Research

Our group uses cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) to investigate the structure of biological systems at molecular resolution. By imaging fully hydrated, unstained specimens at cryogenic temperatures, we obtain near-native views of cells, organelles, and macromolecular complexes. Our research spans synaptic biology, bacterial toxins, parasitology, and method development, and we contribute electron microscopy expertise to a wide range of collaborative projects.

Synaptic Architecture and Neurotransmission

Synaptic transmission relies on the precisely controlled release of neurotransmitters from synaptic vesicles. These vesicles are organized into functionally distinct pools — the readily releasable pool, the recycling pool, and the reserve pool — yet the molecular mechanisms that differentiate them remain poorly understood.

Using cryo-electron tomography, we visualize the three-dimensional architecture of synapses at nanometer resolution, revealing filamentous connectors between vesicles, the organization of the active zone, and structural intermediates of exocytosis. To move beyond animal models, we have established human iPSC-derived neurons as a versatile system for both functional and structural studies, and demonstrated that they form bona fide synapses.

We also develop computational tools for image analysis: CryoVesNet, a deep-learning framework for automated segmentation of synaptic vesicles in cryo-electron tomograms, enables quantitative analysis of vesicle distributions and connectivity across large datasets.

CryoVesNet segmentation of synaptic vesicles in rat hippocampal neurons. (A, B) 3D reconstructions showing spherical (blue) and elliptical (yellow) vesicles in excitatory (A) and inhibitory (B) synapses. (C, D) 2D tomographic slices with individual vesicle labels. Scale bar: 100 nm. From Khosrozadeh et al., J. Cell Biol. (2025).

Key publications

† = equal contribution, * = corresponding author

Rostami I, Leuenberger J, Ott G, Khosrozadeh A, Diab R, Saxena S, Nevian T, Zuber B*. Advancing human iPSC-derived motor neuron models using glutamatergic modulators for synaptic function studies. Preprint (2026). DOI: 10.21203/rs.3.rs-8600072/v1

Khosrozadeh A, Seeger R, Witz G, Radecke J, Sørensen JB, Zuber B*. CryoVesNet: A dedicated framework for synaptic vesicle segmentation in cryo-electron tomograms. Journal of Cell Biology 224(1) (2025). DOI: 10.1083/jcb.202402169

Radecke J†, Seeger R†, Kadkova A, Laugks U, Khosrozadeh A, Goldie KN, Lučić V, Sørensen JB*, Zuber B*. Morphofunctional changes at the active zone during synaptic vesicle exocytosis. EMBO Reports 24(5):e55719 (2023). DOI: 10.15252/embr.202255719

Pore-Forming Toxins

Pore-forming toxins (PFTs) are major virulence factors produced by pathogenic bacteria. They perforate host cell membranes, causing cell damage and death. Understanding how these toxins recognize their receptors, insert into membranes, and assemble into functional pores is essential for developing countermeasures against bacterial infections.

Using cryo-EM single particle analysis, we determine the high-resolution structures of PFTs from several bacterial species. Our recent work includes the structure of aerolysin pores in a lipid environment, the octameric pore of Clostridium perfringens beta-toxin, and the identification of anthrax toxin receptor 2 as the receptor for C. perfringens NetF toxin. In the framework of an interdisciplinary Sinergia project, we combine structural biology with computational chemistry and veterinary pathology to design peptide-based inhibitors against clostridial toxins.

Cryo-EM structure of the C. perfringens NetF pore (yellow) in complex with its receptor ANTXR2 (blue). Each NetF protomer is bound to one ANTXR2 molecule. Oblique view (left), side view (top right), and top view (bottom right). From Wang, Cattalani, Iacovache et al., Nat. Commun. (2026).

