bioRxiv Science⌕ Search

Biology subjects

Cavanagh, A.

Publications and source records attributed to Cavanagh, A..

2 recordsLinked to original sources

CSR Calculator: An R package and Shiny application for assigning plant ecological strategies using trait data

O_LIThe competitor, stress-tolerator, ruderal (CSR) theory, first proposed by John Philip Grime, is a useful framework for understanding plant ecological strategies and predicting responses to environmental changes and pressures. However, current tools for assigning CSR strategies are limited to an Excel sheet format and have yet to be integrated into modern computational platforms that enable reproducible research. C_LIO_LIWe present CSRcalculator (https://github.com/TeddyGaskin/CSRcalculator), an open-source R package and shiny application that calculates CSR scores and assigns strategies based on user-uploaded trait data. CSRcalculator supports CSR assignments according to the three most prominent models: The original soft approach, the global StrateFy, and a morpho-physiological model. C_LIO_LIThe R package outputs a table including CSR scores, assigned strategies and intermediate traits for the selected model. The shiny application produces this same table alongside an interactive ternary plot to visualise the strategy distribution and an optional summary table describing the overall CSR strategy distribution, using metrics such as, the modal strategy, axis means, standard deviations, and ranges. Group-level analyses calculate the same statistics across user-defined categories. C_LIO_LIWe provide a worked example using our tool to assign CSR strategies to plants for an example dataset. C_LI

plant biology↗

Temperature response of Rubisco kinetics in Arabidopsis thaliana: thermal breakpoints and implications for reaction mechanisms

Optimization of Rubisco kinetics could improve photosynthetic efficiency, ultimatly resulting in increased crop yield. However, imprecise knowledge of the reaction mechanism and the individual rate constants limit our ability to optimize the enzyme. Membrane inlet mass spectrometery (MIMS) may offer benefits over traditional methods for determining individual rate constants of the Rubisco reaction mechanism, as it can directly monitor concentration changes in CO2, O2, and their isotopologs during assays. However, a direct comparsion of MIMS to the traditional Radiolabel method of determining Rubisco kinetic parameters has not been made. Here, the temperature responses of Rubisco kinetic parameters from Arabidopsis thaliana were measured using the Radiolabel and MIMS methods. The two methods provided comparable parameters above 25 {degrees}C, but temperature responses deviated at low temperature as MIMS derived catalytic rates of carboxylation, oxygenation, and CO2/O2 specificity showed thermal breakpoints. Here we discuss the variability and uncertainty surrounding breakpoints in the Rubisco temperature response and relavance of individual rate constants of the reaction mechanisms to potential breakpoints.

plant biology↗