Nishio Haruki, Hirano Satoyuki, Kodama Yutaka
Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga, 522‑8522, Japan.
Center for Ecological Research, Kyoto University, Shiga, 520‑2113, Japan.
Plant Methods. 2023 Jul 5;19(1):67. doi: 10.1186/s13007-023-01038-6.
Organelle motility is essential for the correct cellular function of various eukaryotic cells. In plant cells, chloroplasts move towards the intracellular area irradiated by a weak light to maximise photosynthesis. To initiate this process, an unknown signal is transferred from the irradiated area to distant chloroplasts. Quantification of this chloroplast movement has been performed using visual estimations that are analyst-dependent and labour-intensive. Therefore, an objective and faster method is required.
In this study, we developed the cellssm package of R ( https://github.com/hnishio/cellssm.git ), which is a user-friendly tool for state-space modelling to statistically analyse the directional movement of cells or organelles. Our method showed a high accuracy in estimating the start time of chloroplast movement in the liverwort Marchantia polymorpha over a short period. The tool indicated that chloroplast movement accelerates during transport to the irradiated area and that signal transfer speed is uneven within a cell. We also developed a method to estimate the common dynamics among multiple chloroplasts in each cell, which clarified different characteristics among cells.
We demonstrated that state-space modelling is a powerful method to understand organelle movement in eukaryotic cells. The cellssm package can be applied to various directional movements (both accumulation and avoidance) at cellular and subcellular levels to estimate the true transition of states behind the time-series data.
细胞器运动对于各种真核细胞的正确细胞功能至关重要。在植物细胞中，叶绿体向弱光照射的细胞内区域移动，以最大限度地进行光合作用。为启动这一过程，一个未知信号从受照射区域传递到远处的叶绿体。对这种叶绿体运动的量化一直是通过依赖分析人员且劳动强度大的视觉估计来进行的。因此，需要一种客观且更快的方法。
在本研究中，我们开发了R语言的cellssm软件包（https://github.com/hnishio/cellssm.git），它是一种用户友好的状态空间建模工具，用于对细胞或细胞器的定向运动进行统计分析。我们的方法在短时间内估计地钱多歧苔叶绿体运动的开始时间时显示出高精度。该工具表明，叶绿体在向受照射区域运输过程中运动加速，并且信号在细胞内的传递速度不均匀。我们还开发了一种方法来估计每个细胞中多个叶绿体之间的共同动态，这揭示了不同细胞之间的不同特征。
我们证明了状态空间建模是理解真核细胞中细胞器运动的有力方法。cellssm软件包可应用于细胞和亚细胞水平的各种定向运动（积累和回避），以估计时间序列数据背后状态的真实转变。
