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.

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.

Project description:The effect of environmental salinity on the gill proteome was isolated in controlled mesocosm experiments. Salinity-dependent changes in the gill proteome were analyzed by LCMSMS data-independent acquisition (DIA) and Skyline. For this purpose, relative abundances of 1691 proteins representing the molecular phenotype of stickleback gills were quantified using previously developed MSMS spectral and assay libraries in combination with data-independent acquisition (DIA) quantitative proteomics (Li et al. 2018). Osmoregulatory responses were distinguished from general stress responses based on the direction of protein abundance changes. If the abundance of a protein was consistently regulated in opposite directions by hyper- versus hypo-osmotic salinity stress in all six mesocosm experiments then it was considered an osmoregulatory protein. If protein abundance was always increased in all six mesocosm experiments independent of whether salinity was increased or decreased then it was considered a stress response protein. KEGG pathway analysis revealed that the inositol phosphate metabolism, salivary secretion, several endocrine and extracellular signaling, valine, leucine and isoleucine degradation, citrate cycle, and oxidative phosphorylation pathways contain most osmoregulatory gill proteins whose abundance is directly proportional to environmental salinity. Most proteins that were inversely correlated with salinity map to pathways that represent proteostasis, immunity and intracellular signaling processes. General stress response proteins represent fatty and amino acid degradation, purine metabolism, focal adhesion, mRNA surveillance, phagosome, endocytosis, and several intracellular signaling pathways. Some proteins in these general stress response pathways are consistently down-regulated instead of being up-regulated during any type of salinity stress indicating that these KEGG pathways are not uniformly induced or repressed but that their function is being altered more intricately.

Project description:Introduction: A major economic impediment to the aquaculture of marine finfish in land-based recirculating systems is maintaining the system salinity at a range for optimal growth. Florida Pompano (Trachinotus carolinus) are warm water, euryhaline, marine finfish shown to be a suitable candidate for low-salinity culture. Due to its popularity among sport and commercial fishers, high market value, and ability to readily consume pelleted feeds, the Florida Pompano has become a renewed target for commercialized aquaculture. Although the Florida Pompano has been successfully grown at various salinities, its optimal growth salinity has not yet been established. Studies have shown culturing at different salinities has an effect on digestion rates, feed utilization, and lipid biosynthesis. Identifying the optimal salinity for growth would result in decreased energy expenditure on maintaining homeostasis, since osmoregulation is a highly demanding process. This would allow for energy to be spent on the efficient use of nutrients. Methods: Our study was designed to determine how Florida Pompano larviculture at various salinities affects fish health with transcriptomics (RNA-seq) and fatty acid analysis. RNA-seq was used to identify genes actively transcribed and expressed at the time of sampling. After hatching in a salinity of ~ 30 ppt, larvae were reared in 345 L tanks at one of three salinities (10, 20, 30 ppt) in triplicate. Larvae samples for RNA-seq and fatty acid analysis were collected every three days until weaning. Samples for fatty acid composition were analyzed using a gas chromatography-mass spectrometry (GC/MS). RNA was extracted from homogenized whole-body samples using the Qiagen RNeasy Mini kit. Total RNA was sequenced on the Illumina HiSeq 4000 System. Raw sequences were filtered for low-quality sequences, aligned to the S. dumerili reference genome (NCBI Genome: 12614), and quantified. Each sampling day was compared across salinities to establish the differentially expressed genes (DEGs) between salinities. Results & Discussion: The numbers of DEGS in pooled samples was minimal (less than 15 total in each comparison) and the number of DEGS at each dph was variable. There were no significant differences between pooled samples or at each dph according to PERMANOVA analysis, but each dph was statistically different on pairwise analysis. Gene set enrichment analysis revealed that there was a downregulation of immune related genes in lower salinities versus higher salinities suggesting larvae may be dealing with less stress at lower salinities. Most osmoregulation, fatty acid, and immune related genes tested were not significantly different across salinities. This is likely be cause the Florida pompano is euryhaline and has a tolerance to the salinities selected. There was an increase in the expression levels of several immune related genes that may indicate an increase exposure to pathogens at later days post hatch likely related to feeding schedule. There was also an increase in fatty acid biosynthesis genes that corresponded with levels of fatty acids indicating a possible synthesis of essential fatty acids from precursors. Conclusions: From a transcriptomics perspective, the larvae did not show a negative response to lower salinities in comparison to higher salinities, which in fact showed upregulation of immune related genes. Further exploration of Florida pompano’s ability to biosynthesize essential fatty acids is necessary. This study will help enable the optimization of Florida Pompano larviculture using information on the optimal salinity and fatty acid content for growth and facilitate more cost-effective rearing methods.

Dataset Information

Tissue-specific gene signatures of gilthead sea bream (Sparus aurata L.) after hyper- and hypo-osmotic challenges

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets