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1

Ultrastructural Analysis of Listeria monocytogenes

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L. monocytogenes cells, grown to mid-exponential phase, were harvested by centrifugation and resuspended in 20% TSB dissolved in 20 mM NaPO4 (pH 4.5). Following treatment of 5 × 109 cells with 1 mg/ml B2M for 15 min at 37°C cells were pelleted by centrifugation and fixed with 2.5% glutaraldehyde containing 1% saccharose in phosphate buffer (pH 7.3). Samples were washed 5 times with phosphate buffer and postfixed in 2% aqueous osmium tetroxide. After dehydrating the samples in a graded series of 1-propanol, they were blockstained in 1% uranyl acetate and embedded in Epon. Sections were collected on copper grids, contrasted with 0.3% lead citrate for 1 min and imaged in a Zeiss TEM 109 or in a Jeol TEM 1400.
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2

Characterization of Ambient PM2.5 in Hong Kong

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PM2.5 were collected as previously described [19 (link)]. Briefly, in the summer (24 June to 11 July 2017), PM2.5 was collected in the busy roadside in Hong Kong by the URG PM samplers (URG-2000-30EH, 8 L/min) through a 47 mm Teflon (Pall Life Sciences, Ann Arbor, MI, USA) and (800 °C, 3 h) 47 mm quartz-fiber filters (Whatman, Clifton, NJ, USA). PM was extracted from the filters with 90% ethanol and 5 min of sonication and then it was dried overnight by a freeze dryer. The contents of organic carbon and elemental carbon were analysed using a Desert Research Institute Model 2001 Thermal/Optical Carbon Analyzer with the IMPROVE-A protocol. Water-soluble inorganic ions were determined by ion chromatography. PM size was determined by dynamic light scattering (Microtrac252, Montgomeryville, PA, USA). PM morphology was characterised by a transmission electron microscopy (TEM, JEOL TEM-1400, acceleration voltage 120 kV).
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3

Negative Stain Electron Microscopy Sample Prep

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Sample preparation for negative stain electron microscopy was carried out at the FHCRC electron microscopy facility as previously described (Poudel et al., 2016 ). Briefly, nickel grids were glow discharged for 40 sec, after which grids were incubated with samples. Samples were fixed using 0.5x Karnovsky’s fix at 2 minutes. Samples were then washed with one drop of 0.1 M cacodylate buffer, followed by a four-drop H2O wash. One drop of 1% uranyl acetate was touched on the sample. The grids were then carefully dragged through dry filter papers and put in a desiccator overnight to dry. Images were collected in a JEOL TEM 1400 transmission electron microscope, and measurements were done using ImageJ.
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4

Ultrastructural Analysis of Mouse Caudoputamen

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Animals were anesthetized with an intraperitoneal injection of a drug cocktail containing ketamine (100 mg/kg) and xylazine (10 mg/kg) diluted in a 0.9% NaCl solution. After anesthesia, mice were sacrificed with decapitation. Brains were quickly dissected and fixed in 0.1% Glutaraldehyde, 4% PFA, 2% Sucrose in 0.1 M Sorensen Phosphate Buffer for 24 h. The area of interest, caudoputamen, was dissected and fixed again overnight in 2.5% Glutaraldehyde, 0.1% Sucrose in 0.1 M Sorensen Phosphate Buffer. Samples were then washed in PBS and post‐fixed in 2% osmium tetroxide in PBS. After dehydrating the samples in a graded series of isopropanol, they were blockstained in 2% uranyl acetate in ethanol and embedded in Epon. Semi‐thin (500 nm) sections were stained with toluidine blue and analyzed using light microscopy to find the area of interest. Ultra‐thin sections (80 nm) were cut on a microtome using a diamond knife (Leica EM UC7) and collected on carbon‐coated formwar films on 200 mesh copper grids (Plano) contrasted with 0.3% lead citrate for 1 min and imaged using a TEM 1400 (Jeol). For the experiments, only axons localized in axon fiber bundles passing through the caudoputamen were chosen. For the quantification of non‐myelinated axons, only axons with caliber over 200 nm were chosen. Analysis of the images was performed with ImageJ software.
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5

