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12 protocols using epoxy resin

1

Lung Tissue Sampling and Processing

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Sampling and processing of the lungs were carried out as described elsewhere [25 (link),38 (link),39 (link)]. Briefly, each lung was embedded in 2% aqueous agar—agar (Merck, Darmstadt, Germany) and cut from apex to base into parallel slices with a thickness of 2 mm using a tissue slicer. Slices from both lungs were alternatively taken for light and electron microscopy. Lung slices collected for electron microscopy were cut into tissue blocks with a size of 1–2 mm3. After additional immersion fixation, specimens for light and electron microscopy were rinsed repeatedly in cacodylate buffer. Postfixation followed in 1% OSO4 in 0.1 M cacodylate buffer for 2 h. Again specimens were rinsed in cacodylate buffer then in distilled water and stained en bloc overnight at 4–8°C in half-saturated aqueous uranyl acetate solution. Specimens were dehydrated in ascending series of acetone. For ultrastructural analyses tissue blocks were embedded in epoxy resin (Serva Electrophoresis GmbH, Heidelberg, Germany). Prepared 70 nm thin ultra-thin sections were stained with lead citrate and uranyl acetate. For light microscopy whole tissue slices were embedded in the methacrylate resin Technovit 7100 (Heraeus Kulzer GmbH, Hanau, Germany). 1.5 μm sections were cut and stained with toluidine blue.
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2

Transmission Electron Microscopy Protocol

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For electron microscopic analyses, different cell lines were fixed in freshly prepared 2% glutaraldehyde ELMI grade in phosphate buffered saline (PBS; both Sigma-Aldrich) for 2 hours at 4 °C, washed and stored in PBS. Subsequently, samples were post-fixed in 1% veronal-acetate-buffered OsO4 (Merck) for 1 hour, dehydrated in a graded series of ethanol and embedded in epoxy resin (Serva). Ultrathin sections were stained in 1% uranyl acetate or alternatively, in 0.2% OTE (Oolong Tea Extract, Nisshin EM Co.), and subsequently in 8% alkaline lead citrate (both Merck), followed by examination in a transmission electron microscope at 80 kV (Tecnai 20, FEI Company).
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3

Corticospinal Tract Ultrastructural Analysis

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Spinal cord was isolated at the fifth cervical vertebra and the corticospinal tract (CST) was used for electron microscopic (EM) and immunohistochemical (IHC) analyses. For EM, tissue was fixed in 4% PFA/2.5% glutaraldehyde in cacodylate buffer followed by epoxy resin (Serva) embedding for ultrathin cross sections. Myelinated and nonmyelinated axons were quantified at 4400× and 12000× magnifications. Samples for IHC were fixed in 4% PFA and paraffin-embedded for diaminobenzidine (DAB) or fluorescent stainings. The following antibody dilutions were used: OLIG2 1:200 (Dana-Farber Cancer Institute, Boston, MA, USA); CC1 1:50 (Oncogene, La Jolla, CA, USA); Glial Fibrillary Acidic Protein (GFAP) 1:5000 (Dako, Glostrup, Denmark); CD107b (MAC3) 1:400 (BD Pharmingen, San Diego, CA, USA); CD3 1:150 (Serotec, Bicester, United Kingdom).
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4

Ultrastructural Analysis of Myelinated Axons

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Mice were anesthetized using Avertin and perfused using 4% paraformaldehyde, 2.5% glutaraldehyde in 0.1M phosphate buffer. Tissue was dissected and contrasted with 2% osmium tetroxide (OsO4) in 0.1M phosphate buffer and embedded in epoxy resin (Serva Electrophoresis). Using an ultramicrotome (Leica, RM2155), ultrathin sections were cut with a diamond knife (Histo HI 4317; Diatome) and contrasted. Electron microscopic images were taken using LEO EM912 transmission electron microscope and a 208×2048 CCD camera (Proscan). To measure the g-ratio the circumference of the outer layer of myelin, the layer surrounding the inner tongue and of the axon were measured using ImageJ. The diameter, length of compact myelin or circumference was calculated using these data from each individual axon. A minimum of 300 myelinated cross sections were measured per genotype and 100 per animal.
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5

Renal Ultrastructure Analysis

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Electron microscopic analyses were performed on kidneys that were fixed in 4% buffered paraformaldehyde. Tissue was post-fixed with 1% osmium in 0.1 M sodium-cacodylat buffer, stained with 1% uranyl acetate and embedded in epoxy-resin (Serva). Ultra-thin sections were cut (Ultramicrotome, Reichert-Jung) and contrasted with uranyl acetate in methanol followed by lead citrate. Micrographs were generated with a transmission-electron microscope (JEM 1010, JEOL).
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6

