I am a multidisciplinary researcher with over a decade of experience dedicated to advancing responsible aquaculture and fisheries practices. Fueled by a profound passion for aquatic life, my career has centered on unraveling the complexities of fish and their welfare. My focus spans from deciphering fish behavior and social structures to exploring their adaptive responses to environmental challenges. Currently, I am immersed in innovative proteomic techniques aimed at assessing and enhancing the well-being of aquatic species. This research trajectory has deepened my understanding of the physiological and molecular aspects of fish welfare, empowering me to develop and validate strategies for improving welfare management on commercial and global scales. In addition to my scientific contributions, I actively engage in fish welfare training, experimentation, and consultancy.
EDUCATION
2012 – 2016: Ph.D. in Life and Environmental Sciences: Specialty Farming Systems - University of Algarve, Portugal, with distinction and honor.
2004 – 2006: BSc in Marine Biology and Biotechnology (2nd Cycle)
IPL – Escola Superior de Tecnologia do Mar (ESTM), with final grade of 16/20
2001 - 2004: Bachelor’s in marine biology and biotechnology (1st Cycle)
IPL – Escola Superior de Tecnologia do Mar (ESTM), with final grade of 16/20
RESEARCH, TEACHING, or OTHER INTERESTS
Aquatic Science, Agricultural and Biological Sciences, Food Science, Multidisciplinary
Thermal and Nutritional Strategies for Managing Tenacibaculum maritimum in Aquaculture: A Welfare-Oriented Review Raquel Carrilho, Márcio Moreira, Ana Paula Farinha, Denise Schrama, Florbela Soares, et al. Animals, 2025 Disease outbreaks pose a significant challenge in aquaculture, leading to substantial economic losses for producers. Tenacibaculosis, a significant ulcerative bacterial disease caused by Tenacibaculum maritimum, affects a wide range of marine fish species globally. Current disease management relies on antibiotics and chemicals, leading to environmental issues, impaired fish and consumer health, and increased antimicrobial-resistant bacteria. This narrative review critically explores welfare-oriented alternatives, specifically examining the potential of temperature modulation and functional diets. Although thermal strategies show promise for warm-water species through behavioural fever mechanisms, their effectiveness remains limited by species-specific thermal tolerances and lack of commercial validation. Nutritional interventions using marine algae, probiotics, and immunostimulants demonstrate broader applicability but suffer from inconsistent methodologies, limited commercial validation, and significant knowledge gaps. We propose that integration of these approaches could theoretically represent a paradigm shift from pathogen-focused to host-centred disease management, pending empirical validation. However, this integration concept requires rigorous validation, as significant knowledge gaps persists regarding optimal implementation protocols, welfare monitoring frameworks, and economic viability assessments. From our perspective, transitioning to welfare-oriented aquaculture demands rigorous evaluation and validation, commercial-scale trials, economic cost–benefit analysis, and the establishment of regulatory frameworks before these theoretical alternatives can be responsibly implemented.
Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration Cláudia Raposo de Magalhães, Kenneth Sandoval, Ferenc Kagan, Grace McCormack, Denise Schrama, et al. Plos One, 2024 Gilthead seabream (Sparus aurata) is an important species in Mediterranean aquaculture. Rapid intensification of its production and sub-optimal husbandry practices can cause stress, impairing overall fish performance and raising issues related to sustainability, animal welfare, and food safety. The advent of next-generation sequencing technologies has greatly revolutionized the study of fish stress biology, allowing a deeper understanding of the molecular stress responses. Here, we characterized for the first time, using RNA-seq, the different hepatic transcriptome responses of gilthead seabream to common aquaculture challenges, namely overcrowding, net handling, and hypoxia, further integrating them with the liver proteome and metabolome responses. After reference-guided transcriptome assembly, annotation, and differential gene expression analysis, 7, 343, and 654 genes were differentially expressed (adjusted p-value < 0.01, log2|fold-change| >1) in the fish from the overcrowding, net handling, and hypoxia challenged groups, respectively. Gene set enrichment analysis (FDR < 0.05) suggested a scenario of challenge-specific responses, that is, net handling induced ribosomal assembly stress, whereas hypoxia induced DNA replication stress in gilthead seabream hepatocytes, consistent with proteomics and metabolomics’ results. However, both responses converged upon the downregulation of insulin growth factor signalling and induction of endoplasmic reticulum stress. These results demonstrate the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at the transcriptomic level. Furthermore, it provides significant resources for characterizing and identifying potentially novel genes that are important for gilthead seabream resilience and aquaculture production efficiency with regard to fish welfare.
