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13 protocols using propidium iodide

1

Multicolor Biofilm Imaging Technique

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Single and mixed biofilms were developed as described above on 12-well polystyrene plates covered with a sterile coverslip (Velab, Mexico City, Mexico).
Coverslips were recovered and placed in contact with a mixture of fluorochromes. The following fluorochromes were applied: calcofluor white 1 g/L (Sigma-Aldrich St. Louis, MO, USA) for chitin; 10 mM FUN®1 (Life Technologies, Gaithersburg MD, USA) for metabolic activity; 1 mg/mL concanvalin A (conA) (Sigma-Aldrich St. Louis, MO, USA) for glucose and mannose residues; and 1.5 μg/mL DAPI (Vector Laboratories, CA, USA) and propidium iodide (PI) 10 mg/mL (AbD Serotec, Raleigh, NC, USA) for nucleic acids. Samples were observed under CLSM (Carl Zeiss, Germany) with filters: 480-530 nm (FUN®1), 360-460 nm (DAPI), 543-560 nm (PI), 355-433 nm (calcofluor white), and 495-519 (conA). Images were processed with Zeiss LSM Image Brower ver. 4.0 software (Carl Zeiss, Germany).
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2

Epifluorescence Microscopy for Biofilm Analysis

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For the detection of biofilm component by epifluorescence microscopy (EFM), HLFCs were grown over sterile glass coverslips (Velab, Mexico City, Mexico) on 12-well plates. Cells were infected as previously described; fungal biofilm, bacterial biofilm, and mixed biofilm were included. After a biofilm maturation period of 24 h, biofilms were stained with calcofluor white (CW) (1 g/L) (Sigma-Aldrich, St. Louis, MO, USA) for the detection of chitin and N-acetylglucosamine, with Concanavalin A-Alexafluor 488 (ConA) (1 mg/ml) (Sigma-Aldrich St. Louis, MO, USA) for the detection of glucose and mannose residues, while propidium iodide (PI) (10 mg/ml) (AbD Serotec, Raleigh, NC, USA) was used to stain nucleic acids and extracellular DNA. The stained cells were observed under an epifluorescence microscope (Imager.Z2, Apotome 2.0, Carl Zeiss, Germany) at the following wavelengths: CW (λExcitation = 355 nm; λEmission = 433 nm); ConA (λExcitation = 495 nm; λEmission = 519 nm); PI (λExcitation = 535 nm; λEmission = 617 nm). Images were analyzed with the LSM Image Brower version 4.0 software (Carl Zeiss, Germany).
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3

Apoptosis Evaluation of AT2 Cells

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Flow cytometry was used to evaluate the apoptosis of the AT2 cells. Following the treatments, the AT2 cells were collected and washed with PBS, and then resuspended in 500 µl binding buffer containing 5 µl Annexin V-FITC and 10 µl propidium iodide (Bio-Rad Laboratories, Inc.). Following incubation for 30 min in the dark at room temperature, the apoptotic ratio was measured using a FACScan flow cytometer (Cyto-Flex Beckman) according to the protocol provided with the Annexin V/PI kit.
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4

Cell Cycle Analysis of hFOB1.19 Cells

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hFOB1.19 cells were seeded into 6-well plates and cultured for 24 h. Then cells were collected and washed with PBS twice. Cells were immobilized with precooled 70% ethanol, and RNase was added and incubated for 15 min. Then 50 μg/mL of propidium iodide (PI) (Bio-Rad, Hercules, CA, USA) was added to each well and incubated for another 30 min. Finally, cell cycle was detected by flow cytometry (BD Biosciences, Franklin Lakes, NJ, USA) as previously described [25 (link)].
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5

Annexin V-FITC Apoptosis Assay

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After treatment, cells (1×105 cells/well) were collected and resuspended in 500 µl binding buffer containing 5 µl Annexin V-FITC and 10 µl propidium iodide (Bio-Rad Laboratories, Inc.). After incubation at room temperature in the dark for 30 min, cell suspensions were loaded into an FACScan flow cytometer (Becton-Dickinson and Company) according to the manufacturer's protocol of the Annexin V-FITC Apoptosis Detection Kit, cat. no. C1062L, Beyotime Institute of Biotechnology). The results were analyzed by FlowJo software (V10.6; BD Biosciences) to determine the apoptosis rate (early + late apoptosis).
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6

