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72 protocols using thimerosal

1

Quantifying β-Glucan and Chitin in Candida albicans

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β-glucan exposure on C. albicans cells was quantified by flow cytometry27 (link),28 . Briefly, exponential cells were incubated for 5 h under the conditions specified and then fixed with 50 mM thimerosal (Sigma-Aldrich, Dorset, UK). The cells were then stained with Fc-Dectin-1 and anti-human IgG conjugated to Alexafluor 488 (Invitrogen), and the fluorescence of 10,000 events acquired using a BD Fortessa flow cytometer. The gating strategy and axis scales, which remained unchanged throughout, are presented in Supplementary Fig. 4. Median fluorescence intensities (MFI) were determined using FlowJo v.10 software. Each cytometry plot is representative of at least three independent biological replicates.
To examine chitin levels in C. albicans, thimerosal-fixed cells were stained for 60 min in the dark with 10 µg mL−1 CFW (Sigma-Aldrich, Dorset, UK). These cells were imaged by fluorescence microscopy (above) and their fluorescence was quantified by flow cytometry without further staining (above: Supplementary Fig. 4).
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2

Nanoparticle Cytotoxicity Evaluation Protocol

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Cell treatments consisted of 24-hour exposures to their respective culture media plus various doses of Ag-NPs (up to 5 mg/mL) or Au-NPs (up to 50 mg/mL). Vendor supplied NP stock solutions (Ag-NP ¼ 1.8 mg/mL and Au-NP ¼ 1.0 mg/mL) and all other test articles including cadmium nitrate tetrahydrate (Sigma-Aldrich, Saint Louis, Missouri), thimerosal (Sigma-Aldrich), Fluoro-Jade C (Histo-Chem Inc, Jefferson, Arkansas), and N-acetyl cysteine (Sigma-Aldrich) were sterilized via micro-filtration through a 0.2 mm diameter PVDF filter before being vortex-mixed with culture media. Conventional culture medium served as the negative control, whereas 50 mM cadmium nitrate tetrahydrate (Sigma-Aldrich) and 100 mM thimerosal (Sigma-Aldrich) were used as positive controls.
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3

Immunofluorescence Staining for Cell Fixation

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Cells were first fixed with 4% paraformaldehyde for 5 minutes at room temperature. After washing with D-PBS
(Invitrogen, 14190–250) with thimerosal (Sigma, T5125) for 3 times, cells were penetrated with 0.1% saponin (Fluka
Analytical, 47036) plus 1% of either goat or donkey serum for 15 minutes at room temperature. Cells were further blocked with
5% of either goat or donkey serum plus 0.05% saponin for 15 minutes at RT. After incubation with primary antibodies at
4°C overnight, the cells were incubated with secondary antibodies for 30 min at RT. The counts of immunofluorescent
cells were taken from 10 random fields per each replicate, and each sample had three replicates.
Antibodies and dilutions used see Key Resources Table.
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4

Immunohistochemical Analysis of Lung Tissue

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Human LGs from three donors were obtained from Advanced Tissue Services (Phoenix, AZ, USA). The LG were removed ≤24 hours after death. Tissues were preserved immediately in RNAlater and shipped at 4°C overnight. All donors were females, and their ages at the time of death were 62, 84, and 90 years. The LGs were embedded in paraffin, and 5-μm sections were prepared. Endogenous peroxidase activity on rehydrated sections was blocked by treating slides with 3% hydrogen peroxide in absolute methanol for 30 minutes. Antigen retrieval was performed for 40 minutes using 0.01 M citrate (pH 6.39) in a humidified heated chamber. Sections were blocked with 5 g/L casein (Sigma Aldrich) in PBS containing 0.5 g/L thimerosal (Sigma-Aldrich; cat# T5125-25G) for 30 minutes, incubated with primary antibodies, and diluted in casein buffer 1:50 overnight at 4°C. Biotinylated goat anti-rabbit IgG antibodies (Vector Labs, Burlingame, CA, USA) were used at a 1:300 dilution. Visualization was achieved using biotin/avidin-peroxidase (Vector Labs) and Nova Red (Vector Labs). Counterstaining was made with Gill's hematoxylin (Fisher Scientific, San Diego, CA, USA; CS400).
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5

Immunohistochemical Staining of DsRed

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Tissues were fixed immediately and embedded in paraffin in Scripps histology core facility, and 5 μm sections were prepared. Endogenous peroxidase activity on rehydrated sections was blocked by treating slides with 3% hydrogen peroxide in absolute methanol for 30 min. Antigen retrieval was performed for 40 min using 0.01 M citrate (pH 6.0) in a humidified heated chamber. Sections were blocked with 5 g/L casein in PBS containing 0.5 g/L thimerosal (Sigma-Aldrich; cat# T5125-25G) for 30 min, and incubated with anti-DsRed primary antibody, and diluted in casein buffer overnight at 4°Cand anti-dsRed primary antibodies were used for immunostaining. Biotinylated secondary antibodies (Vector Labs, Burlingame, CA) were used at a 1:300 dilution. Visualization was achieved using biotin/avidin-peroxidase (Vector Labs) and Nova Red (Vector Labs). Tissue was counterstained with Gill’s hematoxylin (Fisher Scientific, San Diego, CA; CS400).
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6

