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Life is based on the action and interaction of biomolecules, and measuring their structure and dynamics during their function in the living cell can provide invaluable insights into their mechanism. A prime example for a complex and dynamic protein machinery is clathrin-mediated endocytosis, an essential cellular process for the uptake of molecules from the environment. During endocytosis, more than 50 different proteins in many copies self-assemble into a complex machinery that invaginates the membrane and forms a vesicle. But what are the precise locations of the proteins throughout the process of endocytosis? How can we measure the structural organization and dynamic functional changes of cellular protein assemblies? Current technologies are very limited in answering this question.
Our research vision is to develop optical super-resolution microscopy technologies that will allow us to visualize the structure and the dynamics of molecular machines in living cells on the nanoscale. Our interdisciplinary team of physicists, biologists, computer scientists and engineers are developing new approaches for single-molecule localization microscopy (SMLM) to measure the precise 3D locations of proteins at high throughput and the new MINFLUX technology to probe conformational changes of protein machines in the living cell with nanometer spatial and millisecond temporal resolution. We use these methods to gain mechanistic insights into endocytosis and other cellular protein machines.
Jonas Ries studied physics in Bremen and Konstanz with a specialization in quantum optics. After completing a PhD in biophysics at the TU Dresden in 2008 and a postdoctoral fellowship at the ETH in Zurich in 2012, he joined the EMBL in Heidelberg as a group leader. Since 2023 he is a full professor for Advanced Microscopy and Cellular Dynamics at the Max Perutz labs at the University of Vienna and will start his group in fall 2023.
Contact: Jonas.ries@maxperutzlabs.ac.at
We developed MINFLUX tracking in 2D and 3D to study the 16 nm steps of the motor protein kinesin while it walks on microtubules in living cells. This is a first step towards monitoring functional conformational changes of protein machines at high spatiotemporal resolution in living systems (Deguchi et al., Science, 2023 - free full PDF version).
We developed high-throughput super-resolution microscopy and measured the nanoscale distribution of 23 endocytic proteins from >100 000 snapshots of endocytic structures in budding yeast, providing new insights into structure, assembly process, and force generation of the endocytic machinery (Mund et al., Cell, 2018).
How can we analyze huge super-resolution data sets in a meaningful way? We developed LocMoFit, a tool that enables fitting of super-resolution microscopy data to an arbitrary geometric model. The fit extracts quantitative parameters of individual cellular structures, which can be used to investigate dynamic and heterogenous protein assemblies and to create average protein distribution maps (Wu et al., Nature Methods, 2023).
We used 3D single-molecule localization microscopy to measure the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determined the average trajectory of clathrin remodeling during endocytosis. We developed a new physical model that describes the measured shapes and dynamics and could represent a general mechanism for clathrin coat remodeling (Mund, Tschanz et al., Journal of Cell Biology, 2023).
We developed a software that uses simulator-based inference to localize fluorophores in 3D at high densities, increasing the speed of single-molecule localization microscopy by one order of magnitude. This software outperformed all other software in a public software benchmark on all modalities (Speiser, Müller et al., Nature Methods, 2021).
Direct observation of motor protein stepping in living cells using MINFLUX.
Deguchi, Takahiro; Iwanski, Malina K; Schentarra, Eva-Maria; Heidebrecht, Christopher; Schmidt, Lisa; Heck, Jennifer; Weihs, Tobias; Schnorrenberg, Sebastian; Hoess, Philipp; Liu, Sheng; Chevyreva, Veronika; Noh, Kyung-Min; Kapitein, Lukas C; Ries, Jonas
Field-dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging.
Fu, Shuang; Shi, Wei; Luo, Tingdan; He, Yingchuan; Zhou, Lulu; Yang, Jie; Yang, Zhichao; Liu, Jiadong; Liu, Xiaotian; Guo, Zhiyong; Yang, Chengyu; Liu, Chao; Huang, Zhen-Li; Ries, Jonas; Zhang, Mingjie; Xi, Peng; Jin, Dayong; Li, Yiming
Nanoscale structural organization and stoichiometry of the budding yeast kinetochore.
Cieslinski, Konstanty; Wu, Yu-Le; Nechyporenko, Lisa; Hörner, Sarah Janice; Conti, Duccio; Skruzny, Michal; Ries, Jonas
Systematic identification and functional characterization of transcriptional regulators
The mineralosphere as microhabitat for microbe, mineral and organic matter interaction in soils
Activation and regulation of plant immunity by secreted signaling peptides
Transcription start site selection is environmentally controlled to diversify the proteome in eukaryotes
How evolutionary interplay between sexes can help us define phenotypes and develop drugs
Mining for protein-protein interactions with AlphaFold: Lessons from Genome Maintenance
Title to be announced
The magical Martian Methane mystery and other stories about life on Mars
Probing life at the nanoscale - one molecule at a time
The Underworld of Deep-Sea Hydrothermal Vents
Epigenetic regulation of germline development
Sister chromatid cohesion is mediated by individual cohesin complexes
Origin and evolution of a defensive symbiosis in tortoise leaf beetles
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18th Microsymposium on RNA Biology
The „Microsymposium on RNA Biology“ is an international conference that brings together young scientists, junior and senior group leaders, and company representatives from all over the world to present and discuss their latest findings in the exciting field of small RNAs and beyond. The Microsymposium was founded in 2005 and has established itself as the major small RNA meeting in Europe. It is organized by the four research institutions IMBA, IMP, GMI and the Max Perutz Labs as well as by the RNA community of the Vienna BioCenter.
Transformation Reactions of Organic Contaminants and Oxygen: From Field Sites to Reaction Mechanisms
Title to be announced
Multiscale plant bioimaging using advanced microscopy
Evading ageing: Mitochondrial and proteostatic adaptations in oocytes
Parthenogenesis, cryptobiosis, and the survival in extreme environmental conditions
Ubiquitin & Friends Symposium 2024
The Ubiquitin & Friends Symposium is an annual international meeting taking place in the beautiful capital of Austria, aiming to bring together scholars from various fields studying ubiquitin/Ubl biology and protein degradation in a personal, family-like atmosphere, as suggested by the name.
Genomes in Rhodnius prolixus symbiotic system
Stem cells, immune evasion and metastasis in colorectal cancer
The evolution and development of mollusc shells
Unraveling the Complexity of Crossover Regulation in C. elegans
Dynamics of 3D Genome Structure and Function
How superworms can help to solve our plastic waste crisis
New players in an old pathway: biology of methanogens of the TACK superphylum
Shaping morphogen gradients: from molecules to tissues and back
Studying stressed cells by in situ structural biology
Exploring Microbial Resilience: Unravelling Escherichia coliand#x27;s Stress Response at the Level of Protein Synthesis
Deep homology and deep diversity: Evolving genetic toolkits for making and sensing light
The evolution of cell type identity and tissue microecology at the fetal-maternal interface
The unanticipated roles of PICIs and phages in bacterial evolution
Origin and diversification of gut-derived organs in chordates
Job's Dilemma for the Genome: Why Bad Things Happen to Good Chromosomes
Connections between carbon and nitrogen cycling in the ocean
Understanding how the DNA-loop-extruding protein complex Condensin folds a chromatinized genome into mitotic chromosomes
From Roads to Rivers? Occurrence and environmental fate of tire and road wear particles and of tire-related chemicals
Striking physiology and cell biology of (marine) environmental microorganisms
Mechanisms controlling maintenance of cohesin dependent loops
Title to be announced