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10 protocols using hepes

1

Fibrin Formation and Lysis Assay Protocol

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Fibrin formation and lysis assay were performed as described.22 (link)–24 (link) Cells were counted using an automated cell counter (Countstar, China), and the equal number of cells were plated in a 96-well plate. Culture medium was rapidly removed from the HUVECs. Subsequently, 2 mg/mL fibrinogen (Sigma), 5 mmol/L CaCl2 (Sangon, China), 1 nM thrombin (Sigma), 20 mmol/L HEPES (Sangon, China), and 150 mmol/L NaCl (Sangon, China) were added. For fibrinolysis assays, 1 nM tPA (Sigma) and 50 nM plasminogen (Sigma) were added after fibrin formation. Fibrin formation and lysis were detected by turbidity at 405 nm in microplate readers (TECAN, Austria).
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2

Quantum Dot-Antibody Conjugate Biosensor

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Cadmium oxide (CdO, 99.99%), zinc oxide (ZnO, 99.99%, power), sulfur (S, 99.98%, power), selenium (Se, 99.99%, power), oleic acid (OA, 90%), 1-octadecene (ODE, 90%), and 2-(N-morpholino) ethanesulfonic acid (MES) were purchased from Aldrich. NaOH, HCl, NaCl, KCl, Na2CO3, NaHCO3, KH2PO4, Na2HPO4, H3BO3, Na2B4O7∙10H2O, Tris, Hepes, and Tween-20 were purchased from Shanghai Sangon Ltd (China). Bovine serum albumin (BSA) and calf serum were purchased from Sigma. 1-ethyl-3-(3-(dimethylamino) propyl) carbodiimide (EDC), N-Hydroxysulfosuccinimide (sulfo-NHS) and the microplates were purchased from Thermo Fisher Scientific (USA). Mouse anti C-reaction protein monoclonal antibody and CRP antigen were obtained from Abcam (USA). The fluorescence spectra were detected using SpectraMaxi3 (Molecular Devices, Sunnyvale, USA). Images of electrophoresis gels were taken using a gel imaging system (GenoSens1860, Shanghai, China). The sizes of QDs and QD-antibody probe were recorded using dynamic light scattering (Nano-ZS 90, Malvern Instruments, UK). Purified water (18.2 mΩ, Millipore USA) was used in all experiments.
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3

Characterization of Protein Kinase A Activity

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4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acid (Hepes), ampicillin (Amp), and isopropyl-β-d-thiogalactopyranoside (IPTG) were purchased from Sangon in Shanghai of China. Adenosine triphosphate disodium salt (ATPNa2) was purchased from Solarbio Corporation. Tb3+ solution was obtained from Tb4O7. Tb4O7 was dissolved in concentrated hydrochloric acid and using xylenol orange as an indicator, the solution was titrated with standard EDTA complexation in HAc/NaAc buffer at pH 5.7. Protein kinase A (PKA) is self-purified.43 (link) DNA (pBR322 DNA, calf thymus DNA) was purchased from Sigma. Biochemical reagents in the construction, expression, and purification of proteins were obtained from Trans Gene. Other chemicals were of the highest purity available from local sources.
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4

Purification and Characterization of NDM-1

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Penicillin G, Piperacillin, Ceftriaxone, Cefepime, Cefazolin, Meropenem were purchased from Solarbio Co., Ltd. (Beijing, China). Imipenem was bought from Fresenius Kabi (Bad Homburg, Germany). HEPES was obtained from Sangon Biotech Co., Ltd. (Shanghai, China). All other reagents were purchased from Sigma-Aldrich Co (St. Louis, USA). The controlled pore glass (CPG) beads (125–140 μm particle diameter and 50 nm pore size) were originally purchased from VEB Trisola, Steinach, Germany. The construction of plasmid encoding NDM-1, expression and purification of recombinant NDM-1(rNDM-1) were performed as previously described (Meng et al., 2021a (link); Meng et al., 2021b (link)). The purity of the purified rNDM-1 is > 95%, The unit activity of rNDM-1 to hydrolyze Meropenem is 108 IU/mg.
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5

Isolation of Mouse Skin Cells

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The isolation method of mouse skin primary KCs was described previously68 (link). In brief, shaved back skin was incubated in 1% Typsin without EDTA at 37 °C for 1 h. After separating the epidermis from the dermis, the epidermis was cut into small pieces enough to enter the tip of a 10-ml pipette. Single-cell suspensions were prepared by repeated pipetting with a 10-ml pipette and filtering through a 100-μm cell strainer. Primary KCs were used for protein and RNA extractions.
For isolation of immune cells, mouse back skin was separated at the indicated time point, then cut into small pieces and incubated in RPMI 1640 medium containing 1 mg/ml collagenase IV (Sigma, #C5138), 50 μg/ml DNase I (Sangon Biotech, #A610099, Shanghai, China), 10 mM HEPES (Sangon Biotech, #E607018), and 10% FBS (Gbico, #12657-029) at 37 °C for 90 min. Digested skin pieces were passed through a 74-μm nylon mesh, and the suspensions were added additional RPMI 1640 to inactivate enzyme activity. Skin leukocytes were isolated by 30% and 70% percoll (GE Healthcare, #17-0891-01) at 1260 g for 20 min. The pellets were resuspended in PBS, and the cell number was counted.
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6

