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15 protocols using ceta ccd camera

1

Ultrastructural Analysis of VV-Infected Cells

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For ultrastructural analysis, HeLa and HeLa B2M KO cells grown on 12 mm glass coverslips, and infected with VV for 18h were fixed with a mixture of 2.5% glutaraldehyde and 2% paraformaldehyde in 0.1 M phosphate buffer (pH 7.4) for 1 h at RT. Cells were washed twice at 4°C with phosphate buffer; postfixation was performed with a mixture of 1% osmium tetroxide, 1% potassium ferricyanide in water for 1 h at 4°C and afterwards 0.15% tannic acid for 1 min at RT. Samples were treated with 1% uranyl acetate for 1 h at RT and dehydrated in increasing concentrations of ethanol (50, 75 and 95%) for 10 min each; and 100% ethanol three times for 30 min each, at 4°C. Infiltration in epoxy-resin was done at RT using increasing concentrations of resin (50 and 100%) and polymerization was performed at 60°C for 3 days. Ultrathin sections of the samples were stained following standard procedures with 4% aqueous uranyl acetate and 2% lead citrate. Sections were imaged on a FEI Tecnai 12 electron microscope operated at 120 kV and equipped with a FEI Ceta CCD camera.
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2

Ultrastructural Analysis of Mitochondria-ER Contacts

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HeLa cells were fixed with 2.5% glutaraldehyde in 0,1 M cacodylate buffer (pH 7.4), washed thoroughly in cacodylate buffer and post-fixed in 1% osmium tetroxide (OsO4), 1.5% potassium ferricyanide (K4 [Fe(CN)6]), 0.1 M Na-Cacodylate buffer for 1 h on ice, washed with distilled water (dH2O) and enbloc stained with 0.5% uranyl acetate in dH2O overnight at 4 °C in the dark. Finally, samples were rinsed in dH2O, dehydrated with increasing concentrations of ethanol, embedded in Epon, and cured in an oven at 60 °C for 48 h. Ultrathin sections (70–90 nm) were obtained using an ultramicrotome (UC7, Leica microsystem), collected, stained with uranyl acetate and Sato’s lead solutions, and observed in a Transmission Electron Microscope Talos L120C (FEI, Thermo Fisher Scientific) operating at 120 kV. Images were acquired with a Ceta CCD camera (FEI, Thermo Fisher Scientific). For morphometric analyses of mitochondria and MAMs, the areas and the perimeters (ROIs) of at least 200 mitochondria per sample were drawn using the freehand selections of ImageJ (n = 3). All ROIs were then extended with the enlarge function and the ER cisternae or tubules present within 30 nm or less from the mitochondria selected were scored as a MAM. GraphPad Prism was used to represent the number of contacts.
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3

Immunogold Labeling for Electron Microscopy

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Cells were fixed in 4% PFA EM grade and 0.2 M HEPES buffer for 1 h at RT or in Periodate-lysine-paraformaldehyde (PLP) for 2 h at RT. After three washes in PBS, cells were incubated 10 min with 50 mM glycine and blocked 1 h in blocking buffer (0.2% bovine serum albumin, 5% goat serum, 50 mM NH4Cl, 0.1% saponin, 20 mM PO4 buffer, 150 mM NaCl). Staining with primary antibodies and nanogold-labeled secondary antibodies (Nanoprobes) were performed in a blocking buffer at RT. Cells were fixed for 30 min in 1% GA and nanogold was enlarged with gold enhancement solution (Nanoprobes) according to the manufacturer’s instructions. Cells were post-fixed with OsO4 and processed as described for conventional EM. Images were acquired with Talos L120C TEM (FEI, Thermo Fisher Scientific) operating at 120 kV. Images were acquired with a Ceta CCD camera (FEI, Thermo Fisher Scientific) using Velox 3.6.0 (FEI, Thermo Fisher Scientific).
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4

