Browsing by Author "Silva, Tomé"
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- Data on European seabass fed with methionine-enriched diets obtained through label free shotgun proteomicsPublication . Farinha, Ana Paula; Schrama, Denise; Silva, Tomé; Conceição, Luís E.C.; Colen, R.; Engrola, Sofia; Rodrigues, Pedro; Cerqueira, MarcoThis data article is associated with the research article "Evaluating the impact of methionine-enriched diets in the liver of European seabass through label-free shotgun proteomics". Here it is described the data obtained from proteomic analysis of 36 European seabass juveniles (3 fish x 3 replicate tanks) after 18 days of feeding with experimental diets containing four inclusion levels of methionine (Met): 0.77%, 1%, 1.36% and 1.66% Met (w/w). We analysed this dataset and compared it with that obtained during the long-term feeding period i.e., 85 days. Fish liver proteins were digested with trypsin and purified peptides were analysed by LC-MS/MS. Proteins were identified with at least two peptides at 0.1% Decoy false discovery rate (FDR). In this dataset, we present the analysis of the differential abundant proteins (DAP) with significant differences across treatments after 18 days of feeding (One-Way ANOVA, p < 0.05). Treatment's comparisons were also performed between the 18- and 85-days feeding trials through Two-Way ANOVA (p < 0.05). MS/MS raw data are available via ProteomeXChange with identifiers PXD019610 and 10.6019/PXD019610 (18-days dataset); and PXD019622 and 10.6019/PXD019622 (85-days dataset). This dataset corresponds to fish sampled after 18-days of experimental trial and is made available to support the study conducted in the afore-mentioned article, by performing the analysis during a short-term period of feeding. The data presented may be further used in other nutritional studies e.g., addressing hepatic changes mediated by Met.
- Effects of genotype and dietary fish oil replacement with vegetable oil on the intestinal transcriptome and proteome of Atlantic salmon (Salmo salar)Publication . Silva, Tomé; Cordeiro, O.; Rodrigues, Pedro; Guy, Derrick R.; Bron, James E.; Taggart, John B.; Bell, J. Gordon; Tocher, Douglas R.Expansion of aquaculture requires alternative feeds and breeding strategies to reduce dependency on fish oil (FO) and better utilization of dietary vegetable oil (VO). Despite the central role of intestine in maintaining body homeostasis and health, its molecular response to replacement of dietary FO by VO has been little investigated. This study employed transcriptomic and proteomic analyses to study effects of dietary VO in two family groups of Atlantic salmon selected for flesh lipid content, 'Lean' or 'Fat'.ResultsMetabolism, particularly of lipid and energy, was the functional category most affected by diet. Important effects were also measured in ribosomal proteins and signalling. The long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis pathway, assessed by fatty acid composition and gene expression, was influenced by genotype. Intestinal tissue contents of docosahexaenoic acid were equivalent in Lean salmon fed either a FO or VO diet and expression of LC-PUFA biosynthesis genes was up-regulated in VO-fed fish in Fat salmon. Dietary VO increased lipogenesis in Lean fish, assessed by expression of FAS, while no effect was observed on β-oxidation although transcripts of the mitochondrial respiratory chain were down-regulated, suggesting less active energetic metabolism in fish fed VO. In contrast, dietary VO up-regulated genes and proteins involved in detoxification, antioxidant defence and apoptosis, which could be associated with higher levels of polycyclic aromatic hydrocarbons in this diet. Regarding genotype, the following pathways were identified as being differentially affected: proteasomal proteolysis, response to oxidative and cellular stress (xenobiotic and oxidant metabolism and heat shock proteins), apoptosis and structural proteins particularly associated with tissue contractile properties. Genotype effects were accentuated by dietary VO.ConclusionsIntestinal metabolism was affected by diet and genotype. Lean fish may have higher responsiveness to low dietary n-3 LC-PUFA, up-regulating the biosynthetic pathway when fed dietary VO. As global aquaculture searches for alternative oils for feeds, this study alerts to the potential of VO introducing contaminants and demonstrates the detoxifying role of intestine. Finally, data indicate genotype-specific responses in the intestinal transcriptome and proteome to dietary VO, including possibly structural properties of the intestinal layer and defence against cellular stress, with Lean fish being more susceptible to diet-induced oxidative stress.
- ficoEst – a tool to estimate the body composition of farmed fishPublication . Soares, Filipe; Raposo, Andreia; Mendes, Rodrigo; Azevedo, Marina; Dias, Deborah; Nobre, Ana; Conceição, Luís E. C.; Silva, ToméficoEst - Fish Composition Estimator is a public web tool to estimate the whole-body proximate composition of farmed fish (https://webtools.sparos.pt/ficoest/). The tool was designed for researchers in fish nutrition and fish farmers, and is available for six commercially relevant species: gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), meagre (Argyrosomus regius), rainbow trout (Onchorhynchus mykiss), Atlantic salmon (Salmo salar), and Nile tilapia (Oreochromis niloticus). ficoEst uses three different types of mathematical models (BC1, BC2, and BC3) to estimate the body composition of fish in terms of crude protein, crude lipids, water, ash, phosphorus, and energy. The models differ in the input data used to perform the estimates. BC1 models consider only body weight, BC2 models consider both body weight and water, and BC3 models consider body weight, water, and ash as inputs. The model evaluation results demonstrate that considering water and ash as additional inputs to body weight (BC3 models) significantly improves the accuracy in predicting some body composition components, such as crude lipids (e.g., up to 67.9 % and 28.1 % more accurate, compared to BC1 and BC2 models, respectively, depending on the species considered). ficoEst can be used as a complementary tool to analytical methods to obtain additional information about fish body composition. As a public web tool, ficoEst has the potential to be a valuable resource for researchers and fish farmers interested in estimating the body composition of farmed fish.