Gilthead Seabream Liver Integrative Proteomics and Metabolomics Analysis Reveals Regulation by Different Prosurvival Pathways in the Metabolic Adaptation to Stress Cláudia Raposo de Magalhães, Ana Paula Farinha, Gavin Blackburn, Phillip D. Whitfield, Raquel Carrilho, et al. International Journal of Molecular Sciences, 2022 The study of the molecular mechanisms of stress appraisal on farmed fish is paramount to ensuring a sustainable aquaculture. Stress exposure can either culminate in the organism’s adaptation or aggravate into a metabolic shutdown, characterized by irreversible cellular damage and deleterious effects on fish performance, welfare, and survival. Multiomics can improve our understanding of the complex stressed phenotype in fish and the molecular mediators that regulate the underlying processes of the molecular stress response. We profiled the stress proteome and metabolome of Sparus aurata responding to different challenges common to aquaculture production, characterizing the disturbed pathways in the fish liver, i.e., the central organ in mounting the stress response. Label-free shotgun proteomics and untargeted metabolomics analyses identified 1738 proteins and 120 metabolites, separately. Mass spectrometry data have been made fully accessible via ProteomeXchange, with the identifier PXD036392, and via MetaboLights, with the identifier MTBLS5940. Integrative multivariate statistical analysis, performed with data integration analysis for biomarker discovery using latent components (DIABLO), depicted the 10 most-relevant features. Functional analysis of these selected features revealed an intricate network of regulatory components, modulating different signaling pathways related to cellular stress, e.g., the mTORC1 pathway, the unfolded protein response, endocytosis, and autophagy to different extents according to the stress nature. These results shed light on the dynamics and extent of this species’ metabolic reprogramming under chronic stress, supporting future studies on stress markers’ discovery and fish welfare research.
Fish Processing and Digestion Affect Parvalbumins Detectability in Gilthead Seabream and European Seabass Denise Schrama, Cláudia Raposo de Magalhães, Marco Cerqueira, Raquel Carrilho, Dominique Revets, et al. Animals, 2022 Consumption of aquatic food, including fish, accounts for 17% of animal protein intake. However, fish consumption might also result in several side-effects such as sneezing, swelling and anaphylaxis in sensitized consumers. Fish allergy is an immune reaction to allergenic proteins in the fish muscle, for instance parvalbumin (PV), considered the major fish allergen. In this study, we characterize PV in two economically important fish species for southern European aquaculture, namely gilthead seabream and European seabass, to understand its stability during in vitro digestion and fish processing. This information is crucial for future studies on the allergenicity of processed fish products. PVs were extracted from fish muscles, identified by mass spectrometry (MS), and detected by sandwich enzyme-linked immunosorbent assay (ELISA) after simulated digestion and various food processing treatments. Secondary structures were determined by circular dichroism (CD) after purification by anion exchange and gel filtration chromatography. In both species, PVs presented as α-helical and β-sheet structures, at room temperature, were shown to unfold at boiling temperatures. In European seabass, PV detectability decreased during the simulated digestion and after 240 min (intestinal phase) no detection was observed, while steaming showed a decrease (p < 0.05) in PVs detectability in comparison to raw muscle samples, for both species. Additionally, freezing (−20 °C) for up to 12 months continued to reduce the detectability of PV in tested processing techniques. We concluded that PVs from both species are susceptible to digestion and processing techniques such as steaming and freezing. Our study obtained preliminary results for further research on the allergenic potential of PV after digestion and processing.
