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93 protocols using temcam f416

1

Cryo-EM Structural Analysis of EBOV-Fab Complexes

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Antibody Fab proteins were obtained by recombinant expression as described above or were generated by digestion of the corresponding IgG with papain (ThermoFisher). Fabs of EBOV-515 or EBOV-520 were added in 5 M excess to EBOV GP ΔTM and allowed to bind overnight at 4°C. Complexes were purified subsequently by size exclusion chromatography on an S200 Increase column (GE HealthCare), then deposited on copper mesh grids coated with carbon and stained 2% uranyl formate. Micrographs were collected using a 120KeV Tecnai Spirit with TVIPS TemCam F416 (4k x 4k) at a defocus of about 1.5e-06 defocus and a dose of 25e-/Å2. Micrographs were collected using Leginon (Potter et al., 1999 (link)) and processed on Appion (Lander et al., 2009 (link)). Particles were picked using DoGpicker (Voss et al., 2009 (link)) and aligned with MSA/MRA (Ogura et al., 2003 (link)) where excess Fab or blurry particles were removed. An unbinned, clean dataset was deposited into Relion (Scheres, 2012 (link)) where 3D classification and refinement was performed. Figures were created in Chimera to compare EBOV complexes and show epitope location.
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2

Visualization of Lignin Deposition in Casparian Strips

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Visualization of lignin deposition around Casparian strip was done using permanganate potassium (KMnO4) staining55 (link). The sections were post-stained using 1% of KMnO4 in H2O (Sigma, St Louis, MO, US) for 45 min and rinsed several times with H2O. Micrographs were taken with a transmission electron microscope FEI CM100 (FEI, Eindhoven, The Netherlands) at an acceleration voltage of 80 kV with a TVIPS TemCamF416 digital camera (TVIPS GmbH, Gauting, Germany) using the software EM-MENU 4.0 (TVIPS GmbH, Gauting, Germany). Panoramic were aligned with the software IMOD.
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3

Cryo-EM Specimen Preparation for Liposome-Nanoparticles

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Cryogenic electron microscopy (cryo-EM) was carried out on a JEOL
JEM-2100 transmission electron microscope (JEOL GmbH, Eching, Germany).
Cryo-EM specimens were prepared as follows: a 4 μL drop of liposome–nanoparticles
suspension was deposited on a lacey carbon-coated copper TEM grid
(Electron Microscopy Sciences, Hatfield, PA) and then plunge-frozen
in liquid ethane with a Vitrobot Mark IV (FEI, Eindhoven, The Netherlands)
(conditions: 4 °C and 95% humidity). The vitrified grids were
either directly transferred to the microscope cryotransfer holder
(Gatan, Munich, Germany) or stored in liquid nitrogen. Imaging was
carried out at temperatures around 90 K. The TEM was operated at an
acceleration voltage of 200 kV, and a defocus of the objective lens
of about 0.5–1 μm was used to increase the contrast.
Cryo-EM micrographs were recorded at a number of magnifications with
a bottom-mounted 4k CMOS camera (TemCam-F416, TVIPS, Gauting, Germany).
The total electron dose in each micrograph was kept below 20 e2.
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4

Ultrastructural Analysis of Soleus Muscle

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Sample preparation was performed by the Electron Microscopy Facility at the CBMSO, UAM University, Spain. Soleus muscles were fixed with 4% paraformaldehyde and 2% glutaraldehyde in 0.1 M phosphate buffer and treated with 1% osmium tetroxide at 4 °C for 1 h. Then, they were dehydrated with EtOH and embedded in TAAB812 epoxy resin. Ultrathin 80 nm sections of the embedded tissue were obtained using an ultramicrotome Ultracult E (Leica) and mounted on carbon-coated copper 75-mesh grids. The sections were stained with uranyl acetate and lead citrate and examined at 80 kv in a JEOL JEM 1010 electron microscope. Images were recorded with a TemCam F416 (4k × 4 K) digital camera from TVIPS. Sarcomere and mitochondrial measurements were performed using ImageJ 1.52r software.
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5

Stereological Analysis of Kidney Cortex

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For stereology analysis, 3 kidney cortex pieces per mouse were analyzed, 15 micrographs per sample with a pixel size of 4.08 nm, using a systematic uniform random sampling with a transmission electron microscope (Philips CM100, Thermo Fisher Scientific) at an acceleration voltage of 80 kV with a TVIPS TemCam-F416 digital camera (TVIPS GmbH).
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6

