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7 protocols using aquacide 2

1

Purification of ApoER2 Extracellular Domain

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To produce the ApoER2 ECD fragment, CHO lec 3.2.8.1 cells 45 were transfected with plasmid encoding ApoER2 ECD fused with hGH plus His8 and a TEV recognition site at the N‐terminus (hGH‐ApoER2 ECD) 30 and selected for resistance against 1.5 mg/ml G418. The clone with the highest secretion levels was cultured in a roller bottle (Corning). The culture supernatant was collected in a dialysis tube and concentrated with Aquacide II (Merck Millipore). The hGH‐ApoER2 ECD was purified from the concentrated culture supernatant with Ni‐NTA agarose. After washing the beads with 20 mM Tris‐Cl (pH 8.0), 300 mM NaCl, and 20 mM imidazole, the proteins were eluted with 20 mM Tris‐Cl (pH 8.0), 300 mM NaCl, and 250 mM imidazole. The fusion proteins were treated with His6‐TEV protease to release the hGH plus His8 tag. TEV protease and hGH‐His8 were removed by a second round of Ni‐NTA agarose chromatography. The ApoER2 ECD fragment was further purified by loading onto anion‐exchange chromatography on a MonoQ 5/50GL column (GE Healthcare) equilibrated with 20 mM Tris‐Cl (pH 8.0), and 1 mM CaCl2 and eluting over a linear gradient from 0 to 400 mM NaCl over a 20‐column volume at a flow rate of 1 ml/min.
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2

Purification and Analysis of Biomolecules

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Yeast nitrogen base with ammonium sulfate without amino acids was purchased from Difco Laboratories, Inc. (Detroit, MI). Hipolypepton was purchased from Nippon Shinyaku (Kyoto, Japan). Aquacide II was purchased from Merck Millipore (Burlington, MA, USA). Blue Sepharose 6 Fast Flow column and HiTrap Phenyl HP column were purchased from GE Healthcare Japan (Tokyo, Japan). Sal 1 and RNAiso Plus were purchased from Takara Bio. (Shiga, Japan). A 10% formalin neutral buffer solution was purchased from FUJIFILM Wako Pure Chemical (Osaka, Japan). Heparin sodium was purchased from Mochida Pharmaceutical (Tokyo, Japan). 4′,6-diamidino-2-phenylindole (DAPI) solution was purchased from Invitrogen (Waltham, MA, USA). Masson’s trichrome and Marinol were purchased from Muto Pure Chemical (Fukuoka, Japan). All reagents and solvents were commercially available, special-grade products, and water as a solvent was ion-exchanged water or Milli-Q water.
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3

DENV Plaque Assay on BHK-21 Cells

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Plaque assays were performed on BHK-21 cells. Briefly, BHK-21 monolayers were grown to 80% confluency in 24-well plates and incubated for 1 h at 37°C in 5% CO2 with serially diluted virus supernatants from WT and mutant HAP1 cells infected with DENV, MOI 0.1 for 48 hours. The wells were then overlaid with Dulbecco’s modified Eagle’s medium, 0.8% Aquacide II (EMD Millipore), and 10% FBS; incubated for 7 days; and fixed with 10% formaldehyde. The cells were then stained overnight with crystal violet. Next day the wells were extensively washed with water then dried and the resulting plaques were counted and plaque-forming units (PFU) per ml were calculated. Two independent experiments were performed with triplicate infections and one representative is shown.
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4

