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33 protocols using catalase

1

Quantifying Bacterial Burden in Respiratory Samples

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Bacterial titers in nose, lungs and BAL were determined as described (McCool and Weiser, 2004 (link)). In brief, noses and lungs
were homogenized with a sterile mortar and pestle in 1ml sterile PBS. BAL was performed by
flushing the airway compartment twice with 0.5 ml PBS with 1% FBS. Suspensions
were serially diluted and plated on tryptic soy agar plates with catalase (Worthington
Biochemical Corporation) and neomycin or streptomycin (Sigma). Bacteria were grown
overnight at 37°C with 5% CO2.
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2

Antibiotic Susceptibility Profiling of Isogenic Strains

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MICs of all isogenic strains for 12 clinically relevant antibiotics and ciprofloxacin (SI Appendix, Table S2) were determined in triplicate by broth microdilution according to European Committee on Antimicrobial Susceptibility Testing (EUCAST; http://www.eucast.org) and International Organization for Standardization (ISO) 20776-1:2006 guidelines with two minor modifications. A 1.5-fold testing scale was used to include the standard twofold antibiotic concentrations and their median values, and the cation-adjusted Mueller-Hinton broth (CAMHB; BD) was supplemented with 100 U of catalase (Worthington Biochemical Corporation) instead of 5% lysed horse blood. The lowest antibiotic concentration where no turbidity was observed was scored as the MIC.
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3

Profiling Protein Sulfenylation and Perthiosulfenylation

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For analysis of protein sulfenylation (Cys-SOH) and perthiosulfenylation (Cys-SSOH), cells were lysed in Western solubilization buffer (WSB) containing 1 mM DCP-bio1 (Kerafast or EMD Millipore Sigma), 200 U/mL catalase (Worthington, Lakewood, NJ) and 10 mM N-ethylmaleimide (Sigma) and incubated for 1 h on ice. Equal amounts of cell lysates were mixed with Laemli sample buffer, either in the presence or absence of 25 mmol/L DTT for 30 min, and separated by 10% SDS-PAGE for Western blotting with streptavidin-peroxidase (see below). For analysis of specific proteins of interest, excess DCP-bio1 reagent was removed from DCP-bio1-derivatized lysates by 6 successive washes with 20 mM Tris-HCl (pH 7.4) on Amicon Ultra-0.5 Centrifugal Filter Devices (Millipore). DCP-bio1-tagged proteins were subsequently collected with high capacity NeutrAvidin-agarose beads (Pierce) and washed successively with 1% SDS, 4 mol/L urea, and 1 mol/L NaCl [28] (link). Beads were then washed with 100 mmol/L ammonium bicarbonate either in the presence or absence of 10 mmol/L DTT for 30 min to assess the difference of sulfenic acid and perthiosulfenic acid tagged proteins.
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4

Cell Growth of Fetal PASMC in CDH

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Fetal PASMC from normal and CDH lambs were plated on a 6 well tissue culture plate at 1×106 cells/well in DMEM with 10% FBS and allowed to adhere overnight. On day 0, media was changed to DMEM with 2.5% FBS (as this was the lowest concentration that supported growth). On day 4 cells were removed from the wells using 0.25% trypsin/0.53mM ethylene-diaminetetraacetic acid (EDTA) digestion and counted using a hemocytometer. Absolute cell number on day 4 was compared to cell number at day 0 to determine the relative increase over time. Comparisons were made between control and CDH cells. This assay was repeated twice in the presence or absence of SOD (250U/ml; Sigma Aldrich, St Louis, MO) plus catalase (26.3U/ml; Worthington Biochemical) and Bosentan (a non-selective ET A and B receptor inhibitor) (1mM). Preliminary experiments evaluating the effects of SOD or catalase alone were performed, which revealed that either alone had no effect on either PAEC or PASMC growth (data not shown). For this reason, all experiments were performed with SOD plus catalase in combination.
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5

Pneumococcal and Staphylococcal Infection Models

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Streptococcus pneumoniae (S. pneumoniae) isolate serotype 23F (neomycinR) and a previously described isogenic S. pneumoniae pgdA mutant (kanamycinR and neomycinR) were used throughout the study21 (link). For mouse infections, all pneumococcal strains were grown in tryptic soy (TS) broth (BD) at 37°C without aeration to an optical density of 1.0 at 620 nm. For in vivo bacterial colonization, pneumococci were incubated on TS plates supplemented with 100μl of catalase (30,000 U/ml; Worthington Biomedical) and either 5μg/ml neomycin (FisherScientific) or 125μg/ml kanamycin (Sigma) at 37°C in 5% CO2 overnight. Staphylococcus aureus (S. aureus) strain USA300-JE2 and S. aureus oatA::bursa USA300-JE2 (erythromycinR) were used for infant mouse oral infections. All S. aureus strains were grown overnight, with shaking, at 37°C in 5ml of TS broth, diluted 100-fold next day and subcultured for 4 hours in 5ml of TS broth. For in vivo bacterial colonization S. aureus strains were plated on CHROMID MRSA SMART II agar (bioMérieux), TS or TS+5μg/ml erythromycin and incubated overnight at 37°C.
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6

