Advances in Imaging Plant Cell Dynamics

Komis, George; Novák, Dominik; Ovečka, Miroslav; Šamajová, Olga; Šamaj, Jozef

doi:10.1104/pp.17.00962

Cited by 58 publications

(57 citation statements)

References 122 publications

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“…Recent advances in microscopy that enable resolution below the theoretical diffraction limit are becoming increasingly popular for imaging plant cells [46,47,51]. Depending on the instrument, super resolution microscopy (SRM) imaging can resolve nuclear signals ca.…”

Section: Checklist For a Good Imaging Designmentioning

confidence: 99%

“…In particular, versatile Structured Illumination Microscopy (SIM) [52] is a promising approach. Unlike other SRM approaches that require specific fluorophores, SIM is compatible with regular fluorescent probes due to its relatively fast acquisition rate [46,47,51]. SIM has been successfully applied to image the rapid movements of CRISPR-Cas9-tagged telomeres in the tobacco leaf epidermis [53].…”

Section: Checklist For a Good Imaging Designmentioning

confidence: 99%

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Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Dumur

Duncan

Graumann

et al. 2019

Nucleus

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The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. Abbreviations: 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel

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Section: Checklist For a Good Imaging Designmentioning

confidence: 99%

Section: Checklist For a Good Imaging Designmentioning

confidence: 99%

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Dumur

Duncan

Graumann

et al. 2019

Nucleus

View full text Add to dashboard Cite

show abstract

“…S4B and FP-tagged proteins; Table II) can be visualized with increased precision by clearing plant tissues using new techniques that forgo costly and time-consuming embedding and sectioning steps (Ursache et al, 2018). Although the resolution of confocal microscopes was limited historically by diffraction to greater than 200 nm (Hell, 2007), this barrier has been surpassed in the last decade to enable the imaging of living plant cells at the nanoscale level (Komis et al, 2018). With the advent of superresolution fluorescence microscopy, polysaccharide-binding probes such as S4B can potentially be visualized in the walls of living plant cells at a resolution approaching more invasive methods such as atomic force microscopy and electron microscopy ( Table I; Liesche et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Monitoring Polysaccharide Dynamics in the Plant Cell Wall

2018

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“…To achieve a live imaging of biological samples, various types of confocal microscopies were developed in these 30 years to observe a fluorescence-labeled specimen [1], including the twophoton excitation microscopy [2], the structured illumination microscopy [3], the stimulated emission depletion microscopy [4], and the photoactivated localization microscope [5]. Although these confocal microscopies allowed a time-resolved 3D-imaging of live organisms at spatial resolutions down to 30 nm and were applied to various plant tissues [6], they could visualize only labeled or autofluorescent substances within a limited thickness of samples. Recently, an optical phase-contrast tomography termed "marker-free phase nanoscopy" was developed [7], which enabled an observation of unstained specimens at 90 nm resolution but with a remaining limitation in the sample thickness.…”

Section: Introductionmentioning

confidence: 99%

Visualization of internal 3D structure of small live seed on germination by laboratory-based X-ray microscopy with phase contrast computed tomography

et al. 2020

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Background: The visualization of internal 3D-structure of tissues at micron resolutions without staining by contrast reagents is desirable in plant researches, and it can be achieved by an X-ray computed tomography (CT) with a phase-retrieval technique. Recently, a laboratory-based X-ray microscope adopting the phase contrast CT was developed as a powerful tool for the observation of weakly absorbing biological samples. Here we report the observation of unstained pansy seeds using the laboratory-based X-ray phase-contrast CT. Results: A live pansy seed within 2 mm in size was simply mounted inside a plastic tube and irradiated by in-house X-rays to collect projection images using a laboratory-based X-ray microscope. The phase-retrieval technique was applied to enhance contrasts in the projection images. In addition to a dry seed, wet seeds on germination with the poorer contrasts were tried. The phase-retrieved tomograms from both the dry and the wet seeds revealed a cellular level of spatial resolutions that were enough to resolve cells in the seeds, and provided enough contrasts to delineate the boundary of embryos manually. The manual segmentation allowed a 3D rendering of embryos at three different stages in the germination, which visualized an overall morphological change of the embryo upon germination as well as a spatial arrangement of cells inside the embryo. Conclusions: Our results confirmed an availability of the laboratory-based X-ray phase-contrast CT for a 3D-structural study on the development of small seeds. The present method may provide a unique way to observe live plant tissues at micron resolutions without structural perturbations due to the sample preparation.

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Advances in Imaging Plant Cell Dynamics

Cited by 58 publications

References 122 publications

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

Monitoring Polysaccharide Dynamics in the Plant Cell Wall

Visualization of internal 3D structure of small live seed on germination by laboratory-based X-ray microscopy with phase contrast computed tomography

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