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4 protocols using 3 sialyllactose

1

Comprehensive Glycoprotein Analysis Protocol

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Girard's reagent T (GT), phenylhydrazine, 2,5-dihydroxybenzoic acid (DHB), lactose (Lac), ribonuclease B (RNase B), ovalbumin (chicken egg white albumin), bovine fetuin, 3’-sialyllactose (3’-SL, α2,3-linked sialic acid), 6’-sialyllactose (6’-SL, α2,6-linked sialic acid), 1-ethyl-3-(3-(dimethylamino)propyl)-carbodiimide (EDC) hydrochloride 1-hydroxybenzotriazole (HOBt) hydrate, DL-dithiothreitol (DTT), sodium dodecyl sulfate (SDS), β-cyclodextrin and peptide-N-glycosidase F (PNGase F; supplied glycerol free) were obtained from Sigma (St. Louis, MO, USA). HPLC-grade solvents (acetonitrile, ethanol) were obtained from Fisher Scientific (Fair Lawn, NJ, USA). Water was obtained through a Milli-Q water purification system (Millipore, Bedford, MA, USA). Nonporous graphitized carbon (150 mg/4 mL) solid phase extraction (SPE) columns were obtained from Alltech Associates (Deerfield, IL, USA). Sep-Pak C18 (3 cc) solid phase extraction (SPE) cartridges were obtained from Water Corporation (Milford, Massachusetts, USA). Human serum was obtained from a healthy volunteer in Xi'an Jiaotong Hospital. The research investigations were performed after obtained the informed consent and in accordance with an institutional review board protocol approved by the Human Research Ethic Committee at the Jiaotong Hospital. All other chemicals were purchased from Aladdin Inc. (Shanghai, China).
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2

Influenza Virus Receptor Specificity

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Virus receptor specificity was determined as previously described [16 (link)]. Three biotinylated sialylglycopolymers were used: 3′-sialyllactose (3′SL, Neu5Acα2-3Galβ1-4Glc), 6′-sialyllactose (6′SL, Neu5Acα2-6Galβ1-4Glc), and 6-sialyl-N-acetyllactosamine (6′-SLN, Neu5Acα2-6Galβ1-4GlcNAc) (Sigma). 96-well fetuin-coated (1 μg/well) plates were washed, blocked with PBS containing 1% bovine serum albumin (BSA), and incubated overnight with 32 HA units of influenza viruses at 4°C. Plates were washed, 100 μL of biotinylated glycans were added and incubated at 4°C for 2 h. The plates were washed and incubated with 100 μL of horse-radish peroxidase–conjugated streptavidin at 4°C for 1 h. After a final wash, 50 μL of the tetramethylbenzidine substrate was added and incubated for 10 min at room temperature. The reaction was stopped with 50 μL of 50 mM hydrochloric acid, and absorbance was measured at 450 nm.
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3

Bifidobacterium Carbohydrate Utilization Assay

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Bifidobacterium strains were routinely cultured at 37 °C in Wilkins-Chalgren Anaerobe Broth (Oxoid, Basel, Switzerland) supplemented with soya peptone (5 g L−1, Oxoid), Tween 80 (1 mL L−1, Sigma-Aldrich, Buchs, Switzerland), and fresh sterile filtered l-cysteine hydrochloride (0.5 g L−1, Sigma-Aldrich). Carbohydrate utilization profile of bifidobacteria was investigated in API 50CHL Medium (10 g L−1 bovine/porcine origin polypeptone, 5 g L−1 yeast extract, 1 mL−1 Tween 80, 2 g L−1 dipotassium phosphate, 5 g L−1 sodium acetate, 2 g L−1 di-ammonium citrate, 0.2 g L−1 magnesium sulphate heptahydrate, 0.05 g L−1 manganese sulphate monohydrate, 0.17 g L−1 bromocresol purple; BioMérieux, Genève, Switzerland). The pH of the API medium was adjusted to 7.5 to obtain a final pH of 7 after autoclaving at 121 °C for 15 min. Carbohydrates (concentration as indicated) were filter sterilized and added after autoclaving. Fresh sterile filtered l-cysteine hydrochloride was always added before cultivation (0.5 g L−1). Glucose, lactose, and L-fucose were obtained from Sigma-Aldrich, 2′-fucosyllactose (2′-FL, Fucα1-2Galβ1-4Glc), 3′-fucosyllactose (3′-FL, Fucα1-3Galβ1-4Glc), 3′-sialyl-lactose (3′-SL, NeuAcα2-3Galβ1-4Glc), 6′-sialyl-lactose (6′-SL, NeuAcα2-6Galβ1-4Glc), Lacto-N-neotetraose LNnT (Galβ1-4GlcNacβ1-3Galβ1-4Glc) were donated by Glycom A/S (Lyngby, Denmark).
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4

Structural analysis of PEDV spike with 3'-sialyllactose

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PEDV CV777 S at a concentration of 0.4 mg/ml was incubated with 2 mM 3′-sialyllactose (Sigma-Aldrich) in 2 mM Tris (pH 8.0), 200 mM NaCl, 0.02% NaN3, 0.01% Amphipol A8-35 for 3 h at 4 °C. A 3-μl volume of the spike and 3′-sialyllactose mixture was deposited on a plasma-cleaned CF-2/2 grid before being blotted for 6 s and plunge-frozen in liquid ethane using a Vitrobot Mark IV instrument. The frozen grid was imaged using an FEI Talos transmission electron microscope (Thermo Scientific) equipped with a Ceta 16M detector. Micrographs were collected manually using TIA v4.14 (Thermo Scientific) at a nominal magnification of ×92,000, corresponding to a calibrated pixel size of 1.63 Å/pixel. A full description of the EM data collection parameters can be found in Table 1. CTF estimation, particle picking, 2D classification, ab initio 3D reconstruction, and 3D refinement were performed in cisTEM (49 (link)).
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