The Hakuba Happo samples for geochemical and microbiological analysis were artificially pumped from a drilling well (700 m in depth), which was previously described and named Happo #3 (36°42′N 137°48′E [27 (link)]). For microbiological analysis, two spring water samples were taken at different time points, 233 L taken in July 2016 (labeled HKB701) and 720 L taken in October 2016 (labeled HKB702), respectively. To collect microbial cells, samples were filtered through a 0.1-μm Omnipore membrane filter (Merck Millipore) using a 90 mm diameter stainless-steel filter holder (Merck Millipore) attached to FDA Viton tubing (Masterflex) at a sampling site. After filtration, filters were immediately transferred to sterile tubes and frozen in a dry ice-ethanol bath, transported in dry ice, and stored at −80 °C until DNA extraction. Only in October 2017, water samples for NH3 and amino acid analysis were collected from the same well Happo #3, transferred to dry-heat-sterilized nitrogen-purged 100 ml glass vials, and stored at 4 °C.
Omnipore membrane filter
Manufactured by Merck Group
Sourced in Germany
Omnipore membrane filters are high-quality filtration products manufactured by Merck Group. They are designed for a wide range of laboratory applications that require reliable and consistent filtration performance. The core function of Omnipore membrane filters is to efficiently separate and retain desired substances from liquids or gases, ensuring sample purity and clarity.
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Lab products found in correlation
Sep pak c18 plus short cartridge, by Waters Corporation (3 mentions)
Malvern zetasizer 3000, by Malvern Panalytical (1 mentions)
Hitrap protein g hp column, by GE Healthcare (1 mentions)
Vivaspin, by Sartorius (1 mentions)
Amicon ultra 15, by Merck Group (1 mentions)
Ls6000ta, by Beckman Coulter (1 mentions)
Horse serum, by Thermo Fisher Scientific (1 mentions)
5 bromo 2 deoxyuridine brdu, by Merck Group (1 mentions)
Gentamicin sulfate solution, by Nacalai Tesque (1 mentions)
Helios gene gun, by Bio-Rad (1 mentions)
Vt1200, by Leica (1 mentions)
Mem glutamax, by Thermo Fisher Scientific (1 mentions)
15 protocols using omnipore membrane filter
1
Sampling and Preservation of Hakuba Happo Geochemical and Microbiological Specimens
2
Preparation and Characterization of Chitosan Nanoparticles
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The CNPs were obtained by grinding chitosan sample in a PM 100 CM planetary ball mill (Retsch GMBH, Haan, Germany) in a 125 mL grinding jar containing 5 mm diameter steel balls. A 5 g sample of chitosan and 50 mL of distilled water were placed in the grinding jar and processed for 1 h at 250 rpm. After grinding, the solution containing the CNPs was filtered through an Omnipore membrane filter (Merck Millipore, Darmstadt, Germany; 0.2 μm pore size). The concentration of chitosan nanoparticles in the stock suspension was 0.5 mg/mL, which was the maximum achieved concentration of CNP and stable for a week.
The CNP size was estimated by dynamic light scattering using a Malvern Zetasizer 3000 (Malvern Instruments Ltd, Malvern, Worcestershire, U.K.) and non-invasive backscatter technology. The value of the ζ-potential in water was measured on the same device using the Smoluchowski equation. The results indicated that particles with a diameter of 100 ± 30 nm and ζ-potential of +10 ± 1 mV had been obtained. The particle shape was evaluated using a Tescan S9251G scanning electron microscope (Tescan, Brno, Czech Republic) at an accelerating voltage of 3 kV with an in-beam secondary electron detector (Tescan, Brno, Czech Republic) (Figure 1 ).
