Biology subjects

Schwarz, T. M.

Publications and source records attributed to Schwarz, T. M..

3 recordsLinked to original sources

bioRxiv2026

Nanoscale identification of organic pigments in biogenic calcite by atom probe tomography

Spatially-resolved mass spectrometry could contribute to the understanding of biological processes. Atom probe tomography (APT) is a technique which could, in principle, fill an analytical gap for nanoscale mass spectrometry. Yet, because of a limited understanding of the process of fragmentation of biomolecules, biological or biochemical interpretation of the obtained data has so far not been successful. Here, we report on analyses of synthetic and biogenic pigmented calcite minerals. The purple coloration of Sphaerechinus granularis sea urchin spines is due to the occlusion of polyhydroxylated naphthoquinone (PHNQ) molecules, mainly spinochrome A, within the calcite phase. Peaks relating to these pigments as well as to other intra-crystalline macromolecules were identified by APT analysis of the purple spine region with comparison to measurements of synthetic calcite single crystals, calcite crystals doped with PHNQ, and the uncoloured (white) region of sea urchin spines. To facilitate the molecular identification of peaks appearing solely in purple-coloured spines, which are possible fragments from PHNQ, we introduce novel APT data filtering techniques based on spatial and temporal correlations in the detection of ions of targeted mass-to-charge state ratios. This allows us to discuss the fragmentation of organic molecules under field conditions and improve the identification of peaks in the mass spectrum, while also determining nanoscale spatial distribution of fragments related to specifically targeted biomolecules in 3D and elucidate the relationship these organic pigment molecules have to the calcite lattice and inorganic elements such as magnesium. The study aims to improve identification of complex molecular structures by APT, including organic molecules, with the potential ability to provide structural information at a near-atomic scale for a range of materials.

biophysics↗

bioRxiv2025

Exploring the potential for scanning electron microscopy/focused ion beam - based diffraction for screening cryo-transmission electron microscopy samples

The study of biological and organic materials at high resolution using cryogenic transmission-electron microscopy (cryo-TEM) necessitates vitrification to preserve the native structure. Assessing sample integrity is essential, particularly as ice crystallization during freezing and handling can cause irrecoverable structural damage. Usually, a secondary cryo-TEM is used for initial screening, only possible after a time-consuming sample preparation workflow. In the present work, we propose simple methods that exploit existing workflows developed for materials science analyses and demonstrate on-grid in situ assessment of ice crystallinity with electron backscatter diffraction (EBSD) on a direct electron detector (DED) in a cryo-scanning-electron microscope (SEM). This evaluation step can be performed prior to sample preparation for cryo-TEM by using cryogenic focused ion beam (cryo-FIB) milling. Custom grid holders and jigs were developed to integrate the clipped cryo-TEM grids and evolve the sample preparation workflow. EBSD detects hexagonal ice in some areas of the samples, whereas other areas show an absence of EBSD signal, consistent with vitreous ice, that enable targeting the further steps of sample preparation for cryo-TEM. Off-axis transmission Kikuchi diffraction (TKD) was attempted, but led to severe damage to polished TEM-lamellae and appears unsuitable. A proof-of-concept lift-out from a clipped cryo-TEM grid mounted on a support is introduced, demonstrating possibilities for expanded cryogenic correlative workflows beyond the acceleration of sample screening for cryo-TEM.

molecular biology↗

bioRxiv2020

Filovirus infection induces an anti-inflammatory state in Rousettus bats

The Marburg and Ebola filoviruses cause a severe, often fatal, disease in humans and nonhuman primates but have only subclinical effects in bats, including Egyptian rousettes, which are a natural reservoir of Marburg virus. A fundamental question is why these viruses are highly pathogenic in humans but fail to cause disease in bats. To understand how bats resist the disease caused by filoviruses, we infected one cohort of Egyptian rousette bats with Marburg virus and another cohort with Ebola virus and harvested multiple tissues for mRNA expression analysis. While virus transcripts were found primarily in the liver, Principal component analysis (PCA) revealed coordinated changes across multiple tissues. Gene signatures in kidney and liver pointed at induction of vasodilation, reduction of coagulation and changes in the regulation of iron metabolism. Signatures of immune response detected in spleen and liver indicated a robust anti-inflammatory state signified by macrophages in the M2 state and an active T cell response. Many of the responsive genes were found to be evolutionarily divergent, providing a framework for understanding the differences in outcomes of filovirus infections between bats and humans. In this study, we outline multiple interconnected pathways that respond to infection by MARV and EBOV, providing insights into the complexity of the mechanisms that enable bats to resist the disease caused by filoviral infections. The results have the potential to aid in the development of new strategies to effectively mitigate and treat the disease caused by these viruses in humans.

microbiology↗