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17 protocols using ca2 and mg2 free pbs

1

Bronchoalveolar Lavage Fluid Collection

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At each time point, rats were anesthetized by isoflurane inhalation (Piramal Critical Care) and euthanized by removing blood from the inferior vena cava. The trachea was then cannulated by 14-gauge blunt stainless-steel needle and lavaged in-situ with 8 mL sterile cold Ca2+- and Mg2+-free PBS (Life Technologies) 4 times. The recovery volumes of the first lavage were about 7 mL and the subsequent lavages were about 8 mL. The first lavage was collected separately, and the cell-free supernatant was kept at −70 °C for further assays. Cell pellets from 4 lavages were pooled for total cell counts and cytological evaluation. The total number of cells was counted using a NucleoCounter (Chemometec, Allerod, Denmark); 4 × 104 cells were attached to glass slides by spinning at 27 g for 5 min using a cytospin (Hanil, Seoul, Korea). Slides were then dried, fixed with 100 % methanol, and stained with Diff-Quik (Thermo Fisher Scientific, Waltham, MA, USA). Differential cell counting was performed under a light microscope based on the morphology of cells. A minimum of 300 cells per slide was counted.
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2

Dispersing NiO Nanoparticles in Serum Protein

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Previous studies showed that NPs are tend to agglomerate when dispersed in medium and agglomerations are accelerated in high salt conditions such as PBS and saline [34 (link)]. Therefore, we used serum protein as a dispersion medium to provide protein corona formation, which can improve dispersion of NPs in physiological condition as previously described [34 (link)]. Briefly, the stock solution of NiO NPs was prepared by dispersion at 4000 cm2/mL (4360 μg/mL) in DW. The solution was sonicated for 10 min using a bath sonicator (Saehan-Sonic, Seoul, Korea) and heat-inactivated rat serum collected from healthy 6-week old female Wistar rats (Samtako, Gyeonggi-do, Korea) was added at 3 % of end concentration and sonicated for 5 min. Finally, Ca2+- and Mg2+-free PBS (Life Technologies, Gaithersburg, MD, USA) was added to the NP suspension to achieve pre-determined final concentrations (100, 200, and 400 cm2/mL) for animal experimentation, followed by sonication for 5 min in a bath sonicator (Saehan-Sonic).
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3

Acute Lung Inflammation Assessment

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At 24 h after instillation, the acute lung inflammogenic potential was evaluated by the BALF analysis. Rats were sacrificed by removing blood from the inferior vena cava under deep isoflurane anesthesia. The lung was lavaged in situ, 4 times, using 8 mL of cold sterile Ca2+- and Mg2+-free PBS (Life Technologies; Gaithersburg, MD, USA), after cannulating by using a 14-gauge blunt stainless-steel needle. Then, BALF was centrifuged at 2000 g for 5 min, and the supernatant of the first lavage was kept separately for biochemical analysis. Cell pellets from 4 lavages were pooled and counted, using a NucleoCounter (Chemometec; Allerod, Denmark). Then, 4 × 104 cells were attached onto the glass slides by cytospin centrifugation (Hanil; Incheon, Korea). The slides were then stained with Diff-Quick (Thermo Fisher Scientific; Waltham, MA, USA), and differential cell counting was performed by counting at least 300 nucleated cells under a light microscope based on the morphology of cells.
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4

Lung Lavage and Cell Analysis in Rats

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Twenty-four hour post-instillation, the rats were euthanized via an intraperitoneal injection of tiletamine-zolazepam (Zoletil®, 50 mg/kg) and xylazine (5 mg/kg). The trachea was cannulated with a blunt 14 gauge needle, and the lungs were lavaged in situ four times with cold sterile Ca2+- and Mg2+-free PBS (Life Technologies) at a volume of 8 mL. The first lavage was kept for analysis of LDH, total protein, and pro-inflammatory cytokines. Cell pellets from four lavages were pooled for cell counts. The total number of cells in the BALF was quantified by a nucleocounter (Chemometec, Allerod, Denmark), and 4 × 104 cells were attached to glass slides by cytospin at 27 g for 5 min. The cells were then fixed for 5 min with methanol and stained with Diff-Quik (Thermo Fisher Scientific, Waltham, MA, USA) for the differential cell count.
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5

Intratracheal Instillation Assay for Nanoparticle Toxicity

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The intratracheal instillation model was selected instead of an inhalation study because the former is an easy and reliable method to identify NP toxicity and compare responses to different particle types [32 (link)]. NP suspensions at 80, 200, and 800 μg/mL were prepared by dispersing NPs in sterile Ca2+- and Mg2+-free PBS (Life Technologies, Gaithersburg, MD, USA) and sonicated for 10 min using a bath sonicator (Saehan-Sonic, Seoul, Korea) to break up agglomerates. NP suspensions were prepared and sonicated immediately before use as recommend in a previous study [33 (link)]. Six-week-old specific-pathogen-free female rats were purchased from Samtako (Gyeonggi-do, Korea), maintained, and handled according to the policies approved by the Institutional Animal Care and Use Committee of Dong-A University. The instillation (n = 4 per group) was performed according to a previously described method [24 (link)]. NP suspensions were instilled at doses of 40, 100, and 400 μg/rat by instilling 0.5 mL of the suspensions.
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6