Pneumococcal and Staphylococcal Infection Models

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Streptococcus pneumoniae (S. pneumoniae) isolate serotype 23F (neomycinR) and a previously described isogenic S. pneumoniae pgdA mutant (kanamycinR and neomycinR) were used throughout the study21 (link). For mouse infections, all pneumococcal strains were grown in tryptic soy (TS) broth (BD) at 37°C without aeration to an optical density of 1.0 at 620 nm. For in vivo bacterial colonization, pneumococci were incubated on TS plates supplemented with 100μl of catalase (30,000 U/ml; Worthington Biomedical) and either 5μg/ml neomycin (FisherScientific) or 125μg/ml kanamycin (Sigma) at 37°C in 5% CO2 overnight. Staphylococcus aureus (S. aureus) strain USA300-JE2 and S. aureus oatA::bursa USA300-JE2 (erythromycinR) were used for infant mouse oral infections. All S. aureus strains were grown overnight, with shaking, at 37°C in 5ml of TS broth, diluted 100-fold next day and subcultured for 4 hours in 5ml of TS broth. For in vivo bacterial colonization S. aureus strains were plated on CHROMID MRSA SMART II agar (bioMérieux), TS or TS+5μg/ml erythromycin and incubated overnight at 37°C.
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7

Cell Growth of Fetal PASMC in CDH

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Fetal PASMC from normal and CDH lambs were plated on a 6 well tissue culture plate at 1×106 cells/well in DMEM with 10% FBS and allowed to adhere overnight. On day 0, media was changed to DMEM with 2.5% FBS (as this was the lowest concentration that supported growth). On day 4 cells were removed from the wells using 0.25% trypsin/0.53mM ethylene-diaminetetraacetic acid (EDTA) digestion and counted using a hemocytometer. Absolute cell number on day 4 was compared to cell number at day 0 to determine the relative increase over time. Comparisons were made between control and CDH cells. This assay was repeated twice in the presence or absence of SOD (250U/ml; Sigma Aldrich, St Louis, MO) plus catalase (26.3U/ml; Worthington Biochemical) and Bosentan (a non-selective ET A and B receptor inhibitor) (1mM). Preliminary experiments evaluating the effects of SOD or catalase alone were performed, which revealed that either alone had no effect on either PAEC or PASMC growth (data not shown). For this reason, all experiments were performed with SOD plus catalase in combination.
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8

Pneumococcal Isolate Cultivation Protocols

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Pneumococcal isolates were stored at − 80 °C on Cryobeads (Cryobank, Copan Diagnostics, Murrieta, CA). Strains were routinely grown at 37 °C and 5% CO2 overnight on tryptic soy agar plates supplemented with 5% sheep blood (TSAII) (Thermo Fisher Scientific). Growth in broth culture was performed in BHI (Becton, Dickinson, and Co., Sparks, MD) with and without catalase (5000 units, Worthington Biochemical Corporation, Lakewood, NJ) for aerobic cultivation and with Oxyrase® (Oxyrase, Inc., West Mansfield, OH) diluted 1:10 to create an anaerobic environment.
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9

Murine Pneumococcal Infection Model

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All bacterial strains were animal passaged prior to use in experiments and stored at −80°C in 20% glycerol. Inocula consisted of 10(x005E)7 mid-log-phase PBS-washed bacteria in 10μl PBS and were plated to confirm dose. They were delivered to the nares of unanesthetized mice as previously described (37 (link)). At the indicated time points, mice were sacrificed, their trachea cannulated, and 200μl PBS instilled. Lavage fluid was collected from the nares and serially diluted in PBS for plating on TS agar plates supplemented with catalase (Worthington Biochemicals). The lower limit of detection was either 100 CFU/ml or 20 CFU/ml lavage fluid, depending on the experiment. Blood was collected by cardiac puncture and the serum separated. Serum and lavages were assayed for mMIF by specific ELSIA. Serum was additionally assayed for anti-pneumococcal IgG as previously described (14 (link)).
Recombinant murine MIF (rMIF) was produced as described previously and ensured to be LPS-free (38 (link)). PBS was used to dilute the rMIF to the indicated concentration. As dimethyl sulfoxide (DMSO) was present in the rMIF preparation, an identical amount of DMSO was added to PBS for the vehicle control treatment. Either rMIF or vehicle control were administered in a 10μl volume to the nares of unanesthetized mice for the frequency and duration described.
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10

Pneumococcal Strain Isolation and Characterization

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Types 4 and 6A strains used in the study are described in Table 1. Clinical isolates were confirmed as Spn by sensitivity to ethylhydrocupreine hydrochloride (optochin) and typed using specific antisera (Statens Serum Institute). Pneumococci were grown statically in tryptic soy (TS) broth (Becton, Dickinson) at 37°C. Upon reaching the desired OD620nm of ~1.0, cells were washed and diluted in sterile phosphate-buffered saline (PBS) for inoculation. For quantitative culture, serial dilutions were plated on TS broth agar supplemented with an appropriate antibiotic and either 5% sheep blood or catalase (6,300 U/plate; Worthington Biochemical Corporation) and incubated overnight at 37°C with 5% CO2.
Colonies expressing different amounts of CPS were selected by visual screening using microscopy with oblique, transmitted illumination as described [16 (link)]. Mutants were confirmed by whole-genome sequencing. A corrected mutant (P2752) of the cpsE mutation in P385 was constructed by transforming P385 as previously described [26 (link)] with the cps PCR product of P376 using primers 5’- ACC ATT GTC TCT ACC TCT CAC -3’ and 5’- CGG AAT TCC TGT AAT TGA TGT CAT -3’. The transformation was verified using sequencing primer 5’- GAA GAT TCT CCT ACT TAC AGC AAC -3.
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