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17 protocols using tecnai g2 spirit twin tem

1

Ultrastructural Localization of IFT20 in Splenocytes

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Spleens were extracted from WT mice. Following single-cell isolation, splenocytes were fixed with 2.5% glutaraldehyde in 0.1 M DPBS for 2 h at 4 °C and then postfixed for 2 h in 2% osmium tetroxide. In the process of gradually increasing the concentration of ethanol and propylene oxide, the fixed samples were dehydrated and finally embedded in EMbed-812 resin (Electron Microscopy Sciences, Hatfield, PA, USA). Polymerization was performed at 60 °C for 24 h, and an ultramicrotome (Leica, Wetzlar, Germany) was used to prepare ultrathin (100 nm) sections.
For immunogold labeling, prepared sections were reacted with etching solutions for 1 h and then blocked with Tris-buffered saline containing 4% goat serum, 1% bovine serum albumin, and 0.1% Tween-20. The sections were incubated with a 1:100 dilution of IFT20 antibody overnight at 4 °C. The next day, the sections were stained with a gold-conjugated goat anti-rabbit IgG secondary antibody (AURION, Wageningen, Netherlands) at a 1:100 dilution for 2 h at room temperature. Finally, the sections were sequentially dyed with 2.5% uranyl acetate for 7 min and lead citrate for 3 min. Images were captured with a Tecnai G2 spirit TWIN TEM (FEI Company, Hillsboro, OR, USA) at an acceleration voltage of 120 kV. The antibodies used for immunogold labeling are listed in Supplementary Table 4.
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2

Cryo-TEM Imaging of ASC-Exosomes

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Cryo-TEM images were obtained using a BIO-TEM installed at the Korea Basic Science Institute (Osong, Korea). The isolated ASC-exosomes were applied to Quantifoil grids (Electron Microscopy Sciences, Hatfield, PA, USA) and subsequently blotted using Vitrobot Mark IV (FEI, Hillsboro, OR, USA) with the following settings: 100% humidity, 4 °C, blot time of 5 s, blot force of 5, blot total of 1, wait time of 5 s, and drain time of 0 s. For maintenance of vitrified sample grids at a temperature of around −178 °C within the TEM, a side entry Gatan 626 cryo-holder (Gatan, Pleasanton, CA, USA) was used. The grids were then examined with a Tecnai G2 Spirit Twin TEM equipped with an anti-contaminator (FEI Company, Hillsboro, OR, USA). A 4K × 4K, Ultrascan 4000 CCD camera (Gatan) was used for image recording. A low-dose method (exposures at 1000 electrons per nm2/s) was used for cryo-TEM.
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3

Nanoliposome Characterization and Analysis

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Following the synthesis, the nanoliposomes were diluted 1:5000 and 1:10 for nanoparticle tracking analysis (NTA) and dynamic light scattering (DLS), respectively. NTA measurements were recorded and analyzed using the Nanosight NS300 (Malvern, UK); DLS and Zeta potential measurements were performed using the Brookhaven Zeta-PALS light-scattering analyzer (New York, NY, USA). Fourier-transform infrared spectroscopy was performed using the Perkin Elmer FTIR Spectrum II (Waltham, MA, USA) on lyophilized samples. Absorbance measurements were performed in 96-well plates at various dilutions using the Spectramax i3 (Molecular Devices, San Jose, CA, USA). For transmission electron microscopy, immediately after synthesis, liposomes were drop cast on a carbon-copper grid and stained with uranyl acetate for contrast. The imaging was performed using the FEI Tecnai G2 Spirit Twin TEM (Hillsboro, OR, USA) at a voltage of 120 kV.
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4

Cryo-EM Sample Preparation and Vitrification

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After shipment, quality control of the samples was performed by collecting negative stain EM images on a Tecnai G2 Spirit TWIN TEM (FEI) (Gewering et al., 2018 (link)). For cryoEM, all samples were adjusted to 3.5 mg/mL in 50 mM Tris, pH 7.5, and 200 mM NaCl. OF335 was obtained after reaction with a 4-fold excess of AAC-DNPT; OF978C and 971C were obtained with 10-fold molar excess for 30 min at rt. To trigger NBD dimerization, the QQ constructs were then incubated with 5 mM MgATP for 1 hr at rt prior to grid preparation. For OF971, 5 mM Mg2+ATP/Vi was added to the sample and incubated for 1 hr at rt. Freezing protocol was followed as previously described (Januliene and Moeller, 2021 (link)). All samples were vitrified on freshly glow-discharged CF-1.2/1.3 TEM grids (Protochips, USA) with a Vitrobot Mark IV (Thermo Fisher Scientific, Inc, USA) at 100% humidity and 4°C, with a nominal blot force of –2 and a blotting time of 12 s. Grids were plunged into liquid ethane and stored in liquid nitrogen until further use.
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5

Ultrastructural Analysis of Constipated Colon

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After the induction of constipation, the distal colon of vehicle mice and constipation mice were isolated and fixed at 4 °C in 4% glutaraldehyde/4% paraformaldehyde (PFA) for transmission electron microscopy (TEM) according to the protocol [9 (link)]. Specimens were then rinsed with phosphoric acid, dehydrated with acetone, immersed, embedded in EPON812, and cut into Ultrathin sections (60 nm) using an ultratome. Grids were observed using Tecnai G2 Spirit TWIN TEM (FEI, Oregon USA).
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6