Antibiotic Susceptibility Testing Protocol

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Meropenem (MEM) and ceftazidime (CAZ) were obtained from USP (Rockville, MD, USA). Penicillin G (PEN), cefoxitin (FOX), cefaclor (CEC), ceftriaxone (CTRX), cefepime (FEP) and tazobactam (TAZ) were from Solarbio (Beijing, China). Avibactam (AVI), vaborbactam, fosfomycin (FOS), amikacin (AMK) and imipenem (IMI) were purchased from MedChemExpress (MCE, Monmouth Junction, NJ, USA). The purity of all antibiotics used in this study was higher than 95%. The propylamino-derivatized controlled pore glass (CPG) beads, with a diameter of 125–140 µm and pore size of 50 nm, were obtained from Steinachglas (Steinach, Germany). HEPES was purchased from Sangon Biotech (Shanghai, China). All other chemical reagents were purchased from Sigma-Aldrich (Shanghai, China) unless stated otherwise. Molecular biology enzymes were bought from Takara Bio (Dalian, China), and the primers were purchased from Sangon Biotech (Shanghai, China).
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7

Culturing Colorectal Cancer Cell Lines

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Three human colorectal cancer cell lines: HT29 cells (colorectal adenocarcinoma with p53 and APC mutation), LS174T cells (colorectal adenocarcinoma with KRAS mutation) and HCT116 cells (colorectal carcinoma with KRAS mutation) as well as normal colon, CCD841 CoN cells were obtained from American Type Cell Culture (Manassas, VA, USA). All cell lines were cultured in an incubator under the condition of 37°C temperature, humidified 5% CO2 air atmosphere. Cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) (Corning, NY, USA), supplemented with 10% Fetal Bovine Serum (FBS) (Sigma-Aldrich, St Louis, MO, USA), 25mM HEPES (Sangon Biotech, Shanghai, China) and 1% Penicillin/Streptomycin (Merck, Germany).
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8

Culturing Human Bladder Cancer BIU-87 Cells

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Human bladder cancer BIU-87 cells (a kind gift from Professor Xiaofeng Yang of the Department of Urology, our hospital, China) were cultured in RPMI-l640 medium (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 0.05 g/L streptomycin (North China Pharmaceutical Group Corp., Shijiazhuang, China), 0.05 g/L penicillin (North China Pharmaceutical Group Corp., Shijiazhuang, China), 0.8 g/L NaHCO3 (Tianjin DaMao Chemical Reagent Company), 3.6 g/L HEPES (Sangon Biotech Co. Ltd, Shanghai, China) and 10% fetal bovine serum (Hangzhou Sijiqing Biological Engineering Materials Co. Ltd, Hangzhou, China). The cells were incubated at 37 °C in a humidified environment containing 5% CO2 (NU-5500E incubator, Nuaire, Plymouth, MN, USA). For the experiments, cells in the logarithmic growth phase were digested into suspension with 0.25% trypsin (Sangon Biotech Co. Ltd, Shanghai, China).
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9

ATPase Activity Assay of Purified Proteins

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All ATPase assays were performed using the ATPase/GTPase Activity Assay Kit (Sigma-Aldrich, catalog number MAK113-1KT). Purified SugABC (0.72 μg) or 5.46-μg LpqY-SugABC-E164Q in A8-35 was incubated in a 20-μl reaction volume containing 10 mM Hepes, (pH 7.5), 75 mM NaCl, 1 mM ATP, and 2.5 mM MgCl2 (Sangon Biotech) for 30 min at 37°C. The reaction was stopped by adding 100 μl of reagent (catalog number MAK113A) and incubated for an additional 30 min at room temperature to generate the colorimetric product. Absorbance at 620 nm was measured at room temperature using a SpectraMax iD3 multifunction reader (Molecular Devices). ATPase activity was represented as phosphate (nanomoles) produced by 1 mg of protein per minute. Experiments were performed in triplicate.
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10

Recombinant Protein Expression in E. coli

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Restriction enzymes (BamHI and XhoI) were purchased from Thermo Fisher Scientific (Waltham, USA). E. coli BL21(DE3) chemically competent cells were purchased from TransGen Biotech Corporation (Beijing, China). Luria-Bertani medium, HEPES, Tris, NaCl, ampicillin, imidazole, isopropyl-b-D-thiogalactopyranoside, and dithiothreitol were all purchased from Sangon Biotech (Shanghai, China). NADPH was purchased from Sigma-Aldrich Chemistry (Hamburg, Germany).
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