Thesis and internships

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S2AQUA promotes specialised training and education, so we work with students and recent graduates, offering various opportunities for experimental work in a wide range of areas:

  • Aquaculture
  • Marine Biology
  • Biochemistry
  • Molecular Biology
  • Biomedical
  • among others.

If you are interested in any of these subjects, take a look at the list below and contact us!

  • Development and Optimisation of Intestinal Organoids from Gilthead Seabream (Sparus aurata) and European Seabass (Dicentrarchus labrax) as Functional Models for Aquaculture

    SUPERVISOR DETAILS
    Name: Iris Silva
    E-mail: formacao@s2aquacolab.pt

    SUMMARY OF THE PROPOSED RESEARCH
    Provisional title: Development and Optimisation of Intestinal Organoids from Gilthead Seabream (Sparus aurata) and European Seabass (Dicentrarchus labrax) as Functional Models for Aquaculture

    General objective:

    The intestine plays a central role in fish health, nutrition and immune responses and is directly influenced by factors such as diet, environmental stress and pathogens. However, the study of these processes in fish still relies heavily on in vivo experiments, raising ethical, logistical and economic concerns.

    Intestinal organoids, often referred to as "mini-guts", have emerged as innovative three-dimensional models capable of replicating the architecture and functions of the intestinal epithelium. Although they are widely used in human and mammalian research, their application to marine aquaculture species remains limited, with a clear need for optimised protocols tailored to species such as gilthead seabream and European seabass. This thesis aims to contribute to the development of robust, reproducible and reliable in vitro models for applications in nutrition, toxicology and animal health research.

    Planned tasks:

    • Literature review on intestinal organoids in vertebrates and fish.
    • Isolation and characterisation of intestinal cells from gilthead seabream and European seabass.
    • Optimisation of three-dimensional culture protocols (matrices, growth factors and culture conditions).
    • Morphological and functional characterisation of the resulting organoids.
    • Preliminary assessment of organoid responses to nutritional and environmental stimuli.

      This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Establishment of Salmon Skin Organoids as an Innovative Model for the Study of Epithelial Barriers in Aquaculture

    SUPERVISOR DETAILS
    Name: Iris Silva
    E-mail: formacao@s2aquacolab.pt

    SUMMARY OF THE PROPOSED RESEARCH
    Provisional title: Establishment of Salmon Skin Organoids as an Innovative Model for the Study of Epithelial Barriers in Aquaculture

    General objective: Fish skin constitutes the first line of defence against pathogens and environmental stressors and plays a crucial role in the survival and welfare of fish reared in intensive aquaculture systems. In salmon, skin lesions are frequently associated with infections, parasites and handling practices, with direct impacts on animal health and production performance. Skin organoids represent an emerging tissue engineering approach that enables the study of complex cellular processes in a controlled and biologically relevant system. However, the application of this technology to aquaculture species, particularly salmon, is still at an early stage of development. This thesis aims to develop and optimise protocols for the cultivation of salmon skin organoids, providing new opportunities for research in skin health, toxicology and host-pathogen interactions.

    Planned tasks:

    • Literature review on skin organoids and epithelial models in fish and mammals.
    • Isolation of salmon skin cells.
    • Development and optimisation of three-dimensional culture protocols.
    • Structural and cellular characterisation of the organoids.
    • Assessment of the viability and long-term stability of the established models.


    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Development of a Molecular Tool for the Early Detection of Harmful Microalgae in Marine and Aquaculture Systems

    SUPERVISOR DETAILS
    Name: Iris Silva
    E-mail: formacao@s2aquacolab.pt

    SUMMARY OF THE PROPOSED RESEARCH
    Provisional title: Development of a Molecular Tool for the Early Detection of Harmful Microalgae in Marine and Aquaculture Systems

    General objective: Harmful microalgal blooms pose an increasing threat to marine ecosystems, public health and aquaculture, potentially leading to farm closures and mass mortality events in cultured organisms. Traditional monitoring methods rely on microscopic identification and chemical analyses, which are time-consuming and require a high level of technical expertise. Molecular methods offer a rapid and highly specific alternative for detecting harmful species before visible impacts occur, enabling a more proactive and preventive approach. However, molecular-based early warning systems still require further development and validation across different environmental settings. This thesis aims to develop a sensitive and adaptable molecular method for the early detection of harmful microalgal species of relevance to marine and aquaculture environments.

    Planned tasks:

    • Literature review on harmful microalgae in Portugal and current detection methods.
    • Selection of target species and specific molecular markers.
    • Development and optimisation of different molecular detection methods (qPCR, multiplex qPCR, dPCR, etc.).
    • Evaluation of the sensitivity, specificity and robustness of each method.
    • Application of the developed methods to complex environmental samples.


    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Characterisation and Optimisation of Fish Cell Lines for Cellular Aquaculture Applications

    SUPERVISOR DETAILS
    Name: Joana Rosa
    E-mail: formacao@s2aquacolab.pt

    SUMMARY OF THE PROPOSED RESEARCH
    Provisional title: Characterisation and Optimisation of Fish Cell Lines for Cellular Aquaculture Applications

    General objective: Cellular agriculture, based on the production of animal proteins from cell cultures, is emerging as a promising approach to address future global food security challenges. Within this rapidly developing field, cellular aquaculture, which focuses on the production of cultivated seafood, faces a major limitation due to the limited availability of suitable marine fish cell lines.

    The aim of this project is to optimise the culture conditions of fish cell lines and evaluate their suitability for cellular aquaculture applications. Their potential will be assessed based on proliferation performance, growth in serum-free culture media and their capacity to differentiate into muscle and adipose cell lineages. In addition, the cell lines will be comprehensively characterised using multi-omics approaches, including transcriptomics, proteomics and/or lipidomics.

    Planned tasks:

    • Authentication of fish cell lines through genetic barcoding.
    • Optimisation of cell growth by varying culture temperature and culture media, including measurement of cell doubling time.
    • Evaluation of the differentiation potential of the cell lines into muscle and adipose cells using differentiation protocols and specific staining techniques.
    • Comprehensive characterisation of the cell lines using multi-omics approaches, including transcriptomics, proteomics, lipidomics and related techniques.
    • Establishment and/or optimisation of cryopreservation protocols for fish cell lines.


    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Adaptation and Characterisation of Octopus Cells Cultured in Animal Serum-Free Media Supplemented with Microalgae

    SUPERVISOR DETAILS
    Name: Joana Rosa
    E-mail: formacao@s2aquacolab.pt

    SUMMARY OF THE PROPOSED RESEARCH
    Provisional title: Adaptation and Characterisation of Octopus Cells Cultured in Animal Serum-Free Media Supplemented with Microalgae

    General objective: Replacing foetal bovine serum with sustainable alternatives is one of the major challenges in the production of cultivated foods. Within the field of cellular aquaculture, the use of microalgae-derived supplements has emerged as a promising strategy to reduce dependence on animal-derived components while improving the sustainability and scalability of cell culture processes.

    The aim of this project is to adapt octopus cell cultures to culture media supplemented with microalgae-derived serum alternatives and evaluate the impact of this adaptation on cell performance, as well as on their biological and nutritional characteristics. The adaptation process will be carried out through a gradual replacement of animal serum, assessing parameters such as cell viability, proliferation, genetic stability and morphology. The adapted cells will subsequently be characterised in terms of their differentiation potential, transcriptomic and proteomic profiles, and nutritional composition, to evaluate their suitability for cultivated seafood applications.

    Planned tasks:

    • Progressive adaptation of octopus cells to culture media supplemented with different formulations of microalgae-derived serum alternatives using a gradual weaning strategy.
    • Monitoring of the adaptation process by assessing cell morphology, viability, proliferation and genetic stability.
    • Selection of the microalgae-derived serum formulation that provides the best cellular performance.
    • Evaluation of the differentiation potential of the adapted cells.
    • Molecular characterisation of the adapted cells using transcriptomic and proteomic analyses.
    • Determination of the nutritional profile of cells cultured in the optimised medium and comparison with native tissues to assess their suitability for cellular aquaculture applications.


    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Development and Application of 2D In Vitro Models for the Study of Epithelial Regeneration in Salmon

    SUPERVISOR DETAILS
    Name: Joana Rosa
    E-mail: formacao@s2aquacolab.pt

    SUMMARY OF THE PROPOSED RESEARCH
    Provisional title: Development and Application of 2D In Vitro Models for the Study of Epithelial Regeneration in Salmon

    General objective: Efficient regeneration of the skin epithelium is essential for maintaining fish health and welfare in aquaculture. Two-dimensional (2D in vitro) models provide robust and reproducible tools for investigating the cellular mechanisms involved in wound healing and tissue regeneration.

    The aim of this project is to develop and apply 2D in vitro models based on salmonid epithelial cells to evaluate regenerative processes following tissue injury. Regeneration will be investigated using in vitro wound-healing models (scratch assays), enabling the assessment of the effects of different compounds with regenerative potential. Cellular responses will be characterised by evaluating cell proliferation and viability and further complemented by transcriptomic analyses to identify changes in the molecular pathways associated with epithelial regeneration.

    Planned tasks:

    • Establishment and maintenance of 2D cultures of salmonid epithelial cells.
    • Development of an in vitro epithelial wound model using a scratch assay.
    • Evaluation of the effects of different bioactive compounds, individually and in combination, on epithelial regeneration.
    • Quantification of cell proliferation and viability throughout the regenerative process.
    • Functional characterisation of the 2D models through transcriptomic analysis (RNA-seq).


    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Influence of Developmental Stage on the Establishment and Performance of European Seabass and Gilthead Seabream Cell Lines Derived from Muscle and Fin Tissues

    SUPERVISOR DETAILS
    Name: Joana Rosa
    E-mail: formacao@s2aquacolab.pt

    SUMMARY OF THE PROPOSED RESEARCH
    Provisional title: Influence of Developmental Stage on the Establishment and Performance of European Seabass and Gilthead Seabream Cell Lines Derived from Muscle and Fin Tissues

    General objective: Cellular aquaculture is a promising approach for the sustainable production of seafood. However, its progress is limited by the scarcity of well-characterised fish cell lines that display consistent performance in culture. Tissue source and the developmental stage of the donor organism are key factors influencing the successful establishment of cell cultures, yet their effects have not been systematically investigated in aquaculture species.

    The aim of this project is to evaluate the influence of developmental stage, including larval, juvenile and adult stages, on the establishment efficiency and biological characteristics of cell lines derived from muscle and fin tissues of European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata). The study will compare culture establishment efficiency, proliferative performance and molecular characteristics of the resulting cell lines in order to identify the most suitable combinations of tissue source and developmental stage for cellular aquaculture applications.

    Planned tasks:

    • Selection of European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata) and definition of the developmental stages to be studied.
    • Collection of muscle and fin explants from larval, juvenile and adult individuals.
    • Establishment of primary cultures and development of cell lines using 2D culture systems.
    • Comparative evaluation of culture establishment efficiency according to tissue source and developmental stage.
    • Characterisation of cell growth, including cell proliferation and doubling time analyses.
    • Molecular characterisation of selected cell lines using omics approaches, including transcriptomics and/or proteomics.
      Establishment and optimisation of cryopreservation protocols.


    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Development of an In Vitro Bacterial Challenge Model in European Seabass Epithelial Cells Using Inactivated Vibrio anguillarum

    SUPERVISOR DETAILS
    Name: Joana Rosa
    E-mail: formacao@s2aquacolab.pt

    SUMMARY OF THE PROPOSED RESEARCH
    Provisional title: Development of an In Vitro Bacterial Challenge Model in European Seabass Epithelial Cells Using Inactivated Vibrio anguillarum

    General objective: Bacterial infections are among the leading causes of mortality and economic losses in aquaculture. The initial stages of infection often occur at the skin and mucosal surfaces, where bacteria interact with epithelial cells and trigger local immune responses.

    This project aims to develop a simple in vitro bacterial challenge model based on epithelial cell lines derived from European seabass (Dicentrarchus labrax) exposed to inactivated Vibrio anguillarum. The model will enable the study of the early epithelial response to bacterial exposure by assessing cell viability, cytotoxicity and the expression of genes associated with inflammatory responses and microbial recognition. This platform will serve as a preliminary tool for investigating alternative strategies to reduce the use of antibiotics in aquaculture.

    Planned tasks:

    • Selection and maintenance of a European seabass epithelial cell line (skin or fin).
    • Preparation of Vibrio anguillarum inactivated by heat treatment or chemical fixation.
    • Optimisation of exposure conditions, including bacterial concentration and stimulation time.
    • Assessment of cell viability and cytotoxicity following bacterial challenge.
    • Analysis of the expression of genes involved in inflammatory responses and bacterial recognition (e.g. IL-1β, TNF-α, TLRs and mucins).
    • Integrated interpretation of the results and evaluation of the model as an in vitro platform for studying bacterial infections in fish.


    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Cultivation of macroalgae under controlled conditions

    IDENTIFICATION OF THE SUPERVISOR
    Name: Raquel Quintã, Sandra Ramos 
    E-mail: formacao@s2aquacolab.pt

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     Cultivation of macroalgae under controlled conditions

    Main objective: Investigate the cultivation of Ulva sp. and Gracilaria sp. under controlled and manipulated conditions. 
     
    Planned tasks:  

    • Experimental planning;

    • Preparing the experimental set-up;

    • Maintenance of macroalgae cultivation trials;

    • Sampling cultivated biomass, weighing and drying;

    • Monitoring environmental parameters and water quality during cultivation;

    • Preparation of biomass for CN analysis;

    • Literature review. 

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Temporal and Spatial Dynamics of Phytoplankton in the Ria Formosa and Their Implications for the Carrying Capacity of Bivalve Aquaculture

    SUPERVISOR DETAILS
    Name: Renata Gonçalves 
    E-mail: formacao@s2aquacolab.pt

    SUMMARY OF THE PROPOSED RESEARCH
    Provisional title: Temporal and Spatial Dynamics of Phytoplankton in the Ria Formosa and Their Implications for the Carrying Capacity of Bivalve Aquaculture

    General objective: The aim of this project is to contribute to the assessment of the carrying capacity of the Ria Formosa by investigating the temporal and spatial dynamics of phytoplankton, with a particular focus on food availability for clam farming areas and the seasonal occurrence of potentially harmful algal species. The study will identify and quantify phytoplankton in samples collected by shellfish farmers, assess seasonal and spatial patterns, estimate variability in food availability, and record the presence of potentially toxic genera. The results will be discussed within the ecological and production context of bivalve aquaculture in the Ria Formosa.. 

    Planned tasks:

    • Literature review.
    • Training and calibration in phytoplankton taxonomic identification.
      Processing of phytoplankton samples.
    • Phytoplankton identification and cell counting.
    • Development of a database.
    • Statistical analysis of the results.
    • Thesis writing and preparation of the thesis defence.


    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Optimization of the cultivation condition to produce soft-shell crab

    IDENTIFICATION OF THE SUPERVISOR
    Name: Renata Gonçalves 
    E-mail: formacao@s2aquacolab.pt

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     Optimization of the cultivation condition to produce soft-shell crab 

    Main objective: Determine the most favorable conditions (temperature and feed) for the shell molting process in blue and green crabs
     
    Planned tasks:  

    • In vivo     trials with juvenile blue crabs (Callinectes sapidus) and green crabs (Carcinus maenas) to test the effect of temperature on the carapace molting process;

    • In vivo trials to test the effect of different feeding regimes on the growth of juvenile blue crabs (Callinectes sapidus) and green crabs (Carcinus maenas);

    • Laboratory analyses of physiological indicators (digestive enzyme activity);

    • Analyzing data and reporting results. 

    Work to be carried out at Atlantik Fish's facilities in Castro Marim.

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • On-Site Molecular Diagnosis of Emerging Marine Parasites in Aquaculture Using LAMP Technology

    SUPERVISOR DETAILS
    Name: Iris Silva
    E-mail: formacao@s2aquacolab.pt

    SUMMARY OF THE PROPOSED RESEARCH
    Provisional title: On-Site Molecular Diagnosis of Emerging Marine Parasites in Aquaculture Using LAMP Technology

    General objective: Parasitic diseases are among the major constraints to the sustainability of marine aquaculture, causing high mortality rates and significant economic losses. Parasites such as Amyloodinium ocellatum and pathogenic amoebae are particularly problematic due to their rapid spread and the difficulty of achieving early detection under farming conditions. Currently, diagnosis relies mainly on microscopic examination and laboratory-based molecular methods, such as PCR, which require specialised facilities, trained personnel and turnaround times that are often incompatible with rapid decision-making in commercial aquaculture.

