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19 protocols using costar 3524

1

Whole Blood Stimulation Assay

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In 24 well plates (Costar 3524, Corning Incorporated), 1 ml of heparinised whole blood was stimulated either in the presence of a final concentration of 200 ng/ml of Pam3CSK4 (Invivogen), 1 ng/ml of LPS (from Salmonella Minnesota R595, Enzo Life Sciences) added in a volume of 100 µl with RPMI-1640 with GlutaMAX (Life Technologies). Media control samples were cultured with the addition of 100 µl of RPMI-1640 with GlutaMAX. Samples were incubated at 37°C, 5% CO2 for 0, 1, 3, 6, 12 or 24 hours at which point the contents of the well were thoroughly mixed with 2 mls Tempus Solution (Applied Biosystems/Ambion) to lyse the cells and stabilise the RNA. Samples stored at −80°C until RNA processing.
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2

Caco-2 Cell Culture for Adhesion Assays

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Caco-2 cells (ATCC HTB-37), a human colon adenocarcinoma cell line, were maintained in Dulbecco’s modified Eagle’s medium (DMEM)/F12 media (Gibco, USA) supplemented with 10% (v/v) inactivated (30 min, 56°C) fetal bovine serum, 20 U/ml penicillin and 100 μg/ml streptomycin. Cells were cultured at 37°C in a 5% CO2/95% air atmosphere using a humidified CO2 incubator. Cells were used at post-confluence after 21 days of culture. For adhesion assays as well as inhibition of intestinal cell adhesion and invasion by pathogens, monolayers of Caco-2 cells were prepared in 24-well tissue culture plates (Costar 3524, Corning Inc. NY, USA). Cells were seeded at a concentration of 5 × 104 cells/ml in the DMEM-F12 medium without penicillin and streptomycin.
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3

Quantitative Analysis of Biofilm Formation

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Biofilms were cultivated in Luria-Bertani (LB) broth supplemented with or without the hordenine analogs in 24-well polystyrene plates (Costar 3524, Corning, Corning, NY, USA) using previous methods with minor modifications [19 (link)]. After 24 h of static incubation, cultures and planktonic cells were removed and sessile cells were stained with 0.05% crystal violet, with the excess rinsed off using distilled water. After dissolution with 95% ethanol, biofilm biomass was determined at OD570 [20 (link)].
To investigate cell viability, biofilms were washed with phosphate-buffered saline (PBS) and digested with dextranase (5 units, D8144, Sigma-Aldrich, St. Louis, MO, USA), followed by 30 s of sonication, as described previously [21 (link)]. For S. marcescens NJ01, viable cells in the treated biofilms were counted by plating at 28 °C for 24 h. For P. aeruginosa PAO1, viable cells in the treated biofilms were counted by plating at 37 °C for 24 h.
To observe the biofilm more intuitively, samples were observed using confocal laser scanning microscopy (CLSM, LEICA TCS SP8, LEICA, Germany). Biofilms formed on circular glass coverslips were washed with PBS and subsequently stained with acridine orange (AO). Excess dye was removed using PBS. Stained biofilms were then visualized by CLSM (excitation, 488 nm; emission filter, 501–545 nm).
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4

Dual-Species Biofilm Structural Analysis

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To evaluate the biofilm structure, the dual-species biofilms were formed in 24-well plates (Costar® #3524, Corning Inc., Corning, NY, USA) and evaluated by scanning electron microscopy (SEM). In brief, dual-species biofilms of C. albicans and S. mutans were formed in 24-well plates and exposed to the experimental solutions, as previously described. After the last treatment, the wells were gently washed with NaCl (0.85%), and the biofilms were dehydrated using the following series of ethanol concentrations: 70% for 10 min, 95% for 10 min, and 100% for 20 min, followed by air drying for 20 min [41 (link)]. Next, the bottom of each well was cut with a flame-sterilized scalpel blade (number 11, Solidor, Lamedid Commercial and Services Ltd., Barueri, Brazil), and the biofilms were coated with gold and evaluated using an electron microscope (S-360 microscope, Leo, Cambridge, MA, USA).
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5

Quantitative Biofilm Formation Assay

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Biofilm formation ability was determined by crystal violet staining method as described previously,17 (link) with slight modifications. Briefly, the overnight culture of each strain was diluted to final optical density of 600 (OD600) = 0.1, and then 180 μL of Luria-Bertani (LB) broth (Haibo, Qingdao, China) with 1% glucose (Sigma, USA) and 20 μL of bacterial suspensions were inoculated into 96-well polystyrene microtiter plates (Costar #3524, Corning, NY, USA) in triplicate. After 24 h incubation at 37 °C, the plates were gently washed with phosphate-buffered saline (PBS) for three times and stained with 200 μL of 0.1% crystal violet (Solarbio, Beijing, China) for 20 min. After washing with PBS for three times again, the plates were solubilized with 200 μL of 95% ethanol, followed by shaking slowly at room temperature for 20 min. The absorbance was measured at OD570. The cut-off OD (ODc) was defined as three standard deviations (SD) above the mean OD of the negative control (LB broth only). Following were classification criteria: OD ≤ ODC, non-biofilm producers (-); ODC < OD ≤ 2×ODC, weak biofilm producers (+); 2×ODC < OD ≤ 4×ODC, moderate biofilm producers (++); and OD > 4×ODC, strong biofilm producers (+++).18 (link)
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6

