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77 protocols using ultracut r

1

Ultrastructural Analysis of Surgical Samples

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The samples collected during surgery were taken for primary fixation at 4 °C
for 24 hours in 2.5% glutaraldehyde containing 0.1 M phosphate buffer, and
then washed 3 times for 15 minutes with phosphate buffer. The blocks
obtained were cut at 700 nm thickness with an ultramicrotome (Leica Ultracut
R) and stained with toluidine blue. After determining the areas to be
displayed in transmission electron microscopic (TEM), every subject was
scored according to the criteria shown in Table 1[16 (link)].
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2

Analysis of Cambium-Derived Tissue in Transgenic Plants

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The second internode, 10th internode, and 20th internode (counting from the tip) were taken from 4-month-old wild-type and 35S::PtoCYCD3;3 plants. The samples were fixed in FAA (70% ethanol: glacial acetic acid: formaldehyde: glycerol = 18:1:1:1) for 24 h at room temperature and then dehydrated through a graded ethanol series (70%, 80%, 90%, and 100% ethanol; 20 min each step). Ethanol was replaced with ethanol: acetone (1:1) for 20 min and then with pure acetone for 20 min two times. Afterward, the samples were sequentially infiltrated with acetone: resin (2:1) for 3 h and then with acetone: resin (1:1) and acetone: resin (1:3) for 3 h. The samples were replaced with fresh resin for 12 h. After the resin replacement was repeated two times, stem segments were embedded into the resin for 24 h at 60 °C. One µm sections were obtained with a microtome (Leica ultracut R, Germany). The sections were floated on the water, heat-fixed to glass slides, stained with 0.05% toluidine blue, and observed under a Leica DM4000B light microscope. Data were measured on Image J. We measured five times in different quadrant sectors of the cross-sections about the width of cambium-derived tissues. All statistical analyses were performed using SPSS v16.0. Independent-Samples T-test was used.
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3

Ultrastructural Analysis of Trypanosoma Infection

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RAW macrophages and H9C2 cells were infected with trypomastigotes of the Y strain with 10 parasites per cell (MOI 10) for 24 h. They were then washed to eliminate the parasites that did not cause infection, and a fresh medium was added with or without 10 µM of UA for 24 additional hours. After that, cells were fixed with 2.5% glutaraldehyde (Pelco International, Fresno, CA, USA) in PBS at 10°C and processed by the Servicio de Preparación de Muestras de Microscopía Electrónica, STAN 3371IHEM-CONICET.
Briefly, each sample was washed in the same buffer, post-fixed in 1% OsO for 1 h at room temperature, dehydrated in a graded acetone solution series, and embedded in low viscosity epoxy resin (Pelco International). Then, ultrathin sections with interference color gray were cut by ultramicrotome Leica Ultracut R, mounted on grids, and stained with uranyl acetate and lead citrate (Reynolds 1963 (link)). Grids were examined under a Zeiss 900 electron microscope, with a Gatan digital camera (model Orius SC 1000).
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4

Ultrastructural Analysis of H9c2 Cardiac Cells

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H9c2 cardiac cells with or without homocysteine exposure were fixed with 2.5% glutaraldehyde in PBS for 2 h, then washed with 0.1 M PBS and postfixed with 1% OsO
4 in PBS at 4°C for 1 h. After extensive washes with cold water, the samples were dehydrated in gradient ethanol and embedded in Epon812 for ultrathin sectioning (80±5 nm) by Leica Ultracut R (Wetzler, Germany). After being counterstained with 2% uranyl acetate and lead citrate, the cells were observed under a transmission electron microscope (Hitachi-7500, Tokyo, Japan) to examine their ultrastructure, and images were captured with a CCD imaging system (Megaview-III, Munster, Germany).
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5

Citral Effect on Xcc-KVXCC1 Bacterial Ultrastructure

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In order to prepare Xcc-KVXCC1 cells for evaluating the citral effect on bacteria, overnight cultures of Xcc-KVXCC1 at 28 °C in NB was prepared for transmission electron microscopy (Leo 912 AB) analyses [12 (link)]. The citral was added to the bacterial culture at the MIC value. The bacterial suspensions were centrifuged at 6000 rpm for 7 min and cell pellets were pre-fixed on glutaraldehyde solution 2.5% (with cacodylate buffer 0.1 mol/L) for 24 h at −4 °C. Then samples were washed three times for 10 min with cacodylate buffer and post-fixed on 1.0% osmium tetroxide. The samples, which were washed on cacodylate buffer for 15, 30, and 60 min, were dehydrated in a graded ethanol series (30, 50, 70, 80, and 100%). Later, samples were embedded in propylene oxide and resin in ratios of 1:3, 1:1, 3:1, and pure resin for 12, 4, 12 and 24 h, the sample blocks were polymerized in an oven at 60 °C, for 48 h. Then sections of 75 nm by ultramicrotomy (Ultracut R, Leica, Wetzlar, Germany) were prepared and stained with 1% uranyl acetate and lead (II) nitrate. In this study, no-treated bacterial cells or streptomycin were used as negative and positive control, respectively.
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6

