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 - THES A1 - Nowak, Jacqueline T1 - Devising computational tools to quantify the actin cytoskeleton and pavement cell shape using network-based approaches N2 - Recent advances in microscopy have led to an improved visualization of different cell processes. Yet, this also leads to a higher demand of tools which can process images in an automated and quantitative fashion. Here, we present two applications that were developed to quantify different processes in eukaryotic cells which rely on the organization and dynamics of the cytoskeleton.. In plant cells, microtubules and actin filaments form the backbone of the cytoskeleton. These structures support cytoplasmic streaming, cell wall organization and tracking of cellular material to and from the plasma membrane. To better understand the underlying mechanisms of cytoskeletal organization, dynamics and coordination, frameworks for the quantification are needed. While this is fairly well established for the microtubules, the actin cytoskeleton has remained difficult to study due to its highly dynamic behaviour. One aim of this thesis was therefore to provide an automated framework to quantify and describe actin organization and dynamics. We used the framework to represent actin structures as networks and examined the transport efficiency in Arabidopsis thaliana hypocotyl cells. Furthermore, we applied the framework to determine the growth mode of cotton fibers and compared the actin organization in wild-type and mutant cells of rice. Finally, we developed a graphical user interface for easy usage. Microtubules and the actin cytoskeleton also play a major role in the morphogenesis of epidermal leaf pavement cells. These cells have highly complex and interdigitated shapes which are hard to describe in a quantitative way. While the relationship between microtubules, the actin cytoskeleton and shape formation is the object of many studies, it is still not clear how and if the cytoskeletal components predefine indentations and protrusions in pavement cell shapes. To understand the underlying cell processes which coordinate cell morphogenesis, a quantitative shape descriptor is needed. Therefore, the second aim of this thesis was the development of a network-based shape descriptor which captures global and local shape features, facilitates shape comparison and can be used to evaluate shape complexity. We demonstrated that our framework can be used to describe and compare shapes from various domains. In addition, we showed that the framework accurately detects local shape features of pavement cells and outperform contending approaches. In the third part of the thesis, we extended the shape description framework to describe pavement cell shape features on tissue-level by proposing different network representations of the underlying imaging data. N2 - Aktuelle Entwicklungen in der Mikroskopie haben zu einer verbesserten Visualisierung von verschiedenen Zellprozessen geführt. Dennoch führt das auch zu einem höheren Bedarf an Werkzeugen, die Bilder in einer automatisierten und quantitativen Weise bearbeiten und analysieren können. Hier präsentieren wir zwei Anwendungen, die entwickelt wurden, um verschiedene Prozesse in eukaryotischen Zellen zu quantifizieren, welche von der Organisation und Dynamik des Zytoskeletts abhängig sind. In Pflanzenzellen bilden Mircotubuli und Aktinfilamente das Rückgrat des Zytoskeletts. Diese Strukturen unterstützen die Zytoplasmaströmung, die Organisation der Zellwand und den Transport von zellulärem Material zu und von der Plasmamembran. Um die zugrundeliegenden Mechanismen der Organisation, Dynamik und Koordination des Zytoskeletts zu verstehen, sind Hilfsmittel zur Quantifizierung notwendig. Während das ziemlich ausführlich für Microtubuli getan wurde, bleibt das Aktin-Zytoskelett schwer zu studieren aufgrund seines hoch dynamischen Verhaltens. Das erste Ziel dieser Arbeit war es daher, einen automatisierten Framework zu entwickeln, der die Aktin-Organisation und Dynamik quantifiziert und beschreibt. Wir haben diesen Framework genutzt, um Aktin-Strukturen als Netzwerke zu repräsentieren und haben damit die Transporteffizienz in Arabidopsis thaliana Hypocotylzellen untersucht. Des Weiteren haben wir den Framework genutzt, um den Wachstumsmodus in Baumwollfasern zu bestimmen und um die Aktin-Organisation in Reis-Wildtyp und Mutanten zu vergleichen. Zuletzt haben wir eine grafische Benutzeroberfläche zur einfacheren Benutzung entwickelt. Microtubuli und das Aktin-Zytoskelett spielen auch eine große Rolle in der Morphogenese von epidermalen Blattzellen. Diese Zellen haben hochkomplexe und interdigitale Formen, welche sehr schwer in einer quantitativen Art zu beschreiben sind. Während die Beziehung zwischen Microtubuli, dem Aktin-Zytoskelett und Formgestaltung der Zellen in vielen Studien untersucht wurde, ist es immer noch nicht ganz klar wie und ob die Zytoskelettkomponenten die Ein- und Ausbuchtungen in Blattzellen vorherbestimmen. Um die zugrundeliegenden Zellprozesse zu verstehen, die die Zellmorphogenese koordinieren, sind quantitative Beschreiber von Formen notwendig. Daher war das zweite Ziel dieser Arbeit die Entwicklung eines netzwerkbasierten Gestaltbeschreibers, welcher globale und lokale Gestaltmerkmale erfasst, einen Gestaltvergleich ermöglich und die Komplexität von Formen evaluieren kann. Wir haben nachgewiesen, dass unser Framework benutzt werden kann, um Formen aus verschiedenen Bereichen zu beschreiben und zu vergleichen. Darüber hinaus haben wir gezeigt, dass der Framework lokale Gestaltmerkmale in Blattzellen akkurat ermittelt und andere konkurrierende Methoden hinter sich lässt. Im dritten Teil der Arbeit haben wir den Gestaltbeschreiber erweitert, um Gestaltmerkmale von Blattzellen, bezogen auf das ganze Zellgewebe, zu beschreiben, indem wir verschiedene Netzwerkrepräsentationen der zugrundeliegenden Bilddaten vorstellen. KW - Netzwerke KW - Bildanalyse KW - Pflanzenzellen KW - Aktinzytoskelett KW - Zellform KW - pavement cells image analysis KW - cell shape KW - cell morphogenesis KW - actin cytoskeleton machine KW - learning networks plant KW - cells epidermis Y1 - 2020 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 - TY - GEN 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 T2 - Proceedings of the National Academy of Sciences of the United States of America Y1 - 2017 U6 - https://doi.org/10.1073/pnas.1712371114 SN - 0027-8424 VL - 114 SP - E6732 EP - E6732 PB - National Acad. of Sciences CY - Washington ER -