Biology subjects

Herrero, E.

Publications and source records attributed to Herrero, E..

5 recordsLinked to original sources

bioRxiv2026

Leaf movements as a quantitative metric for early stress detection

Early, precise, and non-destructive stress detection is essential for maintaining crop productivity, particularly in high-density plant growth systems like controlled environment agriculture (CEA), where manual monitoring is often impractical. Using plant motion as a proxy for growth and plant health, we demonstrate a method for early, non-invasive stress detection through quantitative leaf-movement analysis in lettuce and five other CEA relevant crops. Leaf-movement dynamics under stress were imaged with a low-cost, scalable Raspberry Pi imaging setup and quantified using a repurposed open-source motion estimation algorithm; Tracking Rhythms in Plants (TRiP). Our system detected stress-induced changes in leaf-movement within 1 hour of stress, with the timing dependent on the nature of the stress. Sustained reductions in leaf-movement coincide with decreased biomass accumulation. This approach offers a non-invasive, rapid, scalable, and cost-effective solution for continuous crop monitoring, with potential for application in both terrestrial and space farming CEA systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/732190v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@19ee20eorg.highwire.dtl.DTLVardef@b0804org.highwire.dtl.DTLVardef@3b3fa8org.highwire.dtl.DTLVardef@1d04026_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Quantification of leaf-movement dynamics as a high-throughput proxy for plant physiological status, enabling early stress detection and timely intervention to mitigate yield penalties in CEA settings (image made with biorender.org). C_FIG

plant biology↗

bioRxiv2026

Dim Green Light Enables Day-and-Night Monitoring of Leaf Movements

Understanding plant growth dynamics requires imaging across day-and-night cycles to quantify growth, movement and development in the aerial plant body and to capture the rhythmic nature of these processes. This requires imaging in light during the day and in darkness at night without perturbing plant physiology. Nighttime imaging has typically depended on infrared (IR) illumination, producing monochrome datasets that require specialised hardware and separate analysis pipelines when combined with daytime RGB imaging. Here, we evaluated very low-intensity green (dimG) illumination from standard LEDs as a practical alternative for colour-consistent nighttime imaging and assessed its physiological impact in Arabidopsis thaliana and Lactuca sativa (lettuce). We show that high resolution colour images can be obtained under dimG using low- cost cameras, with sufficient consistency between full-spectrum and dimG images to allow direct comparison and unified image analysis. We show that very low-fluence green light (<0.5 mol m-2 s-1) does not sustain circadian oscillations of gene activity under continuous exposure and does not perturb rhythms when applied during the dark phase of diel cycles. DimG imaging enabled accurate detection of diel leaf movement profiles in Arabidopsis circadian mutants, revealing genotype-specific phase differences under varying photoperiods. In lettuce, dimG pulses and continuous dimG enabled accurate quantification of diel leaf movement without affecting growth, stomatal opening, electron transport rate or chlorophyll content. Motion profiles under continuous dimG mirrored those under darkness. Our findings establish dim green illumination as a cost-effective solution for night-time imaging, simplifying phenotyping workflows with minimal impact on physiology.

plant biology↗

bioRxiv2025

Assessing the ligand native-like pose using a quantum mechanical-derived hydropathic score for protein-ligand complementarity

Elucidating the correct binding mode of drug-like compounds is crucial to disclose the molecular determinants that underline the recognition by the target protein and estimate the binding affinity, thus guiding the ensuing hit-to-lead optimization. However, the choice of the near-native binding pose in docking experiments remains a major hurdle. Assuming that the hydropathic complementarity principle is the major driving force in ligand-protein recognition, the suitability of simple hydropathicity-based scoring functions to reveal the near-native pose was examined. A benchmarking dataset of 1000 ligand-protein complexes purposely designed to encompass bioactive and decoy poses was used to assess the performance of 3D hydropathicity atomic descriptors derived from empirical and quantum mechanical models. This strategy led to a predictive accuracy of ca. 90% when the non-negligible influence of the conformational stress is also considered. The results reveal the need to leverage nonpolar/polar chemical features for the successful discrimination of the near-native pose.

bioinformatics↗

bioRxiv2025

Arbor function of TRANSPARENT TESTA GLABRA 1 and LIGHT REGULATED WD scaffold proteins in the Arabidopsis circadian oscillators includes transcriptional repression through PSEUDO RESPONSE REGULATORS

Arabidopsis circadian oscillators contain DNA-binding proteins that function at specific times of day. In contrast, we have discovered a continuous function of WD40-repeat scaffold proteins from the TRANSPARENT TESTA GLABRA-1 (TTG1), LIGHT REGULATED WD1 and LIGHT REGULATED LWD2 subfamily (TLWD) which is essential to maintain circadian rhythms. Gene expression analyses indicate multifunctional activity of TLWD in both transcriptional activation and repression. TLWD proteins interact with an array of circadian oscillator activators and repressors that act sequentially throughout the diel cycle. While TLWD proteins were known to participate in activator complexes, our data indicate a novel role of TLWD in transcriptional repression through complex formation with repressors from the PSEUDO RESPONSE REGULATOR (PRR) family. In an analogy to mechanical clocks, TLWD scaffold proteins constitute an ever-present arbor, or spindle, to which transcription factors, which represent the cogs, bind to sustain circadian rhythms.

plant biology↗

bioRxiv2017

Metabolic Constraints And Quantitative Design Principles In Gene Expression During Adaption Of Yeast To Heat Shock

Microorganisms evolved adaptive responses that enable them to survive stressful challenges in ever changing environments by adjusting metabolism through the modulation of gene expression, protein levels and activity, and flow of metabolites. More frequent challenges allow natural selection ampler opportunities to select from a larger number of phenotypes that are compatible with survival. Understanding the causal relationships between physiological and metabolic requirements that are needed for cellular stress adaptation and gene expression changes that are used by organisms to achieve those requirements may have a significant impact in our ability to interpret and/or guide evolution.\n\nHere, we study those causal relationships during heat shock adaptation in the yeast Saccharomyces cerevisiae. We do so by combining dozens of independent experiments measuring whole genome gene expression changes during stress response with a nonlinear simplified kinetic model of central metabolism.\n\nThis combination is used to create a quantitative, multidimensional, genotype-to-phenotype mapping of the metabolic and physiological requirements that enable cell survival to the feasible changes in gene expression that modulate metabolism to achieve those requirements. Our results clearly show that the feasible changes in gene expression that enable survival to heat shock are specific for this stress. In addition, they suggest that genetic programs for adaptive responses to desiccation/rehydration and to pH shifts might be selected by physiological requirements that are qualitatively similar, but quantitatively different to those for heat shock adaptation. In contrast, adaptive responses to other types of stress do not appear to be constrained by the same qualitative physiological requirements. Our model also explains at the mechanistic level how evolution might find different sets of changes in gene expression that lead to metabolic adaptations that are equivalent in meeting physiological requirements for survival. Finally, our results also suggest that physiological requirements for heat shock adaptation might be similar between unicellular ascomycetes that live in similar environments. Our analysis is likely to be scalable to other adaptive response and might inform efforts in developing biotechnological applications to manipulate cells for medical, biotechnological, or synthetic biology purposes.

systems biology↗