Detailed SEM and TEM Imaging Protocols

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Scanning electron microscopy (SEM) was performed as described previously (Bhar et al., 2021 (link)). Briefly, bacterial pellets were fixed with Trump's fixative, washed with 0.1M sodium cacodylate, pH 7.24 and then fixed with OsO4. The sample is dehydrated in 25%–100% graded ethanol series, dried by Tousimis Autosamdri‐815 and mounted on 12 mm Carbon Conductive Adhesive Tab and aluminum stub with sputter gold/palladium coating before being imaged by Hitachi SU‐5000 FE‐SEM. Negative staining was performed using Transmission electron microscopy (TEM) as described previously (Bhar et al., 2021 (link)). Briefly, purified bacterial OMVs pellet, stool derived bEVs or concentrated MNV‐1 were resuspended in fixating solution and 10 μl droplet of the homogenate was poured onto 400‐mesh carbon coated Formvar nickel grid. The excess solution was removed, and the grid was fixed. The grid was stained using floatation on 10 ml of 1% aqueous uranyl acetate and observed with FEI Tecnai G2 Spirit Twin TEM. Finally, images were obtained using Digital Micrograph software and a Gatan Ultrascan 2kX camera.
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7

SWNT-Amyloid Fibrils Binding Protocol

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To selectively bind the SWNTs functionalized with SpyCatcher on the SpyTag amyloid fibrils, SpyCatcher-SWNT was resuspended in PBS containing 0.05% v/v Tween-20 and 0.1% w/v bovine serum albumin (BSA). Solutions having a 1000:1 SpyCatcher-to-SWNT ratio at given concentrations were incubated on the SpyTag biofilms for 2 ​h at room temperature (24–26 ​°C) with slow rocking. The biofilms were then washed once with the PBS-Tween-BSA buffer and three times with deionized water. For instrumented indentation, the SWNT-integrated biofilms were dried in air at room temperature (24–26 ​°C) for 1 day. For transmission electron microscope (TEM) analysis, the SWNT-assembled biofilms were scraped by pipetting and placed on a lacey carbon TEM grid with copper (Ted Pella, Inc.) for 20 ​min. The amyloid fibrils were stained with 2% uranyl acetate for 10 ​s, washed twice with deionized water, and dried in air for an hour. The images were recorded using a Tecnai G2 Spirit Twin TEM (FEI).
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8

Ultrastructural Analysis of Muscle Tissue

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Q muscles were fixed with 3% glutaraldehyde in 0.1 M cacodylate buffer (pH 7.2) containing 0.1% CaCl2 for 3 h at RT. Fixed muscle tissues were washed five times with 0.1 M cacodylate buffer at 4 °C and then postfixed with 1% OsO4 in 0.1 M cacodylate buffer containing 0.1% CaCl2 for 2 h at 4 °C. After rinsing with cold distilled water, they were dehydrated slowly with an ethanol series and propylene oxide at 4 °C. The samples were embedded in Embed-812 (EMS, PA, USA). After polymerization of the resin at 60 °C for 36 h, serial sections were cut with a diamond knife on an ULTRACUT UC7 ultramicrotome (Leica, Wetzlar, Germany) and mounted on formvar-coated slot grids. Sections were stained with 4% uranyl acetate for 10 min and lead citrate for 7 min. Sections were observed using a Tecnai G2 Spirit Twin TEM (FEI Company, Hillsboro, OR, USA).
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9

Ultrastructural Analysis of Mitochondria

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Mitochondrial structures were observed by transmission electron microscopy (TEM). hPDLSCs were fixed in 2.5% glutaraldehyde in 0.1 M phosphate buffer for 2 h at 4°C. Ultrathin sections were stained with uranyl acetate and lead citrate and photographed with a Tecnai G2 Spirit Twin TEM (FEI, USA). Sections were scanned randomly at 10 different spots per sample at ×18500 magnification. The numbers and sizes of mitochondria were measured using imaging software (ImageJ).
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10

Ultrastructural Analysis of Keloid Tissue

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Keloid tissue samples from patients or rabbits were fixed with 1% glutaraldehyde at 4 °C and then washed with 0.1 M phosphate buffer (pH 7.4) at 4 °C. The washed samples were post-fixed with 1% osmium tetroxide (Electron Microscopy Sciences, EMS) in 0.1 M phosphate buffer solution for 2 h at 4 °C, dehydrated using ethanol solutions (50%, 70%, 75%, 90%, 95%, and 100%), and placed in propylene oxide. The dehydrated samples were embedded progressively in 2:1, 1:1, and 1:2 mixtures of propylene oxide and EMbed-812 resins (Electron Microscopy Sciences, EMS) and polymerized at 70 °C for 24 h. The tissues were sectioned at 80 nm using a Leica Ultramicrotome (Leica, Bensheim, Germany) with diamond knives and mounted on 200 mesh copper grids. Finally, the sectioned samples were post-stained with 2% uranyl acetate and 1% lead citrate, following which the specimens were observed using a Tecnai G2 Spirit Twin TEM (FEI Company, Hillsboro, OR, USA) at 120 kV.
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