    Loop-mediated Isothermal Amplification (LAMP) technology offers a promising alternative by enabling rapid, sensitive and highly specific DNA amplification without the need for complex laboratory equipment. Despite its potential, the application of LAMP for on-site diagnostics in aquaculture remains limited, requiring further protocol optimisation and validation using field samples.

    Planned tasks:

    • Literature review on relevant marine parasites and existing molecular diagnostic methods.
    • Selection of molecular targets for Amyloodinium ocellatum and pathogenic amoebae.
    • Optimisation of LAMP protocols, including primer design, reaction conditions and detection methods.
    • Evaluation of the sensitivity and specificity of the method using laboratory and environmental samples.
    • Application and validation of the developed method under commercial aquaculture conditions.


    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • iOysters – Development and optimization of oyster’s growth in closed systems - not available

    IDENTIFICATION OF THE SUPERVISOR
    Name: Catarina Braga
    E-mail: formacao@s2aquacolab.pt

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     iOysters – Development and optimization of oyster’s growth in closes systems

    Main objective: The general objective of the iOysters project is to optimize oyster production conditions to obtain closed (RAS) and semi-closed production systems that allow oysters to be produced independently of the natural environment. The specific objectives are 1) characterize, evaluate and select the optimum conditions for oyster production; 2) optimize the diets and evaluate the densities and species of microalgae to be fed to the oysters.

    Proposed tasks:

    • Identification of the ideal conditions for oysters’ growth;

    • Exposure of commercially available triploid juveniles of the Japanese oyster (Magallana gigas) to various conditions to assess their impact (individual and combined) in oyster growth. This trial will focus on evaluating the impact of diets, environmental conditions, husbandry practices, handling techniques, as well as the diet provided, assessing the impact of changes in the composition and density of the food provided. These trials will be carried out in a closed system under controlled conditions, where all parameters will be regulated and monitored using sensors and manual measurements. The trials will last for three months and will analyze performance indices, nutritional quality and physiological responses. This activity includes tasks such as:

    - Design and implementation of bivalve production systems;

    - Maintaining shellfish production systems;

    - Routine feeding and cleaning of shellfish production systems;

    - Collecting biotic and abiotic parameters;

    - Collaborating in sampling for data collection;

    - Collaborating in analyzing and interpreting the data collected;

    - Collaborating in the preparation of reports and scientific articles.

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Preliminary cryopreservation studies of macroalgae of economic interest found on the Algarve coast - not available

    IDENTIFICATION OF THE SUPERVISOR
    Name: Iris Silva, Cátia Marques
    E-mail: formacao@s2aquacolab.pt

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     Preliminary cryopreservation studies of macroalgae of economic interest found on the Algarve coast

    Main objective: With the increasing use and production of macroalgae in aquaculture, the development of sustainable production strategies is becoming increasingly necessary. One of the key points in this process is the ability to maintain genetic diversity for the development of breeding programs with the aim of maintaining wild populations. Currently, biobanks are an important tool for strain preservation, biodiversity, conservation, ecosystem restoration and research applications. However, these efforts mainly target microalgae and terrestrial plants and the collections that include macroalgae are small and incomplete. Cryopreservation could be an alternative for long-term storage and preservation of biological species that can be used at any time. The general aim of this thesis is to develop cryopreservation protocols for macroalgae such as Ulva, Gracilaria and Saccorhiza.

    Proposed tasks:

    The aim of this work is to investigate various methods of cryopreserving macroalgae of commercial interest from the Portuguese coast, so that they can be stored and used in subsequent trials and to maintain a stock of genetic diversity. To this end, various tests will be carried out to assess the effect of different cryoprotectants, namely optimum concentrations, equilibrium time, cryopreservation temperature, defrosting temperature, and the regenerative efficiency of the cryopreserved species. Cultures will also be kept in cultivation to serve as control.

