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180 protocols using sodium chloride (nacl)

1

pH Adjustment with Phosphate Buffers

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The pH was adjusted by adding disodium phosphate (10 mM, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) containing sodium chloride (137 mM, FUJIFILM Wako Pure Chemical Corporation) and potassium chloride (2.68 mM, KANTO CHEMICAL, Tokyo, Japan) to potassium dihydrogen phosphate (2.0 mM) containing sodium chloride (137 mM, FUJIFILM Wako Pure Chemical Corporation) and potassium chloride (2.68 mM, FUJIFILM Wako Pure Chemical Corporation).
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2

Genetic Modifications of E. coli Chemotaxis

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The strains and plasmids are listed in Table S1. All strains were derived from the K12 strain RP437, which is wild-type for chemotaxis [14 (link)]. The replacement of the wild-type cheA gene with cheA(M98L) to make CheAS cell [15 (link)], the replacement of the wild-type fliC gene with the fliC-sticky gene [16 (link)], and the replacement of the wild-type cheZ gene with cheZ(F98S) [11 (link)] were carried out using the λ red recombinase and tetracycline sensitivity selection method [17 (link),18 (link)]. LB broth (1% bactotryptone (BD, Sparks, MD, USA), 0.5% yeast extract (BD, Sparks, MD, USA), 0.5% NaCl (Wako, Osaka, Japan)) was used for culture growth, transformations, and plasmid isolation. Tryptone broth (TB) (1% bactotryptone, 0.5% NaCl) was used to grow cells for measurements of motor rotation. Growth conditions were described in Supplemental Methods. For all measurement, the cells were suspended in 10NaMB (10 mM potassium phosphate buffer (Wako, Osaka, Japan), pH 7.0; 0.1 mM EDTA-2K (Wako, Osaka, Japan), pH 7.0; 10 mM NaCl, 75 mM KCl (Wako, Osaka, Japan)).
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3

Hepatocyte Isolation via Collagenase Perfusion

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The preparation of hepatocytes was performed by using the collagenase perfusion method as described previously. Abdominal incisions were performed on the rats under anaesthesia, and 18G catheters (Terumo) were inserted into the PV and IVC. The initial perfusions (100 mL; flow rate, 10–15 mL/min) were performed using the perfusion solution, which included NaCl (136.89 mM, Wako), KCl (5.37 mM, Wako), NaH2PO4/2H2O (0.38 mM, Wako), Na2HPO4/12H2O (0.17 mM, Wako), HEPES (10 mM, DOJINDO), glucose (5 mM, Wako), ethylene glycol tetra-acetic acid (0.5 mM, DOJINDO), NaHCO3 (4.16 mM, Wako), and phenol red (0.017 mM, Sigma-Aldrich Japan).
A secondary perfusion was performed for 8–15 min using collagenase solution (Wako), which contained NaCl (136.89 mM, Wako), KCl (5.36 mM, Wako), NaH2PO4/2H2O (0.38 mM, Wako), Na2HPO4/12H2O (0.17 mM, Wako), CaCl2 (5.06 nM, Wako), HEPES (10 mM, DOJINDO), glucose (5 mM, Wako), NaHCO3 (4.16 mM, Wako), phenol red (0.017 mM, Sigma-Aldrich Japan), and soy bean trypsin inhibitor (0.0025 mM, Sigma-Aldrich Japan). After the secondary perfusion, the liver was split into multiple tissues, and the primary hepatocytes were corrected through mesh filtration (Kawamoto, Osaka, Japan) in 2% FBS MEM.
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4

