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17 protocols using pdc 32g 2

1

Kaolinite Nanoparticle Adsorption Protocols

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Kaolinite powder
(KGa-1) was kindly
provided by T. Hassenkam and S. L. S. Stipp (University of Copenhagen).
A suspension of the powder (∼1.5 mg/mL) is prepared using deionized
water (Millipore Inc.). A 20–30 μL aliquot of this suspension
is drop cast onto sapphire or mica substrates. Kaolinite nanoparticles
have two different facets, a negatively charged silica facet and a
positively charged gibbsite facet (at neutral pH).48 (link) By adsorbing them on sapphire or mica, we can expose either
the gibbsite or silica facet to the fluid. After a residence time
of 2 min, the samples are gently dried by blowing air over them and
rinsed with copious amounts of deionized water to remove loosely bound
clay particles from the substrate. Prior to drop deposition, the sapphire
substrates are cleaned with isopropanol, ethanol, and water and by
subsequent plasma cleaning (PDC-32G-2, Harrick Plasma) for 20–25
min, while the mica substrates are freshly cleaved. Sodium chloride
and calcium chloride (puriss, ACS reagent grade, Sigma-Aldrich) solutions
are prepared by dissolving the salt in deionized water. The pH is
adjusted by adding appropriate amounts of a HCl or NaOH solution.
All experiments are performed in a closed fluid cell that allows for
liquid exchange; the electrolyte solutions are injected and removed
using a syringe. The temperature of the cell is kept constant at T = 22.7 ± 0.5 °C.
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2

Cryo-EM Sample Preparation and Data Analysis

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Samples for cryo-EM study were prepared essentially as described15 (link),52 (link) (Supplementary Table 4). All EM grids were evacuated for 2 min and glow-discharged for 30 s using a plasma cleaner (Harrick PDC-32G-2). Four microliters of spike protein (0.8 mg ml−1) was mixed with the same volume of Fabs (1 mg ml−1 each), and the mixture was immediately applied to glow-discharged holy-carbon gold grids (Quantifoil, R1.2/1.3) in an FEI Vitrobot IV (4 °C and 100% humidity). Data collection was performed using either a Titan Krios G3 equipped with a K3 direct detection camera, or a Titan Krios G2 with a K2 camera, both operating at 300 kV. Data processing was carried out using cryoSPARC (v3.2.1)53 (link). After 2D classification, particles with good qualities were selected for global 3D reconstruction and then subjected to homogeneous refinement. To improve the density surrounding the RBD–Fab region, UCSF Chimera (v1.16)54 (link) and Relion (v3.1)55 (link) were used to generate the masks, and local refinement was then performed using cryoSPARC (v3.2.1). Coot (v0.8.9.2)56 (link) and Phenix (v1.20)57 (link) were used for structural modelling and refinement. Figures were prepared using USCF ChimeraX (v1.3)58 (link) and Pymol (v2.4.0, Schrödinger, LLC.).
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3

Freestanding AgNF Network on PET Substrate

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In a typical procedure, 2 g of polymer polyvinyl alcohol (PVA) was dissolved in 18 mL of deionized water at 60 °C. First, the freestanding PVA nanofiber network was collected through electrospinning (working voltage of 15 kV and receiving distance of 15 cm) on a home-made frame using Cu wire. Then, metallic silver was covered on the PVA nanofiber network by direct current sputtering (JZCK-580) with a silver target of 99.99 at% to obtain a freestanding AgNF network. Polyethylene terephthalate (PET) substrates were ultrasonically cleaned in ethanol and deionized water for 10 min and then concentrated in a plasma cleaner (HARRICK, PDC-32G-2) to improve surface hydrophilicity. Finally, the freestanding AgNF network has adhered to the PET substrate as a flexible transparent current collector.
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4

Extracellular Vesicle Visualization by TEM

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10 μL of sEVs sample was placed on formvar−/carbon-coated grid, which was cleaned in advance with a plasma surface treatment instrument (PDC-32G-2, Harrick Plasma, USA). The sample was allowed to settle for 10 min before stained with 2% phosphotungstic acid for 1 min. Grids were imaged with a JEM 1200EX (Jeol Ltd., Japanese) transmission electron microscope operating at 120 kV.
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5

Fabrication and Injection of CNTs-SS Grafts

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Polydimethylsiloxane (PDMS) precursor (A) and crosslinker (B) were mixed at the ratio of 10:1. The mixture was poured into a 1.5 cm × 1.5 cm square-shaped mold. After being cured at 110 °C for 30 min, a piece of square-shaped PDMS was fabricated. Then a hole with a 3-mm diameter was punched at the centre of the PDMS. After being treated with oxygen PLASMA (PDC-32G-2, Harrick, USA), the punched PDMS was bonded to two pieces of un-punched PDMS to obtain a PDMS cavity. Three disk-shaped CNTs-SS were compressed into small grafts, loaded into the tip of a 16G flat-head needle, and then vertically, obliquely, or horizontally injected into the three PBS-filled PDMS cavities, respectively. All of these PDMS cavities were imaged before, during and after injection.
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6