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Optimizing protocols for culture of fish intestinal organoids - not available

    IDENTIFICATION OF THE SUPERVISOR
    Name: Iris Silva, Cátia Marques
    E-mail: formacao@s2aquacolab.pt

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     Optimizing protocols for culture of fish intestinal organoids

    Main objective: The epithelial cells of the intestine are essential for the digestion and absorption of nutrients, but they also act as a physical and immunological barrier against microorganisms or toxins. The interaction between pathogens of species produced in aquaculture and their hosts is an area that has yet to be explored, which is why it is imperative to develop new methodologies to understand these mechanisms. The use of in vitro systems has emerged as a more practical and sustainable strategy with the aim of reducing the number of animals used in in vivo trials. The general aim of this thesis proposal is to develop protocols for culture of fish intestinal organoids as an in vitro tool to be used in nutritional or immunological response studies

    Proposed tasks:

    • To develop these in vitro systems, the planned tasks involve:

    - Biopsies of the posterior intestine of juvenile sea bream and sea bass;
    - Isolation of the intestinal crypts;
    - Testing of in vitro culture conditions (temperature, atmosphere, culture medium, etc.);

    • Once the intestinal organoids have been established, it will be necessary to:

    - Carry out toxicity tests;

    - Analyze the genetic profile of these cells.

     

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Cultivation of macroalgae in hatcheries - not available

    IDENTIFICATION OF THE SUPERVISOR
    Name: Raquel Quintã, Catarina Braga
    E-mail: formacao@s2aquacolab.pt

    AVAILABLE UNTIL DECEMBER

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     Cultivation of macroalgae in hatcheries

    Main objective: Optimization of macroalgae cultivation techniques in hatcheries for production in the sea, and evaluation of their capacity for bioremediation of dissolved nutrients.

    Proposed tasks:

    • Collection of biomass for propagation, preparation and maintenance of biomass cultivation test on wire (spools) in a controlled and manipulate environment;

    • Biomass sampling, image capture, counts and measurements under magnifying glass/microscope, biomass weighing.

     

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Cultivation of macroalgae in IMTA - not available

    IDENTIFICATION OF THE SUPERVISOR
    Name: Raquel Quintã, Sandra Ramos
    E-mail: formacao@s2aquacolab.pt

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     Cultivation of macroalgae in IMTA

    Main objective: Optimization of the cultivation of Ulva sp. and/or Gracilaria sp. in IMTA in earthen ponds and evaluation of nutrient bioremediation.

    Proposed tasks:

    • Biomass sampling, weighing and drying;

    • Sampling and analyzing dissolved nutrients;

    • Preparation of biomass for CN analysis;

    • Assessment of reproductive state of the cultivated biomass;

    • Monitoring environmental parameters;

    • Preparing and maintaining cultivation systems.

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • A Machine Learning Algorithm for Automated Detection of specific fish blood cells - not available

    IDENTIFICATION OF THE SUPERVISOR
    Name: João Janeiro, Cátia Marques
    E-mail: formacao@s2aquacolab.pt

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     A Machine Learning Algorithm for Automated Detection of specific fish blood cells

    Main objective: This thesis aims to develop a cutting-edge machine learning algorithm designed to automatically detect and classify specific types of blood cells in digitized fish blood samples. The project will involve processing and analysing high-resolution microscopic images using advanced image processing techniques and machine learning models. The successful development of this algorithm could significantly enhance biological research and diagnostics in ichthyology, providing a faster, more accurate alternative to manual microscopy analysis

    Objectives:

    • Gather a comprehensive dataset of digitized fish blood samples, annotated with expert biological input on cell types and characteristics;

    • Design and implement a machine learning model capable of recognizing and classifying various blood cell types in fish;

    • Assess the algorithm's accuracy and efficiency against a set of previously unseen test images, ensuring robustness and reliability;

    • Develop a user-friendly interface that allows biologists and researchers to easily input new images and receive detailed cell analysis;

    • Contribute to the body of knowledge in digital image processing in biological research by publishing a research paper.

    Proposed tasks:

    • Conduct a detailed review of existing techniques in image processing and machine learning applications in biological imaging;

    • Pre-process images to enhance features relevant for machine learning analysis, including segmentation and normalization;

    • Experiment with various machine learning models (e.g., CNNs, SVMs) to determine the most effective approach for cell detection and classification;

    • Train the model using the prepared dataset, perform hyperparameter tuning, and cross-validation to optimize performance;

    • Use metrics such as accuracy, precision, recall, and F1-score to evaluate the model on test data;

    • Develop and test a graphical user interface (GUI) that allows users to interact with the model seamlessly;

    • Paper preparation: Document the research process, model architecture, and evaluation results; prepare a research paper which will be the master thesis.

