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Biology subjects

Ries, J.

Publications and source records attributed to Ries, J..

At least 19 recordsLinked to original sources

Super-resolution mapping of platelet α-granules uncovers non-polarized secretion and differential retention of von Willebrand Factor and thrombospondin-1

Platelet -granules contain hundreds of bioactive proteins that regulate thrombosis, inflammation and tissue repair. The interplay between -granule secretion and platelet biomechanics is central to platelet function but remains incompletely understood. Here we combined complementary super-resolution microscopy methods, computational image simulations and quantitative single-cell analysis to investigate -granule nanoscale organization and secretion in tandem with cytoskeletal remodeling in spreading human platelets. We show that P-selectin, thrombospondin-1 (TSP1) and von Willebrand factor (VWF) occupy distinct subgranular domains and that apparent co-localization strongly depends on imaging resolution. We identify ring-like P-selectin staining as a robust signature of intact -granules and demonstrate that -granule secretion in spreading platelets was confined to the platelet cell body rather than the actively remodeling periphery. Quantitative assessment at the single-cell level showed that degranulation coincided with transitions from filopodia-rich to lamellipodial morphologies. Comparisons across adhesive substrates and perturbations by soluble agonists indicated that these processes are coordinated through overlapping signaling networks rather than direct local coupling. Analysis of secreted cargo revealed distinct extracellular fates despite no evidence for polarized secretion. TSP1 accumulated beneath platelets within diffusion barrier-restricted membrane pockets and around platelets following matrix binding, whereas VWF remained predominantly tethered to platelet membranes and formed short VWF strings. Together, our findings redefine the organization and release of platelet -granules, demonstrate an absence of secretion polarity, and establish cargo-specific retention mechanisms that may influence platelet signaling and thrombus architecture.

cell biology↗

Microscope control with a natural language agent

Microscopy underpins modern biology, but acquiring high-quality data from complex experiments at scale remains challenging. Smart microscopy can standardize and automate data collection, but each experiment-specific solution requires coding expertise and development time. To address this, we present MicroClaw, an AI agent that advises on experiment- and system-specific parameters and approaches and collaboratively plans and executes diverse, complex, and reusable imaging workflows across microscope platforms, without requiring expert knowledge.

biophysics↗

Multi-channel high-density single-molecule localization

Deep learning has enabled single-molecule localization microscopy (SMLM) at high emitter densities, but only for single channel systems. Here we present DECODE-Plex, a deep-learning-based framework to localize dense single molecules with overlapping point spread functions simultaneously in multiple channels. We showcase DECODE-Plex on experimental ultra-high density dual-color and 3D live-cell data. Packaged for ease of use, it will enable many groups to improve imaging speed and quality of multi-channel SMLM.

biophysics↗

Cryo-FIB lamellae enable ultra-high excitation laser intensities for cryogenic super-resolution fluorescence imaging

Super-resolution cryogenic correlative light and electron microscopy (SR-cryo-CLEM) integrates molecular specificity and structure on the single-molecule level, but contemporary approaches require low laser powers to preserve specimen vitrification. Here, we perform SR-cryo-CLEM via single molecule localization microscopy (SMLM) on thin biological lamellae and demonstrate that their geometry and minimally-absorbent composition permit excitation laser powers three orders of magnitude higher than standard cryo-EM grids, allowing improved localization precision and imaging speeds.

molecular biology↗

A stable cryogenic fluorescence microscope for correlative super-resolution light and electron microscopy

Cryogenic correlative light and electron microscopy (cryo-CLEM) enables visualization of biological specimens with molecular specificity while preserving near-native macromolecular structure. However, the severely limited resolution of conventional cryo-fluorescence microscopes restricts the accuracy of correlation with cryo-electron microscopy. Super-resolution cryogenic CLEM (SR-cryo-CLEM) offers a potential solution, but presents substantial technical challenges, including mechanical instability and ice contamination. Here, we introduce a modular cryogenic light microscope optimized for single-molecule localization microscopy (cryo-SMLM) that mitigates such limitations. The system is constructed primarily from off-the-shelf components, enabling straightforward and cost-effective assembly, and is operated using fully open-source Python software for flexible and customizable control. The mechanically and thermally stabilized architecture, combined with an axial focus-lock system, maintains sample positioning within a standard deviation of 40 nm. Ice contamination is minimized by imaging inside a purged enclosure, enabling prolonged acquisitions. Together, the platform provides robust localization precision, reproducible imaging performance, and an accessible solution for SR-cryo-CLEM.

