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19 protocols using glycerol

1

Enzymatic Biotin-Labeling Protocol

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NEB buffer 4 and Nt.BbvCI endonuclease were obtained from New England BioLabs (Ipswich, MA, USA), and the polymerase Klenow fragment exo- was purchased from Thermo Fisher Scientific Inc. (Waltham, MA, USA). Streptavidin-coated 96-well plates were purchased from BEAVER Nano-Technologies (Suzhou, China). 3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonic acid (CHAPS), tris(2-carboxyethyl)phosphine hydrochloride (TCEP), Tween 20, and invertase from baker’s yeast were purchased from Sigma-Aldrich (St. Louis, MO, USA). Ethylene glycol, bis(aminoethyl ether)-N, N, N’, N’ tetraacetic acid (EGTA), glycerol, sulfosuccinimidyl-4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (sulfo-SMCC), bovine serum albumin (BSA), deoxynucleotide triphosphate (dNTP) solution mixture, 40% acrylamide mix solution, ammonium persulfate (APS), and 1,2-bis(dimethylamino)-ethane (TEMED) were obtained from Sangon Biotechnology Co. Ltd. (Shanghai, China). All other chemicals were of analytical grade and were used as received without purification. All water used in this work was RNase-free.
The oligonucleotides used in this assay (Table 1) were synthesized and purified by Sangon Biotechnology Co. Ltd. (Shanghai, China). Buffer I (0.1 M NaCl, 0.1 M sodium phosphate buffer, pH 7.3, 0.05% Tween-20) was used throughout the experiment.
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2

Telomerase Activity Quantification Protocol

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All the oligonucleotides used in this study (Table S1) were synthesized and purified by Sangon Biotechnology Co. Ltd. (Shanghai, China), the modified sequences were HPLC purified, and other sequences without modification were ultraPAGE purified. A telomerase ELISA kit was obtained from Innovation Beyond Limits (Germany). Glycerol, deoxynucleotide triphosphates (dNTPs) solution mixture, 40% acrylamide mix solution, ammonium persulfate (APS), and 1,2-bis(dimethylamino)-ethane (TEMED) were obtained from Sangon Biotechnology Co. Ltd. (Shanghai, China). 4′,6-Diamidino-2-phenylindole (DAPI) was purchased from KeyGen Biotech. Co. Ltd. (Nanjing, China). 3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonic acid (CHAPS), Tween 20 and epigallocatechingallate (EGCG) were bought from Sigma-Aldrich (St. Louis, MO, USA). The transfection reagent, X-tremeGENE, was bought from Roche. All of the chemicals were of analytical grade and were used as received without any purification.
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3

Aeromonas salmonicida subsp. masoucida Vaccine

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Aeromonas salmonicida subsp. masoucida (strain RZ6S-1) was isolated from diseased cultured Atlantic salmon in a farm located in Yantai, Shandong province. The strain was stored in 15% glycerol (Sangon, China) at − 80 ℃ in laboratory until passage on tryptone soy agar supplemented with 1.5% NaCl (w/v) (TSA) for 50 h, immediately before use. Bacteria were cultured in tryptone soy broth supplemented with 1.5% NaCl (TSB) for approximately 12 h at 20 ℃ prior to use during the production of vaccine.
Aeromonas salmonicida subsp. masoucida (strain RZ6S-1) were cultured in TSB medium and centrifuged at 4000 g for 10 min. Bacteria were resuspended in 0.2 M phosphate buffer saline (PBS, 0.145 M Na2HPO4⋅12H2O, 0.055 M NaH2PO4⋅2H2O, pH 7.4), and inactivated with 0.2% formalin at 20 ℃ for 24 h, and 4 ℃ for 72 h. Success of inactivation of bacteria was checked by culturing on TSA for 7 days. Inactivated RZ6S-1 was suspended with PBS to approximately 2 × 109 CFU/mL and emulsified with the oil adjuvant Marcol 52 (MOBIL™, USA) at a ratio of 4:6 to form an oil-based vaccine (Yan et al. 2021 ).
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4

Rifampicin MIC Determination in M. smegmatis

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M. smegmatis was grown in nutritious Middlebrook 7H9 supplemented with 0.5% (v/v) glycerol (Sangon Biotech, Shanghai), 0.05% (v/v) Tween-80 (Sangon Biotech, Shanghai) and 10% (v/v) ADC. MICs were quantified with the resazurin microdilution titration method. Briefly, Middlebrook 7H9 broth was added to 96-well plates to prepare a continuous two fold dilution of rifampicin in triplicate. Each well was inoculated with 105 CFU bacteria for 2–3 days at 37 °C and subsequently mixed with 30 μl 0.01% resazurin (Sangon Biotech, Shanghai) solution to determine the lowest concentration that inhibited bacterial growth. Three different gradients of rifampicin were tested: 600, 300, 150, 75, 37.5, and 18.75 μg/ml; 500, 250, 125, 62.5, 31.25, and 15.625 μg/ml; and 400, 200, 100, 50, 25, and 12.5 μg/ml.
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5

Microinjection of Fluorescent Plasmids

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The injection cocktail containing 20% glycerol (Sangon Co., China), 2 mg/ml Texas red dextran (Invitrogen Co., USA) and 200-300 ng/ml recombined plasmid DNA was microinjected into unfertilized eggs according to our previous report (Liu et al., 2013) . After injection, the eggs were fertilized immediately and then cultured in an incubator at 25°C with 95% humidity. Fluorescent signals were observed under a stereoscope (SZX10, Olympus Co., Japan) and photographed under a high sensitivity confocal microscope (LSM 780-1, Zeiss Co., Germany).
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6