Stressor controllability modulates the stress response in fish Marco Cerqueira, Sandie Millot, Tomé Silva, Ana S. Félix, Maria Filipa Castanheira, et al. BMC Neuroscience, 2021 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).
Thermal and nutritional strategies for managing tenacibaculum maritimum in aquaculture: a welfare-oriented review R Carrilho, M Moreira, AP Farinha, D Schrama, F Soares, P Rodrigues, ... Animals: an Open Access Journal from MDPI 15 (17), 2581 , 2025 2025 Citations: 1
Quantifying the welfare impact of air asphyxia in rainbow trout slaughter for policy and practice C Schuck-Paim, WJ Alonso, PA Pereira, JL Saraiva, M Cerqueira, ... Scientific Reports 15 (1), 19850 , 2025 2025 Citations: 7
Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration C Raposo de Magalhães, K Sandoval, F Kagan, G McCormack, ... PLoS One 19 (3), e0300472 , 2024 2024 Citations: 13
Proteomics for comprehensive analysis of seafood products: Quality, safety, authentication, and allergen detection M Cerqueira, CR de Magalhães, D Schrama, AP Farinha, R Carrilho, ... Handbook of seafood and seafood products analysis, 27-71 , 2024 2024 Citations: 8
Welfare of rainbow trout at slaughter: Integrating behavioural, physiological, proteomic and quality indicators and testing a novel fast-chill stunning method JL Saraiva, F Faccenda, MJ Cabrera-Álvarez, M Povinelli, PC Hubbard, ... Aquaculture 581, 740443 , 2024 2024 Citations: 22
A new window into fish welfare: A proteomic discovery study of stress biomarkers in the skin mucus of gilthead seabream (Sparus aurata) CR de Magalhães, AP Farinha, R Carrilho, D Schrama, M Cerqueira, ... Journal of Proteomics 281, 104904 , 2023 2023 Citations: 19
ASSESSING RAINBOW TROUT WELFARE AT SLAUGHTER: AN INTEGRATIVE APPROACH USING BEHAVIOURAL, PHYSIOLOGICAL, PROTEOMIC AND QUALITY INDICATORS WITH A NOVEL TEMPERATURE STUNNING METHOD J Saraiva, F Faccenda, MJ Cabrera-Álvarez, PC Hubbard, M Cerqueira, ... Balanced diversity in aquaculture development, 1310-1311 , 2023 2023
Gilthead seabream liver integrative proteomics and metabolomics analysis reveals regulation by different prosurvival pathways in the metabolic adaptation to stress C Raposo de Magalhães, AP Farinha, G Blackburn, PD Whitfield, ... International Journal of Molecular Sciences 23 (23), 15395 , 2022 2022 Citations: 25
Fish processing and digestion affect parvalbumins detectability in gilthead seabream and European seabass D Schrama, C Raposo de Magalhães, M Cerqueira, R Carrilho, D Revets, ... Animals 12 (21), 3022 , 2022 2022 Citations: 15
Effect of creatine and EDTA supplemented diets on European seabass (Dicentrarchus labrax) allergenicity, fish muscle quality and omics fingerprint D Schrama, CR de Magalhães, M Cerqueira, R Carrilho, AP Farinha, ... Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 41 … , 2022 2022 Citations: 23
Proteomics for Quality and Safety in Fishery Products AP Farinha, M Moreira, CR de Magalhaes, D Schrama, M Cerqueira, ... Sustainable fish production and processing, 45-78 , 2022 2022 Citations: 8
Stressor controllability modulates the stress response in fish M Cerqueira, S Millot, T Silva, AS Félix, MF Castanheira, S Rey, ... BMC neuroscience 22 (1), 48 , 2021 2021 Citations: 15
