TY - JOUR A1 - Nowak, Jacqueline A1 - Gennermann, Kristin A1 - Persson, Staffan A1 - Nikoloski, Zoran T1 - CytoSeg 2.0 BT - automated extraction of actin filaments JF - Bioinformatics N2 - Motivation: Actin filaments (AFs) are dynamic structures that substantially change their organization over time. The dynamic behavior and the relatively low signal-to-noise ratio during live-cell imaging have rendered the quantification of the actin organization a difficult task. Results: We developed an automated image-based framework that extracts AFs from fluorescence microscopy images and represents them as networks, which are automatically analyzed to identify and compare biologically relevant features. Although the source code is freely available, we have now implemented the framework into a graphical user interface that can be installed as a Fiji plugin, thus enabling easy access by the research community. Y1 - 2020 U6 - https://doi.org/10.1093/bioinformatics/btaa035 SN - 1367-4803 SN - 1460-2059 VL - 36 IS - 9 SP - 2950 EP - 2951 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Yu, Yanjun A1 - Wu, Shenjie A1 - Nowak, Jacqueline A1 - Wang, Guangda A1 - Han, Libo A1 - Feng, Zhidi A1 - Mendrinna, Amelie A1 - Ma, Yinping A1 - Wang, Huan A1 - Zhang, Xiaxia A1 - Tian, Juan A1 - Dong, Li A1 - Nikoloski, Zoran A1 - Persson, Staffan A1 - Kong, Zhaosheng T1 - Live-cell imaging of the cytoskeleton in elongating cotton fibres JF - Nature plants N2 - Cotton (Gossypium hirsutum) fibres consist of single cells that grow in a highly polarized manner, assumed to be controlled by the cytoskeleton(1-3). However, how the cytoskeletal organization and dynamics underpin fibre development remains unexplored. Moreover, it is unclear whether cotton fibres expand via tip growth or diffuse growth(2-4). We generated stable transgenic cotton plants expressing fluorescent markers of the actin and microtubule cytoskeleton. Live-cell imaging revealed that elongating cotton fibres assemble a cortical filamentous actin network that extends along the cell axis to finally form actin strands with closed loops in the tapered fibre tip. Analyses of F-actin network properties indicate that cotton fibres have a unique actin organization that blends features of both diffuse and tip growth modes. Interestingly, typical actin organization and endosomal vesicle aggregation found in tip-growing cell apices were not observed in fibre tips. Instead, endomembrane compartments were evenly distributed along the elongating fibre cells and moved bi-directionally along the fibre shank to the fibre tip. Moreover, plus-end tracked microtubules transversely encircled elongating fibre shanks, reminiscent of diffusely growing cells. Collectively, our findings indicate that cotton fibres elongate via a unique tip-biased diffuse growth mode. Y1 - 2019 U6 - https://doi.org/10.1038/s41477-019-0418-8 SN - 2055-026X SN - 2055-0278 VL - 5 IS - 5 SP - 498 EP - 504 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Song, Yu A1 - Li, Gang A1 - Nowak, Jacqueline A1 - Zhang, Xiaoqing A1 - Xu, Dongbei A1 - Yang, Xiujuan A1 - Huang, Guoqiang A1 - Liang, Wanqi A1 - Yang, Litao A1 - Wang, Canhua A1 - Bulone, Vincent A1 - Nikoloski, Zoran A1 - Hu, Jianping A1 - Persson, Staffan A1 - Zhang, Dabing T1 - The Rice Actin-Binding Protein RMD Regulates Light-Dependent Shoot Gravitropism JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Light and gravity are two key determinants in orientating plant stems for proper growth and development. The organization and dynamics of the actin cytoskeleton are essential for cell biology and critically regulated by actin-binding proteins. However, the role of actin cytoskeleton in shoot negative gravitropism remains controversial. In this work, we report that the actin-binding protein Rice Morphology Determinant (RMD) promotes reorganization of the actin cytoskeleton in rice (Oryza sativa) shoots. The changes in actin organization are associated with the ability of the rice shoots to respond to negative gravitropism. Here, light-grown rmd mutant shoots exhibited agravitropic phenotypes. By contrast, etiolated rmd shoots displayed normal negative shoot gravitropism. Furthermore, we show that RMD maintains an actin configuration that promotes statolith mobility in gravisensing endodermal cells, and for proper auxin distribution in light-grown, but not dark-grown, shoots. RMD gene expression is diurnally controlled and directly repressed by the phytochrome-interacting factor-like protein OsPIL16. Consequently, overexpression of OsPIL16 led to gravisensing and actin patterning defects that phenocopied the rmd mutant. Our findings outline a mechanism that links light signaling and gravity perception for straight shoot growth in rice. Y1 - 2019 U6 - https://doi.org/10.1104/pp.19.00497 SN - 0032-0889 SN - 1532-2548 VL - 181 IS - 2 SP - 630 EP - 644 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Breuer, David A1 - Nowak, Jacqueline A1 - Ivakov, Alexander A1 - Somssich, Marc A1 - Persson, Staffan A1 - Nikoloski, Zoran T1 - System-wide organization of actin cytoskeleton determines organelle transport in hypocotyl plant cells JF - Proceedings of the National Academy of Sciences of the United States of America N2 - The actin cytoskeleton is an essential intracellular filamentous structure that underpins cellular transport and cytoplasmic streaming in plant cells. However, the system-level properties of actin-based cellular trafficking remain tenuous, largely due to the inability to quantify key features of the actin cytoskeleton. Here, we developed an automated image-based, network-driven framework to accurately segment and quantify actin cytoskeletal structures and Golgi transport. We show that the actin cytoskeleton in both growing and elongated hypocotyl cells has structural properties facilitating efficient transport. Our findings suggest that the erratic movement of Golgi is a stable cellular phenomenon that might optimize distribution efficiency of cell material. Moreover, we demonstrate that Golgi transport in hypocotyl cells can be accurately predicted from the actin network topology alone. Thus, our framework provides quantitative evidence for system-wide coordination of cellular transport in plant cells and can be readily applied to investigate cytoskeletal organization and transport in other organisms. KW - actin KW - cytoskeleton KW - Golgi KW - image processing KW - networks Y1 - 2017 U6 - https://doi.org/10.1073/pnas.1706711114 SN - 0027-8424 VL - 114 SP - E5741 EP - E5749 PB - National Acad. of Sciences CY - Washington ER -