Ultrastructural Analysis of C. maluytinae

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One specimen of C. maluytinae with attached soft-parts was fully decalcified by immersion in 4% EDTA for several days. Pieces of the mantle, with their associated periostraca, were excised mainly from the ventral areas. They were CO2-critical-point dried (Polaron CPD 7501), post-fixed in OsO4 (2%) for 2 h at 4 °C and embedded in epoxy resin (Aname Epon 812). Blocks prepared in this way were sectioned with an ultramicrotome LEICA Ultracut R and prepared following standard procedures. Ultrathin sections (50 nm) were stained with uranyl acetate (1%) followed by lead citrate. They were observed with TEM (Zeiss Libra 120 Plus) at the Center for Scientific Instrumentation (CIC) of the University of Granada. Due to shortage of material, no specimen of C. natalyae was available for TEM observation.
The two most complete lamellae prepared by FIB and used for EBSD (see below) were also observed using a double Cs corrected FEI Titan G2 60–300 TEM equipped with an X-field emission gun and a Gatan Ultrascan camera (CIC, UGR). Imaging was performed in TEM mode at 300 kV, and 0.5–1 s exposure.
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7

High-Pressure Freezing and Electron Microscopy of Drosophila Embryos

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Embryos were fixed by the high-pressure freezing and freeze substitution (HPF/FS) method as previously described4 (link), 58 . Briefly, a Bal-Tec device was used to freeze stage 12–14 embryos. Freeze-substitution was performed with 1% osmium tetroxide, 0.1% uranyl acetate in 98% acetone and 2% methanol on dry ice. Fixed embryos were embedded in Epon (Sigma-Aldrich) and cut into thin sections with an ultramicrotome (Ultracut R; Leica). The sections were mounted on copper grids and post-stained with 2% uranyl acetate for 10 min and Sato’s lead solution59 (link) for 1 min to improve image contrast. Images were acquired on a transmission electron microscope (CM120; Philips).
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8

Liver Ultrastructural Analysis in Mice

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Mice were euthanized, and liver was rapidly fixed overnight at 4 °C in 1/2 strength Karnovsky’s (2% paraformaldehyde and 2.5% glutaraldehyde in 0.2 M sodium cacodylate buffer, pH 7.4). Tissues were post-fixed in 2% osmium tetroxide in 200 mM sodium cacodylate for 2 h at 4 °C and rinsed in 0.1 M cacodylate buffer. Samples were then blocked, and stained with 1% uranyl acetate overnight at 4 °C. The pellet was then rinsed with 0.1 M sodium acetate. Samples were dehydrated through a graded series of ethanol, and then infiltrated with Epon resin overnight at room temperature. They were then embedded in resin overnight at 60 °C. Thin sections were cut on a Leica Ultracut R, and collected onto formvar-carbon coated slot grids. Sections were examined on a JEOL 2100 transmission electron microscope. Images were recorded on film at ×5000 magnification.
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9

Multimodal Imaging Protocol

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T6 new century ultraviolet-visible spectrophotometer (Beijing, China), Scanning electron microscope (FEI Quanta 250, USA), Transmission electron microscope (JEM-2100, Japan), Ultramicrotome (Leica ultracut R, Germany).
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10

In vivo Electron Microscopy of Autophagy

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For in vivo electron microscopy experiments, euthanized mice were whole body perfused with cold PBS, followed by 2% paraformaldehyde in 0.1 M phosphate buffer (pH 7.4), and then 2.5% glutaraldehyde. Samples were sectioned into 2 cm cubes, followed by post-fixation for 6 h in 1% osmium tetraoxide. Samples were washed three times with PBS and underwent serial dehydration with graded alcohols. Samples were then embedded in epoxy resin. Each 2 cm tissue cube was sectioned into 70 nm thin sections with a microtome (Ultracut R; Leica), mounted on copper grids and post-stained with 2% uranyl acetate and 1% lead citrate. Sections were then dried and analyzed using a JEM 1011CX transmission electron microscope (Jeol, Peabody, MA). Images were acquired digitally from a randomly selected pool of 10–15 fields from nonischemic and ischemic limbs from WT and KO mice treated with either CQ or PBS. Autophagosomes were identified based on double membrane vesicles distinct from mitochondria and sarcoplasmic reticulum, and myofibers were identified as bundles containing distinct myofibrils. The number of autophagosomes/myofiber was calculated at 30,000x magnification from five images per animal.
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