Polyphenol Effects on Lactic Acid Bacteria Biofilm

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24-well polystyrene plates (Costar 3524, Corning Incorporated) were coated with porcine mucin (10 mg/mL, Sigma) in distilled water (200 μL/well; 4 °C, overnight). After discarding the mucin solution, wells were washed twice with a 150 mM NaCl solution and 1 mL per well of fresh MRS, supplemented or not (vehicle: ethanol) with the indicated polyphenol (at concentrations ranging from 5 to 50 µM) and inoculated with 107 colony forming units (CFUs)/mL of a culture in stationary phase of L. paracasei ATCC334 or L. rhamnosus GG strains. Plates were incubated at 37 °C for 24 h. Cells attached to the well walls were quantified as described previously [16 (link)]. After incubation, the medium was removed from each well, and the plates were washed twice in a 150 mM NaCl solution to remove loosely attached cells. We added 1 mL of a 150 mM NaCl solution to each well before repeated pipetting to detach the biofilm, and serial dilutions of biofilm recovered suspension were spotted onto MRS agar plates. Each strain and/or condition was tested in at least three independent experiments, each with three biological replicates.
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7

Biofilm Formation Quantification and Visualization

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The biofilm formation ability of AP2044 strain and lab-WT was determined by the crystal violet staining method and field-emission scanning electron microscope (FE-SEM) as described previously with minor adjustment. Briefly, the strains were cultured overnight and adjusted to a final OD600 of 0.1. A total of 20 μL of each bacterial suspension and 180 μL of LB broth (Haibo, Qingdao, China) were inoculated into a 96-well polystyrene microtiter plate (Costar#3524, Corning, United States) in triplicate. After incubation at 37°C overnight, the plate was washed with phosphate-buffered saline (PBS, Solarbio, Beijing, China) to remove planktonic cells, and the plate was stained with crystal violet (Solarbio, Beijing, China) and solubilized with 95% ethanol (v/v), after which its absorbance was measured at 570 nm.
In addition, the biofilm formation capacity of each strain was used for SEM analysis. Biofilms were cultured for 24 h on coverslips as described above and planktonic cells were removed using PBS. First, the cells were fixed with 2.5% glutaraldehyde in PBS for 4 h. Second, the cells were gently washed with PBS twice. The samples were then gradually treated with ethanol (30, 50, 70, 80, 90, and 100%) for 20 min at each concentration. The dried samples were coated with platinum and visualized using FE-SEM (Thermo Fisher Scientific, Waltham, Massachusetts, United States).
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8

Transwell Assay for Endothelial Cell Migration

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The evaluation of endothelial cell migration is the most frequent method for studying chemotaxis in angiogenesis using transwell plates (Costar, #3524, Corning Incorporated, Waltham, NY, USA) with 8 μm diameter pores filters. Briefly, the bottom chambers were filled 600 μL with or without VEGF (25 ng/mL) and various concentrations of VH02. The insert filters were placed into the wells by sterile forceps. Then, cells 1 × 104 cells/well were suspended in 100 μL of media and seeded in the upper chambers. The cultures were allowed to migrate at 37 °C for 16 h. After incubation, the chemoattractant medium in the bottom chambers was removed and replaced with 8 μM Calcein AM fluorescent dye in medium at 37 °C for 45 min. The migrated cells were determined by multi-detection microplate reader at excitation 458 nm and emission at 528 nm (BioTek Instrument, Inc., Winooski, VT, USA).
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9

Scanning Electron Microscopy of Biofilms

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SEM was performed on biofilm formed on glass coverslips (0.2 mm thick and 6 mm in diameter) by dispensing 700 μL of the cell suspensions into the wells of 24-well flat bottomed polystyrene plates (Costar 3524; Corning; USA). The plates were incubated at 37°C with shaking. The coverslips were then washed three times with water and fixed using 2.5% glutaraldehyde in 0.1 M sodium phosphate buffer (pH 7.2) for 4 h at 4°C. Next the coverslips were washed three times with 0.1 M sodium phosphate buffer for 15 min each, followed by three 50% ethanol (v/v) washed for 10 min each. The samples were freeze-dried for 5 h and ultimately coated with gold and palladium in an evaporator. The observations were usually performed with a scanning electron microscope (FEI Quanta 200; USA).
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10

Quantification of Biofilm Formation in Acidovorax citrulli

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Biofilm formation was assessed as previously described [35 (link)]. Briefly, 24-well polystyrene cell culture plates (Costar 3524, Corning, NY, USA) were filled with KB broth and then inoculated with a 1:1000 dilution of each A. citrulli strain at a concentration of 3 × 108 CFU/mL. The plates were incubated at 28 °C for 48 h without shaking. After incubation, 0.1% crystal violet was added to each well, and the plate was incubated for 30 min at room temperature. Each well was then gently washed three times with distilled water. To quantify biofilm formation, the stained biofilms were solubilized in 95% ethanol for 2 h, and then the OD575 value of each stained cell suspension was measured with an Evolution 300 UV/VIS spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). There were three biological replicates for each A. citrulli strain in each experiment, and there were three independent replicates of this experiment.
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