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72 protocols using durcupan

1

Ultrastructural Analysis of Dendritic Cell Podosomes

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For electron microscopy analysis of podosomes, DCs grown on PDMS 1:20 and 1:78 were washed with PBS, fixed in 1% GA in 0.1 M cacodylate (pH 7.4) buffer for 1 h at RT, washed and postfixed for 1 h at RT in 1% osmium tetroxide and 1% potassium ferrocyanide in 0.1 M cacodylate buffer. Cells were stained en bloc with 2% uranylacetate for 1 h at RT, washed with MQ, dehydrated in an ascending series of aqueous ethanol solutions and subsequently transferred via a mixture of ethanol and Durcupan to pure Durcupan (Sigma) as embedding medium according to standard procedures. Ultrathin grey sections (60–80 nm) were cut, contrasted with aqueous 2% uranyl acetate, rinsed and counterstained with lead citrate, air dried and examined in a JEOL JEM1400 electron microscope (JEOL) operating at 80 kV.
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2

Ultrastructural Analysis of Malaria Parasites

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For electron microscopy analysis of mitochondria across different ABS parasites and stage V gametocytes, infected red blood cells were fixed in 2% glutaraldehyde in 0.1 M cacodylate (pH 7.4) buffer overnight at 4 °C, washed and cell-pellet was resuspended in 3% ultra-low-gelling agarose, solidified and cut into small blocks. Agarose blocks with cells were postfixed for 1 h at RT in 2% osmium tetroxide and 1.5% potassium ferrocyanide in 0.1 M cacodylate buffer with 2 mM CaCl2, washed in MQ and incubated in 0.5% thiocarbohydrazide solution for 30 min at RT. After washing agarose blocks with cells were again fixed in 2% osmium for 30 min at RT, washed and placed in 2% aqueous uranyl acetate overnight at 4 °C. After washing agarose blocks with cells were placed in lead aspartate solution (pH 5.5) for 30 min at 60 °C, washed, dehydrated in an ascending series of aqueous ethanol solutions and subsequently transferred via a mixture of aceton and Durcupan to pure Durcupan (Sigma) as embedding medium. Ultrathin sections (80 nm) were cut, air dried and examined in a JEOL JEM1400 electron microscope (JEOL) operating at 80 kV.
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3

Electron Microscopy of Human Colon

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Human colon was fixed with 2% glutaraldehyde and 2% paraformaldehyde in 0.1 M cacodylate (pH 7.4) buffer overnight at 4℃. After washing in buffer tissue was postfixed for 1 h at RT in 1% osmium tetroxide and 1,5% potassium ferrocyanide in 0.1 M cacodylate buffer, washed in MQ, followed by one hour staining in en bloc with 2% uranyl acetate on ice. After washing in MQ, tissue was dehydrated in an ascending series of aqueous ethanol solutions and subsequently transferred via a mixture of aceton and Durcupan to pure Durcupan (Sigma) as embedding medium. Ultrathin sections (80 nm) were cut on a Leica Artros ultramicrotome, picked up on grids, stained with 2% uranyl acetate and lead citrate, air dried and examined in a JEOL JEM1400 electron microscope operating at 80 kV.
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4

Glutaraldehyde Fixation and Staining Protocol

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Human colon was fixed with 2% glutaraldehyde in 0.1 M cacodylate (pH 7.4) buffer overnight at 4℃. Tissue was postfixed for 1 h at RT in 1% osmium tetroxide and 1.5% potassium ferrocyanide in 0.1 M cacodylate buffer, washed in MQ, followed by one hour staining in en bloc with 2% uranyl acetate on ice. After washing in MQ, dehydrated in an ascending series of aqueous ethanol solutions and subsequently transferred via a mixture of aceton and Durcupan to pure Durcupan (Sigma) as embedding medium. Ultrathin sections (80 nm) were cut on a Leica ultramicrotome, and picked up on grids, stained with 2% uranyl acetate and lead (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint this version posted February 10, 2021. ; https://doi.org/10.1101/2021.02.09.430377 doi: bioRxiv preprint 5 citrate, air dried and examined in a JEOL JEM1400 electron microscope (JEOL) operating at 80 kV.
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5

Ultrastructural Examination of Epididymal Sperm

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Epidydimal sperm samples were centrifuged and the resulting pellet embedded in 2% agarose for transmission electron microscopy. Thereafter, cells/tissue samples were contrasted using 1% osmium tetroxide in PBS for 45 min at room temperature and 1% uranyl acetate (45 min at room temperature in 70% ethanol). Agar blocks were dehydrated and embedded in epoxy resin (Durcupan, Sigma-Aldrich, Germany). Ultrathin sections were prepared using a Leica UC6 ultra-microtome and analysed using a Philipps CM100 transmission electron microscope.
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6

