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25 protocols using 400 mesh copper grid

1

EDS Characterization of GSAN Formulations

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A JEOL JEM-1400 transmission electron microscope (JEOL, MA. USA, Inc.) operating at an accelerating voltage of 120 kV was used to acquire energy dispersive X-ray spectroscopy (EDS) spectra from GSAN formulations. Briefly, one drop of aqueous dispersions of GSAN formulations was deposited on an ultrathin carbon type-A 400 mesh copper grid (Ted Pella Inc. CA. USA), and the droplet was then dried under ambient conditions. EDS spectra on each GSAN formulation were recorded.
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2

Characterization of Ge Nanocrystal Morphology

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Electron-transparent specimens were prepared by drop-casting dilute suspensions of Ge nanocrystals dispersed in hexanes onto lacy carbon supported by a 400-mesh copper grid (Ted Pella). The grids were dried overnight under an incandescent lamp followed by oven drying at 85 °C to minimize any contamination during electron beam irradiation. The TEM imaging of the samples was performed using a JEOL-JEM 2500SE TEM (JEOL Ltd. Tokyo, Japan) at the Advanced Materials Characterizations and Testing Laboratory (AMCaT) at the University of California, Davis. This instrument is operated at 200 kV and is equipped with a Schottky field-emission electron gun (FEG) and a retractable 1k × 1k Gatan Multiscan CCD camera (model 794). Digital Micrograph software provided by Gatan Inc. was used to capture images. To determine the average particle diameter and respective standard deviation, 200 individual nanocrystals were imaged from different sample areas and multiple sample grids. Particle sizes were measured from intensity line profiles across individual particles in one consistent direction using the Image J software package.
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3

Negative Stain Electron Microscopy of Protein Complexes

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To prepare grids for negative stain electron microscopy, a fresh sample of either MceG-GFP or LucB-GFP was applied to a freshly glow discharged (30 seconds) carbon coated 400 mesh copper grid (Ted Pella Inc., cat. #01754-F) and blotted off. Immediately after blotting, a 2% uranyl formate solution was applied for staining and blotted off on filter paper. Application and blotting of stain was repeated five times. Samples were allowed to air dry before imaging. Data were collected on a Talos L120C TEM (FEI) equipped with a 4K x 4K OneView camera (Gatan) at a nominal magnification of 73,000x corresponding to a pixel size of 2.00 Å /pixel on the specimen, and a defocus range of −1 to −2 μm defocus. For LucB-GFP data, data processing was carried out in cryoSPARC v3.3.160 . Micrographs were imported, particles were picked manually as templates for Template Picking. Particles that were picked by template picking were sorted using 2D Classification.
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4

Germanium Nanocrystal Characterization by TEM and DF-STEM

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Both TEM and DF-STEM samples were prepared by drop-casting the dilute
dispersion of Ge NCs in toluene onto lacey carbon supported by a 400
mesh copper grid (Ted Pella). The grids were dried completely to avoid
carbon contamination of the vacuum chamber during electron beam irradiation.
TEM/DF-STEM images were acquired using a FEI ThemIS 60–300
STEM/TEM (Thermo Fisher Scientific, US) operated at 300 kV at the
National Center for Electron Microscopy within the Molecular Foundry
in Lawrence Berkeley National Laboratory. The ThemIS is equipped with
image aberration corrector optics and a Ceta2 camera (4k × 4k
pixels, and 14-bit dynamic range).
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5

Nanoparticle Characterization by TEM

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Uncoated or serum-coated
NPs (0.05 mg) were dispensed onto a 400-mesh copper grid (Ted Pella
Inc., Redding, CA, USA). Excess solution was removed with a Kimwipe
(Kimberly-Clarke, Iriving, TX, USA) and left to air-dry overnight
at room temperature. Grids were imaged with a JEOL TEM-1011 (JEOL
Ltd., Akishima, TYO, Japan) microscope at 100 kV and 6000 magnification.
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6

