Strengths and Limitations of Period Estimation Methods for Circadian Data

Abstract

A key step in the analysis of circadian data is to make an accurate estimate of the underlying period. There are many different techniques and algorithms for determining period, all with different assumptions and with differing levels of complexity. Choosing which algorithm, which implementation and which measures of accuracy to use can offer many pitfalls, especially for the non-expert. We have developed the BioDare system, an online service allowing data-sharing (including public dissemination), data-processing and analysis. Circadian experiments are the main focus of BioDare hence performing period analysis is a major feature of the system. Six methods have been incorporated into BioDare: Enright and Lomb-Scargle periodograms, FFT-NLLS, mFourfit, MESA and Spectrum Resampling. Here we review those six techniques, explain the principles behind each algorithm and evaluate their performance. In order to quantify the methods' accuracy, we examine the algorithms against artificial mathematical test signals and model-generated mRNA data. Our re-implementation of each method in Java allows meaningful comparisons of the computational complexity and computing time associated with each algorithm. Finally, we provide guidelines on which algorithms are most appropriate for which data types, and recommendations on experimental design to extract optimal data for analysis.

Combined Pharmacological and Genetic Manipulations Unlock Unprecedented Temporal Elasticity and Reveal Phase-Specific Modulation of the Molecular Circadian Clock of the Mouse Suprachiasmatic Nucleus

“…All animal work was licensed under the UK 1986 Animals (Scientific Procedures) Act and subject to local ethical review. SCN slices were isolated from 300-m-thick coronal hypothalamic slices prepared from postnatal day 8 (P8) to P10 mice (either sex) and cultured on Millicell tissue culture inserts (PICMORG50, Millipore) for at least a week at 37°C, as previously described (Yamazaki et al, 2002;Hastings et al, 2005;. Slices were prepared from wild-type and circadian mutant mice, CK1…”

“…Remarkably, SCN tissue explants maintain free-running circadian rhythms more or less indefinitely in suitable culture conditions. This stability and robustness are conferred by tight network communication, mediated through electrical activity and neuropeptidergic signaling (Yamaguchi et al, 2003;Maywood et al, 2006Maywood et al, , 2011aLiu et al, 2007). Thus, synchronization of neuronal subpopulations across the nucleus maintains coherent ensemble molecular and electrophysiological rhythms.…”

Phosphorylation of Phosphoenolpyruvate Carboxylase Is Essential for Maximal and Sustained Dark CO2 Fixation and Core Circadian Clock Operation in the Obligate Crassulacean Acid Metabolism Species Kalanchoë fedtschenkoi

“…The level of delayed fluorescence (DF) has previously been reported to be under robust circadian control in K. fedtschenkoi and provides a simple high-throughput assay for measuring circadian period, robustness, and accuracy (Gould et al, 2009). DF was measured in the wild type, rPPCK1-1, and rPPCK1-3 under LL free-running conditions (Figure 7), and the data were analyzed to calculate key circadian rhythm statistics using Biodare Zielinski et al, 2014). The wild type had a robust DF oscillation ( Figure 7A).…”

“…The luminescence was normalized by subtracting the Y value of the best straight line from the raw Y value. Biodare was used to carry out fast Fourier transform (nonlinear leastsquare) analysis and spectral resampling on each DF time-course series using the time window from 24 to 108 h in order to generate period estimates and calculate the associated RAE Zielinski et al, 2014). The first 24 h of the data were excluded as this represents a bedding-in period for the leaves when transition effects, resulting from the leaves moving from light/dark cycles to constant light and temperature (LL), may be influencing the data.…”

Long-term monitoring of bioluminescence circadian rhythms of cells in a transgenic <i>Arabidopsis</i> mesophyll protoplast culture

“…At the three highest cell densities (2×10 5 -6×10 5 cells), the circadian rhythms were maintained for Circadian rhythms of protoplast-derived cells in MSP+PH medium (n=9 in LL ; n=15 in DD), MSP medium (n=9 in LL; n=18 in DD), W5 solution (n=9 in LL; n=15 in DD), and leaves on NF (n=12 in LL; n=12 in DD) were monitored as described in Figure 2. The period of each rhythm was estimated by FFT-NLLS, a multicomponent cosine fit (Zielinski et al 2014). Luminescence data in the range between 24 h and 96 h in constant conditions were used for the analysis.…”