Biology subjects

Beavis, T.

Publications and source records attributed to Beavis, T..

5 recordsLinked to original sources

bioRxiv2026

A mobile optical coherence microscope for studying aquatic organisms in- and outside the laboratory

High-resolution, three-dimensional imaging of live organisms has largely depended on laboratory-bound microscopes, limiting quantitative analysis of morphology and dynamics to species that survive transport and thrive under lab-controlled conditions. Here we present a mobile optical coherence microscopy (OCM) platform that overcomes this constraint, delivering [~]2.5 {micro}m axial resolution, label-free, volumetric imaging of live aquatic organisms in both laboratory and remote field environments. We demonstrate the platform across a broad range of aquatic organisms from the lab and field, spanning multiple phyla - including cnidarians, poriferans, annelids, arthropods and echinoderms - resolving internal anatomy, tissue boundaries and organismal morphology at micrometer scale without fixation, fluorescent labeling, or specialized sample preparation. High-speed acquisition, with up to 250 kHz A-line rate and 7.7 Hz volume rate, further enabled morphodynamic imaging of live biological processes, including cellular aggregate motility, embryonic cell division, and organ-level peristaltic dynamics in intact, living animals. To demonstrate field deployability, the platform was operated during the EMBL TREC pan-European expedition, enabling on-site, label-free imaging of marine organisms and plankton immediately upon collection. By decoupling high-resolution volumetric imaging from fixed laboratory settings, mobile OCM opens a path toward field-ready quantitative morphological and dynamic phenotyping of aquatic life.

bioengineering↗

bioRxiv2026

An Advanced Mobile Laboratory to enable field-based microbial ecology and cell biology across scales

Microbial biodiversity is central to ecosystem function, yet mechanistic insights into the cell biology of environmental organisms remain limited. The underlying challenges are twofold: most microbes remain uncultivable, and a persistent gap exists between field sampling and laboratory analyses. Here, we introduce the Advanced Mobile Laboratory (AML), a field-deployable platform that integrates confocal microscopy, image-enabled cell sorting, and cryo-preparation for expansion and electron microscopy. This setup enables immediate, standardized processing and analysis of environmental communities directly at the sampling site. We demonstrate its capability using marine eukaryotic plankton, showing how the AML enables multiscale investigations, from live imaging of natural communities to enabling ultrastructural and single-cell omics analyses, while minimizing sample degradation and enabling on-site experimentation. By bringing high-end sample preparation and analytical capacity into the field, the AML enables studying life in its natural context to mechanistically understand lifes diversity in the environment.

cell biology↗

bioRxiv2025

The JEDI marker as a universal measure of planetary biodiversity

Despite its critical importance in the formation and maintenance of ecosystems and homeostasis on Earth, biodiversity remains a complex and non-unified concept. Consequently, standards for measuring global biodiversity are lacking, hindering our capacity to document Earths biota and track its change. Here, we propose the Joint, cellular life-Encompassing DIversity (JEDI) marker as a simple, effective and quantitative measure to assess and monitor biodiversity. The JEDI marker is a ribosomal RNA gene fragment that can be amplified from all domains of life using a single pair of PCR primers. We demonstrate the applicability and effectiveness of this approach for assessing biodiversity across ecological and biological scales, from holobionts to diverse ecosystems. In addition, we provide an automated bioinformatic workflow to support the standardised and reproducible analysis of the JEDI marker in future studies. While this approach is not free from trade-offs, we argue that its advantages outweigh its limitations by providing a unique, operational and scalable solution that builds on established infrastructure to integrate the microbial majority into biodiversity assessments and provide fundamental insights into organismal dynamics and associations across domains of life. Thus, the JEDI marker approach addresses the urgent need for a universal and standardised framework to effectively measure and monitor biodiversity at planetary scales in an era of profound global change.

ecology↗

bioRxiv2025

Diatom ultrastructural diversity across controlled and natural environments

Diatoms are ubiquitous aquatic microalgae critical to our planet, that were amongst the pioneer model organisms in cell biology for their large and transparent cell structure. However, their robust silica cell wall renders diatoms impermeable to many dyes and antibodies, and complicates the intracellular delivery of gene editing tools - driving in part the eventual decline of diatoms as mainstream model species despite their unique cellular physiology and remarkable ecological success. Here, we demonstrate that cryo-fixation combined with ultrastructural expansion microscopy (cryo-ExM) can overcome the silica barrier across diverse diatom species spanning over 80 million years of evolutionary time. We illustrate the potential of cryo-ExM to provide scalable, cost-effective volumetric imaging of diatom ultrastructure in laboratory cultures, as well as field-collected samples from the pan-European TREC expedition. We first reveal striking similarities in interphase microtubule organization across diverse diatom species by characterizing cytoskeletal arrangements throughout cell cycles and populations, uniting both pennate and centric morphologies under shared principles. We further unveil diatom photosynthetic diversity through qualitative and quantitative comparative analysis of chloroplast and pyrenoid morphologies, demonstrating that each diatom species architects unique photosynthetic machinery. Using cryo-ExM on environmental samples further exposes intricate diatom symbioses, revealing tight spatial organisation of ecological interactions. This methodology makes diatoms more accessible for modern and comparative cell biology research, providing new opportunities to investigate the cellular mechanisms of one of Earths most successful photosynthetic groups. HighlightsO_LICryo-ExM successfully overcomes diatom frustule barriers to achieve consistent, high-resolution immunofluorescence across evolutionarily diverse species - allowing for comparative cell biology in one of the most important phytoplankton groups on the planet. C_LIO_LICharacterizing microtubule organisation in asynchronously cycling single cells and colonial chains, reveals core features of interphase microtubule organisation across multiple pennate and centric diatom species. C_LIO_LIComparative analysis of chloroplast and pyrenoid morphologies across species provides qualitative and quantitative insights on photosynthetic diversity, suggesting that photosynthetic architectures are unique to each diatom. C_LIO_LIApplied to environmental samples, cryo-ExM provides detailed insight on spatial organisation of diatom symbioses. C_LI

cell biology↗

bioRxiv2023

Harvesting and amplifying gene cassettes confers cross-resistance to critically important antibiotics

Amikacin and piperacillin/tazobactam are frequent antibiotic choices to treat bloodstream infection, which is commonly fatal and most often caused by bacteria from the family Enterobacterales. Here we show that two gene cassettes located side-by-side in and ancestral integron similar to In37 have been "harvested" by insertion sequence IS26 as a transposon that is already globally disseminated among the Enterobacterales. This transposon encodes the enzymes AAC(6)-Ib-cr and OXA-1, reported, respectively, as amikacin and piperacillin/tazobactam resistance mechanisms. However, by studying bloodstream infection isolates from 769 patients from, three hospitals serving a population of 1.5 million people in South West England, we show that increased enzyme production due to mutation in an IS26/In37-derived hybrid promoter or, more commonly, transposon copy number amplification is required to simultaneously remove these two key therapeutic options; in many cases leaving only the last-resort antibiotic, meropenem. These findings may help improve the accuracy of predicting piperacillin/tazobactam treatment failure, allowing stratification of patients to receive meropenem or piperacillin/tazobactam, which may improve outcome and slow the emergence of meropenem resistance.

microbiology↗