The CNP size was estimated by dynamic light scattering using a Malvern Zetasizer 3000 (Malvern Instruments Ltd, Malvern, Worcestershire, U.K.) and non-invasive backscatter technology. The value of the ζ-potential in water was measured on the same device using the Smoluchowski equation. The results indicated that particles with a diameter of 100 ± 30 nm and ζ-potential of +10 ± 1 mV had been obtained. The particle shape was evaluated using a Tescan S9251G scanning electron microscope (Tescan, Brno, Czech Republic) at an accelerating voltage of 3 kV with an in-beam secondary electron detector (Tescan, Brno, Czech Republic) (
3
Efficient Purification of PMab-2 Antibody
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PMab-2 was purified following a previously described method (Ocampo et al., 2016 (link)) with some modifications. Briefly, 10 g of agroinfiltrated N. benthamiana leaves were ground in liquid nitrogen using a mortar and pestle. The powdered tissue was mixed with 40 ml of extraction buffer (0.5 NaCl, 45 mM Tris-HCl, 1 mM EDTA, 40 mM ascorbic acid, 1 mM PMSF; pH 7.5) and then agitated on ice for 1 h. The suspension was filtered through Miracloth (Meck Millipore), and centrifuged twice at 44,000 ×g for 30 min at 4°C. The supernatant was filtered through an Omnipore Membrane Filter (pore size 0.2 µm; Merck Millipore). PMab-2 was then purified using the AKTA start system equipped with a HiTrap Protein G HP column (GE Healthcare). Once the antibodies had bound to Protein G, the column was washed with the aforementioned extraction buffer without ascorbic acid. The antibodies were eluted with 0.1 M glycine-HCl (pH 2.7) and neutralized with 60 µl of 1 M Tris-HCl (pH 9.0) per ml fraction. The elutant was concentrated using Vivaspin (Sartorius) with 1 × PBS, at approximately 20 times.
4
Concentration of Seawater Samples
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Surface seawater was collected from the coast of Tokyo Bay, Japan (35° 19.170′ N, 139° 39.068′ E) in March 2014. The surface seawater was passed through a 41-μm nylon net filter (Merck Millipore) to separate large particles and debris. The aliquot (approximately 100 mL) was concentrated to approximately 9 mL (approximately 11-fold) by centrifugal ultrafiltration using a 10-kDa pore membrane (Amicon Ultra-15, Merck Millipore). Deep seawater was collected at a depth of 857 m off Hatsushima Island, Sagami Bay, Japan (35° 0.948′ N, 139° 13.310′ E) in April 2014. The deep seawater was passed through a 20-μm nylon net filter (Merck Millipore) and a 10-μm Omnipore membrane filter (Merck Millipore). The aliquot (approximately 200 mL) was concentrated to approximately 0.5 mL (approximately 400-fold) by centrifugal ultrafiltration. Ultrafiltration was performed at 5,000 g for 1–2 h at 4 °C.
5
Carboxylation and Purification of Pristine CNTs
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The purity of the pristine multiwall CNTs was evaluated before [23 (link)]. The CNTs were carboxylated by stirring them in a concentrated H2SO4 and HNO3 solution at a 3:1 (v/v) ratio at 70°C for 24 hours. The removal of these acids from the functionalized CNTs (CNTCOOHs) was performed by filtering the CNTCOOHs across a PTFE membrane filter with a pore size of 0.1 μm (Omnipore Membrane Filter, Merck, Prague, Czech Republic). After being triple washed with MilliQ water, the CNTCOOH suspension was dialyzed against 5 liters of MilliQ water at room temperature (Spectra/Por 7 Dialysis Membrane, molecular weight cutoff of 1 kDa, Carl Roth, Karlsruhe, Germany). The water was exchanged three times every 12 hours.
6
Quantifying Cellular Uracil Uptake
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The efficiency of cellular uracil uptake was assessed as described previously [20 (link),21 (link)]. Cells were cultivated in YES medium at approximate densities of 4 × 106–1 × 107 cells/ml. Cells were collected, and 2 × 107 cells were washed twice with sterile water, suspended in 4 μM [U-14C]uracil (Moravek Biochemicals Inc.) for 1 min at room temperature, then quickly filtered using an Omnipore membrane filter (Millipore Corp., 47 mm diameter and 1 μm pore size). Filters were washed twice with sterile water, and radioactivity was counted using a Beckmann LS6000TA scintillation counter.
7
Entorhino-hippocampal Slice Culture Preparation
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Entorhino-hippocampal slice cultures (300 μm thick) were prepared from postnatal day 14 (P14) Sprague-Dawley rats (SLC, Shizuoka, Japan) as described previously [15 (link)]. Briefly, rat pups were deeply anesthetized with isoflurane and decapitated, and their brains were removed and horizontally cut into 300-μm-thick slices using a DTK-1500 vibratome (Dosaka, Kyoto) in aerated, ice-cold Gay’s balanced salt solution. Entorhino-hippocampal slices were placed on an Omnipore® membrane filter (JHWP02500, Φ25 mm; Millipore) that was laid on an O-shaped plastic plate. Doughnut plates were inserted into six-well plates that were each filled with 1 ml of culture medium, out of which 0.9 ml of medium was changed every 3.5 days. The medium consisted of 50% minimal essential medium, 25% Hank’s balanced salt solution, and 25% horse serum (Thermo Fisher Scientific, Waltham, MA, USA), supplemented with 33 mM glucose. Finally, the slices were cultured at 37°C in a humidified incubator with 5% CO2 and 95% air. To label proliferating cells, the S-phase marker 5-bromo-2’-deoxyuridine (BrdU; 100 mg/kg; Sigma, St. Louis, MO) was subcutaneously injected into rat pups 24 h before slice preparation (P13).
