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Thesis

Available Thesis Projects

Proteomic characterization of human fetal tissues and comparison with publicly available datasets

Project description

This master’s thesis project aims to characterize the proteomic landscape of human fetal tissues analysing mass spectrometry–based proteomics data and to compare these profiles with publicly available proteomic datasets. The goal is to identify proteins and molecular pathways that are specific to fetal development and to investigate how proteomic signatures vary across tissues or gestational stages.

Data and tools

The project would involve the analysis of proteomic datasets generated from human fetal tissues (e.g., neural, muscle, skin). These data will be integrated with publicly available proteomic resources and atlases for comparative analysis. Data will be analysed using established proteomics software for mass spectrometry data processing and protein identification (e.g., MaxQuant), as well as statistical and bioinformatics tools in R for downstream analysis and visualization (e.g., Bioconductor, ggplot).

Main objectives

  • Identify and quantify expressed proteins
  • Compare fetal proteomic profiles with public adult datasets to identify development-specific signatures
  • Perform pathway and functional enrichment analyses to characterize biological processes associated with fetal development

Development of a 3D in vitro model to test drug-induced toxicity

Project description

This master’s thesis project aims to develop a physiologically relevant 3D in vitro model for the assessment of drug-induced toxicity, with a focus on fetal-like tissue environments. The project involves the design and optimization of a functional bioink suitable for cell encapsulation, enabling the creation of reproducible and scalable 3D constructs. By integrating material science, rheology, and cell biology, the study will establish quantitative relationships between bioink properties and molecular transport, and validate the platform for drug screening applications. The final goal is to demonstrate the reliability of the system through pilot toxicity studies using benchmark compounds.

Data and tools

The project will involve the formulation and characterization of hydrogel-based bioinks, including chemical and physical quality control across batches. Rheological analyses (e.g., oscillatory tests for storage and loss moduli, viscosity measurements) will be performed to assess viscoelastic properties. Diffusion studies will be conducted to correlate transport phenomena with material parameters. Cell culture techniques will be used to encapsulate relevant cell types within 3D constructs, followed by viability and functional assays. High-throughput compatibility will be evaluated using multiwell formats, and drug response will be assessed through dose–response experiments. Data analysis will be carried out using statistical tools (e.g., R or Python) for curve fitting and assay performance evaluation.

Main objectives

  • Design and formulate a functional bioink suitable for fetal-like 3D in vitro models
  • Ensure reproducible synthesis and assess chemical stability and batch-to-batch consistency
  • Optimize viscoelastic properties of the bioink for printability and cell compatibility
  • Establish quantitative correlations between rheological parameters (G′, G″, viscosity) and effective diffusion coefficients
  • Develop and validate a cell encapsulation platform compatible with high-throughput screening
  • Demonstrate efficient encapsulation, preservation of cell viability and functionality, and scalability to multiwell formats
  • Conduct pilot drug toxicity screening using benchmark compounds
  • Generate dose–response curves, determine IC50 values, and calculate assay quality metrics (e.g., Z′ factor, signal-to-background ratio)

Characterisation of amniotic fluid–derived stem cells and organoids from healthy and pathological pregnancies

Project description

This master’s thesis project aims to characterise amniotic fluid–derived stem cells (AFSCs) isolated from healthy and pathological pregnancies, evaluating their biological properties under different culture conditions and investigating functional differences linked to the pathological origin of the samples. The project further extends to the generation and characterisation of three-dimensional organoid models derived from the same amniotic fluid sources, with the goal of establishing relevant in vitro systems to study pregnancy-associated conditions.

Data and tools

The project will involve the culture and experimental analysis of AFSCs obtained from both healthy and pathological amniotic fluid samples. Cell behaviour, morphology, proliferation kinetics, and viability will be assessed using standard cell biology techniques, including live/dead assays, growth curve analyses, and microscopy-based imaging. Organoid generation will follow established three-dimensional culture protocols. Data will be analysed and visualised using statistical tools in R and appropriate bioinformatics pipelines where needed.

Main objectives

  • Characterise AFSCs under different culture conditions, evaluating morphology, adaptation, and behaviour in response to distinct in vitro environments
  • Compare stem cells derived from healthy and pathological samples to identify biological and functional differences associated with the pathological origin
  • Quantify cell proliferation, viability, and growth kinetics, including doubling time and proliferation rate
  • Generate and characterise amniotic fluid–derived organoids from both healthy and pathological samples as three-dimensional models for further biological investigation

Cellular and molecular characterization of human amniotic fluid and primary fetal amniotic fluid-derived organoids

Project description

This master’s thesis project aims to characterize the cellular composition of human amniotic fluid (AF) and primary AF-derived fetal organoids using single-cell and bulk transcriptomic approaches. The goal is to map cell types present within the amniotic fluid to investigate development mechanisms in congenital diseases, and to investigate how AF-derived organoids can be used as congenital diseases model.

Data and tools

The project would involve the analysis of large single-cell and bulk RNA sequencing datasets. These data will be integrated with publicly available proteomic resources and atlases for comparative analysis. Data will be analysed using different R packages built for the analysis of single-cell data (e.g. Seurat) and bioinformatics tools in R for downstream analysis and visualization (e.g., Bioconductor, ggplot2), as well as diverse genotype-based demultiplexing tools for multiplexed single-cell data (e.g., Vireo, Souporcell, Freemuxlet).

Main objectives

  • Identify and classify cell types present in human amniotic fluid and AF-derived organoids
  • Investigate gestational-stage–specific changes in cellular composition and molecular signatures relevant to congenital diseases
  • Compare cellular profiles between control and diseased organoids to assess organoid fidelity as disease models