Professional Education

  • Master of Science, Polytechnic University of Turin (2016)
  • Bachelor of Science, Universita Degli Studi Di Padova (2014)
  • Doctor of Philosophy, Technische Universiteit Delft (2021)
  • Master of Science, Polytechnic University of Turin, INP de Grenoble, EPFL (2016)

Stanford Advisors

All Publications

  • Glycogen phase separation drives macromolecular rearrangement and asymmetric division in E. coli. bioRxiv : the preprint server for biology Thappeta, Y., Cañas-Duarte, S. J., Kallem, T., Fragasso, A., Xiang, Y., Gray, W., Lee, C., Cegelski, L., Jacobs-Wagner, C. 2024


    Bacteria often experience nutrient limitation in nature and the laboratory. While exponential and stationary growth phases are well characterized in the model bacterium Escherichia coli, little is known about what transpires inside individual cells during the transition between these two phases. Through quantitative cell imaging, we found that the position of nucleoids and cell division sites becomes increasingly asymmetric during transition phase. These asymmetries were coupled with spatial reorganization of proteins, ribosomes, and RNAs to nucleoid-centric localizations. Results from live-cell imaging experiments, complemented with genetic and 13C whole-cell nuclear magnetic resonance spectroscopy studies, show that preferential accumulation of the storage polymer glycogen at the old cell pole leads to the observed rearrangements and asymmetric divisions. In vitro experiments suggest that these phenotypes are likely due to the propensity of glycogen to phase separate in crowded environments, as glycogen condensates exclude fluorescent proteins under physiological crowding conditions. Glycogen-associated differences in cell sizes between strains and future daughter cells suggest that glycogen phase separation allows cells to store large glucose reserves without counting them as cytoplasmic space.

    View details for DOI 10.1101/2024.04.19.590186

    View details for PubMedID 38659787

    View details for PubMedCentralID PMC11042326

  • Diameter dependence of transport through nuclear pore complex mimics studied using optical nanopores. eLife Klughammer, N., Barth, A., Dekker, M., Fragasso, A., Onck, P. R., Dekker, C. 2024; 12


    The nuclear pore complex (NPC) regulates the selective transport of large biomolecules through the nuclear envelope. As a model system for nuclear transport, we construct NPC mimics by functionalizing the pore walls of freestanding palladium zero-mode waveguides with the FG-nucleoporin Nsp1. This approach enables the measurement of single-molecule translocations through individual pores using optical detection. We probe the selectivity of Nsp1-coated pores by quantitatively comparing the translocation rates of the nuclear transport receptor Kap95 to the inert probe BSA over a wide range of pore sizes from 35 nm to 160 nm. Pores below 55 ± 5 nm show significant selectivity that gradually decreases for larger pores. This finding is corroborated by coarse-grained molecular dynamics simulations of the Nsp1 mesh within the pore, which suggest that leakage of BSA occurs by diffusion through transient openings within the dynamic mesh. Furthermore, we experimentally observe a modulation of the BSA permeation when varying the concentration of Kap95. The results demonstrate the potential of single-molecule fluorescence measurements on biomimetic NPCs to elucidate the principles of nuclear transport.

    View details for DOI 10.7554/eLife.87174

    View details for PubMedID 38376900

  • Dynamin A as a one-component division machinery for synthetic cells. Nature nanotechnology De Franceschi, N., Barth, R., Meindlhumer, S., Fragasso, A., Dekker, C. 2024; 19 (1): 70-76


    Membrane abscission, the final cut of the last connection between emerging daughter cells, is an indispensable event in the last stage of cell division and in other cellular processes such as endocytosis, virus release or bacterial sporulation. However, its mechanism remains poorly understood, impeding its application as a cell-division machinery for synthetic cells. Here we use fluorescence microscopy and fluorescence recovery after photobleaching measurements to study the in vitro reconstitution of the bacterial protein dynamin A inside liposomes. Upon external reshaping of the liposomes into dumbbells, dynamin A self-assembles at the membrane neck, resulting in membrane hemi-scission and even full scission. Dynamin A proteins constitute a simple one-component division machinery capable of splitting dumbbell-shaped liposomes, marking an important step towards building a synthetic cell.

    View details for DOI 10.1038/s41565-023-01510-3

    View details for PubMedID 37798563

  • Synthetic Membrane Shaper for Controlled Liposome Deformation ACS NANO De Franceschi, N., Pezeshkian, W., Fragasso, A., Bruininks, B. H., Tsai, S., Marrink, S. J., Dekker, C. 2022: 966-78


    Shape defines the structure and function of cellular membranes. In cell division, the cell membrane deforms into a "dumbbell" shape, while organelles such as the autophagosome exhibit "stomatocyte" shapes. Bottom-up in vitro reconstitution of protein machineries that stabilize or resolve the membrane necks in such deformed liposome structures is of considerable interest to characterize their function. Here we develop a DNA-nanotechnology-based approach that we call the synthetic membrane shaper (SMS), where cholesterol-linked DNA structures attach to the liposome membrane to reproducibly generate high yields of stomatocytes and dumbbells. In silico simulations confirm the shape-stabilizing role of the SMS. We show that the SMS is fully compatible with protein reconstitution by assembling bacterial divisome proteins (DynaminA, FtsZ:ZipA) at the catenoidal neck of these membrane structures. The SMS approach provides a general tool for studying protein binding to complex membrane geometries that will greatly benefit synthetic cell research.

    View details for DOI 10.1021/acsnano.2c06125

    View details for Web of Science ID 000891678100001

    View details for PubMedID 36441529

    View details for PubMedCentralID PMC9878720

  • Transport receptor occupancy in nuclear pore complex mimics NANO RESEARCH Fragasso, A., de Vries, H. W., Andersson, J., van der Sluis, E. O., van der Giessen, E., Onck, P. R., Dekker, C. 2022; 15 (11): 9689-9703