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53 protocols using calcein am

1

Glyphosate-based Herbicides Cytotoxicity Evaluation

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Analytical-grade glyphosate (N-(phosphonomethyl) glycine, CAS No: 1071-83-6) was purchased from VWR International Kft (Debrecen, Hungary). Samples of three GBHs, namely
were kindly provided by pesticide applicators. Composition data for each formulation were retrieved from the material safety data sheets (MSDS). Chemicals used for the assays and human liver-derived metabolic activation system (S9 fraction) were obtained from Sigma-Aldrich Chemie GmbH (Heidelberg, Germany). Cell culture medium and its supplements were obtained from Biowest (Nuaillè, France). The acetomethoxy derivative of calcein (Calcein AM) and propidium iodide (PIO) fluorescent dyes were purchased from Biotium (Hayward, CA, USA). Heparin-containing vacutainers were purchased from BD Vacutainer Systems (Plymouth, UK).
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2

3D Hydrogel Encapsulation of hS/PC Cells

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Early passages (between 3 and 6) of hS/PC cells were encapsulated at 3 × 106 cell/mL in HyStem® hydrogel (GS311; BioTime/Ascendance Biotechnology). According to manufacturer's instructions, hydrogels were formed by mixing reconstituted thiol-modified hyaluronic acid (5.9 mM) and polyethylene glycol diacrylate (1.5 mM) at a 4:1 volume ratio, and plated on microscope glass slides fitted with pre-sterilized arrays of 50 μL wells made from laser-cut polydimethylsiloxane (PDMS; Sylgard™ 184; Dow Corning) sheets (Figure S1). Hydrogels were removed from the mold then each transferred into individual wells of a 48-well plate and cultured as described above. A typical hydrogel formed a low-profile cylinder measuring 6 mm in diameter and 2 mm in height. Hydrogels also were formed directly on confocal glass bottom dishes (P50G1.54F; MatTek) for live-cell imaging. 3D cultures were maintained until microstructures reached up to ~50 μm in diameter (between 6 and 16 days), a time when most live-tracking experiments were initiated. Viability assays using Calcein AM (80011-3; Biotium) and Ethidium Homodimer-III (40050; Biotium) in accordance with manufacturer guidelines were performed in cell-laden hydrogel cultures. IMARIS 9.2 software (Bitplane) was used to separate and quantify objects (Movie S1).
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3

Cell Adhesion and Detachment Assay

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Adhesion Assays: Detached HET‐1A cells were seeded in 96‐well plates. Simultaneously 100 μl of medium containing DCA or ursodeoxycholic acid (UDCA; Sigma‐Aldrich, St. Louis, MO, USA) was added to each well. After allowing 2 hrs for adhesion, the medium was aspirated, the cells washed, and 100 μl of medium containing 2.5 μM calcein AM (Biotium, Hayward, CA, USA) was added to each well for 1 hr at 37°C. Fluorescence was determined using a Victor luminometer (Perkin Elmer, Waltham, MA, USA). The Millicoat™ ECM screening kit (Millipore, Billerica, MA, USA) was used to determine adhesion to specific ECM proteins.
Detachment and Re‐Adherence Assays: cells were seeded in 12‐well plates and allowed to adhere overnight. After 2 hrs treatment with DCA, the growth medium was aspirated and the wells washed twice with medium to ensure capture of all detached cells. Detached cells were re‐suspended in fresh medium and placed in a new well. Wells containing the residual adherent cells were washed twice, and fresh medium was added to each well. After 24 hrs, images were acquired and cell viability determined using MTT (Sigma‐Aldrich, St. Louis, MO, USA). The original untreated well was used as the reference for comparison.
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Cell Viability and Apoptosis Assay Protocol

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Reagents for cell culture were provided by Biowest (Riverside, MO, USA). TrypLE for cell detachment was from Gibco (Amarillo, TX, USA). Dimethyl sulfoxide (DMSO), phosphate buffered saline (PBS) tablets, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) and formaldehyde were purchased from Sigma-Aldrich (St. Louis, MO, USA). Hoechst 33342 was obtained from Santa Cruz Biotechnology, Inc. (Dallas, TX, USA). Calcein AM and propidium iodide (PI) were from Biotium (San Francisco, CA, USA). Annexin V-FITC Apoptosis Detection Kit was from BD Pharmingen (Franklin Lakes, NJ, USA). Tris was obtained from GE Healthcare (Chicago, IL, USA). Other basic chemical reagents (sodium dihydrogen phosphate, disodium hydrogen phosphate, acetic acid, sodium chloride, glucose, potassium chloride, sodium bicarbonate, disodium hydrogen phosphate, potassium dihydrogen phosphate, magnesium chloride 6 hydrate, magnesium sulfate 7 hydrate) were obtained from the local supplier, Chempur, (Piekary Śląskie, Poland). Agarose was purchased from the local supplier, Blirt (Gdańsk, Poland). These chemicals were of analytical grade, and solutions were prepared using water purified using the Mili-Q system.
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5