Screening Growth Inhibitory Compounds

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S. epidermidis was incubated overnight
in 3 mL of culture medium [1% peptone (BD), 1% beef extract (BD) and
0.5% NaCl (Wako), pH 7.1] on a rotary shaker (37 °C, 300 rpm). E. coli was incubated overnight in 3 mL of culture medium
[0.5% yeast extract (BD), 1% tryptone (BD) and 0.5% NaCl (Wako), pH
7.0] on a rotary shaker (37 °C, 300 rpm). We used 15 × dilutions
of the S. epidermidis culture and 10 × dilutions
of the E. coli culture for the growth assays. The
bacterial strains were seeded in 96-well assay plates (Nunc) with
a 100 μL total reaction volume and incubated in a culture medium
containing each chemical compound, 0.3% DMSO as a negative control
or ampicillin (Sigma) as a positive control in the S. epidermidis and E. coli growth assays. S. epidermidis and E. coli were cultured at 300 rpm at 37 °C.
After 4, 6, and 8 h, we measured the absorbance (595 nm) of the culture
media using a micro plate reader (BioRad).
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5

Weak Gel Formulation and Core-Flooding Evaluation

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The main
agent for the weak gel is sulfonated polyacrylamide (FPAM), which
is illustrated in Figure 1, and provided by SNF Water Science. Other chemicals included
the cross-linking agent, polyethylenimine, with an average molecular
weight of 600 (PEI-600), thiourea (used for the deoxidation of brine),
and NaCl (used to make a brine with a salinity of 0.5 wt % NaCl),
which were acquired from Fujifilm Wako Chemical Corporation, Japan.
Berea Buff sandstone (brine permeability 146–409 mD) prepared
from Kocurek Industries, Inc. Texas, USA, was used in the core-flooding
test.
Major laboratory equipment included a DV2T Brookfield
viscometer
(Brookfield Engineering Laboratories, Inc., Middleboro, MA, USA),
an advection pump, and a VINCI SRP350 apparatus (VINCI Technologies,
Nanterre, France), which was used for the core-flooding test. In the
Micronit microfluidic model (Micronit, Enschede, Netherlands), a simulated
sandstone chip was used for the flooding test. A stirrer, a precision
balance (0.001 g), and a constant temperature chamber were also included
in the lab test equipment.
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6

Enzymatic Activity of RNase H

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Synthetic ssRNA (8-mer: 5’-CGACACCU-3’, 14-mer: 5’-CGACACCUGAUUCC-3’) and ssDNA (8-mer: 5’-AGGTGTCG-3’, 14-mer: 5’-GGAATCAGGTGTCG-3’) were obtained from Biologica Co. A commercial product of recombinant RNase H was from Takara Bio Inc. Ammonium acetate (NH4OAc, MS grade), trifluoroacetic acid (TFA), manganese (II) chloride tetrahydrate (99.99%), magnesium chloride hexahydrate (99.995%), zinc chloride (99.999%), calcium chloride, acetic acid, and trizma base were from Sigma-Aldrich. Sodium chloride, dithiothreitol (DTT) and hydrochloric acid were from Wako. Triethylamine (TEA), SDS, tryptone, dried extract yeast, and 0.2 mol/l-di-sodium dihydrogen ethylenediaminetetraacetate (EDTA) solution were from Nacalai Tesque. Ultrapure water was produced by PURIC-ω (ORGANO) and used for all the experiments.
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7

Protocol for Preparing Ophthalmic Formulations

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Regorafenib, 4‐[4‐ ({[4‐Chloro‐3‐(trifluoromethyl) phenyl]carbamoyl}amino)‐3‐fluorophenoxy]‐N‐methylpyridine‐2‐carboxamide monohydrate, was purchased from Selleck Chemicals Co., Ltd. and Active Biochem, Ltd.. Pazopanib, 5‐[[4‐[(2,3‐dimethylindazol‐6‐yl)‐methylamino]pyrimidin‐2‐yl]amino]‐2‐methylbenzenesulfonamide hydrochloride was purchased from SYNKinase Co., Ltd. Hydroxypropyl cellulose, sodium dihydrogen phosphate, sodium chloride and sodium hydroxide were purchased from FUJIFILM Wako Pure Chemical Corporation (Osaka, Japan). Light liquid paraffin and benzalkonium chloride were purchased from NACALAI TESQUE, Inc (Kyoto, Japan). Polysorbate 80 and D‐mannitol were purchased from Junsei Chemical Co., Ltd. Captisol was purchased from Ligand Pharmaceuticals, Inc. Aflibercept (40 mg/mL EYLEA® Injection For Intravitreal Injection) was purchased from Bayer Yakuhin, Ltd. Mydrin‐P ophthalmic Solution was purchased from Santen Pharmaceutical Co., Ltd.. Scopisol solution was purchased from Senju Pharmaceutical Co., Ltd. (Osaka, Japan). Fluorescite Intravenous Injection 500 mg was purchased from Alcon Japan Ltd. (Tokyo, Japan).
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8