SARS-CoV-2 Plaque Reduction Neutralization Test

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For PRNT50, one day before infection, 1 × 105 Vero cells/ml were seeded in 24‐well plate using MEM containing 10% FBS and antibiotics. 1:5 diluted serum samples were heat‐inactivated for 30 min at 56°C. Four‐fold serial dilution was performed and mixed with an equal volume of 20‐40 pfu of SARS CoV‐2. The serum‐virus mixture was incubated for 1 h at 37°C in a humidified incubator with 5% CO2. After incubation, 100 µL of the mixture was added in duplicate to 24‐well plate and incubated for 1 h at 37°C in humidified incubator with 5% CO2. After incubation, 1 ml of 1% overlay media containing MEM, Aquacide‐II (Merck), 2% FBS and antibiotics was added to the Vero cell monolayer. Plates were incubated for 5 days at 37°C in a humidified incubator with 5% CO2. Five days postinfection, overlay media was discarded, cells were fixed using 3.7% formaldehyde and after washing with PBS, cells were stained using 1% crystal violet. Plates were washed and kept for air dry. Plaques were counted manually and PRNT50 titer was determined using Karber's formula as described earlier.14 Samples with PRNT50 titer ≥20 were considered seropositive.
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5

DENV Plaque Assay on BHK-21 Cells

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Plaque assays were performed on BHK-21 cells. Briefly, BHK-21 monolayers were grown to 80% confluency in 24-well plates and incubated for 1 h at 37°C in 5% CO2 with serially diluted virus supernatants from WT and mutant HAP1 cells infected with DENV, MOI 0.1 for 48 hours. The wells were then overlaid with Dulbecco’s modified Eagle’s medium, 0.8% Aquacide II (EMD Millipore), and 10% FBS; incubated for 7 days; and fixed with 10% formaldehyde. The cells were then stained overnight with crystal violet. Next day the wells were extensively washed with water then dried and the resulting plaques were counted and plaque-forming units (PFU) per ml were calculated. Two independent experiments were performed with triplicate infections and one representative is shown.
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6

Carbohydrate-based Analytical Procedures

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Maltooligosaccharide (G1-4), soluble potato starch, corn starch, bovine serum albumin and ampicillin sodium salt were purchased from Sigma-Aldrich (St. Louis, MO, USA). Tryptone and yeast extract were obtained from Difco (Bacton Dickinson and company, Sparks, MD, USA). β-CD was purchased from AppliChem (Darmstadt, Germany). Standard maltitol and D-sorbitol were obtained from TCI (Toshima, Kita-ku, Tokyo, Japan). Aquacide II, methanol, isopropanol, ethyl acetate, acetonitrile, HPLC-grade water, potassium dihydrogen phosphate, dipotassium phosphate and TLC silica gel 60 F254 glass plates (20 cm in height) were purchased from Merck (Darmstadt, Germany). IPTG, glycine and Tris-HCl were obtained from Vivantis (Sendirian Berhad, Shah Alam, Malaysia). Sulfuric acid was obtained from Carlo Erba Reagents (Val de Reuil, France). The commercial glucose oxidase kit was obtained from Human mit-diagnostics GmbH (Idstein, Germany). Other chemicals used were of an analytical grade.
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7

PRNT Assay for Virus Neutralization

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For PRNT, 1 day before infection, 1 × 105 cells/mL were seeded in a 24-well plate using MEM containing 10% FBS and antibiotics. Serum samples diluted at a ratio of 1:5 were heat inactivated for 30 minutes at 56°C. Four-fold serial dilution was performed and mixed with equal volume of 40 to 80 pfu of virus. The serum–virus mixture was incubated for 1 hr at 37°C in humidified incubator with 5% CO2. After incubation, 100 μL of the mixture was added in duplicate to 24-well plate and incubated for 1 hour at 37°C in humidified incubator with 5% CO2. After incubation, 1 mL of 1% overlay media containing MEM, Aquacide-II (Merck, Darmstadt, Germany), 2% FBS and antibiotics was added to Vero cell monolayer. Plates were incubated for 5 days at 37°C in humidified incubator with 5% CO2. At 5 days postinfection, overlay medium was discarded, cells were fixed using 3.7% formaldehyde, and after washing with phosphate-buffered saline, cells were stained using 1% crystal violet. Plates were washed and air-dried. Plaques were counted manually, and PRNT50 titer was calculated using Karber’s formula, log10 PRNT50 = m − Δ (Σp − 0.5), where m is the log10 of the highest dilution and Δ is the constant interval between dilutions expressed as log10, as previously described.19 (link)
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