Browsing by Author "Silva, Tomé S."
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- Changes in liver proteome expression of Senegalese sole (Solea senegalensis) in response to repeated handling stressPublication . Cordeiro, O.; Silva, Tomé S.; Alves, Ricardo N.; Costas, B.; Wulff, Tune; Richard, Nadège; Vareilles, Mahaut; Conceição, L. E. C.; Rodrigues, PedroThe Senegalese sole, a high-value flatfish, is a good candidate for aquaculture production. Nevertheless, there are still issues regarding this species’ sensitivity to stress in captivity. We aimed to characterize the hepatic proteome expression for this species in response to repeated handling and identify potential molecular markers that indicate a physiological response to chronic stress. Two groups of fish were reared in duplicate for 28 days, one of them weekly exposed to handling stress (including hypoxia) for 3 min, and the other left undisturbed. Two-dimensional electrophoresis enabled the detection of 287 spots significantly affected by repeated handling stress (Wilcoxon–Mann–Whitney U test, p<0.05), 33 of which could be reliably identified by peptide mass spectrometry. Chronic exposure to stress seems to have affected protein synthesis, folding and turnover (40S ribosomal protein S12, cathepsin B, disulfide-isomerase A3 precursor, cell-division cycle 48, and five distinct heat shock proteins), amino acid metabolism, urea cycle and methylation/folate pathways (methionine adenosyltransferase I α, phenylalanine hydroxylase, mitochondrial agmatinase, serine hydroxymethyltransferase, 3-hydroxyanthranilate 3,4-dioxygenase, and betaine homocysteine methyltransferase), cytoskeletal (40S ribosomal protein SA, α-actin, β-actin, α-tubulin, and cytokeratin K18), aldehyde detoxification (aldehyde dehydrogenase 4A1 family and aldehyde dehydrogenase 7A1 family), carbohydrate metabolism and energy homeostasis (fatty acid-binding protein, enolase 3, enolase 1, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase, aconitase 1, mitochondrial ATP synthase α-subunit, and electron-transfer flavoprotein α polypeptide), iron and selenium homeostasis (transferrin and selenium binding protein 1), steroid hormone metabolism (3-oxo-5-β-steroid 4-dehydrogenase), and purine salvage (hypoxanthine phosphoribosyltransferase). Further characterization is required to fully assess the potential of these markers for the monitoring of fish stress response to chronic stressors of aquaculture environment.
- Changes in the soluble bone proteome of reared white seabream (Diplodus sargus) with skeletal deformitiesPublication . Silva, Tomé S.; Cordeiro, O.; Richard, Nadège; Conceição, L. E. C.; Rodrigues, PedroOne of the main constrains for commercial aquaculture production of white seabream (Diplodus sargus) is the high incidence of skeletal malformations in reared fish. The purpose of this study was to obtain a better understanding of the mechanisms involved in the development of these types of skeletal malformations by comparative proteomic analysis of the vertebral column of normal and deformed fish using 2DE for protein separation and MS for protein identification. We observed a 3.2 and 3.4-fold increase in the expression of two tropomyosin isoforms, one of which (tropomyosin-4) is essential for the motility and polarization cycles of osteoclasts. Furthermore, a 1.6, 1.7 and 1.8-fold increase in three parvalbumin spots was detected, suggesting a cellular response to increased intracellular Ca2+ levels. These results can be interpreted as signs of increased cellular activity in the bone of white seabream with skeletal deformities coupled to a higher degree of calcium mobilization, which elicits further studies into the use of these proteins as indicators of skeletal metabolic state.
