Project description:We sequenced and assembled de novo the coding transcriptomes in four species of Notothenioid fish: Neopagetopsis ionah (Jonah’s ice fish), Pseudochaenichtys georgianus (South Georgia icefish), Harpagifer antarcticus (Antarctic spiny plunderfish) and Parachaenichthys charcoti (Charcot’s dragonfish). We sampled 1-4 individuals and 1-14 tissues (brain, white muscle, liver, head kidney, trunk kidney, skin, heart, red muscle, spleen, ovary, testis, whole blood, gill, red blood cells) in each species, depending on tissue availability.
Project description:The effect of different diets (i.e. fish oil based vs vegetable oil based) on liver transcription profiles over the life history stages (freshwater and marine phases) of cultured Atlantic salmon (Salmo salar) were explored. Two groups of fish were raised from first feeding on different lipid containing diets; a) the standard 100% fish oil based diet, the other enriched with a blend of vegetable oils (75%) + fish oil (25%). Liver samples were taken from fish at four time points: two freshwater phase (as parr 36 weeks post hatch (wph); as pre-smolts, 52 wph) and two marine phase ( as post-smolts 55 wph; and as adult fish , 86 wph). A total of 96 cDNA microarray hybridisations - TRAITS / SGP Atlantic salmon 17k feature cDNA microarray - were performed ( 2 diets x 4 time points x 6 biological replicates x 2 -dye swap) using a comon pooled reference contol design.
Project description:In order to identify gene expression difference between marine and freshwater stickleback populations, we compared the transcriptomes of seven adult tissues (eye, gill, heart, hypothalumus, liver, pectoral muscle, telencephalon) between a marine population sampled from the mouth of the Little Campbell river in British Columbia (LITC) and a freshwater population (Fishtrap Creek, FTC) from northern Washington. For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents. Four to five fish from each population were used as biological replicates for each of the seven tissues. For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents. All fish were of similar age and were raised in the same aquarium (salinity: 3.5 ppt), with a plastic divider separating the marine and freshwater groups. One male and four females were sampled from each population. Microarray experiments were performed in a 2-color format on custom Agilent arrays: experimental RNA samples were labeled with Cy5, and the common reference RNA sample was labeled with Cy3. The reference RNA was total RNA isolated from a large number of 7-day-post-hatch embryos from the freshwater population of Bear Paw Lake, Alaska (BEPA). One technical replicate was used for each array, and one of the hypothalamus samples (Hyp_FTC#3) was excluded from further analysis due to poor quality indicators. FTC#1 liver and LITC#2 pectoral muscle samples did not yield RNA of sufficient quality for the microarray experiment, and were also excluded from hybridization.
Project description:White bass (Morone chrysops) are a popular sportfish throughout the southern United States, and one parent of the commercially successful hybrid striped bass (M. chrysops x M. saxatilis). Currently, white bass are cultured using diets formulated for other carnivorous fish, such as largemouth bass (Micropterus salmoides) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-Cision). Significant differential expressed genes and gene ontology of pairwise comparisons between control diet and each test diet are presented and discussed.
Project description:Transcriptional responses to hypoxia were assessed in three species of marine fish (smoothhead sculpin [Artedius lateralis], sailfin sculpin [Nautichthys oculafasciatus] and Pacific staghorn sculpin [Leptocottus armatus]) all of which have previously been shown to share the same level of hypoxia tolerance. To determine if there is convergence in mechanisms underlying phenotypic convergence of hypoxia tolerance, each species was exposed to short-term (8 hours) and long-term (72 hours) hypoxia. Specifically, liver was sampled and mRNA was extracted from each species at normoxia, 3hr, 8hr, 24hr, 48hr and 72hr of hypoxia.
Project description:Ocean global warming affects the distribution, life history and physiology of marine life. Extreme events, like marine heatwaves, are increasing in frequency and intensity. During sensitive developmental windows of fish, the consequences may be long-lasting and mediated by epigenetic mechanisms. Here, we used adult European sea bass as a model to study the effects of a marine heatwave during development. We measured DNA methylation and gene expression in four tissues (brain, muscle, liver and testis) and detected differentially methylated regions (DMRs). Six genes were differentially expressed and contained DMRs three years after exposure to increased temperature, indicating direct phenotypic consequences and representing persistent changes. Interestingly, nine genes contained DMRs around the same genomic regions across tissues, therefore consisting of common footprints of developmental temperature in environmentally responsive loci. These loci are, to our knowledge, the first metastable epialleles (MEs) described in fish. MEs may serve as biomarkers to infer past life history events linked with persistent consequences. These results highlight the importance of subtle phenotypic changes mediated by epigenetics to extreme weather events during sensitive life stages. Also, to our knowledge, it is the first time the molecular effects of a marine heatwave during the lifetime of individuals are assessed. MEs could be used in surveillance programs aimed at determining the footprints of climate change on marine life. Our study paves the way for the identification of conserved MEs that respond equally to environmental perturbations across species. Conserved MEs would constitute a tool of assessment of global change effects in marine life at a large scale.
Project description:The pink salmon (Oncorhynchus gorbuscha) is a commercial anadromous fish species of the family Salmonidae. The species has a peculiar life cycle that includes spawning migration from marine to freshwater environments, which is accompanied by significant adaptive changes in the body, both the physiological and biochemical. This study described and revealed the variability of blood plasma proteomes of female and male pink salmon collected from three different biotopes - marine, estuarine and riverine - that the fish pass through spawning migration. Identification and comparative analysis of pink salmon blood plasma protein profiles were performed using proteomic and bioinformatic approaches. Blood proteomes of female and male spawners collected from different biotopes were qualitatively and quantitatively distinguished. Females differed primarily by proteins associated with reproductive system development (certain vitellogenin and choriogenin), lipid transport (fatty acid binding protein) and energy production (fructose 1,6-bisphosphatase), and males - by proteins involved in blood coagulation (fibrinogen), immune response (lectins) and reproductive processes (vitellogenin). Differentially expressed sex-specific proteins were implicated in proteolysis (aminopeptidases), platelet activation (β- and γ-chain fibrinogen), cell growth and differentiation (a protein containing the TGF_BETA_2 domain) and lipid transport processes (vitellogenin and apolipoprotein). The results obtained are of fundamental and practical importance, providing to the existing knowledge of biochemical adaptations to spawning of pink salmon, representative of the economically important migratory fish species.
Project description:Plant-based protein sources play an important role in aquaculture by dwindling fish meal to sustainable levels. However, the use of such feedstuffs requires nutrient supplementation to fulfil fish nutritional requirements. This work addressed the response in the liver of farmed fish to dietary methionine (Met), assessing at the same time the growth performance. Fish were fed at suboptimal levels of dietary Met (0.77% w/w; M0.65 diet), within (1% w/w Met; M0.85 diet)and above(1.36 % w/w Met (M1.25 diet); 1.66% w/w Met(M1.5 diet)) the estimated requirement for this species, in a total of four tested conditions. The impact of dietary methionine supplementation in seabass juvenile’s performance was assessed through 85 days of trial, between May and August of 2018. Fish were reared in triplicate tanks and three liver samples/tank (9 per treatment) were collected for liver proteome analysis at the end of the trial i.e., after 85 days of feeding.
Project description:The salmon fry was sampled at day 0 (before initial feeding) and day 1 (20h after initial feeding). The fish was about 0.2g, liver and pyloric caeca were dissected and used for RNA-seq. Fish was given standard commercial diets with high PUFA.