Microfluidic Sarbecovirus and RABV Infection

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Xona microfluidic devices (Xona Microfluidics, Cat#SND450) were sterilised and plasma bonded to glass coverslips (24 × 40 mm; Menzel Glaser) using a plasma cleaner (PDC-32G-2, Harrick Plasma). After bonding, the devices were coated with 15 µg/mL poly-L-ornithine (Sigma) and 10 µg/mL laminin (Sigma). HDF51i-509 NPCs were seeded in both panels of a microfluidic device at a density of 8 × 104 cells per panel in BrainPhys™ complete neural differentiation media to initiate differentiation. The media in the wells were replenished every 2–3 days and the differentiation was continued for up to 21 days.
Microfluidic chambers were infected as described previously (Sundaramoorthy et al. 2020a ) with sarbecoviruses or RABV at a MOI 1 at day 20–21 of differentiation. Briefly, media from the panel to be infected was removed and the appropriate volume of viral inoculum in BrainPhys™ neural medium required to infect at MOI 1 was added. A unidirectional flow of media was strictly maintained by a higher volume of media in the non-infected panel (200 µL) and a lower volume in the infected panel (100 µL). Sarbecovirus- or RABV-infected microfluidic chambers were incubated at 37 °C and 5% CO2 for 24 h.
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7

Enhancing HA-PU Composite Coating

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Primarily, the PU films were treated under plasma conditions for 7 min (PDC-32G-2, Harrick Plasma, Ithaca, NY, USA) to increase the bonding strength between the HA solution and PU films. The HA solution was then dispensed onto the PU films to form the base layer and dried at room temperature for 2 h. The TA polymer solution prepared in Section 2.1. was dispensed on the base layer, followed by TA-DMNs shaped by CL. During CL, centrifugation was performed for 3 min at 1300× g while vacuum conditions and a temperature of 4 °C were maintained.
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8

PET Film Preparation and Surface Modification

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Poly(ethylene terephthalate) (PET), with a thickness of 188 µm, was purchased from FilmBank (Gyeonggi-do, Korea). Prior to deposition, the PET films were cleaned with DI water, methanol, and DI water and then dried with compressed air. The cleaned PET substrates were then corona treated using a BD-20C Corona Treater (Electro-Technic Products Inc., Chicago, IL, USA) to impart a negative substrate surface charge, which helped lay down the first primer layer, BPEI [47 (link)]. Single side polished silicon wafers (p-type, 100, University Wafer, Boston, MA, USA) were used for characterizing film thickness and surface structure. Silicon wafers were cleaned with DI water, acetone, and DI water and then finally dried with compressed air. Polyurethane (PU) rubber (0.7 mm thick, WooJinPackage, Seoul, Korea) for SEM imaging and thermoelectric behaviors was rinsed with methanol and DI water before being dried with compressed air. Every PU sheet was then treated with a plasma cleaner (Harrick Plasma, PDC 32G-2, Ithaca, NY, USA) at 25 W for 5 min to enhance the adhesion of the first BPEI layer to the substrate.
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9

Microfluidic Chip Fabrication via Soft Lithography

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A high-aspect ratio mould for the subsequent soft lithography steps was additively manufactured (RGD 720 multipurpose transparent PolyJet photopolymer, Objet Eden260V PolyJet 3D printer), along with the control plates. To produce the microfluidic chip, a 10:1 PDMS-curing agent mixture (Sylgard 184 silicone elastomer kit) was degassed in a vacuum chamber for 1 h, then poured onto the mould and cured at 70 °C for 8 h. The PDMS was then peeled off the mould and trimmed, using a scalpel blade, to desired size. Channel inlet and outlets were formed with a 1.5 mm biopsy punch. Prior to assembly, the surface of the PDMS was activated by exposing it to an 18 W air/oxygen plasma at 0.6–0.8 torr pressure for 21 s, inside a plasma cleaner (PDC-32G-2, Harrick Plasma). The PDMS channels were then covalently bonded to a glass slide, by bringing them in contact immediately after plasma activation, to enclose the bottom of the channel. This creates the microfluidic chip. 8 µl of master mix was then loaded into the microfluidic chip using a syringe (Becton Dickinson 0.5 ml 29G × 12.7 mm Medical Syringe) before assembling the chip with needle, control plates, and fasteners etc. into the main cartridge. Chamber 1 was pre-vacuumed, by compressing the chamber then closing all valves, before deploying.
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10

Atomic Force Microscopy on Mica and Silica

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The mica and silica substrates were glued with epoxy to a steel puck which was magnetically clamped to the piezo stage of the AFM. Muscovite was cleaved with adhesive tape before each experiment. As silica sample surfaces, we used a silicon wafer (1 × 1 cm) with a 30 nm thermally grown oxidized layer. The silica sample was cleaned in an ultrasonic bath for 10 min in a mixture of isopropanol, ethanol, and Millipore water (25/25/50% by volume) and subsequently rinsed with only Millipore water. Then, the substrate was air plasma cleaned (PDC-32G-2, Harrick Plasma, Ithaca, NY, USA) for 20 min. Each experiment was started by flushing the system with purified water. The electrolyte solutions were prepared by dissolving the salts (NaCl, KCl, LiCl and CsCl 99% purity) in purified water. The pH was controlled by adding either NaOH or HCl to the solution. The pH of the electrolyte solutions without adjustment is around 6. All the used chemicals were purchased from Sigma Aldrich.
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