- Development and application of a mechanistic nutrient-based model for precision fish farmingPublication . Soares, Filipe M. R. C.; Nobre, Ana M. D.; Raposo, Andreia I. G.; Mendes, Rodrigo; Engrola, Sofia; Rema, Paulo J. A. P.; Conceição, Luís E. C.; Silva, Tomé S.This manuscript describes and evaluates the FEEDNETICS model, a detailed mechanistic nutrient-based model that has been developed to be used as a data interpretation and decisionsupport tool by fish farmers, aquafeed producers, aquaculture consultants and researchers. The modelling framework comprises two main components: (i) fish model, that simulates at the individual level the fish growth, composition, and nutrient utilization, following basic physical principles and prior information on the organization and control of biochemical/metabolic processes; and (ii) farm model, that upscales all information to the population level. The model was calibrated and validated for five commercially relevant farmed fish species, i.e., gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax), Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), and Nile tilapia (Oreochromis niloticus), using data sets covering a wide range of rearing and feeding conditions. The results of the validation of the model for fish growth are consistent between species, presenting a mean absolute percentage error (MAPE) between 11.7 and 13.8%. Several uses cases are presented, illustrating how this tool can be used to complement experimental trial design and interpretation, and to evaluate nutritional and environmental effects at the farm level. FEEDNETICS provides a means of transforming data into useful information, thus contributing to more efficient fish farming
- Dietary tools to modulate glycogen storage in gilthead seabream muscle: glycerol supplementationPublication . Silva, Tomé S.; Matos, Elisabete; Cordeiro, O.; Colen, Rita; Wulff, Tune; Sampaio, Eduardo; Sousa, Vera; Valente, L. M. P.; Gonçalves, Amparo; Silva, Joana M. G.; Bandarra, N.; Nunes, Maria Leonor; Dinis, Maria Teresa; Dias, J.; Jessen, Flemming; Rodrigues, PedroThe quality and shelf life of fish meat products depend on the skeletal muscle’s energetic state at slaughter, as meat decomposition processes can be exacerbated by energy depletion. In this study, we tested dietary glycerol as a way of replenishing muscle glycogen reserves of farmed gilthead seabream. Two diets were tested in duplicate (n = 42/tank). Results show 5% inclusion of crude glycerol in gilthead seabream diets induces increased muscle glycogen, ATP levels and firmness, with no deleterious effects in terms of growth, proximate composition, fatty acid profile, oxidative state, and organoleptic properties (aroma and color). Proteomic analysis showed a low impact of glycerol-supplementation on muscle metabolism, with most changes probably reflecting increased stress coping capacity in glycerol-fed fish. This suggests inclusion of crude glycerol in gilthead seabream diets (particularly in the finishing phase) seems like a viable strategy to increase glycogen deposition in muscle without negatively impacting fish welfare and quality.
- Dietary vitamin K supplementation and expression of proteins involved in skeleton development of senegalese sole (Solea senegalensis)Publication . Richard, Nadège; Gavaia, Paulo J.; Cordeiro, O.; Silva, Tomé S.; Rodrigues, C.; Rodrigues, Pedro; Conceição, L. E. C.In aquaculture, skeleton deformities are a serious problem as they affect growth, morphology, survival of fish and also increase productions costs and decrease market value of the final products. Since vitamin K is known for playing and important role in bone metabolism, the aim of this study was to investigate the effects of dietary vitamin K1 supplementation on skeleton deformities and on the expression of proteins involved involved in skeleton development of Senegalese sole.
- Effect of harvesting stress and storage conditions on protein degradation in fillets of farmed gilthead seabream (Sparus aurata): a differential scanning calorimetry studyPublication . Matos, Elisabete; Silva, Tomé S.; Tiago, Teresa; Aureliano, M.; Dinis, Maria Teresa; Dias, J.A trial was undertaken to evaluate Differential Scanning Calorimetry (DSC) as a fast analytical tool to differentiate gilthead seabream subjected to variable conditions of slaughter stress and post-mortem storage. Fish were subjected to different harvesting stress conditions: profound anaesthesia (PA, low stress) and net crowding (NC, high stress). Fish were slaughtered in an ice-salt water slurry, and subsequently stored on ice (7 days). Additional NC fish were frozen ( 20 C) and subjected to a freeze–thaw cycle. Dorsal muscle was assessed for cathepsins activity, liquid loss and DSC analysis. It is demonstrated that DSC analysis is capable of differentiating fresh, frozen and thawed-re-frozen fish, while liquid loss and cathepsin B activity are good markers to distinguish fresh from frozen fish. Harvesting stress had little effect on myosin and actin enthalpy transitions, as observed by DSC at 49 and 74 C, respectively, but a lower DH actin/myosin ratio was found in PA fish, suggesting that intense exercise prior to slaughter promoted partial denaturation of muscle myosin.
- Effects of preslaughter stress levels on the post-mortem sarcoplasmic proteomic profile of gilthead seabream musclePublication . Silva, Tomé S.; Cordeiro, O.; Matos, Elisabete; Wulff, Tune; Dias, J.; Jessen, Flemming; Rodrigues, PedroFish welfare is an important concern in aquaculture, not only due to the ethical implications but also for productivity and quality-related reasons. The purpose of this study was to track soluble proteome expression in post-mortem gilthead seabream muscle and to obsere how preslaughter stress affects these post-mortem processes. For the experiment, two groups of gilthead seabream (n = 5) were subjected to distinct levels of preslaughter stress, with three muscle samples being taken from each fish. Proteins were extracted from the muscle samples, fractionated, and separated by 2DE. Protein identification was performed by MALDI-TOF-TOF MS. Analysis of the results indicates changes on several cellular pathways, with some of these changes being attributable to oxidative and proteolytic activity on sarcoplasmic proteins, together with leaking of myofibrillar proteins. These processes appear to have been hastened by preslaughter stress, confirming that it induces clear postmortem changes in the muscle proteome of gilthead seabream.