Quantifying Cell Pyroptosis by Flow Cytometry

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Cell pyroptosis was measured using the FAM fluorescent-labelled inhibitor of caspase-1 assay (FLICA) and propidium iodide (PI) according to manufacturer’s instruction (Bio-Rad, Hercules, CA, USA). The fluorescent signal was detected using flow cytometry, and the percentage of pyroptosis cells was the percentage of active caspase-1-PI double‐positive cells in total cells.
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7

Cell Surface Marker Analysis by Flow Cytometry

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Cells were cultured to 70–80% confluence and detached from the cell culture flasks using EDTA. Cell pellets were obtained and washed with cold phosphate-buffered saline (PBS) containing 1% FCS and 5 mM EDTA. All further steps were performed on ice and all centrifugation steps at 4 °C. Fluorochrome-conjugated monoclonal antibodies against human CD44 (FITC, BD Pharmingen; BV421, BD Pharmingen), Claudin-1 (APC, R&D systems), and their isotype controls were added to the cell suspension at concentrations recommended by the manufacturer (BD Biosciences) and incubated at 4 °C in the dark for 30 min. The labelled cells and CD44 reporter GFP cells were washed in PBS and then were analysed on a FACS Aria (BD Biosciences). Gating was set to relevant isotype control (IgG-FITC)-labelled cells or unstained cells for each cell line. Propidium iodide (Bio-Rad, 1351101) and DRAQ7 (BioLegend, 424001) were used for the dead cell removal.
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8

Formulation and Characterization of Drug-Loaded Nanoparticles

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Sodium alginate and PLGA were purchased from Dae Jung (Korea). CBP was provided by Spectrum Pharmaceuticals. Fluorescein isothiocyanate (FITC), fetal bovine serum, bovine serum albumin, and acetic acid were obtained from Invitrogen (Leiden, The Netherlands). Propidium iodide was obtained from Bio-Rad (Hercules, CA, USA). The other reagents used (and vendors) were as follows: dimethyl sulfoxide (Welgene, Gyeongsangbuk-do, Korea), acetonitrile (HyClone, Logan, UT, USA), methyl thiazolyl tetrazolium (MTT) kit, and Ultrapure water (Milipore, Bedford, MA).
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9

Flow Cytometric Analysis of HT-29 Cells

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HT-29 cells were released from 6-well plates by TrypLE™ Express. Cells were washed with chilled flow buffer (PBS, 25 mM HEPES, 1 mM EDTA, 1 % BSA) and resuspended in 2 μg/mL CXCR4-APC (clone 12G5; BD Pharmingen) and CD26-FITC (clone M-A261; Serotec), combined CD26-FITC (clone M-A261; Serotec), CD44-APC (clone G44-26; BD Pharmingen), CD133-PE (clone AC133; Miltenyi Biotec), or fluorophore-tagged isotype controls (Miltenyi Biotec) for 45 min at 4 °C. Cells were then washed twice with flow buffer and resuspended in BSA-free flow buffer for analysis. Flow cytometry analysis was carried out with a BD FACSCalibur™ flow cytometer (BD Biosciences). Cell debris and aggregates were excluded based on scatter signals and 10,000 events were captured per sample. Data were analyzed using Flowing Software version 2.5.0 (University of Turku, Turku, Finland).
Following labeling with CD26-PE (clone M-A261; Serotec) cells were stained with annexin-V-FITC and propidium iodide (PI) according to manufacturer’s protocol (Roche Diagnostics) for detection of necrotic, apoptotic, and live cells. Analysis was carried using a Guava® easyCyte™ 8HT flow cytometer and associated InCyte software (Millipore).
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10

Yeast Chitin and Nucleic Acid Imaging

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Similarly, from a yeast fungal culture of 18 h incubation under conditions previously described (see microcapsule assays), cells were harvested by centrifugation and washed with 1X PBS. Subsequently, cell samples are placed in a uorochrome mixture containing 10 mg/L propidium iodide (PI) (AbD Serotec Raleigh, NC, USA) to detect nucleic acids and 1 g/L calco uor white (CW) (Merck®, Darmstadt, Germany) to label chitin. Samples were observed on a Confocal Laser Scanning Microscope (CLSM) model 710 (Carl Zeiss, Oberkochen, Germany) with lters of 560 nm for IP and 440 nm for CW.
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