Cell Viability Assessment via Flow Cytometry

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Cells were added to the stain buffer consisting of HBSS with 2 μM calcein AM (Biotium) and 2 μM ethidium Homodimer-1 (Thermo) for 20 min. LSRFortessa (Becton Dickinson) was used to acquire fluorescence signals of samples, followed by analysis with the software Weasel (v.2.7.1; Chromocyte). Percent cell viability was calculated by dividing the number of calcein+ ethidium events by the total event number. In some cases, APC beads (CalibriteTM; Becton Dickinson) with a known number were added in each sample to calculate an absolute number of viable and dead cells.
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6

Analyzing CFTR Modulator Effects on Organoid FIS

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For the FIS assay, organoids were seeded into 96-well plates. After 24 h, the organoids were stained with Calcein AM (Biotium) and stimulated with forskolin (Sigma-Aldrich, USA) at concentrations of 0.128 and 5 µM. The processing lasted for 60 min, and the “fixed” fields were photographed using the Observer. D1 fluorescence microscope (Zeiss, Germany) at 10-min intervals. CFTR correctors VX-809, VX-661 and VX-445 were all added at a concentration of 3.5 µM (Selleckchem, Houston, TX, USA) at the stage of organoids seeding, and CFTR potentiator VX-770 (3.5 µM; Selleckchem, USA)—simultaneously with forskolin. Quantitative analysis of the FIS was carried out using the Image J program (v1.52n state version). The Sigma Plot 12.5 program was used for plotting.
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7

Assessing C. jejuni Impact on HT-29/B6 Viability

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To study effects of C. jejuni on HT-29/B6 viability, Calcein-acetoxymethyl/Hoechst staining was performed. Calcein-acetoxymethyl (Calcein-AM; Biotium) has already been described as a green fluorescent indicator of viable cells in cytotoxicity assays [29 (link), 30 (link)]. Hoechst 33342 (Thermo Fisher Scientific) (hereinafter referred to as Hoechst) is used as a blue fluorescent marker of the nuclei of all cells [53 (link)]. Viability of HT-29/B6 cells was investigated in 96 well plates (Sarstedt). After 7 days differentiation, HT-29/B6 with ~ 80–90% confluence were infected with wild type, ::Cj1492c and ::Cj1507c for 5 h and 24 h as described before. Infected monolayers were washed 3 times with PBS and incubated with 0.4 µM Calcein-AM at 37 ℃ with 5% CO2 for 30 min. 5 µg/ml Hoechst was added to each well and incubated 15 min at room temperature followed by two washes with PBS. Fluorescence micrographs were subsequently captured with a Leica DMI6000 (Leica). The relative viability of host cells was calculated as percentage of the number of viable cells compared to the total cell numbers automatically determined using the ImageJ software as described above [27 (link)]. Presented results are calculated from three individual assays.
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8

Multiparametric Imaging of Cellular Stress Responses

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Hoechst 33342, TMRM, calcein-AM, and Ethidium Homodimer-1 were all purchased from Biotium and applied using manufacturer’s protocol31 (link),57 (link). MitoSOX was purchased from Life Technologies and was applied to cells for a 10-min incubation to assess mitochondrial superoxide31 (link). Calcein-Cobalt Chloride (CoCl2) staining was used to assess mitochondrial permeability transition, which is achieved through quenching cytosolic calcein-AM signal with 5 μM CoCl2 described previously31 (link). Immunofluorescence with Anti-MF-20 (DSHB # AB_2147781) was used with fluorescent secondary antibody conjugated to Alexa Fluor 555 (Themo # A-31570) to assess cardiac hypertrophy in fixed and permeabilized PVNM cells. All imaging experiments were done on an Olympus IX70 inverted microscope with QImaging Retiga SRV Fast 1394 camera using NIS Elements AR 3.0 software. Quantification, scale bars, and processing including background subtraction, was performed on Fiji (ImageJ) software.
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9

Synthesis of Gold Nanoparticles with CTAB

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Gold(III) chloride hydrate (HAuCl4), cetyltrimethylammonium bromide (CTAB), sodium borohydride (NaBH4), hydroquinone, silver nitrate (AgNO3), dopamine hydrochloride, bicine, resazurin, and McCoy's 5A medium were purchased from Sigma-Aldrich (Atlanta, GA, USA). Methoxy poly(ethylene glycol) thiol (HS-mPEG) with molecular weights (Mw) of 2k, 5k, 10k, and 20k were purchased from Nanocs. Dulbecco's modified Eagle's medium (DMEM) was purchased from Thermo Fisher. Calcein AM (4 mM) dissolved in DMSO was purchased from Biotium. Propidium iodide (≥ 95%, PI) was purchased from Combi-Blocks (San Diego, CA, USA). All reagents were used without further purification. Deionized water (18.2 MΩ·cm) purified with a Milli-Q Academic water purification system was used to make aqueous solutions.
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10

Flow Cytometry Cell Viability Assay

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Cells retrieved from gels were added to the stain buffer consisting of HBSS with 2 × 10−6m of calcein AM (Biotium) and 2 × 10−6m ethidium homodimer‐1 (Thermo Fisher Scientific) for 30 min. Samples were then analyzed by flow cytometry using LSRFortessa (Becton Dickinson). An event threshold of 5000 in forward scatter was used to exclude debris. Percent cell viability was calculated by dividing the number of calcein+ ethidium events by the total event number. In some cases, APC beads (Calibrite; Becton Dickinson) with a known number were added in each sample to calculate an absolute number of viable and dead cells.
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