Immunofluorescence Imaging of BBB Monoculture

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For immunofluorescence imaging, the BBB monoculture comprising hCMEC/D3 alone was cultured on the membranes of the static and the dynamic model. At days 3, 5 and 8, the membranes were cut and placed on a microscopic slide and subsequently fixed, blocked, and permeabilized using 4% paraformaldehyde (Sigma), and 0.01 M PBS (pH 7.4) supplemented with 0.05% thimerosal (Sigma), 10% normal horse serum, and 1% Triton X-100 (Sigma), respectively. Next, the cells were stained overnight using the following primary antibodies: a mouse anti-human−1 antibody (1/100) (BD Pharmingen, Erembodegem, Belgium). Next, cells were stained with a secondary fluorescein isothiocyanate (FITC)-labeled donkey anti-mouse antibody (1/100) (Jackson ImmunoResearch, Newmarket, UK) for 2 h at room temperature. Finally, cells were counterstained with 4′,6-diamidino-2-phenylindole (DAPI) (Sigma), and the membrane containing the cells was mounted in citifluor (Citifluor Ltd., London, UK) following its careful removal from the silicon casket of TripleB membranes and the transwell insert, and was subsequently stored at 4 °C. The images were taken using an UltraVIEW confocal microscope system (Perkin Elmer, Waltham, MA, USA). The analysis of the images was performed using the ImageJ software (National Institutes of Health, Bethesda, MD, USA).
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7

Hemagglutination Assay for Av. paragallinarum

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Av. paragallinarum cultured on chocolate agar was incubated in brain heart infusion (BHI) broth (BD, USA) with 5% (v/v) heat-inactivated swine serum (Sigma-Aldrich, USA) and 0.01% nicotinamide adenine dinucleotide (Sigma-Aldrich) at 37℃ for 16 h [14 (link)]. The enriched broth was centrifuged at 4,000 × g for 20 min, then washed 3 times with phosphate buffer solution (PBS) with 0.01% thimerosal (Sigma-Aldrich) and incubated at 4℃ overnight. The hemagglutination test was as follows. PBS (25 µL per well) was added to a 96 well microtiter plate, followed by 25 µL of antigen, and then diluted two-fold. A 25 µL aliquot of fresh chicken RBC made from Alsever's solution was added to each well, after which plates were incubated at room temperature for 40 min after mixing. The concentration of the antigen was diluted to 4 hemagglutinating units (HAU) for the HI test for serovar A.
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8

Inactivation of Candida albicans Germ Tubes

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Wild-type C. albicans SC5314 was maintained as previously described (Leonhardt et al., 2015 (link)). For experiments, colonies were transferred to M199 medium (PAA), pH 4 and cultured at 30°C to stationary phase. Germ tubes were induced by culturing in M199 medium, pH 8 for 1 h at 37°C. Germ tubes were inactivated by washing them in phosphate-buffered saline (PBS) and followed by incubation in PBS containing 0.1% thimerosal (Sigma-Aldrich) for 1 h at 37°C with shaking. Afterwards, germ tubes were washed five times and then re-suspended in RPMI-1640. Killing was confirmed by plate counts on YPD (2% D-glucose, 1% peptone, 5% yeast extract, Roth) agar plates.
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9

Allergen Extract Preparation and Standardization

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Crude allergen extracts, including Betula alba pollen (white birch, cat. no. P6770, Sigma), Corylis avellana pollen (hazel, cat. no. 0127, Allergon AB, Ängelholm, Sweden), Cynodon dactylon pollen (Bermuda grass, cat. no. 0421, Allergon AB), Phleum pratense (timothy grass, cat. no. 0113, Allergon AB), Lolium perenne pollen (perennial rye grass, cat. no. 0214, Allergon AB), Dermatophagoides pteronyssinus allergen (house dust mite, cat. no. 4965, Allergon AB) and Equus caballus allergen (horse dander, cat. no. 2046, Allergon AB) were dissolved in degranulation buffer (25 mM piperazine-N,N′-bis(2-ethanesulfonic acid) (cat. no. 80635, Sigma), 110 mM sodium chloride (cat. no. S7653, Sigma), 5 mM potassium chloride (cat. no. P9541, Sigma) and 0.01% (v/v) thimerosal (cat. no. T8784, Sigma); pH 7.4), and each mixture was stirred at 300 r.p.m. at 4 °C for 16 h. Subsequently, each allergen mixture was centrifuged, the supernatant was filter-sterilized and the total protein concentration was measured using the Bradford assay. The allergen solutions were stored at −20 °C at a concentration of 1 mg ml−1.
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10

Fluorescence Microscopy and TEM Analysis of Candida Albicans Cell Wall

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For fluorescence microscopy, cells were fixed in 50 mM thimerosal (Sigma-Aldrich) and stained for β-glucan (1.5 µg/ml Fc-Dectin-1 plus anti-human IgG conjugated to Alexa Fluor 488; green), chitin (50 µg/ml wheat germ agglutinin conjugated to Alexa Fluor 350; blue), and mannan (25 µg/ml concanavalin A conjugated to Texas Red; red). All samples were examined by phase differential interference contrast (DIC) and fluorescence microscopy using a Zeiss Axioplan 2 microscope. Images were recorded digitally using the Openlab system (Openlab v 4.04: Improvision, Coventry, UK) with a Hamamatsu C4742- 95 digital camera (Hamamatsu Photonics, Hamamatsu, Japan).
High-pressure freeze substitution transmission electron microscopy on normoxic and hypoxic C. albicans cells was performed as described previously (103 (link), 104 (link)), cutting ultrathin sections of 100 nm in thickness. Samples were imaged with a Philips CM10 transmission microscope (FEI, United Kingdom) equipped with a Gatan Bioscan 792 camera, and the images were recorded using a Digital Micrograph (Gatan, Abingdon Oxon, United Kingdom). The thicknesses of the inner chitin-glucan and outer mannan layers of the cell wall were measured by averaging >30 measurements for each cell (n > 30 cells) using ImageJ.
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