Biology subjects

Claydon, W.

Publications and source records attributed to Claydon, W..

4 recordsLinked to original sources

bioRxiv2025

Accurately Programming Complex Light Regimes with Multi-channel LEDs

BackgroundAdvances in LED lighting technologies have allowed researchers to explore increasingly complex light regimes. This has given us greater insight into plants responses to dynamic light, including seasonality and fluctuating conditions, rather than the discrete (i.e. on / off) lighting previously explored. However, there is a need for methods to accurately program multi-channel / waveband LED lighting systems. ResultsWe present a multi-step, multidimensional algorithm to accurately program LED lights. This algorithm accounts for non-linearity between intensity settings and irradiance output, as well as bleedthrough between channels of different wavebands. Our algorithm out-performs other methods which treat waveband channels as independent variables, more accurately predicting intensity settings to achieve a desired irradiance when using multiple LED channels. ConclusionsThis algorithm allows the community to accurately program complex light regimes to probe plant responses to dynamically changing light spectra. We have made this algorithm available to the plant science community as an R package, LightFitR (available on GitHub at: https://github.com/ginavong/LightFitR).

plant biology↗

bioRxiv2024

Harnessing light heterogeneity to optimise controlled environment agriculture

Yield is impacted by the environmental conditions that plants are exposed to. Controlled environmental agriculture provides growers with an opportunity to fine-tune environmental conditions for optimising yield and crop quality. However, space and time constraints will limit the number of experimental conditions that can be tested, which will in turn limit the resolution to which environmental conditions can be optimised. Here we present an innovative experimental approach that utilises the existing heterogeneity in light quantity and quality across a vertical farm to evaluate hundreds of environmental conditions concurrently. It proposes a three-phase workflow for identifying critical light variables, which can guide targeted improvements in yield and energy use. Using an observational study design, we identify features in light quality that are most predictive of biomass in different microgreens crops (kale, radish and sunflower) that may inform future iterations of lighting technology development for vertical farms. The findings suggest that light quality, rather than just light intensity, plays a crucial role in uniform crop yields and that light sensitivities are variety-specific, highlighting the importance of tailored light recipes for different crops.

plant biology↗

bioRxiv2024

Hypocotyl Development in Arabidopsis and other Brassicaceae Displays Evidence of Photoperiodic Memory

Sensing and responding to photoperiod changes is essential for plants to adapt to seasonal progression. Most of our understanding of how plants sense photoperiodic changes is through studies on flowering time. However, other aspects of plant development are regulated by the photoperiod, including hypocotyl elongation. Unlike flowering, hypocotyl elongation displays a greater plasticity to changes in the photoperiod with increases in daylength causing greater inhibition of growth until a threshold is met. Previous studies have only looked at hypocotyl development in the context of a stationary photoperiod. It is unknown if changes in the photoperiod during development influence hypocotyl elongation. Here, we developed a physiological assay to investigate this question. We have discovered that hypocotyl elongation is influenced by a memory of past photoperiod exposure in Arabidopsis and Brassicaceae cultivars used for microgreen agriculture. Photoperiodic memory persisted for multiple days, although it weakened over time, and the strength of the memory was dependent on the genetic background. We identified that phyB and ELF3, key regulators of hypocotyl development, were required for photoperiodic memory. Finally, we identified that the circadian clock is unlikely to function as a repository for photoperiodic memory as circadian rhythms quickly re-aligned with the new photoperiod. In summary, our work highlights for the first-time evidence of a photoperiodic memory that can control plant development.

plant biology↗

bioRxiv2023

An Arabidopsis leaf expression atlas across diurnal and developmental scales

Mature plant leaves are a composite of distinct cell types, including epidermal, mesophyll and vascular cells. Notably the proportion of these cells, and the relative transcript concentrations within different cell types may change over time. While gene expression data at a single-cell level can provide cell-type specific expression values, it is often too expensive to perform this on high resolution time series. Although bulk RNA-seq can be performed in a high resolution time series, the RNA-seq in whole leaves measures the average gene expression values across all cell types in each sample. In this study, we combined single cell RNA-seq data with time-series data from whole leaves to infer an atlas of cell type-specific gene expression changes over time for Arabidopsis thaliana. We inferred how relative transcript concentrations of cell types vary across diurnal and developmental time scales. Importantly this analysis revealed three sub-groups of mesophyll cells that have distinct temporal profiles of expression. Finally, we develop tissue-specific gene networks that form a new community resource: An Arabidopsis Leaf Time-Dependent Atlas (AraLeTa), which allows users to extract gene networks that are confirmed by transcription factor binding data and specific to certain cell types, at certain times of day and certain developmental stages, which is available at: https://regulatorynet.shinyapps.io/araleta/.

plant biology↗