molecular biology↗

Multi-step implementation of meiotic crossover patterning

Crossover formation during meiosis is a tightly controlled process in which genetic information is exchanged between homologous chromosomes to increase the diversity of the progeny. In this process, an excess of double-strand breaks is introduced, but only a limited subset is ultimately processed into crossovers. Imbalances in the distribution of crossovers can lead to errors in chromosome segregation, with devastating consequences on the health of the progeny. However, the selection of which breaks are designated to become crossovers is still poorly understood, as both its timing and the ultimate molecular mechanisms are under debate. Here, we used 3D dual-color single-molecule localization microscopy and real-time confocal imaging, combined with advanced image analysis, to investigate the timing and mechanism of crossover designation in C. elegans. We show that meiotic crossover patterning is not established by a single decision point but depends on a dynamic, multi-layered regulation process. An initial, early selection process restricts potential crossovers to a small subset of double-strand break sites that already exhibit basic patterning features, including assurance and interference. A second, later step fine-tunes this pattern to ultimately ensure genome integrity and promote accurate chromosome segregation. Real-time imaging reveals that although the full process takes more than seven hours, key molecular events occur within minutes, high-lighting how rapid local dynamic changes can give rise to an overall slow but extremely robust crossover regulation program.

cell biology↗

Multiscale imaging of cytokinesis

After separation of duplicated genetic material, animal cells divide by cytokinesis. This process involves several simultaneous and successive steps of molecular reorganization at cell membrane, cortex and the spindle apparatus as the cleavage furrow ingresses and the spindle is transformed into the intercellular bridge. Dozens of proteins play a role in cytokinesis. However, a comprehensive view of their successive nanoscale reorganizations over cytokinesis remains untractable with current microscopy methods. Here, we developed a multimodal imaging and analysis framework to investigate the relative organization of key cytokinetic molecules over time. We extract cytokinetic hallmarks from live-cell lattice light-sheet and expansion microscopy (ExM) to computationally define pseudotime and align nanoscale ExM images of cytokinesis. We discover a cytokinetic substep and create nanoscale maps of the intercellular bridge and the midbody in 6 stages for 20 involved molecules. We thus provide a framework for nanoscale analysis of cytokinesis, a process fundamental to life.

cell biology↗

Chlamydial membrane vesicles deliver the chlamydial porin OmpA to mitochondria to inhibit apoptosis

Chlamydiae are obligate intracellular bacteria that inhibit mitochondrial apoptosis to maintain integrity of the host cell. We have previously reported that a chlamydial outer membrane {beta}-barrel protein, the porin OmpA, can during ectopic expression inhibit mitochondrial apoptosis through direct interaction with the BCL-2-family effectors BAX and BAK. We here show that OmpA from Chlamydia trachomatis (Ctr) uses membrane vesicles for its delivery to the outer mitochondrial membrane during Ctr infection. Using a number of imaging and fractionation techniques, we show that OmpA during infection reaches mitochondria and is inserted into mitochondrial membranes. Purified membrane vesicles (MV) from Ctr-infected cells contained OmpA. When added to uninfected cells, MV fused with mitochondrial membranes, causing the interaction of OmpA with BAK and the cytosolic retro-translocation of BAX. MV addition to uninfected cells protected the cells against apoptosis. We propose a structural model of this BAK inhibition by OmpA that reenacts the inhibition of BAK by the mitochondrial porin VDAC2. The results provide evidence that the porin from Chlamydia, as well as the structurally similar porin from the related Simkania, specifically exploits its relationship to mitochondrial porins to protect the infected cell against apoptosis and to enable intracellular growth of the bacteria in human cells.

cell biology↗

Evaluating MINFLUX experimental performance in silico

MINFLUX is a super-resolution microscopy technique with remarkable resolution for imaging and tracking. Its optical resolution is well understood under idealized conditions, but because of system complexity and experimental imperfections, actual performance can be much worse. Here we present SimuFLUX, a comprehensive and realistic simulator for MINFLUX. We use it to investigate performance limits caused by fluorophore dynamics, background, estimators, and misalignment, and to simulate experiments to optimize parameters and assess feasibility.

biophysics↗

Effects of base temperature, immersion medium, and EM grid material on devitrification thresholds in cryogenic optical super-resolution microscopy