Key publications

† = equal contribution, * = corresponding author

Wang C†, Cattalani F†, Iacovache I†, Naguleswaran A, Farhoosh F, Franzen J, Abrami L, van der Goot FG, Posthaus H*, Zuber B*. Identification and structural characterization of anthrax toxin receptor 2 as the Clostridium perfringens NetF receptor. Nature Communications (2026). DOI: 10.1038/s41467-026-69526-6

Anton JS†, Iacovache I†, Bada Juarez JF, Abriata LA, Perrin LW, Cao C, Marcaida MJ, Zuber B*, Dal Peraro M*. Aerolysin nanopore structures revealed at high resolution in a lipid environment. Journal of the American Chemical Society 147(6):4984–4992 (2025). DOI: 10.1021/jacs.4c14288

Bruggisser J†, Iacovache I†, Musson SC, Degiacomi MT, Posthaus H*, Zuber B*. Cryo-EM structure of the octameric pore of Clostridium perfringens beta-toxin. EMBO Reports 23(12):e54856 (2022). DOI: 10.15252/embr.202254856

Cryo-EM Methods and Technology

We develop tools and methods that push the boundaries of cryo-electron microscopy.

FerriTag is a genetically encoded tag based on a modified ferritin cage that produces a high-contrast signal in cryo-electron tomograms. It enables the specific localization of target proteins in their cellular context, bridging the gap between fluorescence microscopy and cryo-ET.

CEMOVIS (cryo-electron microscopy of vitreous sections) allows the imaging of specimens that are too thick for conventional cryo-EM. Vitreous samples are cut into ultrathin sections (~60 nm) at cryogenic temperatures using a diamond knife and imaged without staining. We have contributed to pushing this technique toward high-resolution in situ structure determination.

CryoVesNet is a deep-learning pipeline based on a U-Net architecture, trained to automatically segment synaptic vesicles in cryo-electron tomograms. It generalizes across different sample types and enables large-scale quantitative analysis.

Cryo-EM visualization of rapamycin-induced FerriTag labeling of a mitochondrial outer membrane protein. Arrowheads point to individual ferritin particles decorating the mitochondrial membrane. Scale bar: 200 nm. From Wang et al., Structure (2025).

Key publications

† = equal contribution, * = corresponding author

Wang C, Khosrozadeh A, Iacovache I, Zuber B*. Genetically encoded FerriTag as a specific label for cryo-electron tomography. Structure 33(12):2146–2156.e4 (2025). DOI: 10.1016/j.str.2025.08.013

Elferich J†, Kaminek M†, Kong L, Odriozola A, Kukulski W, Zuber B*, Grigorieff N*. In situ high-resolution cryo-EM reconstructions from CEMOVIS. IUCrJ 12(Pt 4):502–510 (2025). DOI: 10.1107/S2052252525005196

Khosrozadeh A, Seeger R, Witz G, Radecke J, Sørensen JB, Zuber B*. CryoVesNet: A dedicated framework for synaptic vesicle segmentation in cryo-electron tomograms. Journal of Cell Biology 224(1) (2025). DOI: 10.1083/jcb.202402169

Trypanosome Cell Biology

Trypanosoma brucei, the causative agent of sleeping sickness, harbors a unique mitochondrial genome — the kinetoplast DNA (kDNA) — that is physically connected to the flagellar basal body through the tripartite attachment complex (TAC). This connection ensures faithful segregation of the mitochondrial genome during cell division.

Using cryo-electron tomography, we have revealed the elastic nature of the TAC and contributed to identifying novel proteins involved in kDNA anchoring. This work, in collaboration with the Torsten Ochsenreiter group, provides structural insights into an essential and parasite-specific machinery that represents a potential drug target.

3D segmentation model of the TAC area in T. brucei based on cryo-electron tomograms. Basal body and flagellum (magenta), pro-basal body (pink), microtubule quartets (purple/violet), flagellar pocket (blue), exclusion zone filaments (green), outer mitochondrial membrane (yellow), inner mitochondrial membrane (orange), kDNA (cyan). Scale bar: 200 nm. From Bregy et al., bioRxiv (2023).

