How we approach science
We believe that interdisciplinary approaches hold the largest promise for groundbreaking discoveries in biology. Our team hence brings together scientists with diverse backgrounds in cell biology, biochemistry, physics, and computer science.
We like to ask unconventional questions and therefore often first establish new assays to visualize the respective cell biological processes. We exploit a broad panel of advanced microscopy techniques and combine them into correlative workflows to bridge resolution gaps between molecular and cell biological scales. This has lead us to discover new biological phenomena for which molecular regulators have not yet been described.
To elucidate the molecular foundation of previously undescribed cell biological phenomena, we perform image-based loss-of-function screening. We have implemented a fully automated live-cell microscopy platform and cell phenotype analysis by machine learning. New molecular regulators identified by screening are then systematically characterized in cells using state-of-the-are techniques, as for example CRISPR/Cas9-based genome engineering, functional readouts using biosensors, chemically-induced protein dimerization, and micro-manipulation using intracellular laser surgery.
Once we have gained insights into the cellular functions of novel regulators, we aim to dissect the underlying molecular mechanisms. We characterize molecular properties using a variety of biochemical technologies, including systematic analysis of molecular interactions and posttranslational modifications by mass spectrometry.
We then test lead hypotheses about molecular mechanisms by in vitro reconstitution using purified components. For example, we have established a variety of assays using purified chromatin, DNA-coated beads, and recombinant proteins to study the mechanical properties of mitotic chromosomes. We manipulate the components in this system using microfluidic chambers and magnetic force control, and analyze biophysical properties using light- and atomic-force microscopy. Ultimately, we aim to reconstitute the respective molecular functions by synthetic components that mimic the molecular function of the native cellular proteins.
Pursuing our ideas from a general description of cell biological processes up to the mechanistic details about the molecular components requires a broad range of technologies. This is made possible by the outstanding research infrastructure provided at campus facilities and our strong network of international collaboration partners. Researchers in our laboratory take the lead in developing hypotheses and establish the principal experimental assays and approaches, but they are supported in many experiments by outstanding staff in our facilities.
Technologies and model systems
The cutting-edge technologies provided by 18 scientific facilities at our campus offer unmatched opportunities to focus entirely on the biological questions rather than troubleshooting technical details.
At IMBA, we have free access to a variety of cutting-edge microscopes through the BioOptics, VBCF Advanced Microscopy, and Electron Microscopy facilities. Their large collection of scanning confocal and spinning disc confocal microscopes, automated screening microscopes, laser microsurgery, super-resolution fluorescence, and electron microscopes enable us to approach scientific questions from multiple angles. We are particularly excited about newly emerging imaging techniques such as lattice light-sheet microscopy, which we have implemented at our campus together with the VBCF Advanced Microscopy facility.
Our biochemical experiments are supported by the Protein Chemistry, Protein Technology, and Metabolomics facilities, and chromosome conformation capture approaches are carried out in collaboration with the Next Generation Sequencing facility. Genome engineering and molecular biology services are further supported by Protein Technology and Molecular Biology facilities.
We use human tissue culture cells as a main model system and have developed a large library of cell lines stably expressing various combinations of fluorescent marker proteins for systematic phenotype profiling. Our experiments are typically automated to a very high degree, involving high-throughput transfection and automated microscopy for high-content screening. To extract quantitative phenotype traits from large-scale microscopy experiments, we have developed computer vision and machine learning methods that are disseminated as the open-source software software CellCognition.
We have developed CellCognition as an open source software that combines object detection, single-cell tracking, feature extraction, and classification of morphologies (Figure 1). This enables automated annotation of different cell morphology states, or kinetic readouts of various cell features. CellCognition runs on Windows, Mac OS X, and Linux desktop computers and provides an interface to computing clusters for ultra-high-throughput data analysis. Please reference the CellCognition software by the original publication Held et al., Nature Methods, 2010.
References for computer vision and machine learning methodology
Held M, Schmitz MH, Fischer B, Walter T, Neumann B, Olma MH, Peter M, Ellenberg J, Gerlich DW. (2010). CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. Nat Methods. 7(9):747-54
Zhong Q, Busetto AG, Fededa JP, Buhmann JM, Gerlich DW. (2012). Unsupervised modeling of cell morphology dynamics for time-lapse microscopy. Nat Methods. 9(7):711-3
Sommer C, Held M, Fischer B, Huber W, Gerlich DW. (2013). CellH5: a format for data exchange in high-content screening. Bioinformatics. 29(12):1580-2
Conrad C, Gerlich DW. (2010). Automated microscopy for high-content RNAi screening. J Cell Biol. 188(4):453-61.
Sommer C, Gerlich DW. (2013). Machine learning in cell biology - teaching computers to recognize phenotypes. J Cell Sci. 126(Pt 24):5529-39
References for screening applications
Cuylen, S., Blaukopf, C., Politi, AZ., Müller-Reichert, T., Neumann, B., Poser, I., Ellenberg, J., Hyman, AA., Gerlich, DW. (2016). Ki-67 acts as a biological surfactant to disperse mitotic chromosomes. Nature. 535(7611):308-12
Wurzenberger C, Held M, Lampson MA, Poser I, Hyman AA, Gerlich DW. (2012). Sds22 and Repo-Man stabilize chromosome segregation by counteracting Aurora B on anaphase kinetochores. J Cell Biol. 198(2):173-83
Piwko W, Olma MH, Held M, Bianco JN, Pedrioli PG, Hofmann K, Pasero P, Gerlich DW, Peter M. (2010). RNAi-based screening identifies the Mms22L-Nfkbil2 complex as a novel regulator of DNA replication in human cells. EMBO J. 29(24):4210-22.
Schmitz MH, Held M, Janssens V, Hutchins JR, Hudecz O, Ivanova E, Goris J, Trinkle-Mulcahy L, Lamond AI, Poser I, Hyman AA, Mechtler K, Peters JM, Gerlich DW. (2010). Live-cell imaging RNAi screen identifies PP2A-B55alpha and importin-beta1 as key mitotic exit regulators in human cells. Nat Cell Biol. 12(9):886-93.