Negative Stain Electron Microscopy Protocol

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To prepare grids for negative stain electron microscopy, a fresh sample of either MceG-GFP or LucB-GFP was applied to a freshly glow discharged (30 seconds) carbon coated 400 mesh copper grid (Ted Pella Inc., cat. #01754-F) and blotted off. Immediately after blotting, a 2% uranyl formate solution was applied for staining and blotted off on filter paper. Application and blotting of stain was repeated five times. Samples were allowed to air dry before imaging. Data were collected on a Talos L120C TEM (FEI) equipped with a 4K x 4K OneView camera (Gatan) at a nominal magnification of 73,000x corresponding to a pixel size of 2.00 Å /pixel on the specimen, and a defocus range of -1 to -2 μm defocus. For LucB-GFP data, data processing was carried out in cryoSPARC v3.3.1 60 . Micrographs were imported, particles were picked manually as templates for Template Picking. Particles that were picked by template picking were sorted using 2D Classification.
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7

Cryo-EM of Dengue Virus Particles

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Purified DENV 16681 was placed on an ultra-thin carbon film (<3 nm) supported by a thicker holey carbon film on a 400 mesh copper grid (Ted Pella, Redding, CA). A cryoplunge 3 system (Gatan Inc.,Warrendale, PA) installed in a Class II biological safety cabinet was used to blot (~6 s) and rapidly plunge the grid into liquid ethane maintained in a liquid nitrogen bath. The grid was subsequently transferred to an FEI Titan Krios electron microscope using a cryo holder. The microscope was operated at 300 kV with a total dose of ~20 electrons per Å2 and micrographs were recorded using a 4kx4k CCD camera (Gatan Inc.). Viruses collected 5 d post-infection from both Vero and Vero-furin cells were analyzed further, as these were optimum in purity and virus concentration. Heterogeneity of each sample was analyzed by classifying ~850 particles as mature, partially mature and immature based on their smooth, mosaic or spiky appearances, respectively.
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8

Characterization of Composite Scaffolds

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Composite scaffolds were analyzed with Scanning Electron Microscopy (SEM) to observe the surface morphology and average pore sizes. Microscopic view of inorganic fillers was observed with SEM analysis. In addition, STEM and AFM analyses were performed to observe the morphology of POSS and Si-HAP nanoparticles. Nanoparticles were dispersed in ultrapure water with 10 12 dilution factor. Nanoparticle dispersions were dripped on TEM grids (Ted Pella 400 mesh copper grid supported with ultrathin carbon film) and coverslips. Before SEM analysis, samples were coated with a thin gold layer under Argon gas by using Emitech K550X. The analysis was performed with Quanta FEG 250 (at 7 × 10 -2 mbar and 15 mA). Image J software was used to calculate the average pore sizes. DLS Analysis was performed in a Malvern Zeta-sizer Nano ZS to determine the hydrodynamic sizes of the inorganic fillers. 1% w/v of dispersions were prepared with deionized water and incubated in an ultrasonic bath for 5 min before testing.
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9

Negative-Stain Electron Microscopy of PGAM5

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Homemade grids were prepared for negative-stain experiments by depositing a thin plastic layer on the surface of 400-mesh copper grids (Ted Pella) floated on 2% amyl acetate (EMS)58 . Air-dried grids were then coated with ~3 nm of continuous carbon film, negative glow discharged, and loaded with 2.5 µL of purified PGAM5 (~0.01–0.1 mg/mL). Following a 30 s incubation, grids were briefly dipped in two drops of sample buffer and one drop of 0.75% uranyl formate staining solution with blotting performed between drops by touching the edge of the grid briefly to the surface of Whatman 1 filter paper. Sample grids were dipped in a second drop of stain for 30 s, blotted on filter paper, and air dried prior to imaging. Images were collected using a 120 kV Tecnai T12 (FEI) microscope equipped with a Gatan 4× 4 K CCD camera at 52 K magnification corresponding to a pixel size of 2.21 Å.
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10

Negative Staining for TEM Imaging

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Three μl of the sample was applied on glow-discharged, carbon-coated, and formvar-stabilized 400 mesh copper grids (Ted Pella) and incubated for approximately 30 s. Excess sample was blotted off, and the grid was washed with MilliQ water prior to negative staining using 2% uranyl acetate. TEM imaging was done using Hitachi HT7700 (Hitachi High-Technologies) transmission electron microscope operated at 100 kV equipped with a 2k x 2k Veleta CCD camera (Olympus Soft Imaging System).
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