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12 protocols using bullet blender blue

1

Propagation and Subculture of O. tsutsugamushi strain UT-76

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O. tsutsugamushi strain UT-76 (a Karp-like strain from Thailand) was propagated in T25 cell culture flasks containing a confluent monolayer of L929 cells which were grown in DMEM supplemented with 10% FBS at 35°C with 5% CO2. After 7 days of infection the cells were sub-cultured onto fresh L-929 cell monolayers. The infected flasks were harvested by scraping using a sterile inoculating loop in 1ml spent medium and disrupted to release intracellular bacteria by lysing in a bullet blender (BBX24B, Bullet Blender Blue, Nextadvance, USA) used at power 8 for 1 min. The lysed bacteria were added to a T25 flask (100 μl/flask) containing an uninfected L-929 monolayer at 70–100% confluence. Infected flasks were passaged at a ratio of 1:5 (original culture flask: subculture flask). Bacteria were sub-cultured for a total of <20 passages, where passage 0 was the original clinical isolate.
Antibiotics were only used in the experiment testing the effect of antibiotic addition. Here antibiotics were used at the following concentrations: chloramphenicol 150 μg/ml, penicillin G 100 μg/ml, penicillin G + streptomycin (premix from Sigma-Aldrich) 125 μg/ml + 200 μg/ml.
Cell lines and bacteria were tested for the presence of mycoplasma and confirmed to be mycoplasma-free using the VenorGeM PCR detection kit (Minerva biolabs).
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2

Lung Homogenization and Bacterial Enumeration

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One third lungs were placed in a Bullet Blender Blue (Next Advance, Troy, NY) and homogenized at speed 8 for 4 minutes. Tissue homogenate was plated at a 1:5 dilution on 7H11 agar plates. The limit of detection is 15 CFUs for lungs.
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3

Tissue Homogenization and Biomarker Quantification

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Tissue samples were weighed, and 1 mL of PBS added with 0.05% Tween 20 (Sigma-Aldrich, St Louis, Mo) and 1% protease inhibitor cocktail (Sigma-Aldrich) was supplemented for every 100 mg of tissue. The tissue was then homogenized with a Bullet Blender Blue (Next Advance, Averil Park, NY) at setting 7 for 8 minutes at 4°C. The resulting suspension was centrifuged at 4000 rpm for 20 minutes at 4°C, and supernatants were harvested and stored at −80°C for later analyses.
The levels of FXa (MyBioSource, San Diego, CA), F1+2 (LifeSpan BioSciences, Seattle, WA), TATc (Assaypro, Charles, MO), TF (R&D, Minneapolis, MN), FVII (LifeSpan BioSciences, Seattle, WA), TFPI (R&D, Minneapolis, MN), and eosinophil cationic protein (ECP) (MBL, Woburn, MA) were measured in tissue extracts by the indicated ELISA according to the manufacturer’s instructions.
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4

Hippocampal Metabolite Extraction Protocol

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Each hippocampal tissues sample was weighed, and then homogenized by a bead mill homogenizer (Bullet Blender Blue, Next Advance). The tissue was transferred to a chilled safe-lock microcentrifuge tube. A mass of chilled stainless steel beads equal to the mass of the tissue was added to the tube. Ten-fold (w/v) ice-cold 80% methanol was then added to the tissue and beads. Samples were mixed in the Bullet Blender Blue for 2 min at a speed of eight. The extracts were centrifuged at 12,000 rpm for 10 min at 4°C, and all supernatant were lyophilized and then stored at -80°C until analysis. Samples were resuspended using 100 μl 80% methanol. In order to take into account the signal drift of the mass spectrometer over the run time, the hippocampus samples were injected into UHPLC-QTOFMS system in a random run order.
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5

