for the gills, with the gill-associated lymphoid tissue (GIALT) being mainly composed of B and T cells scattered throughout the epithelium and the lamellae, in some species such as rainbow trout (Oncorhynchus mykiss) or Atlantic salmon (Salmo salar), a more organized structure designated as the interbranchial lymphoid tissue (ILT) is also identified. Yet, although many studies have investigated the immune response of the gill to stimulation or pathogen encounter, which have revealed the activation of both innate and adaptive immune elements, how the gills respond to secondary stimulation or whether memory responses are locally orchestrated is still unknown. To provide insights into this matter, in the current study, we have infected rainbow trout by bath with Lactococcus petauri and then re-infected or mock-infected the survivor fish as well as mock-infected controls. At day 4 after the last infection, the fish were sacrificed and gills used to perform an RNAseq transcriptomic analysis and an IgM and IgT repertoire analysis. The number of cells secreting total and specific IgM in gills was also established by ELIspot. Our results demonstrate that memory responses are locally organized in the rainbow trout gills, given that re-infected fish did not up-regulate genes related to inflammation (as happens in the primary infection), but preferentially modified genes related to adaptive immunity, mainly to B cell function, experiencing a significant IgM and IgT clonal expansion. Accordingly, re-infected fish produced increased levels of specific IgM both locally and in serum, although no clonal selection was apparent. These findings advance our understanding of mucosal immunological memory in teleost fish and reveal the gills as a site of localized adaptive immune regulation during secondary responses.
2026-06-14 | GSE328875 | GEO
Project description:Expression profile of liver of ICR mice (13-week old) treated with control diet (CRF-1) or CRF-1 containing 500 ppm diosgenin for 4 weeks.
2010-10-08 | GSE24580 | GEO
Project description:Gills of teleost fish represent a vital multifunctional organ; however, they are subjected to environmental stressors, causing gill damage. Gill damage is associated with significant losses in the Atlantic salmon aquaculture industry. Gill disorders due to environmental stressors are exacerbated by global environmental changes, especially with open-net pen aquaculture (as farmed fish lack the ability to escape those events). The local and systemic response to gill damage, concurrent with several environmental insults, are not well investigated. We performed field sampling to collect gill and liver tissue after several environmental insults. Using a 44K salmonid microarray platform, we aimed to compare the transcriptomes of pristine and moderately damaged gill tissue. The gill damage-associated biomarker genes and associated qPCR assays arising from this study will be valuable in future research aimed at developing therapeutic diets to improve farmed salmon gill health.
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Project description:Simple cost-effective bacterins are the earliest and most successfully used commercial vaccines in fish. In particular, those prepared from Yersinia ruckeri have proven effective at controlling Enteric Red Mouth Disease (ERM) and yersiniosis in rainbow trout and Atlantic salmon, respectively. However, the emergence of outbreaks of ERM caused by atypical biotypes of Y. ruckeri and reports of vaccine failure resulting in mass mortality of hatchery Atlantic salmon has reinvigorated interest in vaccines against fish bacterial diseases. Therefore the objective of this study was to identify surrogates of protection against yersiniosis using cDNA microarray to characterise the response of host genes in the gills of unvaccinated and vaccinated Atlantic salmon challenged with Y. ruckeri. Differentially expressed genes were identified using two-way ANOVA and restricted to those with >2.5-fold change at P<0.05. Using cDNA microarray we identified the expression of 6 genes in response to infection and 4 genes associated with the protective host response to yersiniosis. Analysis by real-time PCR confirmed that three immunologically relevant genes, namely a cathelicidin (47-fold) and a C-type lectin (19-fold) increased in response to yersiniosis. Including collagenase (17-fold increase), an important tissue remodelling and repair enzyme, these genes represent 3 of 6 non-protective and/or pathological responses to yersiniosis. Genes associated with the protective host response included an immunoglobulin gene and a selenoprotein that showed significant fold changes (15-fold increases each), highlighting the importance of antibody-mediated protection against yersiniosis. These findings provide much needed knowledge of the host-pathogen interaction in response to bacterial infection and immunisation in fish. Significantly, we identified a transcriptional biosignature consisting of predominantly immune-relevant genes (14 up and 3 down-regulated) in the gills of Atlantic salmon after immersion vaccination and before bacterial challenge. This biosignature may be used as a surrogate of protection and therefore as a predictor of vaccine success against yersiniosis.
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