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4 protocols using 0.1 mm diameter glass beads

1

Skin Microcomedone Bacterial DNA Extraction

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Example 3

Skin microcomedone (white head or black head) samples were taken from the skin of the subjects using a specialized adhesive tape. The skin was moistened with water before the adhesive tape was put on. The tape was left on the skin for 15-20 minutes until it became dry. Clean gloves were used for each sampling. After being taken off from the skin, the tape was placed into a 50 mL sterile tube. This can be applied to many skin sites, such as the nose, forehead, chin, and back.

Bacterial DNA Extraction

Microcomedones were individually picked or scraped off from the adhesive tape using sterile forceps and placed in a 2 mL sterile microcentrifuge tube filled with Buffer ATL (Qiagen) and 0.1 mm diameter glass beads (BioSpec Products, Inc., Bartlesville, Okla.). Cells were lysed using a beadbeater for 3 minutes at 4,800 rpm at room temperature. After centrifugation at 14,000 rpm for 5 minutes, the supernatant was retrieved and used for genomic DNA extraction using QIAamp DNA Micro Kit (Qiagen). The manufacturer protocol for extracting DNA from chewing gum was used. Concentration of the genomic DNA was determined by a spectrometer.

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2

Modulation of MEF Gene Expression by Short-Chain Fatty Acids

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C57BL/6 primary MEFs were obtained from 12.5 to 14.5 days post coitus embryos and cultured in Dulbecco’s Modified Eagle’s Medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), and 1% nonessential amino acids (Gibco). MEFs were plated at a density of 2.5 × 105/mL in 24-well plates (Costar) overnight. Live PC members were prepared as before to an OD600 of 0.2, and diluted (1/105 by volume) in MEF containing culture media. PC lysates were prepared by taking live PC culture, bead beating with 0.1-mm diameter glass beads (BioSpec) for 5 min and filtering using Millex-GV 0.22-µm filter (Millipore). Plates were incubated at 37 °C, 5% CO2 for 1, 3, 6, and 14 h for live PC, or 12 h for lysates in the presence of acetic acid (Fisher), butyric acid (Sigma), propionic acid (Sigma), nicotinic acid (Sigma), or valproic acid sodium salt (Sigma) at the indicated concentrations. After incubation, culture media was removed and cells were harvested in Buffer RLT Plus (Qiagen) with 1% 2-Mercaptoethanol (Sigma) and RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions. All MEF experiments were ≥2 independent experiments, with at least two experimental replicates/experiment. The mean fold change for each experiment was plotted and represented as bar graphs.
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3

Fecal DNA Extraction Protocol

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Approximately 200 mg of each stool sample was fully homogenized with 0.1-mm diameter glass beads (Biospec, Orlando, FL, USA). Fecal DNA was subsequently extracted using commercial QIAamp stool DNA extraction kits (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. The concentration and quality of the extracted genomic DNA was determined by agarose gel electrophoresis and spectrophotometric analysis (NanoDrop Technologies, Wilmington, DE, USA). All extracted DNA samples were stored at −20℃ until use in further experiments.
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4

Skin Microcomedone Sampling and Bacterial DNA Extraction

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Example 3

Skin Microcomedone Sampling

Skin microcomedone (white head or black head) samples were taken from the skin of the subjects using a specialized adhesive tape. The skin was moistened with water before the adhesive tape was put on. The tape was left on the skin for 15-20 minutes until it became dry. Clean gloves were used for each sampling. After being taken off from the skin, the tape was placed into a 50 mL sterile tube. This can be applied to many skin sites, such as the nose, forehead, chin, and back.

Bacterial DNA Extraction

Microcomedones were individually picked or scraped off from the adhesive tape using sterile forceps and placed in a 2 mL sterile microcentrifuge tube filled with Buffer ATL (Qiagen) and 0.1 mm diameter glass beads (BioSpec Products, Inc., Bartlesville, Okla.). Cells were lysed using a beadbeater for 3 minutes at 4,800 rpm at room temperature. After centrifugation at 14,000 rpm for 5 minutes, the supernatant was retrieved and used for genomic DNA extraction using QIAamp DNA Micro Kit (Qiagen). The manufacturer protocol for extracting DNA from chewing gum was used. Concentration of the genomic DNA was determined by a spectrometer.

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