Bioengineering Center Institute for Synthetic Biomedicine

2023 Nature Biotechnology

Felix Sigmund, Oleksandr Berezin, Sofia Beliakova, Bernhard Magerl, Martin Drawitsch, Alberto Piovesan, Filipa Gonçalves, Silviu-Vasile Bodea, Stefanie Winkler, Zoe Bousraou, Martin Grosshauser, Eleni Samara, Jesús Pujol-Martí, Sebastian Schädler, Chun So, Stephan Irsen, Axel Walch, Florian Kofler, Marie Piraud, Joergen Kornfeld, Kevin Briggman & Gil Gregor Westmeyer

Genetically encoded barcodes for correlative volume electron microscopy

While genetically encoded reporters are common for fluorescence microscopy, equivalent multiplexable gene reporters for electron microscopy (EM) are still scarce. Here, by installing a variable number of fixation-stable metal-interacting moieties in the lumen of encapsulin nanocompartments of different sizes, we developed a suite of spherically symmetric and concentric barcodes (EMcapsulins) that are readable by standard EM techniques. Six classes of EMcapsulins could be automatically segmented and differentiated. The coding capacity was further increased by arranging several EMcapsulins into distinct patterns via a set of rigid spacers of variable length. Fluorescent EMcapsulins were expressed to monitor subcellular structures in light and EM. Neuronal expression in Drosophila and mouse brains enabled the automatic identification of genetically defined cells in EM. EMcapsulins are compatible with transmission EM, scanning EM and focused ion beam scanning EM. The expandable palette of genetically controlled EM-readable barcodes can augment anatomical EM images with multiplexed gene expression maps.

2022 Nature Cell Biology

Truong, D.-J.J.*, Armbrust, N.*, Geilenkeuser, J., Lederer, E-M., Santl, T., Beyer, M. Ittermann, S., Steinmaßl, E., Dyka, M., Raffl, Phlairaharn, T., Greisle, T., Zivanic, M., Grosch, M., Drukker, M.,, Westmeyer G.G., *equal contribution

Intron-encoded cistronic transcripts for minimally-invasive monitoring of coding and non-coding RNAs ion

2021 Nature Cell Biology

Truong, D.-J.J., Phlairaharn, T., Eßwein, B., Gruber, C., Tümen, D., Baligács, E., Armbrust, N., Vaccaro, F.L., Lederer, E.-M., Beck, E.M., Geilenkeuser, J., Göppert, S., Krumwiede, L., Grätz, C., Raffl, G., Schwarz, D., Zirngibl, M., Živanić, M., Beyer, M., Körner, J.D., Santl, T., Evsyukov, V., Strauß, T., Schwarz, S.C., Höglinger, G.U., Heutink, P., Doll, S., Conrad, M., Giesert, F., Wurst, W., Westmeyer, G.G.

Non-invasive and high-throughput interrogation of exon-specific isoform expression

2021 Nature Materials

Farhadi, A., Sigmund, F., Westmeyer, G.G., Shapiro, M.G.

Genetically encodable materials for non-invasive biological imaging.

2019 ACS Nano

Sigmund, F*., Pettinger, S.*, Kube, M.*, Schneider, F., Schifferer, M., Schneider, S., Efremova, M., Pujol-Martí, J., Aichler, M., Walch, A., Misgeld, T., Dietz, H., Westmeyer, G.G.

Iron-sequestering nanocompartments as multiplexed Electron Microscopy gene reporters.

2018 Nature Communications

Sigmund, F., Massner, C., Erdmann, P., Stelzl, A., Rolbieski, H., Desai, M., Bricault, S., Wörner, T.P., Snijder, J., Geerlof, A., Fuchs, H., Hrabe de Angelis, M., Heck, A.J.R., Jasanoff, A., Ntziachristos, V., Plitzko, J., Westmeyer, G.G.

Bacterial encapsulins as orthogonal compartments for mammalian cell engineering.

2017 Nature Methods

Symvoulidis, P., Lauri, A., Stefanoiu, A., Cappetta, M., Schneider, S., Jia, H., Stelzl, A., Koch, M., Perez, C.C., Myklatun, A., Renninger, S., Chmyrov, A., Lasser, T., Wurst, W., Ntziachristos, V., Westmeyer, G.G.

NeuBtracker-imaging neurobehavioral dynamics in freely behaving fish.

2018 JACS

Roberts, S., Seeger, M., Jiang, Y., Mishra, A., Sigmund, F., Stelzl, A., Lauri, A., Symvoulidis, P., Rolbieski, H., Preller, M., Deán-Ben, X.L., Razansky, D., Orschmann, T., Desbordes, S.C., Vetschera, P., Bach, T., Ntziachristos, V., Westmeyer, G.G.

Calcium Sensor for Photoacoustic Imaging.