Biology subjects

Zimmermann, T.

Publications and source records attributed to Zimmermann, T..

6 recordsLinked to original sources

bioRxiv2026

PinCorr: A high-pressure freezing carrier with intrinsic landmarks for cryo-correlative light and electron microscopy

Cryo-correlative light and electron microscopy methods enable targeted structural analysis of fluorescently labelled features in vitrified specimens. However, correlative workflows on high-pressure frozen samples often remain challenging due to the lack of persistent landmarks for reliable sample tracking and image registration between different microscopes. Standard high-pressure freezing carriers provide little intrinsic reference information, as the exposed sample surface is often smooth and rotationally ambiguous, complicating localisation of regions of interest across imaging platforms. Here, we introduce PinCorr, a 3-mm high-pressure freezing carrier with an integrated coordinate system formed by four asymmetrically arranged pillars with distinct geometries. These built-in landmarks remain visible after freezing and provide a stable, sample-independent reference frame for orientation and correlation between cryo-fluorescence microscopy and electron microscopy. We show that PinCorr supports fluorescence-guided cryo-volume imaging, serial lift-out for cryo-electron tomography and freeze-substitution workflows followed by room-temperature on-section correlation. PinCorr thus provides a hardware-based approach to establishing a persistent spatial reference frame in HPF-based correlative imaging workflows for thick and multicellular specimens.

Molecular Biology↗

bioRxiv2025

Human Lung Alveolar Model with an Autologous Innate and Adaptive Immune Compartment

Lung-resident immune cells, spanning both innate and adaptive compartments, preserve the integrity of the respiratory barrier, but become pathogenic if dysregulated1. Current in vitro organoid models aim to replicate interactions between the alveolar epithelium and immune cells but have not yet incorporated lung-specific immune cells critical for tissue residency2. Here we address this shortcoming by describing human lung alveolar immuno-organoids (LIO) that contain an autologous tissue-resident lymphoid compartment, primarily composed of tissue-resident memory T cells (TRMs). Additionally, we introduce lung alveolar immuno-organoids with myeloid cells (LIOM), which include both TRMs and a macrophage-rich alveolar myeloid compartment. The resident immune cells formed a stable immune-epithelial system, frequently interacting with the epithelium and promoting a regenerative alveolar transcriptomic profile. To understand how dysregulated inflammation perturbed the respiratory barrier, we simulated T-cell-mediated inflammation in LIOs and LIOMs and used single-cell transcriptomic analyses to uncover the molecular mechanisms driving immune responses. The presence of innate cells induced a shift in T cell identity from cytotoxic to immunosuppressive, reducing epithelial cell killing and inflammation. Based on insights obtained with bulk RNA-seq data from the phase 3 IMpower150 trial, we tested whether LIOM cultures could model clinically-relevant but poorly understood pulmonary side effects caused by immunotherapies such as the checkpoint inhibitor atezolizumab3. We observed a decrease in immunosuppressive T cells and identified gene signatures that matched the transcriptomic profile of patients with drug-induced pneumonitis. Given its effectiveness in capturing outcomes and mechanisms associated with a prevalent pulmonary disease, this system unlocks opportunities for studying a wide range of immune-related pathologies in the lung.

cell biology↗

bioRxiv2024

Golden eagles regularly use gravity waves to soar in the Alps: new insights from high-resolution weather data

1Soaring flight developed as a result of behavioural and morphological adaptations that allow birds to reduce the metabolic cost of flight by harnessing the energy available in the atmosphere. Despite an increased attention given in the last decades to the physics and ecology that allow soaring flight, its study has been limited by the generally low spatio-temporal resolution of available atmospheric data. This constrained our ability to quantify the atmospheric conditions that allow soaring, and limited our understanding of its flexibility in different uplift conditions. While the use of updraughts such as thermals and orographic lifting are well described in the literature (albeit only quantified through atmospheric proxies), the use of others, such as gravity waves, was hypothesised but largely undocumented. Recent advancements in high-resolution atmospheric modelling, with hourly output available at the kilometer-scale grid spacing, offer new opportunities to investigate the flexibility of soaring flight in response to complex atmospheric dynamics. In this study, we used a combination of a high-resolution atmospheric analysis and high-resolution GPS tracking data to characterise the updraught sources used by golden eagles, Aquila chrysaetos, in the European Alps. We document that golden eagles in this region repeatedly use gravity waves, and that while thermals were still the main updraught source used for soaring, gravity waves were involved in at least 19% of the inspected soaring segments. In winter, when thermals were more scarce, the quasi-totality of soaring events were powered by gravity waves or orographic lifting, largely expanding the environmental energy available to soaring birds and therefore the landscape connectivity in topographically complex regions. Our results also emphasise the difficulty to distinguish between convective (thermals) and dynamic updraught sources, as these co-occur within the boundary layer over complex terrain.

ecology↗

bioRxiv2023

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↗

bioRxiv2022

CSPP1 stabilizes growing microtubule ends and damaged lattices from the luminal side.

Microtubules are dynamic cytoskeletal polymers, and their organization and stability are tightly regulated by numerous cellular factors. While regulatory proteins controlling formation of interphase microtubule arrays and mitotic spindles have been extensively studied, the biochemical mechanisms responsible for generating stable microtubule cores of centrioles and cilia are poorly understood. Here, we used in vitro reconstitution assays to investigate microtubule-stabilizing properties of CSPP1, a centrosome and cilia-associated protein mutated in the neurodevelopmental ciliopathy Joubert syndrome. We found that CSPP1 preferentially binds to polymerizing microtubule ends that grow slowly or undergo growth perturbations and, in this way, resembles microtubule-stabilizing compounds such as taxanes. Fluorescence microscopy and cryo-electron tomography showed that CSPP1 is deposited in the microtubule lumen and inhibits microtubule growth and shortening through two separate domains. CSPP1 also specifically recognizes and stabilizes damaged microtubule lattices. These data help to explain how CSPP1 regulates elongation and stability of ciliary axonemes and other microtubule-based structures.

cell biology↗

bioRxiv2021

Impact of charge patches on tumor disposition and biodistribution of therapeutic antibodies

This study explores the impact of antibody surface charge on tissue distribution into various tissues including tumor. Tumor-bearing mice were dosed intravenously with a mixture comprising three antibodies engineered to carry negative charge patches, a balanced charge distribution, or positive patches, respectively. Tissue levels were analyzed with a specific LC-MS/MS method. In addition, the antibody mix was administered to non-tumor bearing mice. Muscle and skin interstitial fluid were obtained by centrifugation and analyzed by LC-MS/MS. An in-vitro endothelium model was explored for its feasibility to mimic the observed distribution differences. A balanced charge distribution was optimal in terms of total tumor exposure, while in other tissues negatively charged and balanced charged antibodies gave similar results. In contrast, positive charge patches generally result in increased serum clearance but markedly enhance tumor and organ uptake, leading to higher tissue-to-serum ratios. The uptake and availability in the interstitial space were confirmed by specific assessment of antibody levels in the interstitial fluid of muscle and skin, with similar charge impact as in total tissue. The in vitro model was able to differentiate the transport propensity of this series of antibody variants. In summary, our results show the differential effects of charge patches on an antibody surface on biodistribution and tumor uptake. These insights may help in the design of molecules with biodistribution properties tailored to their purpose and an optimized safety profile.

cancer biology↗