Automated analysis of calcium spiking profiles with CaSA software: two case studies from root-microbe symbioses

BMC Plant Biology

Methodology Article

Eva Sciacca¹  Salvatore Spinella¹  Paola Bonfante²  Andrea Genre²  Giulia Russo² 

[1] Dipartimento di Informatica, Università di Torino, C.So Svizzera, 185, 10149, Torino, Italy;Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Viale P.A. Mattioli 25, 10125, Torino, Italy;

关键词: Arbuscular mycorrhiza;    Calcium signaling;    Medicago truncatula;    Nitrogen fixation;    Phosphate;    Plant-microbe interactions;    Symbiosis;    Automated data analysis;   

DOI  :  10.1186/1471-2229-13-224

 received in 2013-09-24, accepted in 2013-12-11,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundRepeated oscillations in intracellular calcium (Ca2+) concentration, known as Ca2+ spiking signals, have been described in plants for a limited number of cellular responses to biotic or abiotic stimuli and most notably the common symbiotic signaling pathway (CSSP) which mediates the recognition by their plant hosts of two endosymbiotic microbes, arbuscular mycorrhizal (AM) fungi and nitrogen fixing rhizobia. The detailed analysis of the complexity and variability of the Ca2+ spiking patterns which have been revealed in recent studies requires both extensive datasets and sophisticated statistical tools.ResultsAs a contribution, we have developed automated Ca2+ spiking analysis (CaSA) software that performs i) automated peak detection, ii) statistical analyses based on the detected peaks, iii) autocorrelation analysis of peak-to-peak intervals to highlight major traits in the spiking pattern.We have evaluated CaSA in two experimental studies. In the first, CaSA highlighted unpredicted differences in the spiking patterns induced in Medicago truncatula root epidermal cells by exudates of the AM fungus Gigaspora margarita as a function of the phosphate concentration in the growth medium of both host and fungus. In the second study we compared the spiking patterns triggered by either AM fungal or rhizobial symbiotic signals. CaSA revealed the existence of different patterns in signal periodicity, which are thought to contribute to the so-called Ca2+ signature.ConclusionsWe therefore propose CaSA as a useful tool for characterizing oscillatory biological phenomena such as Ca2+ spiking.

【 授权许可】

Unknown   
© Russo et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.