Aeromonas hydrophila Virulence Assay

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Aeromonas hydrophila strains AH33, AH189, AH196, and AH301 (Table 1) were isolated from diseased carps and identified based on gyrB sequences. Strain NJ‐35 was donated by Prof. Yongjie Liu (College of Veterinary Medicine, Nanjing Agricultural University, China) (Pang et al., 2015). Stock cultures were maintained at −80°C in Luria‐Bertani broth (Oxoid, Basingstoke, UK) containing 30% (v/v) glycerol (Sangon Biotech, Shanghai, China). When required, the stocks were streaked on nutrient agar, incubated at 30°C overnight, and single colonies were collected and used in subsequent experiments.
The catecholamine hormone NE (noradrenaline bitartrate) was purchased from Target Molecule (Boston). Before each experiment, NE solutions were freshly prepared with sterilized physiological saline solution and filter‐sterilized using 0.22 μm MCE syringe filters (Sangon Biotech, Shanghai, China).
Serum‐SAPI medium was prepared as described by Lyte and Ernst (1992) and Dong et al. (2016) with slight modification. Briefly, the medium contained 0.4990 g glucose, 0.5003 g NH4NO3, 0.2504 g KH2PO4, 0.2497 g KCl, and 0.1216 g MgSO4 in one liter of 10 mM HEPES buffer, which was supplemented with 10% (v/v) fetal bovine serum (FBS, Zhejiang Tianhang Biotechnology, Hangzhou, China).
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7

Transaminase Enzyme Production Protocol

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Yeast extract and tryptone were purchased from Oxoid (Shanghai, China). Pyridoxal-5’-phosphate (PLP), pyruvate and R-1-phenylethylamine (1-(R)-PEA) were purchased from Aladdin Biochemical Technology Co., Ltd. (Shanghai, China). Choline chloride (ChCl), urea, ethylene glycol (EG), propylene glycol (PG), glycerol, formate, kanamycin sulphate, isopropyl–β-d-thiogalactopyranoside (IPTG), sodium dihydrogen phosphate, disodium phosphate, imidazole, sodium chloride, Ni-NTA Sefinose™ Resin (Settled Resin), Modified Bradford Protein Assay kit and SDS PAGE gel kit were obtained from Sangon (Shanghai, China). Amicon®® Ultra Filter units were obtained from Sigma Aldrich (Shanghai, China). All chemicals were of analytical grade. The transaminase genes from Aspergillus terreus, which were previously transformed in E. coli BL21 (DE3) pRSF-D-AAO competent cells, were stored in our laboratory at −80 °C. The plasmids and the E. coli BL21 (DE3) pRSF-D-AAO competent cells were constructed by Anhui General Biology Company (Anhui, China).
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8

Gut Microbiome Depletion and Transplantation

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Mice were gavaged with the mixture of antibiotics (ampicillin, neomycin (Cayman, Ann Arbor, MI, United States), metronidazole (Sigma, St. Louis, MO, United States) 1mg/L; vancomycin (Cayman, Ann Arbor, MI, United States) (0.5mg/mL) three consecutive days to deplete the gut microbiota. On the fourth day after antibiotics treatment, mice were orally administered 200μL fecal suspension, which was retrieved from RD and HMD mice and was suspended in 30% glycerol (Sangon Biotech, Shanghai, China) diluted in PBS (Gibco, Co Dublin, Ireland) (100mg/1.2mL), for totally four times. Fecal microbiome transplanted mice were used for experiments.
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9

Analytical Protocol for Danhong Injection

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Arachidonic acid (AA), dimethyl sulfoxide (DMSO), and o-dianisdine were purchased from Sigma-Aldrich Inc. (St. Louis, MO, USA). The salvianolic acid B (SaB), danshensu sodium (DSS), lithospermic acid (LA), rosmarinic acid (RA), p-coumaric acid (pCA), and hydroxysafflor yellow A (HSYA) were purchased from Shanghai Winherb Medical Technology Co., Ltd. (Shanghai, China). The aspirin was obtained from Dalian Meilun Biological Technology Co., Ltd. (Dalian, China). The 10 batches of normal danhong injection samples, the danshen component (DS), and the honghua component (HH) were provided by Danhong Pharmaceutical Co., Ltd. (Heze, China), while five batches of abnormal samples were collected from samples that suffered oxidative degradation. The glycerol and the 4% paraformaldehyde fix solution were purchased from Sangon Biotech Co., Ltd. (Shanghai, China). Ultrahigh-purity water was produced by a Millipore Milli-Q System (Milford, MA, USA). Acetonitrile, formic acid, and methanol were obtained from Merck KGaA (HPLC grade, Darmstadt, Germany). 1-phenyl-2-thiourea was purchased from Sigma-Aldrich Inc. (St. Louis, MO, USA).
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10

Isolation and Characterization of Lactic Acid Bacteria

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One gram of sour porridge was put into a conical flask containing 9 mL of sterile sodium chloride (0.9%, w/v) covered with glass beads. Then the slurry was shocked for 30 min in a shaker at room temperature, followed by centrifugation at 2500× g for 15 min. The supernatant was collected, serially diluted, and 1 mL of the suspension from 106 dilution was plated onto the sterilized Man Rogosa Sharpe (MRS) [38 (link)] agar medium (Sangon). The plates were cultured at 30 °C for 1–2 days. Individual colonies were selected and purified. The morphological and physicochemical properties of all pure isolates were analyzed using Gram staining test, endospore test, cellular morphology and colony characteristics, biochemical tests (i.e., catalase, oxidase, nitrate reductase, arginine, amygdalin, etc.), the potentiality to ferment various saccharides such as sucrose, mannitol, glucose, arabinose and so on. All isolates were maintained at −80 °C in MRS broth supplemented with 20% (v/v) glycerol (Sangon).
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