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29 protocols using 0.2 μm syringe filter

1

Antibiotic Impact on Gut Microbiome

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Animal experiments were performed under a protocol approved by the Animal Institutional Care and Use Committee at the Center for Comparative Medicine at the University of Virginia, in line with national standards. Per Fig. 1d, C57BL/6J male mice, 8 weeks of age, (Jackson Laboratories, Farmington, CT, USA) were either untreated or given clindamycin (25 mg/kg/day) for 10 days via oral gavage (n=7 animals per group). Seven days after final antibiotic administration, stool was collected from these mice which was pooled, homogenized, and diluted 1/10 w/v in PBS. This slurry was then sterile filtered using a 0.2 μm syringe filter (EMD Millipore, Darmstadt, Germany). This metabolite milieu from the stool sample was then conditioned with 10 μL of UK1 spores for 24 hours and then diluted 1/10 for analysis by impedance cytometry or CFU determination assays.
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2

GABA Quantification from BSG Fermentation

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Supernatant from the BSG fermentation (100 μl) was obtained by centrifugation (8,000 ×g, 5 min, 4°C), followed by dansylation at 80°C for 40 min after addition of 1 M sodium carbonate–sodium bicarbonate buffer (pH 10.0; 200 μl), dansyl chloride dissolved in acetone at 20 mg/ml (100 μl), and distilled water (600 μl). Then, 10%(v/v) acetic acid (100 μl) was added to terminate the reaction. After centrifugation, the reaction solution was filtered with a 0.2-μm syringe filter (Merck Millipore, USA) and injected into a high-performance liquid chromatography (HPLC) system for analysis at 254 nm and 30°C [29 (link)]. A JASCO HPLC system (JASCO LC-2000 Plus Series, Japan) with a photodiode array detector, an autosampler (JASCO AS-2055 Plus), and an AccQ-Tag C18 column (3.9 × 150 mm, 4 μm; Waters Corporation, UK) was used. Eluent A was prepared by mixing tetrahydrofuran, methanol, and 50 mM sodium acetate–acetic acid buffer (pH 6.2) at a ratio of 1:15:84 (v:v:v), and eluent B was methanol. Eluents A and B were applied at a flow-rate of 1 ml/min for 5 min, 16 min, and 4 min at ratios of 80:20, 45:55, and 0:100, respectively [29 (link)]. The GABA content was calculated using calibration curves determined at five concentrations with GABA standard material (Sigma-Aldrich, USA). All experiments were conducted three times.
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3

Copper Tolerance in Acinetobacter sp. IrC2

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Acinetobacter sp. IrC2 (accession number: JX009134) is a copper-resistant bacterium with a minimum inhibitory concentration of 10 mM CuSO4. Acinetobacter sp. IrC2 was cultivated in Luria Broth (LB; Pronadisa) containing 10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, and 0.1 g/L glucose for growth measurement. The medium was sterilized in an autoclave at 120°C for 15 min. A 1 M stock solution of CuSO4 (Merck) was prepared and filter-sterilized using a 0.2 μm syringe filter (Merck Millipore). Bacterial culture (0.5 ml, OD600 = 0.6) was inoculated into a 50 ml sterile LB medium. Bacterial cultures prepared with 6 mM copper and without copper supplementation were used as control, followed by shaking at 37°C and 100 rpm. Every 3 h, cell turbidity was measured using a spectrophotometer (LaboMed) at a wavelength of 600 nm until the bacteria reached the stationary growth phase. One milliliter of sample from each culture was withdrawn for OD600 measurement for each timepoint. Growth measurement was done in triplicates. The mean value of OD600 of cultures grown in media supplemented with CuSO4 was compared to that of the control group using Student’s t-test.
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4

Affinity Chromatography for mAb Purification

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The purification of mAbs was performed by affinity chromatography. Briefly, novel mouse mAbs were purified by salt fractionation (solid ammonium sulphate ([NH4]2SO4; 45% of saturation - 270 g/L; Fisher Scientific) followed by affinity chromatography using a 5 ml HiTrap Protein G HP column in an ÄKTAprime plus chromatography system (both from GE Healthcare, UK). The antibody sample was loaded into the HiTrap Protein G HP column pre-equilibrated with 25 ml binding buffer (0.1 M phosphate buffer, 0.15 M NaCl, pH 7.4) at a flow rate of 1 ml/min. Unbound proteins were removed by washing the column with 50 ml binding buffer and bound antibodies were eluted with 25 ml elution buffer (0.1 M glycine, pH 2.5). Selected fractions were pooled together and subjected to buffer exchange with PBS using the HiPrep 26/10 Desalting column (GE Healthcare Life Sciences). Following buffer exchange, the purified antibodies were filtered through a 0.2 μM syringe filter (Merck Millipore, UK), aliquoted and stored at -20°C for further studies.
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5

Extraction and Purification of Helminth Excretory/Secretory Proteins

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4hr and overnight supernatants containing E/S products from passage worm cultures were filter sterilised through a 0.2μm syringe filter (Merck, Germany). E/S was then concentrated using Amicon Ultra-15 centrifugal filter units (Merck) by centrifugation at 3,000g at 4°C. Centrifugation was carried out until approximately 20% of the original volume of supernatant remained. E/S was then dialysed against PBS using Slide-A-Lyzer Dialysis cassettes, 3.500 MWCO (Thermo Scientific, UK) at 4°C. The E/S was then filtered sterilised a final time through a 0.2μm syringe filter, the protein concentration measured and aliquoted prior to storage at -80°C
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6

