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!

  • Preliminary cryopreservation studies of macroalgae of economic interest found on the Algarve coast

    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.

  • Optimizing protocols for culture of fish intestinal organoids

    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 1) biopsies of the posterior intestine of juvenile sea bream and sea bass, 2) isolation of the intestinal crypts, and 3) testing of in vitro culture conditions (temperature, atmosphere, culture medium, etc.). Once the intestinal organoids have been established, it will be necessary to 4) carry out toxicity tests and 5) analyze the genetic profile of these cells.

     

  • Validation of a panel of growth biomarkers in sea bream and sea bass

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

    SUMMARY DESCRIPTION OF THE WORK PROPOSAL
    Proposed title:     Validation of a panel of growth biomarkers in sea bream and sea bass

    Main objective: Growth is one of the most important factors for the success of aquaculture production, since producers want to have stocks of fish that reach commercial size as soon as possible and with homogeneous sizes. However, perhaps because it is a multifactorial characteristic (depending on environmental, genetic and nutritional factors, etc.), there is a great heterogeneity of sizes between fish in the same stock. This has a major economic impact, and it is therefore necessary to develop effective strategies for selecting traits that impact aquaculture growth and productivity. Previously, S2AQUA participated in a project where genetic biomarkers related to growth were identified in sea bream and sea bass through mRNA sequencing (RNA-Seq). This thesis proposal aims to validate the panel of growth biomarkers that were previously identified as being differentially expressed between fast-growing and slow-growing fish.

    Proposed tasks:

    To validate the biomarkers selected, it will be necessary to 1) design specific primers for the genes selected in the previous analysis (for both sea bream and sea bass), 2) analyze the efficiency of the primers designed for both species, and 3) quantify the expression of these genes using qPCR tests to compare expression in samples of fat-growing and slow-growing fish, as well as with the results obtained from RNA-seq analysis. The integration of all these results obtained will generate a tool with the aim of assisting the aquaculture industry by enabling the selection of fish lineages with the best growth potential.

  • iOysters – Development and optimization of oyster’s growth in closed systems

    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

  • Cultivation of macroalgae in hatcheries

    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.

     

  • Cultivation of macroalgae in IMTA

    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:

    1. Biomass sampling, weighing and drying.

    2. Sampling and analyzing dissolved nutrients.

    3. Preparation of biomass for CN analysis.

    4. Assessment of reproductive state of the cultivated biomass.

    5. Monitoring environmental parameters.

    6. Preparing and maintaining cultivation systems

     

  • 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:  
    1. Experimental planning. 
    2. Preparing the experimental set-up. 
    3. Maintenance of macroalgae cultivation trials. 
    4. Sampling cultivated biomass, weighing and drying. 
    5. Monitoring environmental parameters and water quality during cultivation. 
    6. Preparation of biomass for CN analysis. 
    7. Literature review. 

  • A Machine Learning Algorithm for Automated Detection of specific fish blood cells

    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:

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

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

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

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

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

    Proposed tasks:

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

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

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

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

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

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

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

     

  • Effects of supplementing cryopreservation media with microalgae extracts and/or bovine milk-derived extracelular vesicles in sea bream (𝘚𝘱𝘢𝘳𝘶𝘴 𝘢𝘶𝘳𝘢𝘵𝘢) spermatozoa

    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.

  • Effects of 𝘎𝘳𝘢𝘤𝘪𝘭𝘢𝘳𝘪𝘢 𝘴𝘱-Based Diets on Enhancing Gonad Production in Sea Urchins (𝘗𝘢𝘳𝘢𝘤𝘦𝘯𝘵𝘳𝘰𝘵𝘶𝘴 𝘭𝘪𝘷𝘪𝘥𝘶𝘴)

    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:

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

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

    3. Conduct histological examination of sea urchin gonads.

    4. Analyze the lipid content of sea urchin gonads.

    5. Analyze results from fatty acids composition.

    6. Perform statistical analyses on obtained results.

     

  • Morphological and molecular identification of pathogenic bacteria isolated from marine animals

    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.

  • 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. 

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