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392 protocols using ultracut uct

1

Detailed Electron Microscopy Specimen Preparation

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Specimens for electron microscopy were immediately fixed in 2.5% phosphate-buffered glutaraldehyde (pH 7.4), post fixed in 1% osmium tetroxide in the same buffer at 4 °C and dehydrated. For transmission electron microscopy, the specimens were embedded in epoxy resin. Ultrathin sections (60–70 nm) were obtained (Leica ultra-cut UCT) and stained with uranyl acetate and lead citrate72 , examined and photographed (JEOL JEM 2100 electron microscope; Jeol Ltd, Tokyo, Japan) in Electron Microscope Research Laboratory (EMRL) of Faculty of Agriculture, El Mansoura University, Egypt.

Toluidine blue stain

Semi-thin sections (1 µm) were also obtained (Leica ultra-cut UCT), stained with toluidine blue and examined by light microscope.
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2

Ultra-structural Analysis of Biological Samples

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Cells were fixed with 2% glutaraldehyde for 5 hrs and postfixed with 0.5% paraformaldehyde; washed with a 0.1 M cacodylate buffer (pH = 7.4), contrasted with a 1% OsO4 solution in a cacodylate buffer (pH = 7.4), dehydrated in an increasing series of ethanol solutions, followed by dehydration with acetone, impregnated, and embedded in Epon-812 (following manufacturer’s instructions). Ultrathin sections (100–200 nm thick) were cut with a diamond knife (Diatome) on an ultramicrotome Ultracut-UCT (Leica Microsystems), transferred to copper 200 mesh grids, covered with formvar (SPI, Washington, DC, USA), and contrasted with lead citrate, according to the Reynolds established procedure [46 (link)]. For the analytical electron microscopy study, contrasting was omitted in some cases.
Ultra-thin sections were examined in transmission electron microscopes JEM-1011 and JEM-2100 (Jeol, Tokyo, Japan) with accelerating voltages of 80 kV and 200 kV, respectively, and magnification of ×13,000–21,000. Images were recorded with Ultrascan 1000XP and Orius SC1000D CCD cameras (Gatan, Pleasanton, CA, USA).
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3

Ultrastructural Skin Analysis in Pups

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P1 pups were anesthetized and perfused with 2.5% glutaraldehyde in 0.1 M sodium cacodylate buffer. 1-mm3 dorsal skin section was taken from the perfused pups and placed in the same fixative for an additional 2 h at 4 °C. The skin samples were rinsed three times in 0.2 M sucrose/ sodium cacodylate buffer and were left in this buffer overnight. The samples were then post-fixed in ferrocyanide-reduced osmium tetroxide for 1 h at 4 °C followed by dehydration with acetone, infiltration with acetone/epon, and embedded in Epon. Sections were cut with Leica Microsystems Ultracut UCT. To examine the sections, FEI Tecnai 12 BioTwin 120 kV Transmission Electron Microscope imaged with an AMT XR80C CCD Camera System.
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Transmission Electron Microscopy Preparation

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Cells were prefixed in 2.5% glutaraldehyde and subsequently fixed in 0.1 M sodium cacodylate buffer (pH 7.4) containing 1% osmium tetroxide for 1 h at 4 °C. The fixed cells were then stained en bloc, postfixed in 1% osmium tetroxide, dehydrated through a graded ethanol series, and embedded in epoxy resin. Ultrathin sections (∼90 nm) were then cut using Ultracut UCT (Leica Microsystems, Wetzlar, Germany), stained with aqueous lead citrate and uranyl acetate, and examined using TEM (JEM 1400; JEOL, Tokyo, Japan) at an acceleration voltage of 75 kV.
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5

Leaf Anatomy Investigation via Histology

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To investigate the internal anatomy of leaves, sections were cut through the leaf midrib. The proximal halves of individual leaves were fixed in 0.3 mg/cm3 paraformaldehyde, 5% ethanoic acid, and 50% ethanol, and then dehydrated in a graded ethanol (50%–95%) series. Sections (1 μm thick) were cut with a micrometre (Ultracut UCT, Leica Microsystems,Welzlar, Germany), stained with toluidine, and imaged with a microscope and imaging system (Optiphot 2 with DS-L1, Nikon, Tokyo, Japan). The cut surface was mid-way between the midrib and margin, near the widest point of the leaf.
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6

