Semiautomatic Segmentation of Plant Golgi Stacks in Electron Tomograms Using 3dmod

Ki, Keith Ka; Kang, Byung-Ho

doi:10.1007/978-1-4939-7262-3_8

Cited by 17 publications

(13 citation statements)

References 18 publications

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“…Tomograms were reconstructed using the etomo interface of the IMOD software package (Boulder Laboratory of 3D Electron Microscopy of the Cell). Tomogram analysis and 3D model reconstruction were performed with the 3dmod graphic module of the IMOD software package (Kang et al ., ; Toyooka and Kang, ; Mai and Kang, ).…”

Section: Methodsmentioning

confidence: 99%

A distinct class of vesicles derived from thetrans‐Golgi mediates secretion of xylogalacturonan in the root border cell

et al. 2017

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Root border cells lie on the surface of the root cap and secrete massive amounts of mucilage that contains polysaccharides and proteoglycans. Golgi stacks in the border cells have hypertrophied margins, reflecting elevated biosynthetic activity to produce the polysaccharide components of the mucilage. To investigate the three-dimensional structures and macromolecular compositions of these Golgi stacks, we examined high-pressure frozen/freeze-substituted alfalfa root cap cells with electron microscopy/tomography. Golgi stacks in border cells and peripheral cells, precursor cells of border cells, displayed similar morphological features, such as proliferation of trans cisternae and swelling of the trans cisternae and trans-Golgi network (TGN) compartments. These swollen margins give rise to two types of vesicles larger than other Golgi-associated vesicles. Margins of trans-Golgi cisternae accumulate the LM8 xylogalacturonan (XGA) epitope, and they become darkly stained large vesicles (LVs) after release from the Golgi. Epitopes for xyloglucan (XG), polygalacturonic acid/rhamnogalacturonan-I (PGA/RG-I) are detected in the trans-most cisternae and TGN compartments. LVs produced from TGN compartments (TGN-LVs) stained lighter than LVs and contained the cell wall polysaccharide epitopes seen in the TGN. LVs carrying the XGA epitope fuse with the plasma membrane only in border cells, whereas TGN-LVs containing the XG and PGA/RG-I epitopes fuse with the plasma membrane of both peripheral cells and border cells. Taken together, these results indicate that XGA is secreted by a novel type of secretory vesicles derived from trans-Golgi cisternae. Furthermore, we simulated the collapse in the central domain of the trans-cisternae accompanying polysaccharide synthesis with a mathematical model.

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Section: Methodsmentioning

confidence: 99%

A distinct class of vesicles derived from thetrans‐Golgi mediates secretion of xylogalacturonan in the root border cell

et al. 2017

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“…The slices within tomogram were manually drawn and contoured to generate a precise 3D reconstruction of the imaging sections. 39,40 Quantification of microvessel characteristics To calculate the microvessel density, we developed a MATLAB code with a graphical user interface (GUI). The GUI was used to set parameters to filter out objects that were not microvessels (such as single cells).…”

Section: Microscopymentioning

confidence: 99%

Differential functional roles of fibroblasts and pericytes in the formation of tissue-engineered microvascular networks in vitro

et al. 2020

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Formation of a perfusable microvascular network (μVN) is critical for tissue engineering of solid organs. Stromal cells can support endothelial cell (EC) self-assembly into a μVN, but distinct stromal cell populations may play different roles in this process. Here we describe the differential effects that two widely used stromal cell populations, fibroblasts (FBs) and pericytes (PCs), have on μVN formation. We examined the effects of adding defined stromal cell populations on the self-assembly of ECs derived from human endothelial colony forming cells (ECFCs) into perfusable μVNs in fibrin gels cast within a microfluidic chamber. ECs alone failed to fully assemble a perfusable μVN. Human lung FBs stimulated the formation of EC-lined μVNs within microfluidic devices. RNA-seq analysis suggested that FBs produce high levels of hepatocyte growth factor (HGF). Addition of recombinant HGF improved while the c-MET inhibitor, Capmatinib (INCB28060), reduced μVN formation within devices. Human placental PCs could not substitute for FBs, but in the presence of FBs, PCs closely associated with ECs, formed a common basement membrane, extended microfilaments intercellularly, and reduced microvessel diameters. Different stromal cell types provide different functions in microvessel assembly by ECs. FBs support μVN formation by providing paracrine growth factors whereas PCs directly interact with ECs to modify microvascular morphology.

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“…The resulting contours were smoothened, and their excess points were deleted with the drawing tool plug-in (http://www.andrewnoske.com/student/downloads/imod/drawingtools.html). This semiautomatic modeling method is explained by Mai and Kang (2017). Thylakoid membranes were outlined in every 4th slice, and obvious errors in the outlines were corrected before the contours were meshed to generate 3D models with the imodmesh command.…”

Section: Dual-axis Electron Tomography Tomogram Reconstruction Modementioning

confidence: 99%

Thylakoid-Bound Polysomes and a Dynamin-Related Protein, FZL, Mediate Critical Stages of the Linear Chloroplast Biogenesis Program in Greening Arabidopsis Cotyledons

et al. 2018

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Biogenesis of the complex 3D architecture of plant thylakoids remains an unsolved problem. Here, we analyzed this process in chloroplasts of germinating cotyledons using 3D electron microscopy and gene expression analyses of chloroplast proteins. Our study identified a linear developmental sequence with five assembly stages: tubulo-vesicular prothylakoids (24 h after imbibition [HAI]), sheet-like pregranal thylakoids that develop from the prothylakoids (36 HAI), proliferation of pro-grana stacks with wide tubular connections to the originating pregrana thylakoids (60 HAI), structural differentiation of pro-grana stacks and expanded stroma thylakoids (84 HAI), and conversion of the pro-grana stacks into mature grana stacks (120 HAI). Development of the planar pregranal thylakoids and the pro-grana membrane stacks coincides with the appearance of thylakoid-bound polysomes and photosystem II complex subunits at 36 HAI. ATP synthase, cytochrome, and light-harvesting complex II proteins are detected at 60 HAI, while PSI proteins and the curvature-inducing CURT1A protein appear at 84 HAI. If stromal ribosome biogenesis is delayed, prothylakoids accumulate until stromal ribosomes are produced, and grana-forming thylakoids develop after polysomes bind to the thylakoid membranes. In () mutants, in which thylakoid organization is perturbed, pro-grana stacks in cotyledons form discrete, spiral membrane compartments instead of organelle-wide membrane networks, suggesting that FZL is involved in fusing membrane compartments together. Our data demonstrate that the assembly of thylakoid protein complexes, CURT1 proteins, and FZL proteins mediate distinct and critical steps in thylakoid biogenesis.

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Semiautomatic Segmentation of Plant Golgi Stacks in Electron Tomograms Using 3dmod

Cited by 17 publications

References 18 publications

A distinct class of vesicles derived from thetrans‐Golgi mediates secretion of xylogalacturonan in the root border cell

A distinct class of vesicles derived from thetrans‐Golgi mediates secretion of xylogalacturonan in the root border cell

Differential functional roles of fibroblasts and pericytes in the formation of tissue-engineered microvascular networks in vitro

Thylakoid-Bound Polysomes and a Dynamin-Related Protein, FZL, Mediate Critical Stages of the Linear Chloroplast Biogenesis Program in Greening Arabidopsis Cotyledons

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