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Effects of supplementing cryopreservation media with microalgae extracts and/or bovine milk-derived extracelular vesicles in sea bream (𝘚𝘱𝘢𝘳𝘶𝘴 𝘢𝘶𝘳𝘢𝘵𝘢) spermatozoa - not available

    IDENTIFICATION OF THE SUPERVISOR
    Name: Sandra Ramos, Renata Gonçalves
    E-mail: formacao@s2aquacolab.pt

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     Effects of supplementing cryopreservation media with microalgae extracts and/or bovine milk-derived extracellular vesicles in sea bream (Sparus aurata) spermatozoa

    Main objective: Explore innovative techniques in fish sperm cryopreservation, particularly (1) the effects of microalgae extracts and (2) bovine milk-derived extracellular vesicles (EVs) in frozen gilthead sea bream spermatozoa. By leveraging the bioactive compounds in microalgae extracts (such as carotenoids, polyunsaturated fatty acids (PUFAs), phenolic compounds, terpenes, proteins, and sulphated polysaccharides) and in EVs (proteins, lipids, RNA, and microRNAs), the aim is to enhance sperm cell resilience and improve overall cryopreservation success rates, contributing to higher fertilization rates.

    Proposed tasks:

    Broodstock management techniques.

    • Sperm collection, cryopreservation and thawing procedures;

    • Fertilizations and possible induction of females to maturate and ovulate;

    • Evaluation of the quality of cryopreserved sperm by:

    - Assessing fertilization and hatching percentages of eggs;

    - Larval survival in 96-well plates;

    - Total and progressive motility and velocity;

    - Cell viability;

    - Lipid peroxidation;

    - Presence of Reactive Oxygen Species (ROS);

    - DNA integrity;

    - Cell apoptosis;

    • Perform statistical analyses on obtained results.

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Effects of 𝘎𝘳𝘢𝘤𝘪𝘭𝘢𝘳𝘪𝘢 𝘴𝘱-Based Diets on Enhancing Gonad Production in Sea Urchins (𝘗𝘢𝘳𝘢𝘤𝘦𝘯𝘵𝘳𝘰𝘵𝘶𝘴 𝘭𝘪𝘷𝘪𝘥𝘶𝘴) - not available

    IDENTIFICATION OF THE SUPERVISOR
    Name: Sandra Ramos, Florbela Soares
    E-mail: formacao@s2aquacolab.pt

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     Effects of Gracilaria sp-Based Diets on Enhancing Gonad Production in Sea Urchins (Paracentrotus lividus)

    Main objective: To investigate the effects of different diets, particularly fresh Gracilaria sp and its inclusion in a pelleted diet, on enhancing gonad production in sea urchins (Paracentrotus lividus).

    Objectives:

    • Conduct a sea urchin feeding trial over approximately three months, from January to March 2025.

    • Perform biometric measurements on sea urchins, including test diameter, wet weight, gonad weight, and Gonadosomatic Index (GSI), along with assessment of gonad color.

    • Conduct histological examination of sea urchin gonads.

    • Analyze the lipid content of sea urchin gonads.

    • Analyze results from fatty acids composition.

    • Perform statistical analyses on obtained results.

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

  • Morphological and molecular identification of pathogenic bacteria isolated from marine animals - not available

    IDENTIFICATION OF THE SUPERVISOR
    Name: Iris Silva, Florbela Soares
    E-mail: formacao@s2aquacolab.pt

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     Morphological and molecular identification of pathogenic bacteria isolated from marine animals

    Main objective: The planned tasks involve 1) pathological analysis of diseased fish samples, in collaboration with the pathology laboratory, as well as 2) cultivation techniques, isolation and 3) morphological and biochemical characterization of the isolated bacteria. Subsequently, 4) cryopreservation methods and cataloguing will be carried out so that the samples can be added to the S2AQUA BIOBANK. For molecular identification, the tasks will focus on 5) searching databases for genetic sequences of the species in question, 6) designing primers, and 7) optimizing PCR protocols. It may also be necessary to analyze sequencing results.

    This thesis/internship proposal is academic in nature (curricular) and and is not remunerated.

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