Cryogenic correlative light and electron microscopy (cryo-CLEM) is an imaging strategy that integrates specific molecular labeling and molecular resolution structural information. However, there is a resolution gap of more than two orders of magnitude between diffraction-limited fluorescence microscopy and electron microscopy (EM). Single-molecule localization microscopy (SMLM) performed at cryogenic temperatures promises to bridge this resolution gap. Nevertheless, the high excitation laser powers required for SMLM risk the devitrification of frozen biological samples, leading to perturbation of their native-like state. Here, we investigate how base cooling temperature, immersion medium, and EM grid support materials influence sample devitrification. Using finite element simulations and experimental validation, we show that a cryo-immersion medium enhances heat dissipation for carbon supports, while metallic supports in a cold nitrogen gas medium tolerate higher laser intensities due to lower base temperatures. Gold supports illuminated at 640 nm exhibit markedly high laser thresholds, similar to silver-coated grids. Additionally, metallic supports maintain efficient heat dissipation in vacuum-based cryostats. Our findings provide quantitative insights that aid in optimization of cryo-SMLM setups for improved cryo-CLEM imaging.

molecular biology↗

Continuum architecture dynamics of vesicle tethering in exocytosis

Essential for eukaryotic organisms, multiple copies of the exocyst complex tether each secretory vesicle to the plasma membrane (PM) in constitutive exocytosis. The exocyst higher-order structure (ExHOS) that coordinates the action of these multiple exocysts remains unexplored. We integrated particle-tracking, super-resolution microscopy and cryo-electron tomography in a model that time-resolves the continuum conformational landscape of the ExHOS and functionally annotates its different conformations. We found that 7 exocysts form flexible ring-shaped ExHOS that tether vesicles at <45 nm from the PM. The ExHOS, initially 19 nm in radius, rapidly expands while it pulls the vesicle towards the PM. Subsequently, the ExHOS stabilizes, securing the vesicle at [~]4 nm from the PM. After fusion, Sec18 mediates the ExHOS disassembly when its radius is 38 nm. By resolving the fundamental biophysical principles of tethering we bridged the gap between static isolated structures and the dynamic and multimeric nature of exocytosis.

cell biology↗

Fast and robust 3D MINFLUX excitation with a variable phase plate

MINFLUX has achieved record resolution in superresolution imaging and single fluorophore tracking. It is based on localizing single fluorophores by rapid probing with a patterned beam that features a local intensity minimum. Current implementations, however, are complex and expensive and are limited in speed and robustness. Here, we show that a combination of an electro-optical modulator with a segmented birefringent element such as a spatial light modulator produces a variable phase plate for which the phase can be scanned on the MHz timescale. Bisected or top-hat phase patterns generate high-contrast compact excitation point-spread functions for MINFLUX localization in the x,y, and z-direction, respectively, which can be scanned around a fluorophore within a microsecond and alternated among different excitation wavelengths. We discuss how to compensate for non-optimal performance of the components and present a robust 3D and multi-color MINFLUX excitation module with record speed, which we envision as an integral component of a high-performance and cost-effective open-source MINFLUX.

biophysics↗

Universal inverse modelling of point spread functions for SMLM localization and microscope characterization

The point spread function (PSF) of a microscope describes the image of a point emitter. Knowing the accurate PSF model is essential for various imaging tasks, including single molecule localization, aberration correction and deconvolution. Here we present uiPSF (universal inverse modelling of Point Spread Functions), a toolbox to infer accurate PSF models from microscopy data, using either image stacks of fluorescent beads or directly images of blinking fluorophores, the raw data in single molecule localization microscopy (SMLM). The resulting PSF model enables accurate 3D super-resolution imaging using SMLM. Additionally, uiPSF can be used to characterize and optimize a microscope system by quantifying the aberrations, including field-dependent aberrations, and resolutions. Our modular framework is applicable to a variety of microscope modalities and the PSF model incorporates system or sample specific characteristics, e.g., the bead size, depth dependent aberrations and transformations among channels. We demonstrate its application in single or multiple channels or large field-of-view SMLM systems, 4Pi-SMLM, and lattice light-sheet microscopes using either bead data or single molecule blinking data.

biophysics↗

Automated 3D multi-color single-molecule localization microscopy

Since its inception, single molecule localization microscopy (SMLM) has enabled imaging scientists to visualize biological structures with unprecedented resolution. Particularly powerful implementations capable of 3D, multi-color and high-throughput imaging have yielded key biological insights although widespread access to such technologies has been limited. The purpose of this protocol is to provide a guide for interested researchers to establish high-end SMLM in their laboratories. We detail the initial configuration and subsequent assembly of the SMLM, including instructions for alignment of all optical pathways, software/hardware integration and operation of the instrument. We describe validation steps including the preparation and imaging of test- and biological samples with structures of well-defined geometry and assist the user in troubleshooting and benchmarking performance. Additionally, we provide a walkthrough of the reconstruction of a super-resolved dataset from acquired raw images using the Super-resolution Microscopy Analysis Platform (SMAP). Depending on the instrument configuration, the cost of components is in the range $80,000 - 160,000, a fraction of the cost of a commercial instrument. A builder with some experience of optical systems is expected to require 3 - 6 months from the start of system construction to attain high-quality 3D and multi-color biological images.