- Enhanced dietary formulation to mitigate winter thermal stress in gilthead sea bream (Sparus aurata): a 2D-DIGE plasma proteome studyPublication . Schrama, Denise; Richard, Nadège; Silva, Tomé S.; Figueiredo, Filipe A.; Conceição, Luís E. C.; Burchmore, Richard; Eckersall, David; Rodrigues, PedroLow water temperatures during winter are common in farming of gilthead sea bream in the Mediterranean. This causes metabolic disorders that in extreme cases can lead to a syndrome called "winter disease." An improved immunostimulatory nutritional status might mitigate the effects of this thermal metabolic stress. A trial was set up to assess the effects of two different diets on gilthead sea bream physiology and nutritional state through plasma proteome and metabolites. Four groups of 25 adult gilthead sea bream were reared during winter months, being fed either with a control diet (CTRL) or with a diet called "winter feed" (WF). Proteome results show a slightly higher number of proteins upregulated in plasma of fish fed the WF. These proteins are mostly involved in the immune system and cell protection mechanisms. Lipid metabolism was also affected, as shown both by plasma proteome and by the cholesterol plasma levels. Overall, the winter feed diet tested seems to have positive effects in terms of fish condition and nutritional status, reducing the metabolic effects of thermal stress.
- Impact of dietary protein hydrolysates on skeleton quality and proteome in Diplodus sargus larvaePublication . Vareilles, Mahaut; Richard, Nadège; Gavaia, Paulo J.; Silva, Tomé S.; Cordeiro, O.; Guerreiro, Inês; Yúfera, M.; Batista, I.; Pires, C.; Pousão-Ferreira, P.; Rodrigues, Pedro; Rønnestad, I.; Fladmark, K. E.; Conceição, L. E. C.In order to investigate the effects of dietary protein hydrolysates (PH) on larval growth performance, skeleton quality and proteome expression, triplicate groups of white seabream (Diplodus sargus) larvae were co-fed from first-feeding with live feed and three microencapsulated diets differing in the molecular weight of their PH fraction (Control – inclusion of CPSP-90; H – inclusion of a high amount in 0.5–30 kDa hydrolysates; L – inclusion of a high amount in <0.5 kDa hydrolysates). At 15 days after hatching (DAH), proteome expression changes were assessed in entire larvae by twodimensional gel electrophoresis and the quality of larval skeleton was analysed at 28 DAH through double staining of cartilage and bone. Dietary PH fractions tested affected growth, the larvae fed diet L being significantly larger than those fed diet H, but it did not affect the incidence of deformed larvae, nor the number of deformities per fish. Two-dimensional analysis of larvae proteome allowed the detection and the comparative quantification of a total of 709 protein spots having a pI between 4 and 7, around half of which had an expression significantly affected by dietary treatment, the main difference being between proteome of Control larvae with those of both groups L and H. From these spots, 52 proteins involved in diverse processes such as cytoskeletal dynamics, energetic, lipoprotein, amino acid (AA), and nucleotide metabolisms, protein chaperoning and degradation, and signal transduction, were identified. This study revealed that the molecular weight of the dietary protein hydrolysate fraction had a minor impact on skeletal deformities in white seabream larvae, but affected growth performance and had a strong impact on larvae whole body proteome.
- Inclusion of protein hydrolysates in the diet of white seabream (Diplodus sargus) larvae: impacts on skeleton quality and larvae proteome expressionPublication . Richard, Nadège; De Vareilles, M.; Gavaia, Paulo J.; Silva, Tomé S.; Cordeiro, O.; Yúfera, M.; Rodrigues, Pedro; Conceição, L. E. C.In order to investigate the effects of dietary protein hydrolysate on larval skeleton quality and larvae proteome expression, triplicate groups of white seabream (Diplodus sargus) larvae were co-fed from first-feeding onwards with live feed and three microencapsulated diets ir differing only on the molecular weight of their protein hydrolysate fraction.