Cryogenic TEM Imaging of Biological Samples

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Cryogenic transmission electron microscopy samples were prepared by rapid immersion in liquid ethane using a Vitrobot Mark IV (FEI; Hillsboro, OR, USA) set to room temperature and 95% humidity. Quantifoil 200 mesh R1.2/1.3 TEM grids (Electron Microscopy Science; Hatfield, PA, USA) were rendered hydrophobic by glow-discharging for 30 seconds at 15 mA with a PELCO easieGlow (Ted Pella; Redding, CA, USA). Samples (3 μL) were spotted on grids, incubated in the Vitrobot chamber for 10 seconds, briefly blotted with Whatman 595 filter paper, and then plunged into ethane. Grids were imaged using a 200 kV Thermo Fisher Scientific Talos Arctica G3 and SerialEM software (Boulder Laboratory for 3D Electron Microscopy of Cells; Boulder, CO, USA) under low-dose conditions. To align the microscope, a cross-gradient TEM grid under parallel illumination conditions at spot size 3 with the 70 μm condenser and 100 μm objective aperture was used. A Ceta CCD camera (FEI; Hillsboro, OR, USA) at −3 μm defocus, 92,000× nominal magnification corresponding to a pixel size of 1.6 nm with a total dose of 62 e-/Å2 was used to acquire images. Intermediate magnification images were acquired at 85,000× nominal magnification at −15 μm defocus.
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5

Transmission Electron Microscopy of MEFs

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MEFs were seeded on alcian blue-coated glass coverslips and fixed in double-strength fixative into the media (4% PFA EM grade, 5% GA in Na-cacodylate buffer 0.1 M, pH 7.4) for 20 min at RT. After removing the mixture, cells were incubated with single-strength fixative (2% PFA, 2.5% GA in Na-cacodylate buffer 0.1 M, pH 7.4) for 3 h at RT. After several washes in cacodylate buffer, cells were post-fixed in 1% osmium tetroxide (OsO4), 1.5% potassium ferricyanide (K4[Fe(CN)6]) in 0.1 M Na-cacodylate buffer for 1 h on ice, washed with distilled water (dH2O) and enbloc stained with 0.5% uranyl acetate in dH2O overnight at 4 °C in the dark. Samples were rinsed in dH2O, dehydrated with increasing concentrations of ethanol, embedded in Epon resin and cured in an oven at 60 °C for 48 h. Ultrathin sections (70–90 nm) were collected using an ultramicrotome (UC7, Leica microsystem, Vienna, Austria), stained with uranyl acetate and Sato’s lead solutions and observed in a Transmission Electron Microscope Talos L120C (FEI, Thermo Fisher Scientific) operating at 120 kV. Images were acquired with a Ceta CCD camera (FEI, Thermo Fisher Scientific). Image analysis was performed using Microscopy Image Browser45 (link).
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6

Cryogenic TEM Imaging of LVFF Nanofibers

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Cryogenic TEM cryogrids were prepared by rapid immersion in liquid ethane using a Vitrobot Mark IV (FEI, Hillsboro, OR) set to room temperature and 95% humidity. Quantifoil 200 mesh R1.2/1.3 TEM grids (Electron Microscopy Science, Hatfield, PA) were rendered hydrophobic by glow-discharging for 30 seconds at 15 mA with a PELCO easieGlow (Ted Pella, Redding, CA). Before cryo-plunging, samples (3 μL) were applied to the carbon side of the TEM grid and then incubated in the Vitrobot chamber for 10 seconds. Samples were blotted for 2–4 seconds with Whatman 595 filter paper. Cryogrids were imaged with a 200 kV Thermo Fisher Scientific Talos Arctica G3 under low-dose conditions using the software platform SerialEM (Boulder Laboratory for 3D Electron Microscopy of Cells, Boulder, CO). The microscope was aligned using a cross-gradient TEM grid under parallel illumination conditions at spot size 3 with the 70 μm condenser and 100 μm objective aperture. Images were acquired with a Ceta CCD camera (FEI, Hillsboro, Oregon) at −3 μm defocus, 92,000× nominal magnification corresponding to a pixel size of 1.6 nm with a total dose of 62 e-/Å2. Contours of 200 randomly selected nanofibers were manually traced using representative cryogenic TEM images of LVFF 25 mole % nanofibers. Measurements were input to calculate nanofiber length based on methods previously described. [61 (link)]
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7