HUVEC Culture and PECNP Uptake

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ACLAR film slides (Redding, CA, USA) were placed in 24-well plates and 1 × 105 HUVEC were seeded on top in 1 mL media and incubated for 24 h at 37 °C, 5% CO2, and 95% relative humidity. A volume of 25 µL of a 2 mM PECNP dispersion was added to the media (final dilution 1:40) for 4 h. Incubation was stopped by the addition of a primary fixative (4% formaldehyde,2% glutaraldehyde and 1 mM MgCl2, in 100 mM sodium phosphate buffer at pH 7.2). Following two post-fixations steps, buffered OsO4 (1%) and ethanolic uranyl acetate (0.5%), respectively, samples were flat-embedded in epoxy resin (Serva, Heidelberg, Germany) for ultrathin sectioning. Sections were post-stained with uranyl and lead and investigated by TEM (EM912, Carl Zeiss, Oberkochen, Germany).
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7

Peripheral Nerve Fixation and Staining

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Peripheral nerves were fixed in 2.5% glutaraldehyde and 4% PFA in 0.1 M phosphate buffer for 1 week. Then, they were contrasted with osmium tetraoxide and embedded in epoxy resin (Serva) and 0.5 µm semi-thin sections were cut (Leica RM 2155) using a diamond knife (Histo HI 4317, Diatome). Afterwards sections were stained according to Gallyas (1971 (link)) and with Methylene blue/Azur II for 1 min. Analysis was performed on total nerve cross sections using FIJI (NIH).
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8

Ultrastructure of Canine Endometria in Pyometra

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Samples of healthy (n = 3) and pyometra affected canine endometria (n = 3) were fixed in 3% buffered glutaraldehyde (pH 7.4, Merck). After washing in 0.1 M phosphate buffer (Soerensen, pH 7.4) samples were postfixed in 1% osmium tetroxide (Electron Microscopy Sciences, Hatfield, PA, USA) for 2 hours at room temperature. Afterwards, samples were embedded in epoxy-resin (Serva). Semi-thin sections were cut at 0.8 μm, stained with toluidine blue (Merck) for general histological evaluation. Ultrathin sections were prepared (70 nm) and contrasted with uranyl acetate (Fluka Chemie AG, Buchs, Switzerland) and lead citrate (Merck), and evaluated by a transmission electron microscope (Zeiss EM900, Zeiss, Oberkochen, Germany). Images from surface and glandular epithelium were made to assess the amount of LDs (LDs/nuclei) and to measure LDs diameter (ImageSP-TRS, Moorenweis, Germany).
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9

Ultrastructural Analysis of Organoid Polarity Reversal

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To further analyse polarity reversal of organoids, basal‐out and apical‐out organoids at day three after induction of polarity reversal were used. All samples were fixed in 3% buffered glutaraldehyde (pH 7.4, Merck). Organoids were then pre‐embedded in 1.5% agarose. After being washed in 0.1 M Soerensen buffer (pH 7.4), the samples were postfixed for 2 h at room temperature in 1% osmium tetroxide (Electron Microscopy Sciences). This was followed by dehydration in an ethanol series along with an increasing series of propylene oxide (Sigma‐Aldrich) before embedding and polymerisation in epoxy resin (Serva) for 48 h at 60°C. Ultrathin sections (70 nm) were cut for transmission electron microscopic evaluation and contrasted in methanolic uranyl acetate (Fluka Chemie AG) and alkaline lead citrate (Merck). For imaging, a transmission electron microscope (EM 900, Zeiss) equipped with a slow‐scan CCD camera (2k Wide‐angle Dual Speed, TRS) and ImageSP Professional software (SYSPROG, TRS) were used.
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10

Plant Sample Preparation for TEM

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Plant samples were fixed according to Karnovsky (1965 ), and subsequently post-fixed in 2% OsO4 for 2 h at 4 °C, dehydrated in an ethanol series, substituted by propylene oxide and embedded in glycidyl ether 100 epoxy resin (Serva) equivalent to the former Epon812. The resin polymerization was performed at 65 °C for 24 h. Semi-thin sections were prepared using Jung RM 2065 microtome, and stained with methylene blue and azure A prior to examination under a light microscope (Olympus-Provis). Ultra-thin sections were prepared with Ultracut UCT Leica microtome, stained with uranyl acetate and lead citrate, and examined under a transmission electron microscope (Morgagni 268D).
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