Nitric Oxide Donor Assay for STEC

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NO was generated by four NO donors, namely DETA‐NONOate (DETA/NO) (Cayman Chemical Company, MI, USA), NOC12 (Dojindo Laboratories, Kumamoto, Japan), Spermine‐NONOate (Sper/NO) (Cayman Chemical Company), and PROLI‐NONOate (PROLI/NO) (Cayman Chemical Company). When a heat‐inactivated DETA/NO was prepared, it was dissolved in hydrochloric acid solution (0.1 mol/L) and then incubated for 4 hr at 60°C. The NOS inhibitor NG‐Monomethyl‐L‐arginine (L‐NMMA) (Dojindo Laboratries) and an iron‐chelating agent, deferoxamine (Sigma‐Aldrich, MO, USA) were used. NaNO2 and NaNO3 were purchased from Wako (Tokyo, Japan). LB broth was dissolved in 10 g of Tryptone (Nacalai Tesque, Japan), 5 g of yeast extract (Nacalai Tesque), and 10 g of sodium chloride (Wako) in 1 L of DW, adjusted to pH 7.2 and autoclaved. Polyclonal antisera for Stx1 and Stx2 were prepared as described previously (Noda, Yutsudo, Nakabayashi, Hirayama, & Takeda, 1987; Yutsudo et al., 1987). The anti‐Stx1 and anti‐Stx2 antisera primarily reacted with the A subunit of Stx1 and Stx2, respectively. Anti‐RNA α and anti‐RecA antibodies were obtained from NeoClone Biotechnology International (Madison, WI, USA) and Bio Academia (Osaka, Japan).
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9

Fabrication of Microfluidic Devices

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Hen egg-white lysozyme (>95% purity) was
purchased from Hampton Research (Aliso Viejo, CA, USA). We used lysozyme
without further purification. Sodium chloride, sodium acetate, acetic
acid, glycerol, acetone, and 2-propanol were purchased from Wako Pure
Chemical Industries, Ltd. (Osaka, Japan). Trichloro(1H,1H,2H,2H-perfuluorooctyl)silane
was purchased from Sigma-Aldrich (St. Louis, MO, USA). Polydimethylsiloxane
(PDMS; SILPOT 184 W/C) was purchased form Dow Corning Toray Co., Ltd.
(Tokyo, Japan). We purchased a SU-83010, a SU-83050, and a SU-8 developer
from Nippon Kayaku Co., Ltd. (Tokyo, Japan). Silicon wafers were obtained
from Global Top Chemical (Tokyo, Japan).
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10

Synthesis and Characterization of Cyclodextrin Derivatives

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FPB-βCyD, PB-βCyD, and 1 were synthesised according to our previous reports.5–7 (link) Dimethyl sulfoxide (DMSO, Luminasol®, Dojindo Laboratories), sodium chloride (Fujifilm Wako Chemicals), disodium hydrogen phosphate (Fujifilm Wako Chemicals), sodium hydrogen carbonate (Fujifilm Wako Chemicals), sodium carbonate (Fujifilm Wako Chemicals), d-fructose (Fujifilm Wako Chemicals), d-glucose (Fujifilm Wako Chemicals), d-galactose (Fujifilm Wako Chemicals), d-mannose (Fujifilm Wako Chemicals), d-ribose (Fujifilm Wako Chemicals), d-xylose (Fujifilm Wako Chemicals), hydrogen chloride aq. (Fujifilm Wako Chemicals), 50% sodium hydroxide solution (super special grade, Fujifilm Wako Chemicals), and Milli-Q water were used for spectroscopic measurements.
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