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13 protocols using morada soft imaging system

1

Ultrastructural Analysis of Nerve Fibers

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To analyse the ultrastructural characteristics of the nerve fibres, one decalcified sample from each group was randomly selected after isolation of the implants. Following fixation with 2% glutaraldehyde in 0.05 mol⋅L−1 cacodylate buffer (pH 7.3), samples were post-fixed in 2% osmium tetroxide for 1 h and stained with 2% uranyl acetate in 10% acetone for 20 min. Subsequently, the samples were subjected to a dehydrating series of graded concentrations of acetone and embedded in araldite. Serial ultrathin sections (∼0.06 µm) were mounted on 0.7% Formvar-coated copper grids, contrasted with 0.5% uranyl acetate and a stabilized solution of lead citrate, and examined in a transmission electron microscope (EM 208; Philips, Eindhoven, The Netherlands) operated at 80 kV. The microscope was provided with a Morada Soft Imaging System (Olympus, Tokyo, Japan) camera to acquire high-resolution images of the evaluated samples. The images were processed digitally with iTEM-FEI software (Morada Soft Imaging System; Olympus, Tokyo, Japan).
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2

Swarming Motility and Flagella Visualization in Campylobacter jejuni

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The optical density at 600 nm (OD600) of the bacterial cultures to be tested was adjusted to 0.4 and spotted onto soft agar (0.8% [wt/vol]). Plates were incubated for 24 h at 37°C, and the swarming diameter of the tested strain was compared to those of the wild-type strain and the nonmotile C. jejuni ΔmotA mutant strain. Bacterial flagella were visualized by negative staining and transmission electron microscopy (TEM). Briefly, bacterial cells were pelleted (2,000 rpm for 2 min) and resuspended in prewarmed phosphate-buffered saline (PBS). Samples were directly applied to glow-discharged carbon-coated 200-mesh Cu grids and stained using 2% phosphotungstic acid (pH 7.0). Images were acquired using 10,000-fold to 35,000-fold magnification on a Tecnai Biotwin TEM (FEI Company) at 80 kV. Images were collected using a Morada Soft Imaging system and a 6-M-pixel charge-coupled-device (CCD) camera (Olympus).
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3

Transmission Electron Microscopy of RNA Samples

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Transmission electron microscopy (TEM) was performed from the collected RNA 1 and RNA 2-positive gradient fractions at the microscopy department of Centro de Investigación Principe Felipe (CIPF, Valencia, Spain). Glow Discharge (30 s, 7.2 V, using a Bal-Tec MED 020 Coating System (BalTec AG, Pfäffikon, Switzerland) was applied over Carbon-coated copper grids, and grids were immediately placed on top of sample drops for 10 min. After two brief distilled water washes, grids were contrasted with 1% uranyl acetate for 5 min. Excess fluid was removed, and grids were allowed to dry before examination with a transmission electron microscope FEI Tecnai G2 Spirit (Thermo Fisher Scientific, Waltham, MA, USA). Finally, photomicrographs were obtained under a transmission electron microscope (FEI Tecnai G2 Spirit Biotwin) using a digital camera Morada Soft Imaging System (Olympus, Tokio, Japan).
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4

Immunogold Labeling of Venus-Positive Dendrites

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For pre-embedding immunogold staining, mice were perfused with 4% paraformaldehyde/0.5% glutaraldehyde, post-fixed in 4% paraformaldehyde, and 50 -µm sections were cut on a vibratome (Leica). Pre-embedding immunogold staining was performed by incubating sections in chicken anti-GFP primary antibody (1:200, Aves Lab) and in the appropriate colloidal gold-conjugated secondary antibody (1:50; UltraSmall; Aurion). The samples were post-fixed in 1% osmium and 7% glucose for 30 min, rinsed, dehydrated, and embedded in araldite (Durcupan; Fluka). For the ultrastructural characterization of Venus-positive dendrites, serial ultrathin sections (60–70 nm) were cut with a diamond knife, stained with lead citrate, and examined under a transmission electron microscope (Tecnai Spirit G2; FEI) and images recorded using a digital camera (Morada, Soft Imaging System; Olympus). Adjustment of brightness and contrast of the pictures, if needed, was performed with Adobe Photoshop (Adobe Systems).
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5

Ultrastructural Analysis of HeLa Cells

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HeLa cells were seeded at 3 × 104 cells per chamber in a Lab-Tek chamber slides of 4 wells (Nalge Nunc International) and treated as indicated in each case. Then, the cells were fixed for 1 h in 3.5% glutaraldehyde at 37°C and postfixed for 1 h in 2% OsO4 at room temperature. Cellular staining was performed at 4°C for 2 h in 2% uranyl acetate in the dark. Finally, cells were rinsed in sodium phosphate buffer (0.1 mol/L, pH 7.2), dehydrated in ethanol, and infiltrated overnight in Araldite (Durcupan, Fluka). Following polymerization, embedded cultures were detached from the chamber slide and glued to Araldite blocks. Serial semi-thin (1.5 μm) sections were cut with an Ultracut UC-6 (Leica), mounted onto slides and stained with 1% toluidine blue. Selected semi-thin sections were glued (Super Glue, Loctite) to araldite blocks and detached from the glass slide by repeated freezing (in liquid nitrogen) and thawing. Ultrathin (0.07 μm) sections were prepared with the Ultracut and stained with lead citrate. Finally, photomicrographs were obtained under a transmission electron microscope (FEI Tecnai Spirit G2) using a digital camera (Morada, Soft Imaging System, Olympus).
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6