Transmission Electron Microscopy of Cells

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The cells were processed for transmission electron microscopy as described previously [23 (link)]. Briefly, the cells were fixed in 3% glutaraldehyde (in 0.1 M cacodylate buffer, pH 7.2; Sigma) for 3 h at room temperature. Subsequently, the cells were washed in cacodylate buffer (0.1 M, pH 7.2) and post-fixed in 1% OsO4 (in 0.1 M cacodylate buffer, pH 7.2; Sigma) for 1 h at room temperature. After the rinsing procedure, the cells were dehydrated in graded alcohols (50%, 75%, 96%, and 100%), clarified in propylene oxide, and embedded in a mixture of Epon 812 and Durcupan (Sigma; polymerization for 3 days at 60 °C). Toluidine blue was used to stain the semithin sections. Ultrathin sections were cut on Ultrotome Nova (LKB, Vienna, Austria). These sections were then collected onto formvar carbon-coated copper grids, counterstained with uranyl acetate and lead citrate, and examined under a JEOL JEM-1400Plus transmission electron microscope (at 120 kV, JEOL, Tokyo, Japan). The images were taken with the integrated 8Mpix CCD camera and processed further using the software TEM Center (Ver. 1.7.3.1537, JEOL, Tokyo, Japan).
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7

Transmission Electron Microscopy of Fixed Cells

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Cell samples were fixed in 4% paraformaldehyde plus 1% glutaraldehyde in 0.1 M phosphate buffer overnight. After contrasting using 1% osmium tetroxide in 0.1 M phosphate buffer (45 minutes at room temperature) and 1% uranyl acetate (in 70% ethanol, room temperature), samples were dehydrated in an ascending ethanol series and embedded in epoxy resin (Durcupan, Sigma-Aldrich). Ultrathin sections of approximately 70 nm thickness were prepared using a Leica Ultracut UC6. For imaging, a Philips CM100 transmission electron microscope was used.
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8

Proventriculus Ultrastructural Analysis

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Dissected proventriculi with garland nephrocytes attached were fixed in 3.2% paraformaldehyde, 0.5% glutaraldehyde, 1% sucrose, and 0.028% CaCl2 in 0.1 N sodium cacodylate, pH 7.4 for overnight at 4°C, postfixed in 0.5% osmium tetroxide for 1 hr and in half-saturated aqueous uranyl acetate for 30 min, dehydrated in a graded series of ethanol and embedded into Durcupan (Fluka - Sigma Aldrich) according to the manufacturer’s recommendations. 70-nm sections were stained in Reynold’s lead citrate and viewed on a transmission electron microscope (JEM-1011; JEOL, Tokyo, Japan) equipped with a digital camera (Morada; Olympus) using iTEM software (Olympus).
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9

Histological and Ultrastructural Analysis of Skeletal Muscle

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For microscopic analysis, the paraformaldehyde fixed PM muscle tissues were trimmed, paraffin-embedded, sectioned, and mounted on polylysine-coated slides. Then, the slides were rehydrated by a series of incubations in xylene and ethanol solutions and subjected to hematoxylin and eosin (H&E) and Masson trichrome staining as described in our previous studies (Xing et al., 2021a (link),c ). Images were captured under identical conditions at the same magnification using a light microscope (Axio Scope.A1, Carl Zeiss, Oberbochen, Germany).
The glutaraldehyde fixed PM muscle tissues were excised transverse to the long axis of the muscle fibers for ultrastructural analysis according to Qi et al. (2018) (link). Briefly, the obtained small blocks were postfixed and stained in 1% osmium tetraoxide and 1% uranyl acetate for 1 h at room temperature. After dehydration in graded series of ethanol, the specimens were infiltrated and polymerized in epoxy resin (Durcupan; Sigma-Aldrich, Shanghai, China). Thereafter, ultrathin sections were sliced and stained with lead citrate and uranyl acetate. The sections were observed using an H-7650 transmission electron microscope (Hitachi, Tokyo, Japan).
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10

Ultrastructural Analysis of Mouse Cerebellum

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Four C57BL/6 mice of either sex with an age between P23–P28 were sacrificed, followed by transcardial perfusion with saline and consecutively a fixative containing 4% paraformaldehyde and 2% glutaraldehyde in phosphate-buffered saline (PBS). After removal of the brain, the tissue was allowed to post-fix over night at 4°C and sagittal sections of the cerebellum were prepared at a thickness of 60 µm using a Leica microtome (Leica Microsystems, Wetzlar, Germany). The sections were stained in 0.5% osmium tetroxide in PBS for 30 min followed by dehydration in graded alcohol and another staining step with 1% uranyl acetate in 70% ethanol. After further dehydration, the tissue was embedded in durcupan (Sigma-Aldrich), which was allowed to polymerize for 48 hr at 56°C between coated microscope slides and cover glasses. Regions of interest were identified by light microscopy, cut and transferred onto blocks of durcupan to obtain ultra-thin sections using an Ultramicrotome (Leica Microsystems). Ultra-thin sections were transferred onto formvar-coated copper grids and stained with lead citrate. Ultrastructural analysis was performed using a Zeiss SIGMA electron microscope (Zeiss NTS, Oberkochen, Germany) equipped with a STEM detector and ATLAS software.
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