Henning Paul-Julius Stahlberg

Mission We use high-resolution cryo-electron microscopy to study neurodegeneration and other protein systems. We also develop novel imaging technology in the areas of electron microscopy hardware and applications, sample preparation, data collection schemes, and data analysis software systems. The Stahlberg group is supported by the University of Lausanne, Faculty of Medicine and Biology, and by the EPFL, Faculty of Basic Sciences, Physics Institute. The LBEM is a research laboratory of both UNIL and EPFL. Education PhD | Chemistry Department 1997 – 1997 EPFL, Lausanne, Switzerland Diploma | Solid State Physics 1993 – 1993 Technical University, Berlin, Germany Professionals experiences Full Professor 2020–2020 EPFL, Lausanne, SwitzerlandAssistant Professor (TTAP) 2003–2007 UC Davis, California, USAPostDoc 1998–2002 University of Basel, Switzerland ResearchAutomation of electron microscopy data analysis The Stahlberg group has built a suite of programs to process cryo-electron microscopy images. The software system 2dx [1] was able to fully automatically process cryo-EM images of two-dimensional membrane protein crystals, resulting in a high-resolution 3D structure of the membrane protein while data are being collected. 2dx is based on the MRC software suite and was extended by additional programs, e.g., to apply single particle and maximum likelihood algorithms to 2D crystal geometries. We have further developed FOCUS [2], which establishes an interface between cryo-EM data collection and data processing. FOCUS monitors a cryo-EM instrument, and once an image or a movie or tilt series is recorded, FOCUS will submit it to a fully automated and user-adaptable processing pipeline. Daniel Castano in our group has also developed the DYNAMO software package [3] for sub-volume analysis of Cryo-electron tomography datasets. DYNAMO is now widely used by a large user community [1] Gipson, B., Zeng, X., Zhang, Z. Y., & Stahlberg, H. (2007). 2dx-User-friendly image processing for 2D crystals. Journal of Structural Biology, 157(1), 64&72.[2] Biyani, N., Righetto, R. D., McLeod, R., Caujolle-Bert, D., Castano-Diez, D., Goldie, K. N., & Stahlberg, H. (2017). Focus: The interface between data collection and data processing in cryo-EM. Journal of Structural Biology, 198(2), 124&133.[3] Castaño-Díez, D., Kudryashev, M., Arheit, M., & Stahlberg, H. (2012). Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. Journal of Structural Biology, 178(2), 139& 151.Ultrastructural characterization of alpha-synuclei Our group has also studied fibrils of aSyn, which were grown in-vitro de-novo or after seeding with human brain sample (PMCA). We have determined the atomic structures of several aSyn fibril conformations (prionoid strains) [1-4]. [1] New insights on the structure of alpha-synuclein fibrils using cryo-electron microscopyGuerrero-Ferreira, R., Kovacik, L., Ni, D., Stahlberg, H.Current Opinion in Neurobiology 61, 89-95 (2020)[2] Two new polymorphic structures of alpha-synuclein solved by cryo-electron microscopyGuerrero-Ferreira, R., Taylor, N., Arteni, A.-A., Kumari, P., Mona, D., Ringler, P., Britschgi, M., Lauer, M.E., Verasdock, J., Riek, R., Melki, R., Meier, B.H., Böckmann, A., Bousset, L., Stahlberg, H.eLife 8:e48907, (2019)[3] Cryo-EM structure of alpha-synuclein fibrilsGuerrero-Ferreira, R., Taylor, N., Mona, D., Ringler, P., Lauer, M. E., Riek, R., Britschgi, M., Stahlberg, H.eLife 7(e36402), (2018)[4] Cryo-EM structure of alpha-synuclein fibrils amplified by PMCA from PD and MSA patient brainsBurger, D., Fenyi, A., Bousset, L., Stahlberg, H., Melki, R.bioRxiv 2021.07.08.451588, (2022)Microfluidic sample preparation for cryo-EM Our lab has developed microfluidics-based sample preparation for cryo-EM. The cytosol of a single, hand-picked neuronal cell or small nanoliter volumes of sample can be aspired with a capillary. Target proteins can optionally be purified via magnetic beads coupled to FAB antibody fragments from the sample. Finally, the miniature