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40 protocols using μquant microplate spectrophotometer

1

Bacterial Killing Assay of Serum

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We measured the in vitro bacterial killing ability of serum against Escherichia coli. The method was previously described in detail in ref. 102 (link). Briefly, serum samples were serially diluted with phosphate-buffered-saline (PBS), resulting in eight dilutions from 1:2 to 1:265. Each well of a 96-well-plate was filled with 44 μl and mixed with 10 μl of a bacterial working solution of ~1.5 × 105 colony-forming units (CFU)/ml. After incubation for 30 min at 37 °C, tryptic soy broth was added to each well. Absorbance was measured with a spectrophotometer (Biotek; μQuant Microplate Spectrophotometer) to determine background absorbance and again after the plates had been incubated for 12 hours at 37 °C. Bacterial killing capacity was calculated for each dilution of serum against a positive control (wells that contain only bacteria without serum). Ranks were assigned to each dilution before killing capacity dropped from 100% to 0%, such that dilution 1:2 corresponded to rank 1, the usually lowest rank, dilution 1:4 to rank 2, etc. If bacterial killing did not reach 100% even at dilution 1:2, rank 0 was assigned.
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2

Evaluating Steroid-Mediated LNCaP Cell Proliferation

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LNCaP cells were purchased from the American Type Culture Collection (ATCC) (Manassas, VA). Cells were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (Corning, Corning, NY). Cells were maintained in a 37°C, 5% CO2 humidified chamber. LNCaP cells (passage 28) were seeded (2.5 × 104 cells) in 96-well plate. After 96 hours, the RPMI-1640 medium was removed. Cells were washed with phosphate-buffered saline (PBS) and resuspended in RPMI 1640 media containing 10% charcoal: dextran stripped FBS. 24 hours later, steroids were added to the media as a DMSO solution to a final concentration of 0.1 nM or 10 nM. The final DMSO content was 1% v/v of the medium. The MTS cell proliferation assay colorimetric kit (Abcam, Cambridge, England) was performed according to the manufacturer’s instructions 24 and 72 hours after steroids were added. Briefly, 10 μL of MTS reagent was added to each well, and incubated for three hours (either 21 or 69 hours after adding the steroids). The plate was briefly shaken and the absorbance was measured at 490 nm by a μQuant Microplate Spectrophotometer (BioTek, Winooski, VT). The experiments were performed in triplicate with four independent experiments. Cell proliferation was calculated as a percentage of cells treated with steroids compared to the cells that were treated with the vehicle (1% DMSO).
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3

Measurement of Avian IgY Levels

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Total IgY, the avian equivalent to mammalian IgG, was measured using a sensitive ELISA with commercial anti-chicken antibodies38 (link),40 (link). Ninety six-well high-binding ELISA plates (82.1581.200, Sarstedt) were coated with 100 µl of diluted serum sample (2 samples per bird 1:16,000 diluted in carbonate–bicarbonate buffer) and incubated first for 1 h at 37 °C and then overnight at 4 °C. After incubation, the plates were washed with a 200 µl solution of phosphate buffer saline and PBS–Tween, before 100 µl of a solution of 1% gelatine in PBS–Tween was added. Plates were then incubated at 37 °C for 1 h, washed with PBS–Tween and 100 µl of polyclonal rabbit anti-chicken IgY conjugated with peroxidase (A-9046, Sigma) at 1:250 (v/v) was added. Following 2 h incubation at 37 °C, the plates were washed again with PBS–Tween three times. After washing, 100 µl of revealing solution [peroxide diluted 1:1000 in ABTS (2,20-azino-bis- (3-ethylbenzthiazoline-6-sulphonic acid))] was added, and the plates were incubated for 1 h at 37 °C. The final absorbance was measured at 405 nm using a photometric microplate reader (μQuant Microplate Spectrophotometer, Biotek) and subsequently defined as total serum IgY levels41 (link).
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4