Key publications

† = equal contribution, * = corresponding author

Bregy I, Radecke J, Noga A, van den Hoek H, Kern M, Haenni B, Engel BD, Siebert CA, Ishikawa T, Zuber B*, Ochsenreiter T*. Cryo-electron tomography sheds light on the elastic nature of the Trypanosoma brucei tripartite attachment complex. bioRxiv (2023). DOI: 10.1101/2023.03.06.531305

Amodeo S†, Bregy I†, Hoffmann A†, Fradera-Sola A, Kern M, Baudouin H, Zuber B, Butter F, Ochsenreiter T*. Characterization of two novel proteins involved in mitochondrial DNA anchoring in Trypanosoma brucei. PLoS Pathogens 19(7):e1011486 (2023). DOI: 10.1371/journal.ppat.1011486

Collaborative Projects

Our group contributes cryo-EM and electron microscopy expertise to a range of collaborative projects across disciplines.

Serial Block Face Scanning Electron Microscopy (SBFSEM)

SBFSEM enables three-dimensional ultrastructural imaging of large tissue volumes at ~20–30 nm resolution. A resin-embedded sample mounted on an ultramicrotome inside a scanning electron microscope is iteratively cut and imaged, building a 3D dataset of the specimen. We apply SBFSEM to synapse biology, vascular biology, and parasitology. Researchers interested in using this technique are welcome to contact us.

 

SBFSEM of CD4+ T cells interacting with brain endothelial cells (pMBMECs) under physiological flow. Top: a T cell sending a subendothelial protrusion across the endothelial monolayer. Middle: a T cell undergoing diapedesis, with the nucleus already partly beneath the endothelium. Bottom: quantification of T cell protrusions. Serial frontal sections are false-colored: endothelial cells (red), extracellular matrix (green), T cell cytoplasm (light blue), T cell nucleus (bright blue). Yellow arrows indicate mitochondria. Scale bars: 1 μm. From Castro Dias et al., J. Cell Sci. (2021).

Selected Collaborations

Supramolecular DNA nanostructures

With the Robert Häner group (Dept. of Chemistry, University of Bern): cryo-EM characterization of self-assembled nanostructures from amphiphilic DNA and organic chromophore conjugates.

† = equal contribution, * = corresponding author

Thiede J, Schneeberger T, Iacovache I, Langenegger SM, Zuber B, Häner R*. Supramolecular assembly of phenanthrene-DNA conjugates into light-harvesting nanospheres. New Journal of Chemistry 48(36):15731–15734 (2024). DOI: 10.1039/d4nj02411g

Thiede J, Rothenbühler S, Iacovache I, Langenegger SM, Zuber B, Häner R*. Supramolecular assembly of pyrene-DNA conjugates: influence of pyrene substitution pattern and implications for artificial LHCs. Organic & Biomolecular Chemistry 21(39):7908–7912 (2023). DOI: 10.1039/d3ob01375h

Blood-brain barrier

With the Britta Engelhardt group (Theodor Kocher Institute, University of Bern): electron microscopy of the glia limitans and tricellular junctions as sites of immune cell diapedesis.

† = equal contribution, * = corresponding author

Hélie-Legoupil P†, Kloster F†, Pareja J, Vladymyrov M, Mapunda JA, Bouillet E, Oetiker Y, Spera I, Barcos S, Brenna A, Odriozola A, Baert A, Fankhauser C, Haenni B, Proulx ST, Zuber B, Deutsch U, Engelhardt B*. In vivo imaging of the barrier properties of the glia limitans during health and neuroinflammation. Nature Communications 16(1):8895 (2025). DOI: 10.1038/s41467-025-63945-7

Castro Dias M, Odriozola Quesada A, Soldati S, Bosch F, Gruber I, Hildbrand T, Sönmez D, Khire T, Witz G, McGrath JL, Piontek J, Kondoh M, Deutsch U, Zuber B, Engelhardt B*. Brain endothelial tricellular junctions as novel sites for T cell diapedesis across the blood-brain barrier. Journal of Cell Science 134(8) (2021). DOI: 10.1242/jcs.253880