Exosome Immunogold Labeling for EM

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For exosome immunogold labeling for electron microscopy, exosomes were prepared and labeled according to the protocol of Thery et al [41 ]. In brief, isolated exosomes were resuspended in 2% paraformaldehyde (PFA), adsorbed unto nickel Formvar-carbon coated electron microscopy grids (200 mesh), blocked with PBS/5% (w/v) BSA and incubated with antibodies for Her-2 (MSK044, Zytomed Systems, Berlin, Germany), ERα (sc-8002, Santa Cruz Biotechnology, Santa Cruz, CA, USA) and Glypican-1 (sc-101827, Santa Cruz Biotechnology, Santa Cruz, CA, USA) for 30 min. Subsequently grids were washed, blocked and incubated with Donkey Anti-Mouse IgG H&L 10nm Gold antibody (Abcam, Cambridge, United Kingdom). Grids were washed, fixed with 1% glutaraldehyde, contrasted with 4% uranyl acetate and finally embedded in a mixture of 4% uranyl acetate and 2% methyl cellulose.
Grids were visualized on a Morgagni 268 Electron Microscope (FEI, Eindhoven, The Netherlands) and photographed with the Morada Soft Imaging System (Olympus Corporation, Hamburg, Germany).
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7

Immunogold Labeling of Exosomes

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For immunogold labeling for electron microscopy, exosomes were prepared and labeled according to previous described protocols. In brief, isolated exosomes were resuspended in 2% paraformaldehyde (PFA), adsorbed unto nickel Formvar-carbon coated electron microscopy grids (200 mesh), blocked with PBS/5% (w/v) BSA and incubated with CD30 antibody (DAKO, A/S, Denmark) for 30 min. Subsequently, grids were washed, blocked and incubated with Donkey Anti-Mouse IgG H&L 10 nm Gold antibody (Abcam, Cambridge, United Kingdom). Grids were washed, fixed with 1% glutaraldehyde, contrasted with 4% uranyl acetate and finally embedded in a mixture of 4% uranyl acetate and 2% methyl cellulose. Grids were visualized on a Morgagni 268 Electron Microscope (FEI, Eindhoven, The Netherlands) and photographed with the Morada Soft Imaging System (Olympus Corporation, Hamburg, Germany).
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8

Ultrastructural Analysis of Mouse Brain

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For TEM, mice were fixed as described in Supplemental Experimental Procedures. Brains were rinsed in 0.1 M phosphate buffer (PB) and cut into 200-μm sections. Sections were post-fixed in 2% osmium tetroxide, dehydrated, and embedded in Durcupan resin (Fluka; Sigma-Aldrich). Semithin sections (1.5 μm) were cut with a diamond knife and stained with 1% toluidine blue for light microscopy. Ultrathin sections (70–80 nm) were cut, stained with lead citrate, and examined under an FEI Tecnai G2 Spirit transmission electron microscope (FEI Europe) using a digital camera (Morada Soft Imaging System; Olympus). For pre- and post-embedding immunogold stainings, mice were perfused with 4% paraformaldehyde (PFA)/0.5% glutaraldehyde. Pre-embedding immunogold stainings were carried out as previously described (Sirerol-Piquer et al., 2012 (link)). Post-embedding immunogold stainings are described in Supplemental Experimental Procedures.
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9

Ultrastructural Analysis of Human PSD I Pellets

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Human PSD I pellets prepared from one GW23 sample were fixed with 3% glutaraldehyde (Electron Microscopy Sciences (EMS)) for 10 min at 4 °C, washed three times with 0.1 M phosphate buffer and post-fixed with 2% osmium tetroxide (EMS) in 0.1 M phosphate buffer for 1 h at room temperature. Dehydration in graded series of ethanol (30, 50 and 70%) was followed by 2% uranyl acetate (EMS) incubation for 2.5 h. Samples were rinsed with 70%, 96% and 100% ethanol, washed two times with propylene oxide (EMS), embedded in Durcupan resin (Sigma-Aldrich) and allowed to polymerize at 69 °C for 72 h. Ultrathin sections (60–70 nm) were sectioned with a diamond knife (DiATOME) in a UC7 ultramicrotome (Leica), stained with lead citrate and examined under a transmission electron microscope (Tecnai Spirit G2, FEI) using a digital camera (Morada, Soft Imaging System, Olympus).
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10

Ultrastructural Analysis of Spinal Cord Injury

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For transmission electron microscopy (TEM) analysis, uninjured (ut) R-stage and NR-stage animals and after 2, 6, 10 and 20 after spinal cord injury (n = 2/3 each point) were anesthetized and immersed (R-stage) or perfused with 0.83 PBS (NR-stage) followed by incubation in 2% PFA and 2.5% glutaraldehyde (EMS, Hatfield, PA). Spinal cords were micro-dissected and post-fixed overnight in the same fixative. Spinal cords were processes as described before [48 (link)]. Briefly, spinal cords at different days post injury were post-fixed in 2% osmium for 2 h, rinsed, dehydrated, and embedded in araldite (Durcupan; Fluka, Buchs, Switzerland). Semi-thin horizontal sections (1.5 mm) were cut with a diamond knife and stained with toluidine blue. To study the cellular response to injury at the different days and stages, ultrathin sections (60–70 nm) were cut with a diamond knife, stained with lead citrate, and examined under a transmission electron microscope (TEM) (Tecnai Spirit G2; FEI, Eindhoven, The Netherlands) by using a digital camera (Morada, Soft Imaging System; Olympus, Tokyo, Japan). Brightness and contrast adjustment of the pictures was performed with Adobe Photoshop (Adobe Systems, San Jose, CA).
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