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

Abstract

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.

An endophytic Fusarium–legume association is partially dependent on the common symbiotic signalling pathway

“…S5 illustrates the distribution of waiting time autocorrelation values in our populations of spiking profiles. A high number of cells in all treatments demonstrated negative autocorrelation values, indicating that spiking responses to all fungal exudates are in most cases irregular, in analogy to what was described for AM fungal‐induced spiking profiles, and in contrast with the mostly regular rhizobium‐induced calcium spiking signals in the same experimental system (Russo et al , ). Statistical analysis showed no dependency between the distribution of waiting time autocorrelation values and the fungal exudate tested.…”

“…Calcium spiking measurements were analyzed further using CaSA software (Russo et al , ). The generation of at least three peaks was the threshold for discrimination between responding and nonresponding cells.…”

Nutrient Exchange and Regulation in Arbuscular Mycorrhizal Symbiosis

“…However, high levels of Pi do not affect root calcium-spiking responses to AM fungi, indicating that Pi might not affect presymbiotic signaling through the common signaling pathway, which is required for AM fungi infection. Recently, a significant inhibition of presymbiotic signaling, such as the percentage of the calcium-spiking cells and average number of peaks in response to high Pi level, was also reported (Balzergue et al, 2013;Russo et al, 2013). Interestingly, it was reported that Pi inhibition of the arbuscular specific phosphate transporter gene PhPT5 may underlie reduced arbuscule colonization in Petunia hybrida, because the repression of PhPT5 precedes the reduction of AM colonization (Breuillin et al, 2010).…”

CaSiAn: a Calcium Signaling Analyzer tool

“…Available tools for such an automatic analysis of spiking data are typically tailored towards spiking dynamics of neuronal membrane potentials ( Cajigas et al , 2012 ) but do not reflect the specific needs for Ca 2+ signals that often exhibit more noise and slow underlying trends. A recent approach addresses Ca 2+ spike recognition by Matlab scripts ( Russo et al , 2013 ), but without an interactive graphical user-interface (GUI), limiting the application to computational scientists. In particular, these approaches do not allow for an intuitive optimization of signal analysis nor a systematic analysis of the σ- T av relation.…”