8
Ion Exchange Synthesis of YCrB4
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Polycrystalline was fabricated by the arc melting method [20 (link)]. Rare earth metals, Y (890 mg), Cr (520 mg), and B (432 mg) were loaded in a Cu hearth with an atomic ratio of 1:1:4, and melted under the Ar atmosphere. In total, the resulting polycrystals were 1.632 g and were milled in an attritor by 5 mm diameter -based balls, reduced to µm-sized powders. The crystalline features were confirmed by X-ray diffraction (XRD).
The ion exchange reaction was prepared as follows. 100 mg powders of were mixed with a 20 mL cation ion-exchange resin (0.5–1.0 mm, Amberlite IR120B hydrogen form, Organo Corp., Tokyo, Japan) into a 50 mL solvent of acetonitrile (99.5%, Wako Pure Chemical Industries, Ltd., Osaka, Japan). Then, 1 mol/L HCl (0 mL/0.5 mL/1 mL) of hydrochloric acid was added to the solvent. The reaction was continuously stirred (250 rpm) using a magnetic stirrer under inert gas (Ar) at room temperature. The filtration was conducted after ion exchange reaction (0.2 µm pore filter, Omnipore Membrane Filters, Merck Millipore, Billerica, MA, USA).
The ion exchange reaction was prepared as follows. 100 mg powders of were mixed with a 20 mL cation ion-exchange resin (0.5–1.0 mm, Amberlite IR120B hydrogen form, Organo Corp., Tokyo, Japan) into a 50 mL solvent of acetonitrile (99.5%, Wako Pure Chemical Industries, Ltd., Osaka, Japan). Then, 1 mol/L HCl (0 mL/0.5 mL/1 mL) of hydrochloric acid was added to the solvent. The reaction was continuously stirred (250 rpm) using a magnetic stirrer under inert gas (Ar) at room temperature. The filtration was conducted after ion exchange reaction (0.2 µm pore filter, Omnipore Membrane Filters, Merck Millipore, Billerica, MA, USA).
9
Mouse Hippocampal Slice Culture Preparation
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Mouse hippocampal slice cultures were prepared as previously described (Koyama et al., 2007 (link); Kasahara et al., 2016 (link)) from P6 C57BL/6J mice or P10 Thy1-mGFP mice. Briefly, the posterior part of the mouse brain was cut into 400-μm thick transverse slices with a DTK-1500 vibratome (Dosaka, Kyoto, Japan) in aerated, ice-cold Gey’s balanced salt solution (GBSS) containing 36 mM glucose. The slices were incubated for 30–90 min at 4°C in incubation medium containing minimal essential medium (MEM) and HBSS at a ratio of 2:1, 9.0 mM Tris, 22.9 mM HEPES, and 63.1 mM glucose supplied with penicillin/streptomycin. Following this incubation, the slices were placed on Omnipore® membrane filters (JHWP02500; Merck Millipore) on doughnut plates (Hazai-Ya, Tokyo, Japan) in a solution containing 50% MEM, 25% horse serum, 25% HBSS, 6.6 mM Tris, 16.9 mM HEPES and 4.0 mM NaHCO3 supplemented with 29.8 mM glucose and 1% gentamicin sulfate solution (16672-04; Nacalai Tesque, Kyoto, Japan). Finally, the slices were cultured at 35°C in a humidified incubator with 5% CO2 and 95% air. The culture medium was changed twice weekly.
10
Extraction and Analysis of Root Exudates
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The preparation of root extracts and exudates was performed according to the procedure previously described by Sugiyama et al. (2016 ). The medium containing root exudates was filtered through Omnipore membrane filters (Millipore). The medium was passed through a Sep‐Pak C18 Plus short cartridge (Waters), which was eluted with 2 ml of MeOH. The eluant was dried under nitrogen and reconstituted in 50 µl of MeOH for LC‐MS/MS analysis.
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