quantities of sample can be written in a loss-less manner onto a cryo-EM grid. The toolchain developed by Dr. Thomas Braun and student co-workers in the Stahlberg lab allowed to aspire < 1 microliter of HeLa cell cytosol, purify endogenous 20S proteasome sample out of that, and write the resulting 9 nanoliters of pure protein onto a cryo-EM grid, which allowed us to determine the atomic structure of the human 20S proteasome [1]. The patents from this work are now licensed to CryoWrite AG (Basel, Switzerland), who offers this technology as a commercial instrument: The CryoWriter. [1] Schmidli, C., Albiez, S., Rima, L., Righetto, R., Mohammed, I., Oliva, P., Kovacik, L., Stahlberg, H., & Braun, T. (2019). Microfluidic protein isolation and sample preparation for high-resolution cryo-EM. Proceedings of the National Academy of Sciences of the United States of America, 116(30), 15007&15012.Development of novel electron microscopy technolog We have studied the brain tissue obtained after autopsy of patients who died from Parkinson's disease or other synucleinopathies. We identified the large alpha-synuclein-rich aggregates in brain tissue (Lewy bodies), but surprisingly found by correlative light and electron microscopy (CLEM) that these in the majority of cases are primarily composed of densely packed membrane fragments, with aSyn fibrils contributing only in same cases a minor fraction [1]. In contrast, the brain of Multiple System Atrophy (MSA) patients contains aSyn-rich GCI aggregates that indeed are composed of fibrillar material. We also developed and implemented tools to study the structure of human neurodegenerative brain tissue and applied these to various neurodegenerative tissues [2-4]. [1] Lewy pathology in Parkinson's disease consists of a crowded organellar membranous medleyShahmoradian, S., Lewis, A., Genoud, C., Graff, A., Pérez Navarro, P., Goldie, K., Sütterlin, R., Castano-Diez, D., Ingrassia, A., Rozemuller, A.J.M., Paepe, A.D., Erny, J.Staempfli, A., Hoernschemeyer, J., Niedieker, D., El-Mashtoly, S.F., Gerwert, K., Bohrmann, B., Britschgi, M., Stahlberg, H., van de Berg, W.D.J., Lauer, M.E.*Nature Neuroscience 22, 1099-1109 (2019) =corresponding authors[2] Alterations in sub-axonal architecture between normal aging and Parkinson's diseased human brains using label-free cryogenic X-ray nanotomographyTran, H.T., Tsai, E.H.R., Lewis, A., Moors, T., Bol, J.G.J.M., Rostami, I., Diaz, A., Joker, A.J., Guizar-Sicairos, M., Raabe, J., Stahlberg, H., van de Berg, W.D.J., Holler, M., Shahmoradian, S.Frontiers in Neuroscience 14 (570019), (2020)[3] Imaging of post-mortem human brain tissue using electron and X-ray microscopyLewis, A., Genoud, C., Pont, M., van de Berg, W.D.J., Frank, S., Stahlberg, H., Shahmoradian, S., Al-Amoudi, A.Current Opinion Structural Biology 58, 138-148 (2019)[4] Cerebral Corpora amylacea are dense membranous labyrinths containing structurally preserved cell organellesPérez Navarro, P., Genoud, C., Castano-Diez, D., Graff-Meyer, A., Lewis, A., de Gier, Y., Lauer, M.E., Britschgi, M., Bohrmann, B., Frank, S., Hench, J., Schweighauser, G., Rozemuller, A.J.M., van de Berg, W.D.J., Stahlberg, H., Shahmoradian, S.*Scientific Reports 8(18046), (2018). *=corresponding authors Teaching & PhD PhD Students Vishal Kumar, Qishan Xie, Lukas van den Heuvel, Kazadi Ekundayo, Chinmaya Kavalakodu Venkatesh Past EPFL PhD Students Domenic Burger, Daniel Stähli, Marta Di Fabrizio, Berk Küçükoglu, Notash Shafiei Courses Physics of life PHYS-468 Life has emerged on our planet from physical principles such as molecular self-organization, thermodynamics, stochastics and iterative refinement. This course will introduce the physical methods to study life and will discuss the quantitative and physical concepts that make life possible. Practical - Stahlberg Lab BIO-603(SH) Cryo-electron microscopy structural analysis of proteins. The course aims at demonstrating the workflow from sample purification to determining the atomic structure of a soluble or membrane protein.