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10 protocols using formvar carbon coated 200 mesh copper grids

1

Visualizing SARS-CoV-2 in Gut Bacteria

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Gut bacteria derived from healthy donors were infected with the supernatant derived from COVID-19 affected individuals, containing bacteria and SARS-CoV-2 particles. Biological sample was directly deposited in a 3 µL drop on Formvar Carbon coated 200 mesh copper grids (Agar Scientific, USA), let to dry overnight in a desiccator, and the day after the sample was washed with ultrapure water and again let to dry overnight before analysis by JEOL JEM-2100 HR-transmission electron microscope at 120 kV (JEOL, Italy). TEM analysis conducted on unfiltered stock supernatants of Peptide samples demonstrated the presence of SARS-CoV-2 particles on the surface and inside gut bacteria (Supplementary Figure 2).
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2

Transmission Electron Microscopy of Extracellular Vesicles

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Fractions 6-9 (800 µL) of isolated EVs on SEC were pooled and subsequently concentrated to 150µl using Amicon® Ultra 2 centrifugal filter units (10 kDa) (Merck Millipore Ltd.). A previously described method [39 (link)] was followed for transmission electron microscopy (TEM) analysis. A droplet from the purified EV samples was deposited on Formvar-carbon-coated 200 mesh copper grids (Agar Scientific, Essex, UK) and allowed to absorb for 20 min. The sample was fixed on a grid in 2% paraformaldehyde (Sigma-Aldrich) and 1% glutaraldehyde (Polysciences, Warrington, PA, USA), contrasted in uranyl oxalate (a mixture of 4% uranyl acetate (Polysciences) and 0.15 M oxalic acid (Sigma-Aldrich)) and embedded in a mixture of methylcellulose (Sigma-Aldrich) and uranyl acetate (Polysciences). Samples were observed with a JEM 1400 transmission electron microscope (JEOL Ltd. Tokyo, Japan) at 80 kV, and digital images were acquired with a numeric camera (Morada TEM CCD camera, Olympus, Germany).
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3

Transmission Electron Microscopy Characterization

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Particles were characterized by transmission electron microscopy (TEM). Images were obtained using a JEOL JEM 2100 microscope (JEOL, Milan, Italy) operating at 120 kV, placing a 3 µL drop of 2 µg/mL suspensions (AH and AH-NPs) on a Formvar Carbon coated 200 mesh copper grids (Agar Scientific, Stansted, UK), previously irradiated by Leica EM ACE200 (Leica Microsystems, Milan, Italy) for 30 s, 10 mA and dried in a desiccator at room temperature overnight.
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4

Transmission Electron Microscopy of Extracellular Vesicles

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Five microliters of each EVs suspension were diluted in 45 μL, and then two 25-μL droplets of EVs preparations were allowed to adsorb onto formvar/carbon-coated 200 mesh copper grids (Agar Scientific, Essex, UK) for 1 min at room temperature. Grids were then washed twice with distilled water. For negative staining, grids were transferred to a 50-μL droplet of 2% uranyl acetate for 20 s, followed by blotting the excess liquid, and air-dried. TEM visualizations were performed at the National Center for Electron Microscopy of the Universidad Complutense de Madrid (ICTS-CNME-UCM) using a JEOL JEM1010 (100 kV) transmission electron microscope (Jeol Ltd., Tokyo, Japan) equipped with a Megaview II CCD camera integrated into iTEM Olympus Soft Imaging Solutions software (Olympus, Tokyo, Japan).
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5

Transmission Electron Microscopy of EVs

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EV suspension was deposited on Formvar-carbon-coated 200 mesh copper grids (Agar Scientific, Stansted, UK). The method described by Thery et al. 2018 [7 (link)] was followed for transmission electron microscopy (TEM) analysis. Before contrasted in uranyl oxalate (mixture of 4% uranyl acetate (Polysciences, Warrington, PA, USA) and 0.15 M oxalic acid (Sigma-Aldrich, Schnelldorf, Germany)) and embedded in a mixture of methylcellulose (Sigma-Aldrich, Schnelldorf, Germany) and uranyl acetate (Polysciences, Warrington, PA, USA), EVs were fixed on grids in 2% paraformaldehyde (Sigma-Aldrich, Schnelldorf, Germany) and 1% glutaraldehyde (Polysciences, Warrington, PA, USA). Samples were observed with a JEM 1400 transmission electron microscope (JEOL Ltd. Tokyo, Japan) at 80 kV, and digital images were acquired with a numeric camera (Morada TEM CCD camera, Olympus, Germany).
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6