biophysics↗

Skp1 proteins are structural components of the synaptonemal complex in C. elegans

The synaptonemal complex (SC) is a hallmark of meiotic prophase that plays a crucial role in regulating crossovers between homologous chromosomes. Here, we demonstrate that two Skp1-related proteins in C. elegans, SKR-1 and SKR-2, serve as structural components of the SC, independent of their canonical functions within the Skp1-Cul1-F-box (SCF) ubiquitin ligase complex. SKR-1 and SKR-2 localize to the central region of the SC, and synapsis requires their dimerization through a hydrophobic interface that overlaps with the binding sites for CUL-1 and F-box proteins. Using in vitro reconstitution and in vivo analysis of mutant proteins, we show that SKR proteins interact with the other SC proteins using their C-terminal helices to form a soluble complex, which likely represents a basic building block for SC assembly. Our findings demonstrate how conserved Skp1 proteins are repurposed as part of the SC and may provide insight into how synapsis is coupled to cell cycle progression.

cell biology↗

Field dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging

Single-molecule localization microscopy (SMLM) in a typical wide-field setup has been widely used for investigating sub-cellular structures with super resolution. However, field-dependent aberrations restrict the field of view (FOV) to only few tens of micrometers. Here, we present a deep learning method for precise localization of spatially variant point emitters (FD-DeepLoc) over a large FOV covering the full chip of a modern sCMOS camera. Using a graphic processing unit (GPU) based vectorial PSF fitter, we can fast and accurately model the spatially variant point spread function (PSF) of a high numerical aperture (NA) objective in the entire FOV. Combined with deformable mirror based optimal PSF engineering, we demonstrate high-accuracy 3D SMLM over a volume of ~180 x 180 x 5 m3, allowing us to image mitochondria and nuclear pore complex in the entire cells in a single imaging cycle without hardware scanning - a 100-fold increase in throughput compared to the state-of-the-art.

biophysics↗

Direct observation of motor protein stepping in living cells using MINFLUX

Dynamic measurements of molecular machines can provide invaluable insights into their mechanism, but have been challenging in living cells. Here, we developed live-cell tracking of single fluorophores with nanometer spatial and millisecond temporal resolution in 2D and 3D using the recently introduced super-resolution technique MINFLUX. This allowed us to resolve the precise stepping motion of the motor protein kinesin-1 as it walks on microtubules in living cells. In addition, nanoscopic tracking of motors on microtubule of fixed cells enabled us to resolve their spatial organization with protofilament resolution. Our approach will enable future in vivo studies of motor protein kinetics in complex environments and super-resolution mapping of dense microtubule arrays, and pave the way towards monitoring functional conformational changes of protein machines at high spatiotemporal resolution in living systems.

biophysics↗

MicroFPGA: an affordable FPGA platform for microscope control

Modern microscopy relies increasingly on microscope automation to improve throughput, ensure reproducibility or observe rare events. Automation requires in particular computer control of the important elements of the microscope. Furthermore, optical elements that are usually fixed or manually movable can be placed on electronically-controllable elements. In most cases, a central electronics board is necessary to generate the control signals they require and to communicate with the computer. Fur such tasks, Arduino microcontrollers are widely used due to their low cost and programming entry barrier. However, they are limiting in their performance for applications that require high-speed or multiple parallel processes. Field programmable gate arrays (FPGA) are the perfect technology for high-speed microscope control, as they are capable of processing signals in parallel and with high temporal precision. While plummeting price made the technology available to consumers, a major hurdle remains the complex languages used to configure them. In this work, we used an affordable FPGA, delivered with an open-source and friendly-to-use programming language, to create a versatile microscope control platform called MicroFPGA. It is capable of synchronously triggering cameras and multiple lasers following complex patterns, as well as generating various signals used to control microscope elements such as filter wheels, servomotor stages, flip-mirrors, laser power or acoustooptic modulators. MicroFPGA is open-source and we provide online Micro-Manager, Java, Python and LabVIEW libraries, together with blueprints and tutorials.

biophysics↗