Department Bionanoscience
Principal investigator Gijsje Koenderink
E-mail address g.h.koenderink@tudelft.nl
Website https://tudelft.nl/koenderinklab
Cytoskeletal crosstalk in confined cancer cells
Supervisor: Anouk van der Net, j.j.p.vanderNet@tudelft.nl
Confinement parameters of extracellular matrix in the local tumor microenvironments can impact tumor cell migration strategies and therefore also invasion efficiency and metastatic potential. To better understand the effect of confinement on cancer cell morphology and mechanics, we use live-cell confocal microscopy to study the localization of different cytoskeletal networks and their crosstalk in genetically manipulated cancer cells that are confined on 2D micropatterns that mimic 3D collagen migration tracks. Via image analysis, we aim to elucidate strategies employed by cancer cells to survive extreme confining conditions via the cytoskeletal networks.
Techniques
- Micropatterning
- Live-cell confocal microscopy
- Mammalian cell culture
- Electroporation
- Image analysis
Further reading
Ndiaye, A.B., et al. (2022). Frontiers in Cell and Developmental Biology, 11(10), 882037. DOI: 10.3389/fcell.2022.882037.
Building a living cell from scratch using microfluidics
Supervisor: Bert van Herck, b.vanherck@tudelft.nl
To shed light on the fundamental blueprint of a cell and get a better understanding of the governing principles of cellular life, we are aiming to build a synthetic cell from the bottom-up using molecular building blocks. Towards this end, we use a microfluidic technology, Octanol-assisted Liposome Assembly, to produce cell-sized liposomes. This project will focus on the expansion of this microfluidic technology in order to obtain a lab-on-a-chip system to establish a cycle of growing and dividing liposomes, mimicking a continuous life cycle of a living cell. In this experimental and multidisciplinary project, you will gain experience working in a wetlab, learn how to operate a microfluidic setup, and perform fluorescence microscopy-based experiments.
Techniques
- Microfluidics
- Fluorescence microscopy
- Image analysis
Further reading
Deshpande, S., et al. (2016). Nature Communications, 7(10447). DOI: 10.1038/ncomms10447.
Establishing programmable liposome fusion to enable synthetic cell growth
Supervisor: Bert van Herck, b.vanherck@tudelft.nl
To accomplish sustained growth and division, synthetic cells must expand their membrane surface. Providing extra lipids from the outside is a necessity to supply additional membrane area. We are developing a membrane fusion protocol based on complementary DNA strands with a cholesterol tag to induce binding and fusion between GUVs and LUVs. To characterize this process, we use fluorescence imaging (confocal laser scanning, FRET, FLIM) and quantitative image analysis. The project will focus on the development of a content mixing and a leakage assay to further assess vesicle fusion. Further, we plan to integrate this fusion system into a microfluidic device to improve our control over the experimental parameters.
Techniques
- Confocal fluorescence microscopy
- FRET
- FLIM
- Image analysis
- Microfluidics
Further reading
Lira, R.B., et al. (2019). Biophysical Journal, 116(1), 79-91. DOI: 10.1016/j.bpj.2018.11.3128.
Mechanobiology of in vitro cartilage tissues
Supervisor: Irene Nagle, i.nagle@tudelft.nl
In connective tissues, cells are embedded in a support matrix composed of a complex 3D network of extracellular macromolecules and proteins. Cells receive various biophysical stimuli through this extracellular matrix (ECM) such as topographic cues or mechanical stimulation. For instance, chondrocytes, specialized collagen-secreting cells responsible for the maintenance of cartilaginous tissues within joints, are constantly exposed to mechanical loading (compression, shear). This project aims at understanding the interplay between cell behaviour and ECM properties using in vitro model systems based on 3D cultures of chondrocytes in cartilage-mimicking hydrogels and/or the influence of controlled external loading on the cell response. The goal is to gain insights into chondrocyte mechanobiology in healthy but also in diseased conditions.
Techniques
- Light microscopy
- Mammalian cell culture
- Mechanical testing in the context of biological tissues
Further reading
Muntz, I., et al. (2022). Physical Biology, 19(2), 021001. DOI: 10.1088/1478-3975/ac42b8.
Engineering an actin cytoskeleton in synthetic cells for electroporation
Supervisor: Nikki Nafar, n.nafar@tudelft.nl
This project focuses on the role of the actin cytoskeleton in electroporation, a key technique for delivering materials into cells. Electroporation uses electric pulses to destabilize the cell membrane, but the underlying actin cytoskeleton, a complex structural network, might significantly influence this process. You will employ the eDICE technique to create an actin cortex within synthetic cells and then modify this structure using actin-binding proteins. The aim is to understand how these alterations impact the synthetic cells’ response to electroporation.
Techniques
- GUV fabrication (eDICE: emulsion droplet interface crossing encapsulation)
- Fluorescent (+ super-resolution) microscopy
- Electroporation
Further reading
Perrier, D.L., et al. (2019). Scientific Reports, 9(1), 8151. DOI: 10.1038/s41598-019-44613-5.
Model intercellular bridge with septin and other proteins
Supervisor: SaFrye Reese, s.d.r.mxreese@tudelft.nl
In the intercellular bridge, proteins are important for the recruited and organized in the intercellular bridge. In our group, we use cell-sized giant unilamellar vesicles (GUVs) as a model to investigate biological proteins spatiotemporal interactions in a bottom-up approach. By utilizing microfluidic traps, the geometry of the plasma membrane is altered to investigate the shape deformations. Experimentally you can learn about encapsulation of proteins, such as septin and anillin, to model the intercellular bridge. Additionally, you can improve the quantification of the co-localization of multiple proteins to each other or the membrane.
Techniques
- Protein encapsulation
- Confocal microscopy
- Image analysis
- Python coding
Further reading
Panagiotou, T.C., et al. (2022). Cell Reports, 40(9), 111274. DOI: 10.1016/j.celrep.2022.111274.
Evolutionary approach to building a synthetic cell
Supervisor: Marijn van den Brink, m.vandenbrink@tudelft.nl
We aim to build a synthetic cell via a directed evolution approach. We express small but smart DNA libraries inside liposomes using a cell-free expression system (PURE system) and sort the vesicles displaying improved phenotypes, so we can identify the responsible genotypes. Because the genetic modules essential to a synthetic cell are linked to multidimensional phenotypes, including dynamic behaviours, cell shapes and protein localizations, we are developing an imaging-based vesicle selection technique. Possible student project directions: (1) develop microscopy-based method to sort gene-expressing liposomes (wet lab), (2) perform directed evolution experiments to optimize synthetic cell modules (wet lab), (3) train and test AI-based object detection/video classification algorithms (dry lab).
Techniques
- Cell-free gene expression
- Liposome preparation
- Microscopy
- Flow cytometry
- PCR/qPCR
- DNA library design and synthesis
Further reading
Abil, Z. & Danelon, C. (2020). Frontiers in Bioengineering and Biotechnology, 8, 927. DOI: 10.3389/fbioe.2020.00927.