Freeze-Substitution Microscopy Protocol

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Cells in the log phase were sandwiched between copper disks and frozen in liquid propane. The frozen cells were then freeze-substituted with acetone containing 2% glutaraldehyde and 2% tannic acid. After washing with acetone, samples were further fixed with 2% osmium tetroxide in acetone and dehydrated with ethanol. Samples were then infiltrated with propylene oxide twice and with a 70:30 mixture of propylene oxide and resin (Quetol-651; Nisshin EM, Tokyo, Japan), and the propylene oxide was volatilized. Samples were transferred to fresh 100% resin, and the resin was polymerized at 60 °C. Ultrathin sections (70 nm thick) of the blocks were prepared with an ultramicrotome (Ultracut UCT, Leica Microsystems, Wetzlar Germany). The sections were placed on copper grids, stained with lead stain solution (Sigma), and observed under a transmission electron microscope (JEM-1400Plus, JOEL, Tokyo, Japan).
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Ultrastructural Analysis of Phage-Infected Cells

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Samples of non-infected cells and phiKZ-infected cells after 15 and 30 min of infection were chemically fixed using a mixture of glutaraldehyde (0.1%) and formaldehyde (2%) for 30 min at room temperature. The cells were collected by centrifugation at 5000× g and 4 °C. Then, cell pellets were washed twice with sterile PBS and subjected to LR White (Polyscience, Inc., Warrington, PA, USA) embedding, according to the manufacturer’s protocol. Thin sections were cut with a diamond knife (Diatome) on the ultramicrotomes Ultracut-UCT (Leica Microsystems, Buffalo Grove, IL, USA), transferred to copper 200 mesh grids, covered with formvar (SPI, Washington, DC, USA). Some sections were contrasted with lead citrate.
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8

Ultrastructural Analysis of Plant Cuticles

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For TEM analysis of cuticles, the apical 3 mm regions of 7-day-old dark-grown hypocotyls from diploid and tetraploid plants were excised and fixed at 4°C overnight in 0.05 M cacodylate buffer (pH 7.4) containing 2% glutaraldehyde and 2% paraformaldehyde. Samples were next fixed with 1% tannic acid in cacodylate buffer for 1 h at 4°C and were then rinsed four times in 0.05 M cacodylate buffer (30 min per wash). Finally, samples were fixed in 1% osmium tetroxide for 3 h at 4°C. After dehydration in graded ethanol solutions (50%, 70%, 90%, and 100%), samples were embedded in epoxy resin Quetol-651 (Nisshin EM Co. Ltd., Japan). Thin sections (80 nm thickness) were prepared using an ultramicrotome (Ultracut UCT, Leica Microsystems), collected on copper grids, stained with 2% uranyl acetate and lead citrate, and examined with a transmission electron microscope (JEM-1400Plus, JEOL Ltd., Japan).
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9

Ultrastructural Analysis of Plant Leaves

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Leaves were cut into small pieces and rapidly immersed in 0.05 M cacodylate buffer (pH 7.4) containing 2% paraformaldehyde and 2% glutaraldehyde at 4 °C overnight. After fixation, samples were rinsed 3 times with 0.05 M cacodylate buffer, followed by post-fixation with 2% osmium tetroxide in 0.05 M cacodylate buffer at 4 °C for 4 h. Samples were dehydrated in a graded ethanol series, infiltrated with propylene oxide, and finally embedded in Quetol-651 (Nisshin EM Co.). Ultrathin sections were cut with a diamond knife using an ultramicrotome (Ultracut UCT; Leica Microsystems), picked up on copper grids, and stained with uranyl acetate and lead citrate. Sections were observed under a transmission electron microscope (JEM-1200EX; JEOL Ltd) at an acceleration voltage of 80 kV. Digital images were taken with a CCD camera (Veleta; Olympus Soft Imaging Solutions GmbH).
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10

Leaf Anatomy Investigation via Histology

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To investigate the internal anatomy of leaves, sections were cut through the leaf midrib. The proximal halves of individual leaves were fixed in 0.3 mg/cm3 paraformaldehyde, 5% ethanoic acid, and 50% ethanol, and then dehydrated in a graded ethanol (50%–95%) series. Sections (1 μm thick) were cut with a micrometre (Ultracut UCT, Leica Microsystems,Welzlar, Germany), stained with toluidine, and imaged with a microscope and imaging system (Optiphot 2 with DS-L1, Nikon, Tokyo, Japan). The cut surface was mid-way between the midrib and margin, near the widest point of the leaf.
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