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14 protocols using ultracut ultramicrotome

1

Placental Tissue Preparation for Microscopy

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Some fragments of placentas were fixed in a buffered, 2.5% paraformaldehyde solution. After it was rinsed in a phosphate buffer, the material was additionally fixed in buffered osmium (VIII) oxide–OsO4 for 1 h. The tissues were washed twice (2 × 30 min) with phosphate buffer and dehydrated in the alcohol-acetone series. Finally, the material was embedded in epoxy resin. After a polymerization lasting 3 days at 60 °C, semi-thin sections (0.5 µm thick) were obtained using a Reichert-Jung Ultracut ultramicrotome and stained with methylene blue solution.
Both paraffin sections and semi-thin sections were analyzed using an Olympus BX60 light microscope equipped with an
DP74 digital camera. Microphotographic documentation was obtained using the Olympus cellSens Standard software version 3 [23 (link)].
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2

Scanning Electron Microscopy of Rare Flowers

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Flowers of 12 selected microspecies collectively representing seven of the nine macrospecies were either collected by us in the field (most in Crete in 2017) or, in five cases, selected from among samples previously collected by knowledgeable individuals and deposited in the Spirit Collection of the Royal Botanic Gardens Kew.
Preparation for scanning electron microscopy involved selecting flowers from each inflorescence for dehydration through an alcohol series to 100% ethanol. They were then stabilised using an Autosamdri 815B critical-point drier, mounted onto stubs using double-sided adhesive tape, coated with platinum using an Emtech K550X sputter-coater, and examined under a Hitachi cold-field emission SEM S-4700-II at 2 kV. The resulting images were recorded digitally for subsequent aggregation in Adobe Photoshop.
In addition, flowers of a representative member of macrospecies Fusca from Sicily were prepared for anatomical light microscopy. Alcohol-fixed flowers were transferred through an ethanol series to 100% ethanol, followed by an ethanol–LR-White resin series, then embedded in LR-White resin using a vacuum oven set at 60 °C. Semi-thin sections were cut using a Reichert-Jung Ultracut ultramicrotome and a glass knife before mounting on glass slides. Sections were stained with Alcian Blue and imaged using a Leica DM6000B light microscope.
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3

Immunofluorescence Analysis of Wheat Gluten

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Semi‐thin sections were cut using a Reichert‐Jung Ultracut ultramicrotome, collected on drops of distilled water on multiwell slides coated with poly‐L‐lysine hydrobromide (Sigma) and dried on a hot plate at 40°C. Sections were stained with 0.01% (w/v) toluidine blue in 1% (w/v) sodium tetraborate, pH9. Immunofluorescence analysis was carried out as described in Tosi et al. (2011), using the antibodies R2–HMG rabbit polyclonal (specific for high‐molecular‐weight (HMW) glutenin subunits) and IFRN 0610 mouse monoclonal (recognizing epitopes present on gliadins and low‐molecular‐weight (LMW) glutenin subunits).
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4

Morphological Characterization of Strain SBC82T

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Morphological observations of 10-, 20- and 40-day-old cells of strain SBC82T were made with a Zeiss Axioplan 2 microscope and Axiovision 4.2 software (Zeiss, Germany).
For preparation of ultrathin sections, 14-day-old and 30-day-old cells of strain SBC82T were collected from plates and pre-fixed with 1.5% (w/v) glutaraldehyde in 0.05 M cacodylate buffer (pH 6.5) for 1 h at 4 °C and then fixed with 1% (w/v) OsO4 in the same buffer for 4 h at 20 °C. After dehydration in an ethanol series, the samples were embedded into Epon 812 epoxy resin. Sections were obtained using the Reichert-Jung Ultracut ultramicrotome (Austria). Sections were mounted on the support grids, contrasted for 30 min in a 3% solution of uranyl acetate in 70% alcohol, additionally contrasted by lead citrate at 20 °C for 4–5 min, and examined in the JEM-1400 transmission electron microscope (JEOL, Japan) at accelerating voltage of 80 kV at the UNIQEM Collection Core Facility, Research Center of Biotechnology of the Russian Academy of Science.
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5

Transmission Electron Microscopy of Brain Tissue

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Brain tissue was fixed for 2 hours in 3% glutaraldehyde buffered in sodium cacodylate (pH 7.4) and post-fixed in 1% osmium tetroxide in cacodylate buffer, dehydrated in graded ethanol solutions, and embedded in Araldite. Thin sections were cut on a Reichert-Jung Ultracut ultramicrotome, mounted on 300-mesh copper grids, and stained in saturated uranyl acetate in alcohol for 10 minutes and lead citrate for 8 minutes. Sections were examined using a transmission electron microscope (H-600A-2; Hitachi, Tokyo, Japan).
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6

