Biology subjects

Field, N.

Publications and source records attributed to Field, N..

4 recordsLinked to original sources

bioRxiv2025

Plant cells at the organ surface use mechanical cues to activate a specific growth control programme

During morphogenesis of multicellular organs, cells acquire distinct identities that meet specific functional requirements. Epidermal identity is widely considered essential for plant morphogenesis due to the role of the epidermis in both restricting and promoting growth. In the root, epidermal cells are partially covered by a protective root cap, and partially positioned at the organ surface. Here, we propose that epidermal cells at the organ surface have unique requirements for growth control due to high mechanical tension, while covered epidermal cells are mechanically shielded by the root cap. We present in silico and in vivo evidence that plants use surface mechanical cues to activate a cell-type specific growth control programme involving the small GTPase RAB-A5c, allowing them to maintain directional growth at the organ surface. Positional mechanical cues may thus be used to control expression of a sub-population of epidermal genes, linking gene regulation to surface-specific functional requirements.

plant biology↗

bioRxiv2024

Biom3d, a modular framework to host and develop 3D segmentation methods

U-Net is a convolutional neural network model developed in 2015 and has proven to be one of the most inspiring deep-learning models for image segmentation. Numerous U-Net-based applications have since emerged, constituting a heterogeneous set of tools that illustrate the current reproducibility crisis in the deep-learning field and that remain slow to spread in application fields such as 3D bioimaging. Here we propose a solution named Biom3d, a modular deep learning framework facilitating the integration and development of novel models, metrics, or training schemes for 3D image segmentation. The development philosophy of Biom3d provides an improved code sustainability and reproducibility in line with the FAIR principles and is available as a graphical user interface and an open-source deep-learning framework to target a large community of users, from end users to deep learning developers.

bioinformatics↗

bioRxiv2022

A dynamic epibiont community associated with the bone eating worm Osedax

Osedax, the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, that help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-year study, we reveal a dynamic, yet persistent, succession of Campylobacterales integrated into the epidermis of Osedax, that change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species of Osedax, which comprise 67% of the bacterial community on the trunk, are initially dominated by the genus Arcobacter (at early time points < 24 months), the Sulfurospirillum at intermediate stages (~ 50 months), and the Sulfurimonas at later stages (>140 months) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests a transition from heterotrophy to autotrophy along the successional gradient, and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free living relatives, the Osedax epibionts were highly enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms

microbiology↗

bioRxiv2018

Immune profiling of cord blood after prolonged rupture of membranes.

We hypothesised that foetal immune responses to an infectious challenge may be detected by genome-wide transcriptional profiling of cord blood. In order to test this hypothesis, we sought to identify transcriptomic changes in post-natal cord blood samples following prolonged pre-labour rupture of membranes (PROM) as a surrogate for increased risk of infection. By comparison to controls we found increased levels of blood transcripts in a subset of prolonged PROM cases, significantly enriched for innate immune system signalling pathways. These changes were idiosyncratic, suggesting qualitative and quantitative variation in foetal immune responses which may reflect differences in exposure and/or in host genetics. Our data support the view that PROM represents an infection risk to the foetus. In addition, we propose that cord blood transcriptional profiling offers exciting opportunities to identify immune correlates of clinical outcome following potential in utero exposures to infection. These may be used to elucidate the mechanisms of immunological protection and pathology in the foetus and identify biomarkers to stratify the risk of adverse outcomes.

immunology↗