EV Preparation for TEM Imaging

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JAr EVs for
TEM imaging were
prepared as described before46 (link) with modifications.
Briefly, 20 μL of the EV suspension was deposited on formvar-carbon-coated
200 mesh copper grids (Agar Scientific, Essex, U.K.) for 20 min and
fixed in Karnowski fixatives (a mixture of 2% paraformaldehyde and
1% glutaraldehyde) for 5 min. Next, EVs were contrasted for 5 min
in uranyl oxalate [1:1 mixture of 4% uranyl acetate (21447-25, Polysciences,
Warrington) and 0.15 M oxalic acid (75688, Sigma-Aldrich, Schnelldorf,
Germany)] and embedded in a mixture (9:1) of 2% methylcellulose (M6385,
Sigma-Aldrich, Schnelldorf, Germany) and 4% uranyl acetate (21447-25,
Polysciences, Warrington). The EVs were imaged using a JEM 1400 TEM
(JEOL Ltd. Tokyo, Japan, with Morada TEM CCD camera, Olympus, Germany)
at 80 kV.
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7

Transmission Electron Microscopy of EVs

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EVs isolated using SEC (FF EVs and JAr EVs) were concentrated and deposited on Formvar-carbon-coated 200 mesh copper grids (Agar Scientific, Stansted, UK). The method described by Thery et al., 2018 [35 (link)], was used for transmission electron microscopy (TEM) analysis. In brief, EVs were fixed on grids in 2% paraformaldehyde (Sigma-Aldrich, Schnelldorf, Germany) and 1% glutaraldehyde (Polysciences, Warrington, PA, USA) before being contrasted in uranyl oxalate (a mixture of 4% uranyl acetate (Polysciences, Warrington, PA, USA) and 0.15 M oxalic acid (Sigma-Aldrich, Schnelldorf, Germany) and embedded in a mixture of methylcellulose (Sigma-Aldrich, Schnelldorf, Germany) and uranyl acetate (Polysciences, Warrington, PA, USA). Samples were observed with a JEM 1400 transmission electron microscope (JEOL Ltd. Tokyo, Japan) at 80 kV and digital images were acquired with a numeric camera (Morada TEM CCD camera, Olympus, Germany).
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8

TEM Analysis of Nanoparticles and Complexes

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For transmission electron microscopy (TEM) analysis of NPs and NP-Protein complexes, the TEM instrument JEOL JEM 2100 (JEOL, Italy) was used operating at 120 kV. Three microliter of each suspension were dropped on a Formvar Carbon coated 200 mesh copper grids (Agar Scientific, USA) and kept in a desiccator overnight for water evaporation. The size distribution was assessed by ImageJ/Fiji software (open-source, https://imagej.net/software/fiji) using NanoDefine ParticleSizer plugin (Thorsten Wagner, https://imagej.net/plugins/particlesizer) and the data were elaborated by Origin software (OriginLab, Northampton, MA, USA).
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9

Visualizing Phage Samples via TEM

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Formvar/carbon-coated 200 mesh copper grids (Agar Scientific) were prepared via glow discharge (10 mA, 10 s) using a Q150R ES sputter coater (Quorum Technologies). Phage suspensions (15 µl) were pipetted onto the grid surface for 30 s before removal using filter paper. Samples were stained using 15 µl of 2 % phosphotungstic acid. Excess stain was removed using filter paper and grids were air-dried. Samples were visualized using a JEOL JEM-2100Plus (JEOL) TEM and an accelerating voltage of 200 kV. Images were analysed and annotated using ImageJ (https://imagej.net/Fiji).
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10

Evaluating Nanoparticle Cellular Uptake

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The cellular uptake and distribution of CNPs was qualitatively evaluated by TEM analysis. RAW 264.7 murine macrophages were incubated for 24 h with 40 µg/ml and for 48 h with 160 µg/ml of CNPs. At the end of exposure, cells were washed, detached and re-suspended in 2% Karnovsky solution. Before analysis, Karnovsky solution was removed and cells re-suspended in osmium tetroxide solution in 0.1 M cacodilate pH 7.3 for 1 h. After three washes in cacodilate, 0.05 M of 10 min each, cells were dehydrated in a series of ethanol solutions in MilliQ water (30%; 50%; 75%; 95% for 15 min each, and 100% for 30 min), incubated in absolute propylene oxide for 20 min and embedded in a solution of 1: 1 epoxy resin -propylene oxide for 90 min.
This mixture was renewed with pure epoxy resin over night at room temperature and later polymerized at 60 °C for 48 h. Ultrathin sections (50-70 nm) were obtained using Leica UCT ultramicrotome (Leica, Italy) and stained for 25 min with uranyl acetate and lead citrate for 20 min, washed and dried. Ultrathin sections were collected on Formvar Carbon coated 200 mesh copper grids (Agar Scientific, USA) and imaged by JEOL JEM-2100 h-transmission electron microscope at 120 kV (JEOL, Italy).
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