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1.
Nat Commun ; 12(1): 458, 2021 01 19.
Artigo em Inglês | MEDLINE | ID: mdl-33469016

RESUMO

Cell shape is crucial for the function and development of organisms. Yet, versatile frameworks for cell shape quantification, comparison, and classification remain underdeveloped. Here, we introduce a visibility graph representation of shapes that facilitates network-driven characterization and analyses across shapes encountered in different domains. Using the example of complex shape of leaf pavement cells, we show that our framework accurately quantifies cell protrusions and invaginations and provides additional functionality in comparison to the contending approaches. We further show that structural properties of the visibility graphs can be used to quantify pavement cell shape complexity and allow for classification of plants into their respective phylogenetic clades. Therefore, the visibility graphs provide a robust and unique framework to accurately quantify and classify the shape of different objects.


Assuntos
Forma Celular , Processamento de Imagem Assistida por Computador/métodos , Folhas de Planta/citologia , Algoritmos , Arabidopsis/citologia , Microscopia/métodos , Software
2.
Bioinformatics ; 36(9): 2950-2951, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-31971582

RESUMO

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. AVAILABILITY AND IMPLEMENTATION: CytoSeg 2.0 is open-source software under the GPL and is available on Github: https://github.com/jnowak90/CytoSeg2.0. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Projetos de Pesquisa , Software , Citoesqueleto de Actina , Razão Sinal-Ruído
3.
Plant Physiol ; 181(2): 630-644, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31416828

RESUMO

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.


Assuntos
Actinas/metabolismo , Gravitropismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Brotos de Planta/crescimento & desenvolvimento , Citoesqueleto de Actina/fisiologia , Luz , Oryza/crescimento & desenvolvimento , Oryza/efeitos da radiação , Plastídeos/fisiologia
4.
Nat Plants ; 5(5): 498-504, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31040442

RESUMO

Cotton (Gossypium hirsutum) fibres consist of single cells that grow in a highly polarized manner, assumed to be controlled by the cytoskeleton1-3. 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 growth2-4. 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.


Assuntos
Fibra de Algodão , Citoesqueleto/ultraestrutura , Gossypium/ultraestrutura , Actinas/ultraestrutura , Proteínas de Fluorescência Verde , Imageamento Tridimensional , Microscopia Intravital/métodos , Microtúbulos/ultraestrutura
5.
Proc Natl Acad Sci U S A ; 114(28): E5741-E5749, 2017 07 11.
Artigo em Inglês | MEDLINE | ID: mdl-28655850

RESUMO

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.


Assuntos
Citoesqueleto de Actina/metabolismo , Arabidopsis/citologia , Hipocótilo/citologia , Células Vegetais/metabolismo , Transporte Biológico , Citoplasma/metabolismo , Complexo de Golgi/metabolismo , Processamento de Imagem Assistida por Computador , Imageamento Tridimensional , Microtúbulos/metabolismo , Modelos Estatísticos , Organelas/metabolismo , Fenótipo , Transporte Proteico , Análise de Regressão
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