Wagner Lucas, Schmal Christoph, Staiger Dorothee, Danisman Selahattin
Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany ; Institute for Theoretical Biology, Charité Universitätsmedizin, Berlin, Germany.
Plant Methods. 2017 Jan 3;13:2. doi: 10.1186/s13007-016-0153-3. eCollection 2017.
The analysis of circadian leaf movement rhythms is a simple yet effective method to study effects of treatments or gene mutations on the circadian clock of plants. Currently, leaf movements are analysed using time lapse photography and subsequent bioinformatics analyses of leaf movements. Programs that are used for this purpose either are able to perform one function (i.e. leaf tip detection or rhythm analysis) or their function is limited to specific computational environments. We developed a leaf movement analysis tool-PALMA-that works in command line and combines image extraction with rhythm analysis using Fast Fourier transformation and non-linear least squares fitting.
We validated PALMA in both simulated time series and in experiments using the known short period mutant (-). We compared PALMA with two established leaf movement analysis tools and found it to perform equally well. Finally, we tested the effect of reduced iron conditions on the leaf movement rhythms of wild type plants. Here, we found that PALMA successfully detected period lengthening under reduced iron conditions.
PALMA correctly estimated the period of both simulated and real-life leaf movement experiments. As a platform-independent console-program that unites both functions needed for the analysis of circadian leaf movements it is a valid alternative to existing leaf movement analysis tools.
分析叶片昼夜运动节律是研究处理或基因突变对植物生物钟影响的一种简单而有效的方法。目前，使用延时摄影和随后对叶片运动的生物信息学分析来分析叶片运动。用于此目的的程序要么只能执行一种功能（即叶尖检测或节律分析），要么其功能仅限于特定的计算环境。我们开发了一种叶片运动分析工具——PALMA，它在命令行中运行，并结合了图像提取以及使用快速傅里叶变换和非线性最小二乘法拟合的节律分析。
我们在模拟时间序列和使用已知短周期突变体（-）的实验中验证了PALMA。我们将PALMA与两种已建立的叶片运动分析工具进行了比较，发现它表现得同样出色。最后，我们测试了缺铁条件对野生型植物叶片运动节律的影响。在此，我们发现PALMA成功检测到了缺铁条件下的周期延长。
PALMA正确估计了模拟和实际叶片运动实验的周期。作为一个独立于平台的控制台程序，它整合了分析叶片昼夜运动所需的两种功能，是现有叶片运动分析工具的有效替代方案。