Metabolic plasticity of gilthead seabream under different stressors: Analysis of the stress responsive hepatic proteome and gene expression C Raposo de Magalhães, D Schrama, C Nakharuthai, ... Frontiers in Marine Science 8, 676189 , 2021 2021 Citations: 22
Evaluating the impact of methionine-enriched diets in the liver of European seabass through label-free shotgun proteomics AP Farinha, D Schrama, T Silva, LEC Conceição, R Colen, S Engrola, ... Journal of proteomics 232, 104047 , 2021 2021 Citations: 22
Data on European seabass fed with methionine-enriched diets obtained through label free shotgun proteomics AP Farinha, D Schrama, T Silva, LEC Conceição, R Colen, S Engrola, ... Data in Brief 34, 106675 , 2021 2021 Citations: 1
Fish pathology research and diagnosis in aquaculture of farmed fish; a proteomics perspective M Moreira, D Schrama, AP Farinha, M Cerqueira, ... Animals 11 (1), 125 , 2021 2021 Citations: 76
Mid-infrared spectroscopic screening of metabolic alterations in stress-exposed gilthead seabream ( Sparus aurata ) CR de Magalhaes, R Carrilho, D Schrama, M Cerqueira, ... Scientific reports 10 (1), 16343 , 2020 2020 Citations: 23
How tryptophan levels in plant-based aquafeeds affect fish physiology, metabolism and proteome M Cerqueira, D Schrama, TS Silva, R Colen, SAD Engrola, ... Journal of proteomics 221, 103782 , 2020 2020 Citations: 55
Protein changes as robust signatures of fish chronic stress: a proteomics approach to fish welfare research C Raposo de Magalhães, D Schrama, AP Farinha, D Revets, A Kuehn, ... BMC genomics 21 (1), 309 , 2020 2020 Citations: 114
Cognitive appraisal in fish M Cerqueira, S Millot, A Felix, T Silva, GA Oliveira, CCV Oliveira, S Rey, ... Proceedings: Biological Sciences 287 (1923), 1-9 , 2020 2020 Citations: 17
MOST CITED SCHOLAR PUBLICATIONS
Protein changes as robust signatures of fish chronic stress: a proteomics approach to fish welfare research C Raposo de Magalhães, D Schrama, AP Farinha, D Revets, A Kuehn, ... BMC genomics 21 (1), 309 , 2020 2020 Citations: 114
Cognitive appraisal of environmental stimuli induces emotion-like states in fish M Cerqueira, S Millot, MF Castanheira, AS Félix, T Silva, GA Oliveira, ... Scientific Reports 7 (1), 13181 , 2017 2017 Citations: 87
Thermal preference predicts animal personality in Nile tilapia Oreochromis niloticus M Cerqueira, S Rey, T Silva, Z Featherstone, M Crumlish, S MacKenzie Journal of animal ecology 85 (5), 1389-1400 , 2016 2016 Citations: 84
A Proteomics and other Omics approach in the context of farmed fish welfare and biomarker discovery CSF Raposo de Magalhães, MAC Cerqueira, D Schrama, MJV Moreira, ... Reviews in Aquaculture 12 (1), 122-144 , 2020 2020 Citations: 81
Fish pathology research and diagnosis in aquaculture of farmed fish; a proteomics perspective M Moreira, D Schrama, AP Farinha, M Cerqueira, ... Animals 11 (1), 125 , 2021 2021 Citations: 76
Use of conditioned place preference/avoidance tests to assess affective states in fish S Millot, M Cerqueira, MF Castanheira, Ø Øverli, CIM Martins, RF Oliveira Applied Animal Behaviour Science 154, 104-111 , 2014 2014 Citations: 59
How tryptophan levels in plant-based aquafeeds affect fish physiology, metabolism and proteome M Cerqueira, D Schrama, TS Silva, R Colen, SAD Engrola, ... Journal of proteomics 221, 103782 , 2020 2020 Citations: 55
