Biology subjects

Kirchweger, P.

Publications and source records attributed to Kirchweger, P..

8 recordsLinked to original sources

bioRxiv2026

3dcon: tomogram denoising by deconvolution

Cryo-electron tomography is an expanding technology for the study of macromolecules, viruses, and cells. It is often applied to specimens that are too large or heterogeneous for methods based on 2D image averaging such as single particle analysis, e.g., intracellular membranes or organelles. Current practice records a tilt series of projection images in rotation. Reconstruction is normally an ill-posed mathematical problem. Particularly for the under-determined case of sparse data, discrete tilt angles, and a limited tilt range, characteristic artifacts appear in the reconstructed slices. Much of what appears as noise is in fact structural: the projection of contrast from different planes. Various schemes are employed to regularize the reconstruction, including machine-learning frameworks built on neural networks. To the extent that the noise is structural, it might be suppressed by deconvolution with a suitable kernel. This was demonstrated and has been used regularly in cryo-STEM tomography of thick specimens where the under-sampling problem is particularly acute. Here we present 3dcon as an open-source extension of the entropy-regularized deconvolution algorithm that had been adopted from fluorescence microscopy. It takes advantage of modern computing hardware for convenient and fast processing. Deconvolution is entirely algorithmic, meaning that successful processing of the data does not depend on the data itself. As such it should be robust in a wide variety of applications.

biochemistry↗

bioRxiv2025

Azimuthal Segment Imaging in cryo-STEM Tomography

Cryo-electron microscopy is transitioning from investigation of isolated macromolecules to in situ studies bridging the realms of structural and cellular biology. Newly available detector technologies enable unconventional contrast modes with particular advantages. Here we demonstrate application of quadrant diode detectors to visualize a range of biological specimens by cryo-Scanning Transmission Electron Tomography (cryo-STET). Theoretically, we decompose coherent contrast by parallax analysis to isolate phase and amplitude contributions in specimens too thick for energy-filtered TEM. We thereby expand the cryo-STEM toolchest to parallax-filtered bright field (pBF) and parallax-filtered integrated differential phase contrast ({pi}DPC) and demonstrate their advantages in tomography using T4-bacteriophages, whole cells, and cryo-lift-out lamellae of cellular multilayers. The results show significant improvements over traditional STEM modalities in a realm where conventional wide-field transmission EM imaging methods are not applicable. The commercial availability of such detectors and the relative ease and speed of image reconstruction should make this realm accessible to the broader community in life science EM and beyond. TeaserParallax-corrected cryo-STET imaging provides coherent phase and amplitude contrast of thick biological specimens.

cell biology↗

bioRxiv2025

Refractive index as an indicator for dynamic protein condensation in cell nuclei

Protein condensation is the basis for formation of membrane-less organelles in the cell. Most famously, weak, polyvalent interactions, often including RNA, may lead to a liquid-liquid phase separation. This effect greatly enhances local concentrations and is thought to promote interactions that would remain rare in dilute solution. Synthetic systems provide a means to clarify the underlying biophysical mechanisms at play, both in vitro and in the cell via exogenous expression. In this regard, ferritin is a useful substrate, as its composition of 24 subunits with octahedral symmetry supports self-assembly by close packing in 3D. The conventional diagnostic tool for protein condensation is fluorescence imaging. In this work we explore the use of refractive index mapping to detect states of condensation and decondensation. Using two related ferritin-based self-assembly systems, we find that refractive index is a sensitive indicator for reversible condensation. Surprisingly, refractive index indicates a rapid decondensation even when molecular dispersal kinetics are slow according to fluorescence. Conversely, in a photo-activated condensation where long activation results in slow decondensation kinetics, the refractive index provides reliable evidence for the physical state independent of fluorescence. The observations suggest a distinction between condensation to a sparse biomolecular network, or to a material continuum that supports an optical polarizability distinct from that of the dilute phase in solution.

biophysics↗

bioRxiv2024

Snapshots of Mitochondrial Fission Imaged by Cryo-Scanning Transmission Electron Tomography

Mitochondria undergo constant remodeling via fission, fusion, extension, and degradation. Fission, in particular, depends on the accumulation of the mitochondrial fission factor (MFF) and subsequent recruitment of the dynamin-related protein Drp1. We used cryo-scanning transmission electron tomography (cryo-STET) to investigate mitochondrial morphologies in MFF mutant cells (MFF-/-) in ATP-depleting conditions that normally induce fission. The capability of cryo-STET to image through the cytoplasmic volume to a depth of 1 {micro}m provides visualization of mitochondria and their surroundings intact. We imaged changes in mitochondrial morphology and cristae structure and contacts with endoplasmic reticulum, degradative organelles, and cytoskeleton at stalled fission sites. We found disruption of the outer membrane at contact sites with endoplasmic reticulum and degradative organelles at sites of mitophagy. We identified fission sites where the inner mitochondrial membrane is already separated while the outer is still continuous. While MFF is a general fission factor, these observations demonstrate that mitochondrial fission can proceed to the final stage in its absence. The use of cryo-STET allays concerns about the loss of structures due to sample thinning required for cryo-TEM tomography. Summary StatementImaging the whole cytosol in three dimensions greatly aids in understanding cellular processes. Here, we applied cryo-scanning transmission electron tomography to study stages of mitochondrial fission in the absence of the mitochondrial fusion factor protein.

