Biology subjects

Spichal, L.

Publications and source records attributed to Spichal, L..

5 recordsLinked to original sources

bioRxiv2026

A hyperbolic topological atlas reveals polyamine steering of a shared developmental manifold in Arabidopsis

High-throughput plant phenotyping captures development at scale, yet image-rich screens are still often reduced to static trait summaries. We tested whether nutrient availability, polyamine priming, concentration, and their transport reshape Arabidopsis rosette development by generating distinct morphologies or by changing residence along a common trajectory. We analyzed 138,223 time-resolved rosette images from Col-0 and five mutants involved in polyamine transport (put1-5) primed to putrescine, spermidine, spermine, dose, and nutrient regimes using a self-supervised vision backbone, Poincare embedding, hyperbolic Mapper, and manifold straightening. The data form a single connected developmental manifold with 410 nodes and 746 edges, organized from an early, low-nutrient-biased hub through high-betweenness transition corridors to two late, nutrient-enriched terminal regions. Polyamine identity stratifies this manifold by developmental phase: putrescine enriches early states, spermidine occupies transition corridors, and spermine marks late compact rosettes. Nutrient richness and dose change distal occupancy, whereas put genotypes alter dwell time within shared regions rather than producing separate topologies. Manifold straightening resolves these effects into a short early lateral deflection followed by convergence, yielding two scalar readouts, early transverse offset and distal occupancy, that summarize treatment action on a common morphodynamic scale. The framework converts large image screens into interpretable developmental geometry for image-based phenomics.

bioinformatics↗

bioRxiv2026

LOCOPOTS: a low-cost high-throughput screening platform for in vitro potato phenotyping under abiotic stress

Potato crop is highly vulnerable to abiotic stresses like salinity and low nutrient availability. Rapid identification of stress-resilient genotypes is therefore essential for breeding, yet conventional phenotyping is often slow, space-demanding and expensive. We present LOCOPOTS -- a LOw-COst high-throughput screening platform for in vitro POTatoes under abiotic Stress -- which combines individual in vitro plant culture, low-cost RGB imaging and machine-learning-based automatic segmentation using a trained model of a convolutional neural network, based on U-Net architecture. LOCOPOTS enabled the automated extraction of growth, colour, and vegetation-index traits and demonstrated robust performance across independent phenotyping rounds. We screened 30 potato varieties under control, low-nutrient and saltinity conditions, identifying contrasting growth and physiological responses. Integrated traits such as final area and height, Area_AUC and height_AUC, together with GLI, Chol, cive and chlorophyll fluorescence parameters, discriminated genotype performance under stress. Metabolic profiling further revealed genotype-specific reprogramming in carbon and nitrogen metabolism under low nutrition and salt stress, including changes in fructose, myo-inositol, {beta}-aminobutyric acid, {gamma}-aminobutyric acid, proline, and certain polyamines, identifying them as specific chemical biomarkers of plant stress responses. LOCOPOTS provides a scalable, affordable and space-efficient platform for early screening of potato genetic diversity and identification of candidate traits associated with stress resilience.

plant biology↗

bioRxiv2024

Decrypting the complex phenotyping traits of plants by machine learning

Phenotypes, defining an organisms behaviour and physical attributes, arise from the complex, dynamic interplay of genetics, development, and environment, whose interactions make it enormously challenging to forecast future phenotypic traits of a plant at a given moment. This work reports AMULET, a modular approach that uses imaging-based high-throughput phenotyping and machine learning to predict morphological and physiological plant traits hours to days before they are visible. AMULET streamlines the phenotyping process by integrating plant detection, prediction, segmentation, and data analysis, enhancing workflow efficiency and reducing time. The machine learning models used data from over 30,000 plants, using the Arabidopsis thaliana-Pseudomonas syringae pathosystem. AMULET also demonstrated its adaptability by accurately detecting and predicting phenotypes of in vitro potato plants after minimal fine-tuning with a small dataset. The general approach implemented through AMULET streamlines phenotyping and will improve breeding programs and agricultural management by enabling pre-emptive interventions optimising plant health and productivity.

plant biology↗

bioRxiv2020

Sucrose promotes etiolated stem branching through activation of cytokinin accumulation followed by vacuolar invertase activity

The potato (Solanum tuberosum L.) tuber is a swollen stem. Sprouts growing from the tuber nodes represent dormancy release and loss of apical dominance. We recently identified sucrose as a key player in triggering potato stem branching. To decipher the mechanisms by which sucrose induces stem branching, we investigated the nature of the inducing molecule and the involvement of vacuolar invertase (VInv) and the plant hormone cytokinin (CK) in this process. Sucrose was more efficient at enhancing lateral bud burst and elongation than either of its hexose moieties (glucose and fructose), or a slowly metabolizable analog of sucrose (palatinose). Sucrose feeding induced expression of the sucrose transporter gene SUT2, followed by enhanced expression and activity of VInv in the lateral bud prior to its burst. We observed a reduction in the number of branches on stems of VInv-RNA interference lines during sucrose feeding, suggesting that sucrose breakdown is needed for lateral bud burst. Sucrose feeding led to increased CK content in the lateral bud base prior to bud burst. Inhibition of CK synthesis or perception inhibited the sucrose-induced bud burst, suggesting that sucrose induces stem branching through CK. Together, our results indicate that sucrose is transported to the bud, where it promotes bud burst by inducing CK accumulation and VInv activity.

plant biology↗

bioRxiv2019

Cytokinin fluoroprobe and receptor CRE1/AHK4 localize to both plasma membrane and endoplasmic reticulum

The plant hormone cytokinin regulates various cell and developmental processes, including cell division and differentiation, embryogenesis, activity of shoot and root apical meristems, formation of shoot and root lateral organs and others 1. Cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Based on the subcellular localization of cytokinin receptors in various transient expression systems, such as tobacco leaf epidermal cells, and membrane fractionation experiments of Arabidopsis and maize, the endoplasmic reticulum (ER) membrane has been proposed as a principal hormone perception site 2-4. Intriguingly, recent study of the cytokinin transporter PUP14 has pointed out that the plasma membrane (PM)-mediated signalling might play an important role in establishment of cytokinin response gradients in various plant organs 5. However, localization of cytokinin HK receptors to the PM, although initially suggested 6, remains ambiguous. Here, by monitoring subcellular localizations of the fluorescently labelled natural cytokinin probe iP-NBD 7 and the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin fluoroprobes and receptors can enter the secretory pathway and reach the PM. We demonstrate that in cells of the root apical meristem, CRE1/AHK4 localizes to the PM and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. Our results provide a new perspective on cytokinin signalling and the possibility of multiple sites of perception at PM and ER, which may determine specific outputs of cytokinin signalling.

plant biology↗