Open projects at Department of Biotechnology & Biomedicine

• Link to webpage: https://www.bioengineering.dtu.dk/research/research-sections/section-for-medical-biotechnology/cell-signaling-architecture and https://www.chiarafrancavilla.eu/
• The Cell Signalling Architecture team studies the principles and the regulation of cellular signalling in a variety of mammalian cell models using a multi-disciplinary approach which combines cell biology with quantitative omics – specifically phosphoproteomics - and bioinformatics. We focus on how the cellular microenvironment affects signalling cascades, protein localization, metabolism, gene regulation, and cell survival. The final goal of our research is to identify and characterize novel proteins with key roles in cellular signalling and cell survival which can be targeted for personalized intervention in human diseases. Furthermore, we will use our data to improve mammalian cell engineering and to increase our understanding of vesicles properties for nanomedicine. 

• Link to webpage: https://www.bric.ku.dk/research-groups/Research/ochs-group/
• The aim of the Fena Ochs’ laboratory is to decipher the molecular interplay of DNA repair and 3D chromatin organization, and to understand how dysregulation of 3D chromatin organization leads to genome instability and cancer. We develop and apply cutting-edge super-resolution microscopy technology for single molecule imaging in intact cell and tissue samples, with the ambition that our findings may contribute to the development of new clinical treatment strategies.

• What?
  • To study how changes in nutrients in the cellular microenvironment affect cell signalling cascades in breast cancer cells
  • To uncover how changes in nutrients affect the localization of signalling molecules both a global and a molecular level
  • To determine how changes in nutrients affect cell fate decisions including the balance between cell proliferation, motility, death
• How? (Methodological approaches and used technologies)
  • Mammalian cell culture in two and three dimensions
  • Biochemistry methods
  • Advanced imaging methods and data analysis
  • Quantitative proteomics and phosphoproteomics technologies
  • Bioinformatics tools for data analysis
• Why?
  • Nutrients in the extracellular environment determine cell fate, including formation of metastasis and response to therapies, but we do not know the molecular determinants underlying changes in signalling, protein localization, metabolism or gene regulation. This project will reveal such molecular determinants by combining cutting-edge quantitative phosphoproteomics and advanced imaging methods with bioinformatics for data analysis and functional assays.

The candidate will mainly work in the laboratory of Chiara Francavilla learning and applying cell biology, biochemistry, proteomics/phosphoprotoemics, and bioinformatics methods. The project is in collaboration with a wet lab-based postdoc and a bioinformatician who will offer not only training in such methods but also an international and collaborative environment to discuss results and ideas. Here, the candidate will combine a system biology and a target approach to reveal how changes in nutrients availability affect signalling outputs. Once the candidate will find novel protein targets, the candidate will be trained in the lab of Fena Ochs for a period to be discussed in advanced imaging methods and data analysis and will focus on the spatial aspect of signalling regulation upon changes in nutrients availability. The novel proten targets will be validated by advanced imaging methods  in terms of cellualr localization and mobility. Regular meetings with the main supervisors, ad hoc meetings with all the supervisor team, and participation to both group lab meetings will be planned since the beginning and warmly encouraged.