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README.md

{RoPod}, a customizable toolkit for non-invasive root imaging, reveals cell type-specific dynamics of plant autophagy

Arabidopsis root is a classic model system in plant cell and molecular biology. The sensitivity of plant roots to local environmental perturbation challenges data reproducibility and incentivizes further optimization of imaging and phenotyping tools. Here we present RoPod, an easy-to-use toolkit for low-stress live time-lapse imaging of Arabidopsis roots. RoPod comprises a dedicated protocol for plant cultivation and a customizable 3D-printed vessel with integrated microscopy-grade glass that serves simultaneously as a growth and imaging chamber. RoPod reduces impact of sample handling, preserves live samples for prolonged imaging sessions, and facilitates application of treatments during image acquisition. We describe a protocol for RoPods fabrication and provide illustrative application pipelines for monitoring root hair growth and autophagic activity. Furthermore, we showcase how the use of RoPods advanced our understanding of plant autophagy, a major catabolic pathway and a key player in plant fitness. Specifically, we obtained fine time resolution for autophagy response to commonly used chemical modulators of the pathway and revealed previously overlooked cell type-specific changes in the autophagy response. These results will aid a deeper understanding of the physiological role of autophagy and provide valuable guidelines for choosing sampling time during end-point assays currently employed in plant autophagy research.

Publication Details

  • DOI: 10.1038/s41598-024-63226-1
  • Title: {RoPod}, a customizable toolkit for non-invasive root imaging, reveals cell type-specific dynamics of plant autophagy
  • Authors: Guichard, Marjorie and Holla, Sanjana and Wernerová, Daša and Grossmann, Guido and Minina, Elena A.
  • Journal: Scientific Reports

Data Availability

The different functional designs of RoPod chambers, as well as an illustrated step-by-step protocol for their 3D printing are presented in Supplementary File S1 and Supplementary Methods. Updates of the designs and of the printing protocols depending on the model of 3D printer used are available in the dedicated GitHub repository: https://github.com/AlyonaMinina/RoPod.Hardware.

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

License

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.