Spectrophotometric Assay for MAO Inhibition

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A slightly modified continuous spectrophotometric method [27 (link)] was used to determine the selectivity of tyramine oxidation by hMAO-A or hMAO-B inhibited by GST. DEP was used as a standard control for this assay. Briefly, after optimizing tyramine used concentration for hMAO-A, 5x substrate and peroxidase chromogen reagent were mixed (1 : 1) for final of 0.5 mM tyramine HCl. In 96-well plates, 25 μL of GST serial dilutions up to 46 μM final concentrations were mixed with 50 μL isozyme for 0.7 U/mL final concentrations (0.09 U per reaction). After 40 min incubation at RT, 50 μL of the reagent/substrate mix was added to initiate the reaction and to make the final concentrations. The developing color (H2O2 indicator) was monitored over time at 490 nm by the μQuant Microplate Spectrophotometer (Bio-Tek, USA).
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5

Anti-GAA IgG1 ELISA and BAFF Assay

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Anti-GAA IgG1 ELISA were performed as previously described (9 (link)). 96-well plates (Thermo-Scientific: 3855) were coated with rhGAA (1 μg/mL) for experimental samples or a standard curve of IgG1κ (Sigma: M9269; 4000ng/mL - 62.5 ng/mL) and incubated overnight at 4 °C. Samples were diluted 1:50 and incubated for 2 hours at 37 °C. HRP-conjugated rat anti-mouse IgG1 heavy chain secondary detection antibody (AbD Serotec: MCA336P) was incubated for 2 hours at 37 °C. Plates were developed with Sigmafast OPD tablets (Sigma: P9187) and read using a μQuant microplate spectrophotometer (BioTek Instruments, Winooski, VT, USA) at 450 nm. Mouse BAFF immunoassay was performed using manufacturer's protocol (R&D Systems: MBLYS0). Spleens were filtered through a 40 μm nylon mesh filter (Fisher: 22363547) to obtain a single cell suspension for FACS. Cells were blocked with Fc block (clone: 2.4G2; BD Biosciences, San Jose, CA, USA) for 30 minutes at 4 °C prior to labeling. Cells were labeled for 30 minutes at 4 °C with the following antibodies: FITC-CD21/CD35 (clone: 4E3) and APC-IgM (clone: II/41) from eBioscience (San Diego, CA, USA), and Pacific Blue-B220 (clone: RA3-6B2) from Biolegend (San Diego, CA, USA). FACS was performed on a LSRII (BD Biosciences, San Jose, CA, USA) and analyzed using FCS Express 4 (De Novo Software, Glendale, CA, USA).
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6

Microbroth Dilution Method for Antimicrobial Susceptibility

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Bacteria used in this study were Staphylococcus aureus ATCC 29213, Escherichia coli ATCC 25922, Escherichia coli K12, Staphylococcus aureus ATCC 33591, Pseudomonas aeruginosa ATCC 27853, and Enterococcus faecalis ATCC 29212. All compounds were tested by the microbroth dilution method following Clinical and Laboratory Standards Institute guidelines.1 (link) Briefly, Mueller-Hinton broth (Difco Laboratories, Becton Dickinson) was inoculated with each organism and incubated at 37 °C with shaking to establish logarithmic growth. Following incubation, each culture was pelleted by centrifugation (3,500 × g for 5 min) and resuspended in 0.85% sterile saline solution to an optical density at 625 nm of 0.1. Samples were tested in triplicate using 96 well microplates (Corning Costar Corp. Cambridge, MA), yielding final bacterial concentrations of 5×105 CFU/mL, and incubated for 24 h at 37 °C. Following incubation, optical densities of each well were determined with a μQuant microplate spectrophotometer (BioTek Instruments, Inc., Winooski, VT) at 625 nm. The MIC was defined as the lowest concentration needed to completely inhibit growth as compared to no treatment controls.
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7