Morphological Analysis of Plasma-Derived EVs

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Morphological evaluations of isolated Pre and Post derived-EVs were performed using Transmission Electron Microscopy (TEM) negative staining. EVs derived from 200 μl of plasma were diluted 1:100 and absorbed on a glow-discharged carbon-coated formvar copper grid and negatively stained with 2% uranyl acetate. EVs pictures were examined by a Talos L120C (FEI, Thermo Fisher Scientific) operating at 120 kV. Images were acquired with a Ceta CCD camera (FEI, Thermo Fisher Scientific).
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8

Cryo-TEM imaging of LUV50s

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A 4 µL sample containing 300 µM (lipid concentration) LUV50s consisting of 5% PI3P, 65% POPC, 25% POPE, 5% POPS) with or without 100 nM each of WIPI4 and ATG2A was placed onto a grow-discharged lacey formvar/carbon-coated EM grid (PELCO TEM) and vitrified as described above. The grids were imaged with a 200-keV Talos TEM (Thermo Fisher Scientific) equipped with a Ceta CCD camera at a magnification of 73,000 ×. Data were acquired with an electron dose of ~40 e-/Å2 with a defocus of −3.0 or −5.0 µm.
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9

Structural Analysis of Virus-Like Particles

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VLP samples were diluted to ~0.1 mg/mL with 10 mM HEPES, pH 7.0, and 150 mM NaCl. Higher dilutions, in the range of 0.01–0.05 mg/mL, were used when dissociated VLP fragments or Fab fragments were present. Material was adsorbed to a glow-discharged carbon-coated copper grid, washed with the same buffer, and negatively stained with 0.75% uranyl formate. Datasets were collected at magnifications of 50,000 and 100,000 (pixel size: 0.44 and 0.22 nm, respectively) using SerialEM35 (link) on an FEI Tecnai T20 electron microscope equipped with a 2k × 2k Eagle CCD camera and operated at 200 kV, as well as at a magnification of 57,000 (pixel size: 0.25 nm) using EPU on a ThermoFisher Talos F200C electron microscope equipped with a ThermoFisher Ceta CCD camera and operated at 200 kV. Particles were picked automatically using in-house developed automatic software (unpublished) or using e2boxer from the EMAN2 software package36 (link), followed by manual correction. Reference-free 2D classifications and 3D reconstructions were performed using Relion37 (link).
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10

Structural Analysis of Protein Complexes

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X18 UFO-8ANC195, X16 UFO-8ANC195 and X18 UFO-F6 protein complexes to be examined were diluted to an appropriate concentration (0.01-0.03 mg/mL) and dropped onto a freshly glow-discharged carbon-coated grid. After rinsing twice with buffer (25 mM HEPES, 300 mM NaCl, pH 7.5), the grid was stained with 2% uranyl formate (pH 7.0) and then loaded onto a 120 kV TEM for examination.
To visualize the F6-induced disassembly of X18 UFO and Q769 UFO, X18 UFO-8ANC195, Q769 UFO-8ANC195, X18 UFO-F6 and Q769 UFO-F6 protein complexes sampled after 1, 7 and 18 h incubation at room temperature were diluted to an appropriate concentration (0.01–0.03 mg/mL) and dropped onto a freshly glow-discharged carbon-coated grid. After rinsing twice, the grid was stained with 2% uranyl formate (pH 7.0) and then loaded onto a 120 kV TEM for examination. 15–71 representative images for each sample at different time points were manually collected at 73,000 × nominal magnification (1.96 Å/pixel) with a defocus range of −2 to −3 μm, using a Talos C-Twin electron microscope (Thermo Fisher Scientific) operated at 120 kV and equipped with a 4 K × 4 K Ceta CCD camera.
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