Ultrastructural Analysis of Liver Mitochondria

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Liver fragment from each genotype (n = 3/group) was obtained and fixed in 3% glutaraldehyde (Acros Organics, Thermo Fisher Scientific, Waltham, MA, USA) diluted in 0.1 M Sorensen phosphate buffer (pH 7.4) at 4 °C overnight. Subsequently, the livers were post-fixed with 1% osmium tetroxide in 0.1 M Sorensen phosphate buffer for 30 min, dehydrated, and araldite embedded (Fluka, Sigma Aldrich, St. Louis, MO, USA). Ultrathin sections were obtained with an Ultra-cut ultramicrotome (Reichert-Jung, Leica, Microsystems GmbH, Wetzlar, Germany), stained with uranyl acetate and lead citrate, and observed with Talos 120 (Thermo Fisher Scientific). The TEM images were acquired at 6700X magnification in randomly selected fields. Results are expressed as diameter (µm) and number of mitochondria per area for each analyzed section and were quantified by ImageJ software [36 (link)].
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7

Ultrastructural Analysis of Wheat Grains

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Transverse sections (approximately 1 mm thick) were cut in fixative (2.5% (w/v) paraformaldehyde, 0.5% (w/v) glutaraldehyde in 0.1M Sorenson's phosphate buffer, pH 7.2) from the middle of the grain. Sections were fixed at room temperature for 4 h and then rinsed three times in buffer before dehydration in an ethanol series immediately followed by infiltration with LR White resin (medium grade, TAAB L012) for several days. Resin‐infiltrated samples were polymerized in polyethylene capsules (TAAB) at 55°C.
The embedded wheat grains were sectioned using a Reichert‐Jung Ultracut ultramicrotome to a thickness of 1 micron, collected on drops of distilled water on silicon wafers and dried on a hot plate at 40 °C to stretch them flat. To prevent charging during NanoSIMS analysis, the samples and substrates were coated with 10 nm of platinum before loading into the NanoSIMS.
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8

Ultrastructural Analysis of Plant Tissues

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Ten portions of both roots and rhizome were used. Fixation was performed in glutaraldehyde 2.5%–paraformaldehyde 2% for 24 h at 4 °C. Subsequently, the samples were osmicated in 1% osmium tetroxide, dehydrated in acetone, and embedded in Spurr. To orient the specimens properly, semithin sections (1 mm) were cut transversally or tangentially with a glass knife, stained with methylene blue, covered with Durcupan, and observed on an Olympus CX41. Ultrathin (around 100 nm) sections of the samples were then obtained by using a diamond knife (Diatome) with an Ultracut Ultramicrotome from Reichert-Jung. Sections were double-stained with uranyl acetate and lead citrate and viewed with a Jeol JEM 1010 at 80 kV. Images were obtained with a Bioscan camera model 792 (Gatan) at the University of Barcelona technical services.
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9

Electron Microscopy Sample Preparation

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Cell pellets were centrifuged at 14,000 rpm for 3 min, resuspended in 1 mL of 2.5% (v/v) glutaraldehyde in 0.1 M potassium phosphate solution (pH 7.2) and incubated for 1 h. A series of washing steps with increasing alcohol concentration (50–100% v/v) followed. Sedimented cells from the last dehydration step were embedded in resin by infiltration of the pellet with a solution containing 50% (v/v) Mollenhauer [29 (link)] resin in propylene oxide (Agar Scientific) on a rotator (Type N, TAAB) operated at 4 rpm for 12 h in a fume cupboard, followed by curing in undiluted Mollenhauer resin at 60 °C for another 48 h. Thin sections (120 nm) were cut from the resin block using diamond knives on a Reichert-Jung UltraCut Ultramicrotome. The cut sections were examined using a JEOL 1200EX TEM electron microscope operated at 80 keV, in the transmission mode, with the beam current at 60 μA.
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10

Ultrastructural Analysis of Lobster Statocysts

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For the TEM analysis, we used 5 animals (10 statocysts) of both sexes. The lobsters were anaesthetized and sacrificed with an overdose of 2-phenoxyethanol. The statocysts were dissected, fixed, and processed by routine procedures for analysis by TEM. Fixation was performed in 2.5% glutaraldehyde–2% paraformaldehyde for 24 h at 4 °C. Subsequently, the samples were osmicated in 1% osmium tetroxide, dehydrated in acetone, and embedded in Spurr. To orient the specimens properly, semithin sections (1 mm) were cut transversally or tangentially with a glass knife, stained with methylene blue, covered with Durcupan, and observed on an Olympus CX41 microscope. Ultrathin (around 100 nm) sections of the samples were then obtained by using a diamond knife (Diatome) with an Ultracut Ultramicrotome from Reichert-Jung. The sections were double-stained with uranyl acetate and lead citrate and viewed with a Jeol JEM 1010 microscope at 80 kV. Images were obtained with a Bioscan camera model 792 (Gatan, Pleasanton, CA, USA) at the University of Barcelona technical services.
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