Quantification of Cartilage Composition

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For measurement of DNA and characterization of the cartilage extracellular matrix (n = 12 per group), cartilage and bone were separated, freeze dried, and digested in 100 mM sodium phosphate buffer/10 mM Na2EDTA/10 mM L-cysteine/0.125 mg/mL papain overnight at 60 °C. DNA was analyzed by fluorescence assay using bisBenzimide (DNAQF, Sigma). Fluorescence was read using a Glomax Multi Jr Detection System (Promega, Madison, WI). DNA content was quantified by comparison to a standard curve generated using known amounts of calf thymus DNA. Cartilage GAG content was determined using the Blyscan Glycosaminoglycan Assay based on binding to dimethylmethylene blue dye (Biocolor, Carrickfergus, County Antrim, UK). Precise quantities were determined from a standard curve developed using the chondroitin sulphate supplied with the kit. Cartilage collagen content was determined using the chloramine-T hydroxyproline assay according to Reddy and Enwemeka [19 (link)]. Colorimetric results were obtained using a μQuant Microplate Spectrophotometer (Biotek, Winooski, VT). Hydroxyproline was used to develop a standard curve, and the amount of collagen was calculated assuming 12.5% of collagen is hydroxyproline. DNA, GAG, and collagen contents were normalized to tissue dry weight.
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8

Pseudomonas aeruginosa Motility and Biofilm Assays

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Assays to measure swimming, twitching55 (link), and biofilm formation56 , were conducted according to standard protocols. Transformed P. aeruginosa clinical isolates were grown in appropriate media supplemented with gentamicin (30 mg/L), and with or without IPTG (1 mM). Motility and biofilm assays were conducted at 37 °C for 24 h. Images of motility assays were obtained with IVIS-50 (Perkin Elmer) and colony diameter was measured with Living Image software (Perkin Elmer). To study biofilm formation, overnight cultures were diluted 1:3 in LB broth with appropriate conditions, grown for 3 h at 37 °C with shaking. Log-phase cultures were diluted 1:50 into M63 minimal media with 0.4% arginine and 1 mM MgSO4 (30 mg/L gentamicin and 1 mM IPTG included for transformed cultures), and 100 µl added per well to a U-bottom 96-well plate and plates incubated at 37 °C for 24 h. Biofilms were stained with 0.1% crystal violet at RT, extracted in 95% ethanol, and absorbance was measured at 550 nm with a μQuant microplate spectrophotometer (BioTek).
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9

MTT Assay for DSA-Induced Growth Inhibition

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DSA-induced growth inhibition in the AML cell lines was evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) Cell Proliferation Kit I (Roche Diagnostics, Mannheim, Germany) according to the manufacturer’s instructions. Molm-14 cells were harvested from culture and seeded in a 96-well cell culture plate at a density of 5 × 103 cells/well and treated with vehicle (DMSO) or increasing concentrations of DSA (0–1000 pM) for 72 h in a 5% CO2 incubator at 37 °C. HL-60 cells were harvested from culture and seeded in a 96-well cell culture plate at a density of 5 × 103 cells/well and treated with vehicle (DMSO) or increasing concentrations of DSA (0–1000 pM) for 72 h. Subsequently, the cells were labeled with the MTT labeling reagent for 4 h followed by the addition of a solubilization buffer for ~12–16 h (overnight). The plate was then read using the μQuant microplate spectrophotometer (BioTek® Instruments, Inc., Winooski, VT, USA) and the absorbance was read at 570 nm wavelength using 650 nm as the reference wavelength.
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10

Gut Hormone Plasma Analysis Protocol

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In the responder study, the plasma levels of gut hormones were analyzed using commercial radioimmunoassay kits according to the manufacturer’s instructions. Kit GLP1T-36HK (Merck Millipore, Billerica, MA, USA; lower detection limit: 3 pM) was used to measure total GLP-1, while kit GLP1A-35HK (Merck Millipore; lower detection limit: 3 pM) was used to measure the biologically active form of GLP-1 namely GLP-1(7–36) amide or GLP-1 (7–37). Kit RMPYY-68HK (Merck Millipore; lower detection limit 15.6 pg/mL) was used to measure both biologically active forms of PYY, i.e., PYY (1–36) and PYY (3–36). For the non-responder study, plasma PYY was analyzed using Millipore’s MILLIPLEX® MAP Rat Metabolic Hormone Magnetic Bead panel following the manufacturer’s instructions and using a Luminex 200 instrument (Merck Life Science UK Limited, Gillingham, Dorset, UK). Plasma GLP-1 was analyzed using a total GLP-1 ELISA kit (Merck Life Science UK Limited, Gillingham, Dorset UK; cat no EZGLP1T-36K) also following the manufacturer’s instructions and using a μQuant Microplate Spectrophotometer (Biotek, Winooski, Vermont, USA).
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