Ntshangase, S. | bioRxiv Science

bioRxiv2026

Enhancing Lipid Detection and Spatial Accuracy in Carotid Plaques Using Mass Spectrometry Imaging Techniques

Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) is a powerful technique for studying lipid distribution in carotid plaques, key to understanding atherosclerosis. This study aimed to improve sample preparation for MALDI-MSI-based spatial lipidomics of carotid plaques by improving both matrix application and tissue handling. Human carotid plaques were collected from endarterectomy patients with ethical approval and sectioned at 10 {micro}m thickness for MALDI-MSI. We compared eight sample preparation methods, including hydroxypropyl methylcellulose-polyvinylpyrrolidone (HPMC-PVP) embedding media and Cryofilm-type IMS(R) to provide support and maintain tissue structural integrity during sectioning. Methods were assessed for signal intensity, lipid diffusion, lipid coverage, tissue morphology, and image co-registration which each criterion scored from 1-3. Cryofilm-based methods scored highest for preserving tissue morphology and minimising folding artifacts (2.9-3.0) but were limited in co-registration (2.0) due to reliance on adjacent sections. Sublimation methods generally produced greater lipid coverage with reduced lateral diffusion, while automated sprayer methods scored higher in signal intensity/sensitivity (3.0) but had increased lipid delocalisation, particularly for highly hydrophobic species such as triacylglycerols and sterols. The results highlight clear trade-offs between tissue structural preservation, lipid detection sensitivity, and spatial integrity in MALDI-MSI. Because spatial integrity cannot be compromised for imaging lipids in carotid atherosclerotic plaques, Cryofilm combined with sublimation offers a clear advantage. This work strengthens MALDI-MSI workflows enabling more precise spatial mapping and deeper biological interpretation of atherosclerotic lipid distributions.

molecular biology↗

bioRxiv2021

Hybridisation and chloroplast capture between ancient Themeda triandra ecotypes in Australia

Ecotypes are distinct populations within a species which are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. A chloroplast phylogeny confirms that Australia was colonised by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of gene-flow among the ecotypes, largely restricted to two geographic areas. In northern Queensland there appears to be a hybrid zone with admixed nuclear genomes and shared plastid haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal plastid and interior clade nuclear genomes. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. A stable hybrid zone in the east, and the displacement of one ecotype in the west, highlights the unpredictable nature of hybrid zones, with repeated contacts between the same ecotypes producing different outcomes.

evolutionary biology↗