- Selection criteria of Zebrafish male donors for sperm cryopreservationPublication . Diogo, Patricia; Martins, Gil; Eufrásio, Ana; Silva, Tomé; Cabrita, Elsa; Gavaia, PauloSelection criteria for sperm cryopreservation are highly relevant in zebrafish since sperm quality is particularly variable in this species. Successful cryopreservation depends on high-quality sperm, which can only be ensured by the selection of breeders. Consequently, male selection and management are a priority to improve cryopreservation, and therefore, this study aimed to characterize optimal age and sperm collection frequency in zebrafish. For this purpose, males from wild type (AB) and from a transgenic line [Tg(runx2:eGFP)] were sampled at 6, 8, 12, and 14 months. For each age, sperm were collected at time 0 followed by samplings at 2, 7, and 14 days of rest. Sperm quality was assessed according to motility and membrane viability parameters. Quality assessment showed that Tg(runx2:eGFP) displayed significantly higher motility than AB and younger males showed higher motility in both lines. Sperm collection frequency affected membrane viability. While AB fish recovered sperm viability after 14 days of rest, Tg(runx2:eGFP) could not recover. Consequently, it may be important to study the sperm quality of each zebrafish line before sperm cryopreservation. Taking into consideration the results achieved in both lines, sperm collection should be performed between 6 and 8 months of age with a minimum collection interval of 14 days.
- Stressor controllability modulates the stress response in fishPublication . Cerqueira, Marco; Millot, Sandie; Silva, Tomé; Félix, Ana S.; Castanheira, Maria Filipa; Rey, Sonia; MacKenzie, Simon; Oliveira, Gonçalo A.; Oliveira, Catarina; Oliveira, Rui F.Background In humans the stress response is known to be modulated to a great extent by psychological factors, particularly by the predictability and the perceived control that the subject has of the stressor. This psychological dimension of the stress response has also been demonstrated in animals phylogenetically closer to humans (i.e. mammals). However, its occurrence in fish, which represent a divergent vertebrate evolutionary lineage from that of mammals, has not been established yet, and, if present, would indicate a deep evolutionary origin of these mechanisms across vertebrates. Moreover, the fact that psychological modulation of stress is implemented in mammals by a brain cortical top-down inhibitory control over subcortical stress-responsive structures, and the absence of a brain cortex in fish, has been used as an argument against the possibility of psychological stress in fish, with implications for the assessment of fish sentience and welfare. Here, we have investigated the occurrence of psychological stress in fish by assessing how stressor controllability modulates the stress response in European seabass (Dicentrarchus labrax). Results Fish were exposed to either a controllable or an uncontrollable stressor (i.e. possibility or impossibility to escape a signaled stressor). The effect of loss of control (possibility to escape followed by impossibility to escape) was also assessed. Both behavioral and circulating cortisol data indicates that the perception of control reduces the response to the stressor, when compared to the uncontrollable situation. Losing control had the most detrimental effect. The brain activity of the teleost homologues to the sensory cortex (Dld) and hippocampus (Dlv) parallels the uncontrolled and loss of control stressors, respectively, whereas the activity of the lateral septum (Vv) homologue responds in different ways depending on the gene marker of brain activity used. Conclusions These results suggest the psychological modulation of the stress response to be evolutionary conserved across vertebrates, despite being implemented by different brain circuits in mammals (pre-frontal cortex) and fish (Dld-Dlv).
- Sustainable fish meal-free diets for gilthead sea bream (Sparus aurata): integrated biomarker response to assess the effects on growth performance, lipid metabolism, antioxidant defense and immunological statusPublication . Fernandes, Ana M.; Calduch-Giner, Josep Àlvar; Pereira, Gabriella V.; Fachadas Gato Coelho Gonçalves, Ana Teresa; Dias, Jorge; Johansen, Johan; Silva, Tomé; Naya-Català, Fernando; Piazzon, Carla; Sitjà-Bobadilla, Ariadna; Costas, Benjamin; Conceição, Luís E. C.; Fernandes, Jorge M. O.; Pérez-Sánchez, JaumeThe growth of the aquaculture industry requires more sustainable and circular economy-driven aquafeed formulas. Thus, the goal of the present study was to assess in farmed gilthead sea bream (Sparus aurata L.) how different combinations of novel and conventional fish feed ingredients supported proper animal performance in terms of growth and physiological biomarkers of blood/liver/head kidney. A 77-day feeding trial was conducted with three experimental diets (PAP, with terrestrial processed animal protein from animal by-products; NOPAP, without processed animal protein from terrestrial animal by-products; MIX, a combination of alternative ingredients of PAP and NOPAP diets) and a commercial-type formulation (CTRL), and their effects on growth performance and markers of endocrine growth regulation, lipid metabolism, antioxidant defense and inflammatory condition were assessed at circulatory and tissue level (liver, head kidney). Growth performance was similar among all dietary treatments. However, fish fed the PAP diet displayed a lower feed conversion and protein efficiency, with intermediate values in MIX-fed fish. Such gradual variation in growth performance was supported by different biomarker signatures that delineated a lower risk of oxidation and inflammatory condition in NOPAP fish, in concurrence with an enhanced hepatic lipogenesis that did not represent a risk of lipoid liver degeneration.
- Visualization and Differential Analysis of Protein Expression Data Using R.Publication . Silva, Tomé; Richard, NadègeData analysis is essential to derive meaningful conclusions from proteomic data. This chapter describes ways of performing common data visualization and differential analysis tasks on gel-based proteomic datasets using a freely available statistical software package (R). A workflow followed is illustrated using a synthetic dataset as example.