Bacterial DNA Extraction Protocol

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The supernatant were removed from infected flasks and replaced with 6–8 ml pre-warmed media. Infected cells were harvested by mechanical scraping and then lysed using a bullet blender (BBX24B, Bullet Blender Blue, Nextadvance, USA) operated at power 8 for 1 min. Host cell debris was removed by centrifugation at 300xg for 3 minutes, and the supernatant was filtered through a 2.0 μm filter unit (Puradisc, GE Whatman, USA). 10 μl of 1.4 μg/μl DNase (Deoxyribonuclease I from bovine pancreas, Merck, UK) was added per 1 ml of bacterial solution, then incubated at room temperature for 30 minutes. This procedure removed excess host cell DNA. The bacterial sample was then isolated by centrifugation at 14,000xg for 10 min at 4 oC, and washed two times with 0.3M sucrose (Merck). After the washing steps were completed DNA was extracted using a QIAGEN DNeasy Blood & Tissue Kit (QIAGEN, UK) following the manufacturer’s instructions.
Purified DNA samples were analysed by gel electrophoresis using 0.8% agarose gel, in order to assess the DNA integrity. The yield of genomic DNA was quantified using a nanodrop (Nanodrop 2000, Thermo Scientific, UK) and Qubit Fluorometric Quantitation (Qubit 3.0 Fluorometer, Thermo Scientific).
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6

RNA Extraction and qPCR Protocol

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For RNA extraction, accessory lobes were lysed and homogenized using Bullet Blender Blue (Next Advance, USA), and RNA was extracted using RNeasy Mini kit (QIAGEN). Extraction of RNA from sorted cells was performed using RNeasy Micro kit (QIAGEN). Primers were designed using the Universal Probe Library Assay Design center program (Roche). Quantitative real-time PCR (qPCR) was performed using Light Cycler 480 II (Roche). Hypoxanthine guanine phosphoribosyl transferase (Hprt) was used to normalize gene expression. Primers used for qPCR are shown in Table S1.
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7

RNA Extraction and qPCR Protocol

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For RNA extraction, accessory lobes were lysed and homogenized using Bullet Blender Blue (Next Advance, USA), and RNA was extracted using RNeasy Mini kit (QIAGEN). Extraction of RNA from sorted cells was performed using RNeasy Micro kit (QIAGEN). Primers were designed using the Universal Probe Library Assay Design center program (Roche). Quantitative real-time PCR (qPCR) was performed using Light Cycler 480 II (Roche). Hypoxanthine guanine phosphoribosyl transferase (Hprt) was used to normalize gene expression. Primers used for qPCR are shown in Table S1.
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8

Tissue Homogenization and Protein Extraction

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Freshly obtained tissue specimens were weighed and 1 mL of PBS supplemented with 0.05% Tween 20 and protease inhibitor cocktail (Sigma-Aldrich, St. Louis, MO) was added for every 100 mg of tissue. The tissue was then homogenized with a Bullet Blender Blue (Next Advance, Averil Park, NY) at setting 7 for 8 min at 4°C. After homogenization, the suspension was centrifuged at 2000 x g for 20 min at 4°C, and supernatants were stored at −80°C until analyzed.
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9

Quantification of Inflammatory Mediators

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Freshly obtained tissue specimens were weighed, and 1 ml of PBS supplemented with 0.05 % Tween 20 (Sigma-Aldrich, St. Louis, MO) and 1% protease inhibitor cocktail (PIC, PN; P8340, Sigma-Aldrich) was added for every 100 mg of tissue. Tissue extracts were prepared by homogenization with a Bullet Blender Blue (Next Advance, Averill Park, NY) as described previously.14 (link) Nasal lavage fluids (NLF) were obtained from patients before surgery. After suctioning the nasopharynx, 8 ml of PBS was sprayed through a syringe toward the middle meatus, and the resultant fluid was collected as described previously.14 (link) Before analysis, tissue extracts and NLFs were centrifuged at 16,000g for 5 minutes and supernatants were used for each assay.
The protein concentrations of eosinophil cationic protein (ECP), neutrophil elastase (NE) and myeloperoxidase (MPO) were measured by commercial ELISA kits from MBL (Woburn, MA), Hycult Biotech, (Wayne, PA) and R&D systems (Minneapolis, MN), respectively. The minimal detection limits for ECP, NE and MPO are 125, 400 and 62.5 pg/ml, respectively. The concentration of these proteins in tissue extracts was normalized to the concentration of total protein as detected by BCA protein assay kit (Thermo Fisher Scientific, Rockford, IL).
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10

Nasal Lavage for Biomarker Analysis

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Nasal lavage fluid (NLF) was obtained from patients before surgery. After suctioning the nasopharynx, 8 ml of PBS was sprayed through a syringe toward the middle meatus, and the resultant fluid was collected. Tissue extract was prepared by homogenization with a Bullet Blender Blue (Next Advance, Averill Park, NY). The protein concentrations of each biomarker in cell free supernatants were determined by commercial ELISA and Luminex kits. Detailed methods are shown in this article’s Online Repository.
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