cell biology↗

bioRxiv2024

Optimizing contrast in automated 4D-STEM cryo-tomography

4D-STEM is an emerging approach to electron microscopy. While it has been developed principally for high resolution studies in materials science, the possibility to collect the entire transmitted flux makes it attractive for cryo-microscopy in application to life science and radiation-sensitive materials where dose efficiency is of utmost importance. We present a workflow to acquire tomographic tilt series of 4D-STEM datasets using a segmented diode and an ultra-fast pixelated detector, demonstrating the methods using a specimen of T4 bacteriophage. Full integration with the SerialEM platform conveniently provides all the tools for grid navigation and automation of the data collection. Scripts are provided to convert the raw data to mrc format files, and further to generate a variety of modes representing both scattering and phase contrast, including incoherent and annular bright field, integrated center of mass (iCOM), and parallax decomposition of a simulated integrated differential phase contrast (iDPC). Principal component analysis of virtual annular detectors proves particularly useful, and axial contrast is improved by 3D deconvolution with an optimized point spread function. Contrast optimization enables visualization of irregular features such as DNA strands and thin filaments of the phage tails, which would be lost upon averaging or imposition of an inappropriate symmetry.

biophysics↗

bioRxiv2022

Bridging the light-electron resolution gap with correlative cryo-SRRF and dual-axis cryo-STEM tomography

Cryo-electron tomography (cryo-ET) is the prime method for cell biological studies in three dimensions (3D) at high resolution. We have introduced cryo-scanning transmission electron tomography (CSTET), which can access larger 3D volumes, on the scale of 1 micron, making it ideal to study organelles and their interactions in situ. Here we introduce two relevant advances: a) we demonstrate the utility of multi-color super-resolution radial fluctuation light microscopy under cryogenic conditions (cryo-SRRF), and b) we extend the use of deconvolution processing for dual-axis CSTET data. We show that cryo-SRRF nanoscopy is able to reach resolutions in the range of 100 nm, using commonly available fluorophores and a conventional widefield microscope for cryo-correlative light-electron microscopy (cryo-CLEM). Such resolution aids in precisely identifying regions of interest before tomographic acquisition and enhances precision in localizing features of interest within the 3D reconstruction. Dual-axis CSTET tilt series data and application of entropy regularized deconvolution during post-processing results in close-to isotropic resolution in the reconstruction without averaging. We show individual protein densities in a mitochondrion-ER contact in a cell region 850 nm thick. The integration of cryo-SRRF with deconvolved dual-axis CSTET provides a versatile workflow for studying unique objects in a cell.

cell biology↗

bioRxiv2021

A chemotactic sensor controls Salmonella-host cell interaction

Intimate cell contact and subsequent type three secretion system-dependent cell invasion are key steps in host colonization of Salmonella. Adhesion to complex glycostructures at the apical membrane of polarized cells is mediated by the giant adhesin SiiE. This protein is secreted by a type 1 secretion system (T1SS) and needs to be retained at the bacterial surface to exert its adhesive function. Here, we show that SiiE surface expression was linked to the presence of L-aspartate sensed by the Salmonella-specific methyl-accepting chemotaxis protein CheM. Bacteria lacking CheM were attenuated for invasion of polarized cells, whereas increased invasion was seen with Salmonella exposed to the non-metabolizable aspartate analog -methyl-D, L-aspartate (MeAsp). While components of the chemotaxis phosphorelay or functional flagella were dispensable for the increased invasion, CheM directly interacted with proteins associated with the SiiE T1SS arguing for a novel non-canonical signaling mechanism. As a result, CheM attractant signaling caused a shift from secreted to surface-retained and adhesion-competent SiiE. Thus, CheM controls the virulence function of SiiE in a precise spatio-temporal fashion depending on the host micro-milieu.

microbiology↗

bioRxiv2019

Structural and functional characterisation of SiiA, an auxiliary protein from the SPI4-encoded type 1 secretion system from Salmonella enterica

Salmonella invasion is mediated by a concerted action of the Salmonella pathogenicity island 4 (SPI4)-encoded type one secretion system (T1SS) and the SPIl-encoded type three secretion system (T3SS-1). The SPI4-encoded T1SS establishes the first contact to the host membrane. It consists of five proteins (SiiABCDF) that secrete the giant adhesin SiiE. The exact mechanism by which the T1SS enables host cell recognition remains unclear. Here, we investigated structure-function relationships in SiiA, a non-canonical T1SS subunit located at the inner membrane (IM). We observe that SiiA consists of a membrane domain, an intrinsically disordered periplasmic linker region and a folded globular periplasmic domain (SiiA-PD). The crystal structure of SiiA-PD shows homology to that of MotB-PD and other peptidoglycan (PG)-binding domains. Indeed, SiiA-PD binds PG in vitro albeit at an acidic pH, only, whereas MotB-PD binds PG from pH 5.8 to 8. Mutation of Arg162 in SiiA impedes PG binding and reduces Salmonella invasion efficacy of polarized epithelial cells. SiiA forms a complex with SiiB at the IM, and the SiiA-MotB homology is likely paralleled by a SiiB-MotA homology. We show that, in addition to PG binding, the SiiAB complex translocates protons across the IM. Substituting Asp13 in SiiA impairs proton translocation. Overall, SiiA displays many properties previously observed in MotB. However, whereas the MotAB complex uses the proton motif force (PMF) to energize the bacterial flagellum, it remains to be shown how the use of the PMF by SiiAB assists T1SS function and ultimately Salmonella invasion.

microbiology↗