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8 protocols using spurr

1

Electron Microscopy Preparation of Microbial Samples

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Overnight cultures of microbial samples harvested by centrifugation at 6000× g for 10 min were washed with PBS (pH 7.4). Microbial cells treated with chitosan, PDI, or chitosan applied after PDI were pre-fixed with 3% glutaraldehyde for 2 h. Samples were washed with PBS three times and then fixed with 1% osmium tetroxide for 1.5 h, followed by dehydration for 5 min in a graded acetone series (30% and 50%), and 15 min in a graded acetone series (70%, 90%, and 100%), then incubated for 15 min each in acetone. A 3:1 (overnight), 1:1 (4 h), and 1:3 (4 h) mixture of acetone and Spurr (Electron Microscopy Sciences, Hatfield, PA, USA) were added in the dehydrated sample during the infiltration. Samples were embedded, trimming with Ultracut E (Leica, Wetzlar, Germany) and mounted on copper grids. Samples were observed using a transmission electron microscope (Hitachi Ltd., Tokyo, Japan). The control experiment was conducted in absence of any treatment.
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2

Yeast Strain Generation and Sporulation

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Yeast strains and plasmids used in this study are listed in Supplemental Table S1. Haploid yeast strains were generated by tetrad dissection or using a PCR-based transformation approach (Longtine et al., 1998 (link)). Transformants were selected on synthetic complete with dextrose (SCD)-dropout medium at 30°C, and the integration of genes was further confirmed by colony PCR. Haploid strains of two mating types were mated to generate diploid strains. Sporulation condition refers to cells that were grown on either YPD or SCD–Ura+CA (0.67% yeast nitrogen base, complete amino acids without uracil, 2% glucose, and 0.2% casamino acids) plates for 3–4 d and subjected directly to CSH SPO medium (1% KOAc, 0.1% yeast extract, 0.05% glucose) with a starting OD600 of ∼2.0. BODIPY 493/503 was from Thermo Fisher Scientific (Waltham, MA), osmium tetraoxide and Spurr were from Electron Microscopy Sciences (Hatfield, PA), uranyl acetate was from SPI-CHEM (West Chester, PA), and acetone was from Merck (Kenilworth, NJ). All other reagents were from Sigma-Aldrich (St. Louis, MO).
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3

Electron Microscopy Sample Preparation

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Samples were fixed in 2.5% glutaraldehyde (Electron Microscopy Sciences, Hatfield, PA, USA) in 0.1 M cacodylate buffer at pH 7.4 for 12 h, post-fixed in 1% osmium tetroxide for 60 min using the same buffer. Dehydrated samples were embedded in Spurr (Electron Microscopy Sciences). Ultrathin sections (60–70 nm) were cut and mounted on 150 mesh copper grids (Electron Microscopy Sciences). Unstained samples were observed with Talos F200S G2 transmission electron microscope (Thermo Fisher Scientific, Waltham, MA, USA).
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4

Lung Morphometric Analysis Protocol

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Volume of the intact fixed right lung was measured by saline immersion (Yan et al., 2003 (link)). The lung was serially sectioned (3mm intervals) starting with a random orientation; the cut surfaces were imaged using a digital camera. Volume of the sectioned lung was estimated from the images using the Cavalieri principle (Yan et al., 2003 (link)); this tension-free volume was used in subsequent morphometric calculations. Lung slices were divided into roughly equal cranial and caudal regions. Using a systematic sampling scheme with a random start, 2 tissue blocks were sampled from each region (total of 4 blocks per lung), post-fixed with 1% osmium tetroxide in 0.1M cacodylate buffer, treated with 2% uranyl acetate, dehydrated through graded alcohol, and embedded in Spurr (Electron Microscopy Sciences, Hatfield, PA). Each block was sectioned (1µm) and stained with toluidine blue.
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5

Ultrastructural Analysis of Cell Samples

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Cells were grown to 90% confluence before being washed, scraped, pelleted, and fixed in 2.5% glutaraldehyde in 0.1 M sodium cacodylate buffer (pH 7.2) overnight. Samples were post fixed in 1% osmium tetroxide for 2 h, stained in bloc with 0.5% uranyl acetate, rinsed, and dehydrated in graded ethanol. After immersion in propylene oxide, samples were embedded in epoxy resin (Spurr, Electron Microscopy Sciences, EMS, Hatfield PA, USA) and polymerized for 42 h at 75 °C. Ultrathin sections were stained with lead citrate and uranyl acetate and examined in a FEI Tecnai G20 Electron microscope at 200 kVA.
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6

Transmission Electron Microscopy of Extracellular Vesicles

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Cells were grown to 90% confluence before being washed and cultured in serum-free medium for 24 hours. Cells were then scraped off, pelleted, fixed in 2.5% glutaraldehyde in 0.1 M sodium cacodylate buffer (pH 7.2) overnight, and postfixed in 1% osmium tetroxide in the same buffer for 2 hours. Samples were then washed in distilled water, stained in bloc with 0.5% uranyl acetate, rinsed and dehydrated in graded ethanol. After immersion in propylene oxide, samples were embedded in epoxy resin (Spurr, Electron Microscopy Sciences, EMS, Hatfield PA, USA) and polymerized for 42 hours at 75°C. Sections (0.5 μm-thick) were stained with 1.0% toluidine blue in 1.0% aqueous sodium borate for light microscopic examination. Ultrathin sections were stained with lead citrate and uranyl acetate and examined in a JEOL 1010 transmission electron microscope (Jeol Inc., Peabody, MA, USA) at 80 kV.
Extracellular vesicles were obtained and pelleted by centrifugation as described above, suspended in PBS, and 5 μl of samples were deposited on carbon coated copper grids (CF100-Cu, EMS), incubated at room temperature overnight, and fixed with 2.5% glutaraldehyde for 5 minutes. Grids were washed with distilled water several times and stained with 1% uranyl acetate for 5 minutes, followed by TEM analysis.
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7

Conventional TEM Imaging of Vitellogenic Oocytes

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For conventional transmission electron microscopy (TEM), vitellogenic oocytes were fixed in freshly prepared 4% formaldehyde, 2.5% glutaraldehyde diluted in 0.1 M sodium cacodylate buffer pH 7.3 (Electron Microscopy Sciences) at 4ºC for 24 h, and then embedded in epoxy resin (Spurr) (Electron Microscopy Sciences), sectioned and stained using standard methods. For freeze fracture, the yolk organelles were obtained and processed as described in [35 (link)]. All samples were examined in a JEOL 1200 EX transmission electron microscope, operating at 80 kV.
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8

Cashew Pseudofruit Cuticle Ultrastructure

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Skin transversal samples from the equatorial regions of the three cashew pseudofruits were fixed in Karnovsky’s solution with modifications (2.5% glutaraldehyde, 2.5% paraformaldehyde, and 0.05 mM CaCl2 in sodium cacodylate buffer (0.1 M, pH 7.2)) [46 (link)] for 48 h. The samples were post-fixed in 1% osmium tetroxide for 2 h, dehydrated in increasing acetone series up to 100%, and infiltrated in resin (Spurr, Electron Microscopy Sciences, Hat Field, PA, USA). The blocks were sectioned in the ultramicrotome (UC6, Leica, Vienna, Austria). Sections were mounted on 200-mesh copper screens and contrasted with 5% uranyl acetate and 2% lead citrate for 30 min in each step [50 (link)]. Observations and electron micrographs of the epidermis and cuticle were performed using a transmission electron microscope (JEM 1011, JEOL, Akishima, Japan) with a coupled Gatan 830 J46W44 video camera operating at 60 Kv.
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