Department Bionanoscience
Principal investigator Arjen Jakobi
E-mail address a.jakobi@tudelft.nl
Website http://cryoem.tudelft.nl
Deep learning for cryo-EM image processing
Supervisor: Maarten Joosten, m.j.joosten@tudelft.nl
Cryo-EM is a technique that is heavily dependent on the computational algorithms that allow us to pick, classify and reconstruct particles to obtain a 3D representation of a protein or protein complex. The images are noisy and heterogeneous, making it very challenging to find robust computational solutions. We therefore often work with simulated data to test the capabilities of our algorithms. This data needs to be as realistic as possible. In this project you will evaluate how good our simulated data is and optimise it by applying machine learning. You will (learn to) work with Python to build image processing scripts, build neural networks and run them on our high-performance computing environment. You will also get experience working with cryo-EM image processing software, and there are possibilities to complement computational work with work on the microscope and/or in the wetlab.
Techniques
- Cryo-EM
- Image processing
- Machine learning/AI
- Neural networks
- Structural biology
Further reading
Zhong, E. D., et al. (2021). Nature methods, 18(2), 176–185. DOI: 10.1038/s41592-020-01049-4.
Resolving the structural mechanisms of GBP heterodimer formation
Supervisor: Lennart Pagani, l.l.pagani@tudelft.nl
Guanylate-binding proteins (GBPs) are key components of cell-autonomous immunity and protect host-cells from intracellular pathogens by encapsulating bacteria and initiating bacteriolysis and inflammation. The seven GBP orthologues are hierarchically recruited to the bacterial membrane via heterodimerization, but direct molecular evidence is missing. Hence, structural information of GBP heterodimers would be very valuable in our goal to understand the role of GBPs in cellular self-defence. In this project you will try to isolate a GBP heterodimer (GBP1-GBP3) and to resolve the structure by cryo-EM. Within this project you can learn how to clone, culture cells, purify protein and all the other basics of biochemistry. Additionally, you can learn the basics of cryo-EM and image processing.
Techniques
- Cryo-EM
- Fluorescence microscopy
- Protein biochemistry
- Structural biology
- Biophysical characterisation
- Cell culture
Further reading
Kuhm, T., et al. (2023). BioRxiv. DOI: 10.1101/2023.03.28.534355v1.
Elucidating the membrane-binding mechanism of human GBP4
Supervisor: Lennart Pagani, l.l.pagani@tudelft.nl
Guanylate-binding proteins (GBPs) are key components of cell-autonomous immunity and protect host-cells from intracellular pathogens by encapsulating the bacteria and initiating bacteriolysis and inflammation. For decades it has been known that GBP1/2/5 bind membranes through the C-terminal end by having a lipid-moiety attached post translation, yet the membrane-binding mechanism of their family members (GBP4/6/7) is still completely unknown. Through bioinformatic analysis we believe the latter all bind bacterial membranes through amphipathic helices at the C-terminal end. In this project you will try to experimentally show how these GBPs binds membranes. Within this project you can learn how to clone, culture cells, purify protein and all the other basics of biochemistry.
Techniques
- Cryo-EM
- Fluorescence microscopy
- Protein biochemistry
- Structural biology
- Biophysical characterisation
- Cell culture
Further reading
Kuhm, T., et al. (2023). BioRxiv. DOI: 10.1101/2023.03.28.534355v1.
Visualizing antibacterial protein coats at high resolution
Supervisor: Clémence Taisne, c.m.taisne@tudelft.nl
In our lab a key project focuses on studying guanylate-binding proteins (GBPs) involved in cytosolic host defense against intracellular bacteria. Certain pathogens like Salmonella hyphimurium and Shigella flexneri evade vacuoles to thrive in the cell cytosol. Host cells counteract this by recruiting GBPs around pathogen membranes. Using cryo-electron microscopy, our lab has solved the structure of GBP1 and its binding with lipopolysaccharides (LPS). This project aims to further characterise this interaction through high-resolution fluorescence and electron microscopy obtained in infected cells. Using cryo-tomography and super-resolution imaging you will visualise the GBP1 coat binding around different gram-negative bacteria, shedding light on an intricate host defense mechanism that is crucial in the fight against intracellular pathogens.
Techniques
- Cryo-EM/ET
- Fluorescence microscopy
- Cell culture
- Microbiology
- Infection biology
Further reading
Kuhm, T., et al. (2023). BioRxiv. DOI: 10.1101/2023.03.28.534355v1.