Purification of Fc-Containing Protein

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The reaction mixture was adjusted to pH 7.0 using 1 N HCl. The Fc-containing protein was separated from SrtAΔ1–59 and unreacted PLP peptide using protein G affinity chromatography. The column was first equilibrated using TBS, pH 7.0. Then the reaction mixture was loaded onto the Protein G column, and the captured Fc protein was washed with 500 mL of 50 mM Tris and 500 mM NaCl, pH 7.0. Then the Fc-containing protein (unreacted LABL-Fc-ST and product LABL-Fc-ST-PLP) was eluted using 0.1 M glycine-HCl buffer pH 2.7 and immediately dialyzed against TBS, pH 7.5. The protein was then passed through a Detoxi-Gel endotoxin removal column (Thermo Scientific) to remove endotoxin contaminants that may have been introduced during the expression and/or purification steps.52 (link) The flow through from the endotoxin removal column was concentrated using an EMD Millipore 10 kDa MWCO centrifugal concentrator (USA). Concentration was stopped when the volume of the protein solution was 2 mL because precipitation was observed. The concentrated protein was dialyzed against 4 L of 1× PBS pH 7.4 with one buffer change at 4°C overnight and then filtered through an EMD Millipore 0.2 μm syringe filter. The concentration of the end product was determined to be 168 μM (9.6 mg/mL, 19 mg total) by optical density of the solution at 280 nm (MW = 57128.3 Da, ε280 = 82570 M−1cm−1).51 (link)
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7

Coal Composition and Water Analysis

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The coal composition was analysed at the Bureau Veritas Australia Pty Lt, Cardiff, NSW, Australia. Scanning electron microscopy (SEM) was performed according to Hazrin-Chong, Manefield [27 (link)]. Coal formation water was filtered through a 0.2 μm syringe filter (Millipore, Australia) and aliquots for cation analyses were subsequently acidified with formic acid (10% v/v; Sigma-Aldrich, Australia) to a pH < 2 and stored at −20 °C until further processing. Anion (F, Cl, Br, NO2, NO3, PO4, SO4) and cation (B, Ca, Fe, K, Mg, Mn, Na, P, S, Si) concentrations were analysed using ion chromatography (IC) with conductivity detection and inductive coupled plasma optical emission spectroscopy (ICP-OES) at the Mark Wainwright Centre (UNSW, Sydney, Australia). The instrument detection limits were 0.02 mg/L for B, Si and Mn, 0.2 mg/L for Fe and P, 0.5 mg/L for Ca, K, Mg, Na and S, 2 mg/L for F, NO2, NO3 and Br, and 5 mg/L for Cl and PO4.
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8

Isolating Trophoblast Exosomes from Conditioned Media

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When the confluency of trophoblast cells reached 50%, the growth medium was replaced with 5% (v/v) exosome-depleted FBS (Gibco) and the cells were incubated in it for 48–72 h until cell confluency reached 100%, post which the CM was collected. The CM was then filtered with a 0.2 μm syringe filter (Millipore, Billerica, MA, USA) before use. Exosomes were isolated from the collected CM using an exosome isolation kit (ExoQuick-TC™, Systemic Biosciences, Palo Alto, CA, USA), according to the manufacturer’s protocol. Briefly, CM was centrifuged at 1000× g for 5 min to remove the cells and filtered using a 0.22 μm syringe filter. The ExoQuick-TC™ solution was added to the supernatant in a ratio of 1:5, mixed carefully, and then left at 4 °C for 16 h. The exosomal pellets were precipitated by means of centrifugation at 3000× g for 30 min, resuspended in phosphate buffered saline (PBS), and used immediately or stored at −80 °C until use.
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9

Feederloss Culture of Human ESCs

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Mitotically inactivated buffalo FF cells (treated
with 10 μg/ml mitomycin-C) were cultured in T-25
flasks (Iwaki) with addition of ES medium for 7
days. Buffalo fibroblast-conditioned medium was
collected every day, centrifuged at 200 g for 3 minutes,
filtered with a 0.2 μm syringe filter (Millipore,
Watford, England) and frozen at -80˚C. After
thawing, the medium was equilibrated for 2 hours
at 5% CO2 and 37˚C and then used for the feederfree
culture of human ES cells.
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10

Exosome Isolation from Cell Supernatant

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FBS was centrifuged at 10,000 g overnight and then filtered through a 0.2 μm syringe filter (Millipore, Burlington, MA, USA). The exosome-deficient FBS was used for cell culture (DMEM supplemented with 10% exosome-free FBS). To isolate exosomes, the cell supernatant was collected and centrifuged at 2000 g and 10,000 g for 30 minutes at 4°C. The final supernatant was filtered through a 22 μm syringe filter (Millipore, Burlington, MA, USA) and centrifuged at 120,000 g for 70 minutes. Afterwards, the spheroidized vesicles were washed with PBS and centrifuged again at 120,000 g for 70 minutes. Finally, the extracellular markers were detected by Western blotting to validate the result.
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