Nickel Ion-Induced Pulmonary Eosinophilia

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Because we hypothesized that NiO NPs can produce eosinophilia via the accumulation of nickel ions in the phagolysosomes of phagocytes, NiCl2 were instilled into lungs of rats to demonstrate the direct effect of nickel ions. Our previous studies also showed that instillation CoCl2 and ZnCl2 produced similar magnitude of eosinophilia as observed in CoO and ZnO at an equal metal concentrations [8 (link), 11 (link)]. Although NiO NPs in the lung might not completely dissolved in the lung within 3 days after instillation, we selected the dose of NiCl2 at 378.0 μg/rat (171.1 μg Ni/rat), which is equivalent nickel concentration of 200 cm2/rat of NiO NPs to evaluate whether the dissolved nickel from NiO NPs directly induce pulmonary eosinophilia or not. NiCl2 (Sigma-Aldrich) dissolved in sterile Ca2+- and Mg2+-free PBS (Life Technologies) was intratracheally instilled into the lungs of rats and then sacrificed at 24 h post-instillation to collect the BALF and serum.
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7

Agglutination Assay for Gliadin and Zein Digests

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The human erythroleukemic cell line K562(S) from ATCC, was maintained in RPMI-1640 (Roswell Park Memorial Institute) medium (Gibco, Carlsbad, CA, USA) supplemented with 10% fetal calf serum (Gibco), 1% 100× penicillin streptomycin and subcultured every 3 days to maintain a cell density of 10 × 105/mL.
Cells were harvested and washed twice by centrifugation with Ca2+ and Mg2+-free PBS (Gibco) for the agglutination experiments [33 (link)]. The test was conducted with resuspended cells at a concentration of 10 × 107 cells/mL in the same PBS. Briefly, 25 µL of cell suspension was additioned to each well of a 96-well microtiter plate containing digested gliadin (0.75–3 mg/mL) or zein digest (6 mg/mL) concentrations obtained by serial dilution (1:1) with PBS, and then 25 μL PBS was added in each well. The inhibition test was carried out by adding rice hydro-alcoholic extracts (3 mg/mL) instead of 25 μL PBS before the addition of cells to the digested gliadin wells.
The obtained total volume was 100 µL. The cell suspension was incubated at room temperature for 30 min.
Clumped and single cells were counted on the microscope slide after the application of a drop of suspension. Control cells were included, as appropriate. Unless otherwise specified, the agglutination test was repeated twice [33 (link)].
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8

Measuring CRISPR Guide RNA Activity

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Reporters containing target sequences of interest were prepared as previously described (Ramakrishna et al. 2014 (link)). Briefly, oligonucleotides containing target sequences (Fig. 1; Supplemental Fig. S3) were synthesized (Bioneer) and annealed in vitro in a thermocycler. The annealed oligonucleotides were ligated into the pRGS vector (Ramakrishna et al. 2014 (link)) predigested with EcoR1 and BamH1. HEK293T cells were transfected with mixtures of the Cas9-puro, U6-sgRNA, and reporter plasmids at a weight ratio of 1:1:1 using Neon electroporation (Invitrogen). Three days after transfection, adherent cells were trypsinized and resuspended in Ca2+- and Mg2+-free PBS (Gibco-BRL) supplemented with 2% FBS. Single-cell suspensions were analyzed with FACSAria II (BD Biosciences). We then calculated the percentage of mRFP+eGFP+ cells among the total population of mRFP+ cells, which represented the activity of the guide RNA on the target sequence.
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9

Quantifying Cell Proliferation via BrdU Incorporation

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PSCs were passaged at low density in T175 tissue culture flasks and allowed to grow till approximately 50% confluency. Cells were pulsed with 10 μM BrdU (Sigma) for 30 min, Trypsinized, and collected by centrifugation (300g, 5 mins). Cells were washed in Ca2+ and Mg2+ free PBS (Gibco) and then resuspended in ice-cold 70% ethanol dropwise whilst vortexing and stored at -20°C at least overnight. Cells were incubated sequentially in 1% Triton X-100 PBS (PBST) for 20-30 mins (permeabilization), 2M HCl for 20 mins at room temperature and then washed in PBS-Tween(0.1%). They were then incubated in 0.1M Na2B4O7 for 20 min at RT and washed in PBS-T. Samples were stained with 100 μl α-BrdU (Dako, 0744) diluted in PBS-T for 20 mins, washed twice in PBS-T and then incubated in anti-mouse Alexa fluor 488 secondary antibody (Invitrogen) for 20 mins each. RNA was digested (100 μg/ml RNase 37°C for 15 min) and DNA stained with 50 μg/ml propidium iodide (Sigma-Aldrich) prior to flow cytometry (BD Fortessa) and data analysis (FlowJo).
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10

Bleomycin-Induced Lung Injury Model

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Male C57BL/6 animals were anaesthetized by i.p. ketamine/xylazine administration and received an intratracheal (i.t.) injection of bleomycin (80 μl, 1 mg/ml) or vehicle (saline) as a negative control. Animals were treated with uridine (80 μl, 24 μg/ml; Sigma Aldrich, Germany) or vehicle at the indicated time points. Mice were sacrificed at different time points (see results section) via i. p. injection of thiopental. BAL was performed with 3 × 1ml of Ca2+ and Mg2+ free PBS (Gibco, Paisley, UK) supplemented with 0.1 mM sodium EDTA (Sigma Aldrich, Germany), followed by lung resection and storage in OCT freezing medium. BAL cells were counted, differential cell counts were done by FACS analysis, as described previously [12 (link)]. Frozen lung sections were stained with hematoxylin and eosin for histological analysis.
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