Cell Ultrastructure Analysis via TEM

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Cells were cultured with BN NP and HAP for different time periods (8, 12, and 24 hrs) according to the experimental conditions. They were then treated in a step-by-step manner (Buffer wash, post fixation, dehydration, and resin implantation). The cultured cells were fixed using 3% Glutaraldehyde (10 min) and rinsed twice using 0.1 M Cacodylate buffer (20 min). Then they were treated with 1% Osmium Tetroxide for an hour. They were rinsed again with UHQ water thrice (10 min each) before being treated with 1% Uranyl Acetate for an hour. Cells were then dehydrated by multiple exchange of ethanol, using progressively higher ethanol concentration starting from 50% to 100%. This was followed by resin (LX112) implantation in the culture dish. The concentration of the resin was varied from a low to high resin ethanol ratio (1:2, 1:1, 2:1). Finally the cells were treated with 100% percent resin (1 h) before being placed in the oven to be moulded at 70 °C (24 hrs).
The processed samples were then sectioned in 80 nm thickness using the Leica UC7 Ultramicrotome. The sectioned samples were placed in a 400 mesh carbon grids and taken to JEOL TEM 1400 for imaging. Samples were then carefully placed in the TEM holder and secured; making sure they would not be displaced inside the microscope.
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6

Characterizing CMC-ACP Nanoparticles by TEM

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Nickel grids (EMCN, Beijing, China) were loaded with 5 μL of selected CMC-ACP dispersions after 48 h, air-dried, and characterized by TEM (TEM1400; JEOL, Japan) with an accelerating voltage of 120 kV. Selected area electron diffraction (SAED) analyses were performed on a JEOL microscope with an accelerating voltage of 120 kV to determine the phase of the nanoparticles.
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7

TEM Imaging of TGF-β1 Treated Cells

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Cells cultured in 35 mm2 dishes in complete medium ±
TGF-β1 for 4 days were fixed in half-strength Karnovsky fixative
overnight at 4°C, washed with 0.1M cacodylate buffer, and post-fixed in a
1:1 solution of 2% osmium tetroxide and 0.2M cacodylate buffer. After another
wash in buffer, cells were dehydrated with an ascending series of ethanol
washes, including a propylene oxide step, and embedded in Epon 812. Inverted
beam capsules were utilized in the embedding process, and 1μm sections on
slotted grids were stained with uranyl acetate and lead citrate. Sections were
viewed on a TEM 1400 transmission electron microscope (JEOL USA, Peadbody, MA).
Images were captured at 5000× using DigitalMicrograph version 2.1 (Gatan
Inc., Pleasanton, CA) and presented without alteration.
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8

Characterization of Nanomaterial Properties

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Based on nitrogen sorption measurements on a Quadrasorb SI (Quantachrome) the BET surface area and NL-DFT (equilibrium kernel for silica with cylindrical pores) pore size distribution of the particles was calculated. Particle morphology and particle size was visualized by transmission electron microscopy on a TEM 1400 (Jeol). Dynamic light scattering was used to measure the hydrodynamic diameter as well as the zeta potential of the particles in a dispersion of particles (0.1 mg/mL) in 2-[4-(2-hydroxyethyl)-1-piperazinyl]-ethanesulfonic acid (HEPES) buffer solution (25 mM, pH 7.2) from Merck KGaA (Darmstadt, Germany) on a Zetasizer Nano-ZS ZEN 3600 (Malvern Instruments).
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9

Microscopic Analysis of Mineralized Collagen

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The morphologies of the surface and inner-section of mineralized collagen scaffolds were imaged with a cold-field emission SEM (JSM-6330F, JEOL, Tokyo, Japan) operated at an accelerating voltage of 10.0 kV. Prior to the observations, all specimens were sputter-coated with gold.
TEM was performed to investigate the intra- and extrafibrillar mineralization of different scaffolds. Mineralized collagen scaffolds were crushed to fine-grained powders in liquid nitrogen, dispersed in ethanol and dropped on nickel grids; half of them were contrasted for 1 min with 1% uranyl acetate (SPI-Chem™, Structure Probe, West Chester, PA, USA). All the samples were analysed using a TEM (TEM1400; JEOL, Japan) with an accelerating voltage of 120 kV in bright-field and SAED modes.
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10

Electron Microscopic Analysis of Fly Thorax Mitochondria

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Electron microscopic analyses of thorax mitochondria were performed as previously described (Esposito et al., 2013 (link)). In brief, thoraxes of adult flies were fixed in paraformaldehyde/glutaraldehyde, postfixed in osmium tetroxide, dehydrated, and embedded in epon. 80-nm-thick sections were stained with uranylacetate end lead citrate, sections were imaged using a transmission electron microscope (TEM 1400; JEOL) at room temperature and a bottom-mounted camera (11 MP; Quemesa; Olympus), and iTEM 5.2 software (ResAlta Research Technologies) was used to acquire micrographs. Mitochondrial morphology was analyzed using ImageJ and scored in a blinded fashion as normal mitochondria with organized cristae or as swollen mitochondria devoid of cristae from five flies. For each fly, five sections were analyzed.
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