Cognitive appraisal in fish: stressor predictability modulates the physiological and neurobehavioural stress response in sea bass M Cerqueira, S Millot, A Felix, T Silva, GA Oliveira, CCV Oliveira, S Rey, ... Proceedings of the Royal Society B: Biological Sciences 287 (1923) , 2020 2020 Citations: 52
Dietary Creatine Supplementation in Gilthead Seabream ( Sparus aurata ): Comparative Proteomics Analysis on Fish Allergens, Muscle Quality, and Liver D Schrama, M Cerqueira, CS Raposo, AM Rosa da Costa, T Wulff, ... Frontiers in physiology 9, 1844 , 2018 2018 Citations: 51
Short-term impact of bait digging on intertidal macrobenthic assemblages of two south Iberian Atlantic systems S Carvalho, R Constantino, M Cerqueira, F Pereira, MD Subida, P Drake, ... Estuarine, Coastal and Shelf Science 132, 65-76 , 2013 2013 Citations: 42
Are personality traits consistent in fish?—The influence of social context MF Castanheira, M Cerqueira, S Millot, RA Gonçalves, CCV Oliveira, ... Applied Animal Behaviour Science 178, 96-101 , 2016 2016 Citations: 41
Behavioural Stress Responses Predict Environmental Perception in European Sea Bass ( Dicentrarchus labrax ) S Millot, M Cerqueira, MF Castanheira, Ø Øverli, RF Oliveira, CIM Martins PLoS One 9 (9), e108800 , 2014 2014 Citations: 33
Is surface orientation a determinant for colonisation patterns of vagile and sessile macrobenthos on artificial reefs? A Moura, LC Da Fonseca, J Cúrdia, S Carvalho, D Boaventura, ... Biofouling 24 (5), 381-391 , 2008 2008 Citations: 30
Gilthead seabream liver integrative proteomics and metabolomics analysis reveals regulation by different prosurvival pathways in the metabolic adaptation to stress C Raposo de Magalhães, AP Farinha, G Blackburn, PD Whitfield, ... International Journal of Molecular Sciences 23 (23), 15395 , 2022 2022 Citations: 25
Effect of creatine and EDTA supplemented diets on European seabass (Dicentrarchus labrax) allergenicity, fish muscle quality and omics fingerprint D Schrama, CR de Magalhães, M Cerqueira, R Carrilho, AP Farinha, ... Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 41 … , 2022 2022 Citations: 23
Mid-infrared spectroscopic screening of metabolic alterations in stress-exposed gilthead seabream ( Sparus aurata ) CR de Magalhaes, R Carrilho, D Schrama, M Cerqueira, ... Scientific reports 10 (1), 16343 , 2020 2020 Citations: 23
Welfare of rainbow trout at slaughter: Integrating behavioural, physiological, proteomic and quality indicators and testing a novel fast-chill stunning method JL Saraiva, F Faccenda, MJ Cabrera-Álvarez, M Povinelli, PC Hubbard, ... Aquaculture 581, 740443 , 2024 2024 Citations: 22
Metabolic plasticity of gilthead seabream under different stressors: Analysis of the stress responsive hepatic proteome and gene expression C Raposo de Magalhães, D Schrama, C Nakharuthai, ... Frontiers in Marine Science 8, 676189 , 2021 2021 Citations: 22
Evaluating the impact of methionine-enriched diets in the liver of European seabass through label-free shotgun proteomics AP Farinha, D Schrama, T Silva, LEC Conceição, R Colen, S Engrola, ... Journal of proteomics 232, 104047 , 2021 2021 Citations: 22
Habituation and conditioning in gilthead sea bream ( Sparus aurata ): Effects of aversive stimuli, reward and social hierarchies O Folkedal, A Fernö, MAJ Nederlof, JE Fosseidengen, M Cerqueira, ... Aquaculture Research 49 (1), 335-340 , 2018 2018 Citations: 20