Polymerization Reaction Imaging

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Polymerization reaction
samples were added to a Formvar (400 mesh) carbon-coated grid for
5 min. The grid was stained with 2% uranyl acetate for 40 s. The grids
were examined with a JEM1010 (Jeol) transmission electron microscope.
Images were taken with a TemCam F416 (TVIPS) camera at a magnification
of 20,000×.
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7

Transmission Electron Microscopy Sample Preparation

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For TEM analysis,
the cells were fixated in 4% paraformaldehyde + 2.5% glutaraldehyde
in PHEM buffer (60 mM PIPES, 25 mM HEPES, 10 mM EGTA, 2 mM MgCl2, 4% glutaraldehyde, 1% formaldehyde) and incubated for 3
h at room temperature.40 In a laboratory
microwave (Pelco BioWave Pro+, Ted Pella, Redding), they were washed
three times in PHEM buffer, incubated using 1% OsO4 in
PHEM buffer, washed in water, contrasted with 1% uranyl acetate in
water, washed in water and via an ethanol chain,
and acetone-embedded in EponTM. After overnight polymerization, 55
nm-thick sections were cut on an EM UC7 ultramicrotome (Leica, Wetzlar,
Germany) and mounted on 200 MESH copper grids. Post-contrastation
in an automated grid stainer (EM AC20, Leica) and drying, ultrathin
sections were analyzed and micrographed on a Jeol JEM 1400 Plus TEM
equipped with a TemCam-F416 (TVIPS, Gauting, Germany).
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8

Yeast Cell Ultrastructure Preparation for EM

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For EM, the yeast cells were precultured at 30°C in selective liquid medium containing 2% glucose (1.7 g/liter yeast nitrogen base, 2 g/liter His dropout mix, 5 g/liter ammonium sulfate, and 20 g/liter glucose). The cells were then transferred into selective liquid medium containing 3% glycerol (1.7 g/liter yeast nitrogen base, 2 g/liter His dropout mix, 5 g/liter ammonium sulfate, and 30 g/liter glycerol) and harvested in the logarithmic growth phase. The yeast cells were fixed for 30 min in 2% glutaraldehyde. After several washing steps, the cells were incubated with Zymolyase solution (0.1 mg/ml Zymolyase 100T and 0.5% 2-mercaptoethanol in 1× PBS/10% sorbitol [wt/vol]) for 15 min at room temperature to remove the cell wall. After a second fixation with 1% osmium tetroxide (30 min), the cells were poststained with 1% uranyl acetate for 2 h. After dehydration in a graded ethanol series and propylene oxide, the cells were embedded in epoxide resin (Agar 100; Plano). Ultrathin sections were examined using a transmission electron microscope (CM 120; Philips), and images were taken with a CMOS camera (TemCam F416; TVIPS).
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9

Visualizing Tau Protein Polymerization

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For the visualization of polymerization reactions samples were added to a Formvar (400 mesh) copper-coated grids ionized in BAE 120 Evaporator (Bal-Tec). Samples were adsorbed for 5 min, washed with milli Q water and left for 40 s in 2% uranyl acetate. Visualization was performed in JEM1400 Flash Transmission Electron Microscope (Jeol). Images were taken with a TemCam F416 (TVIPS) camera at a magnification of 20,000X. The extent of tau polymerization was analyzed using the image processing and analysis software Image J (Image J, NIH). Ten random fields from each condition were taken for image analysis. All analyses were performed in a blind manner. Each experiment was repeated at least three times.
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10

Negative Staining for Small Extracellular Vesicles

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To visualize small EVs, the fractions were negatively stained. For negative staining, a glow-discharged carbon-coated (2 nm carbon) formvar grid was placed on a 20 μL drop of sample and allowed to adsorb to the carbon for 10 s. The sample was then washed three times briefly on a drop of water, stained with 3% w/v uranyl acetate in water, and dried. Micrographs were recorded using a transmission electron microscope (JEM 1400; JEOL Ltd, Freising, Germany) with a bottom-mounted high-sensitivity 4K CMOS camera (TemCam F416; TVIPS, Gauting, Germany) [60 (link)].
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