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916 protocols using mgcl2

1

Hairy Root Elicitation with Methyl-β-cyclodextrin, Methyl Jasmonate, and H2O2

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Thirty-five-day old hairy root cultures of line U-D2 grown in 250 mL flasks with 50 mL of MSV medium were used for elicitation. The old spent culture medium was removed and replaced by 100 mL fresh MSV medium containing three different groups of elicitors. Group-I: 18 g/L methyl-β-cyclodextrin (CD; CAVASOL® W7 M, Wacker, Munich, Germany), 125 µM methyl jasmonate (MeJA; Sigma-Aldrich, St. Louis, MO, USA), 3 mM H2O2 (Fisher Scientific, Waltham, MA, USA), and additional 1 mM MgCl2 (Sigma-Aldrich, St. Louis, MO, USA), group-II: 18 g/L CD, 125 µM MeJA, and additional 1 mM MgCl2, and group-III: 18 g/L CD, 3 mM H2O2 and additional 1 mM MgCl2. A control group was also analyzed by only refreshing MSV medium without adding any of the elicitors mentioned above. Each group had four flasks as biological replicates.
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2

Inner Ear Tissue Staining and Imaging

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Mice were euthanized and inner ears removed and fixed for 2 h at 4°C in 0.1 M phosphate buffer containing 1% paraformaldehyde (Sigma-Aldrich), 2 mM MgCl2 (Sigma-Aldrich), 0.25% glutaraldehyde (Sigma-Aldrich) and 5 mM EGTA (Merck Millipore). Ears were then washed in 0.1 M phosphate buffer containing 2 mM MgCl2 (Sigma-Aldrich) and 0.02% NP-40 (Fluka). Staining was performed overnight at room temperature (RT) in a solution of 0.1 M phosphate buffer containing 2 mM MgCl2 (Sigma-Aldrich), 5 mM potassium ferrocyanide (Sigma-Aldrich), 5 mM potassium ferricyanide (Sigma-Aldrich), 0.02% NP-40 and 1 mg/ml 5-bromo-4-chloro-indolyl-β-D-galactopyranoside (X-Gal) (Sigma-Aldrich). Post-staining, ears were decalcified in 4.3% EDTA in 0.1 M phosphate buffer (Sigma-Aldrich) for 48 h at 4°C, before paraffin embedding and sectioning at 10 µm. Sections and whole-mount dissected cochlea were imaged on a Zeiss Axio Observer Z-1 microscope using extended focus image capture.
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3

Apoptotic Marker Analysis in C. auris

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For studying apoptotic markers, protoplasts of C. auris MRL6057 were prepared as explained previously [21] (link). Briefly, cells grown for 8 h were then exposed for 4 h to ¼ MIC, ½ MIC and MIC of test compounds. For the purpose of washing and resuspending yeast cells different protoplast buffers (PB) were prepared. After exposure with test compounds, cells were washed and incubated in PB-1 (1 M sorbitol, (Sigma Aldrich Co., USA), 0.05 M tris base (Merck, Germany), 0.01 M MgCl2 (Sigma Aldrich Co., USA), 0.03 M DTT (Merck, Germany), pH 7.4) for 10 min at room temperature. Post-incubation, cells were harvested at 1500 rpm for 5 min and pellet was mixed and incubated in PB-2 (1 M sorbitol, 0.05 M tris base, 0.01 M MgCl2, 0.001 M DTT, pH 7.4) supplemented with lyticase enzyme (1 μg/mL; Sigma Aldrich Co., USA) at room temperature for 1 h. Next, cell suspensions were centrifuged, and pellets were resuspended and incubated in PB-3 (1 M sorbitol, 0.05 M tris base, 0.01 M MgCl2, pH 7.4) at room temperature for 20 min. Post-incubation cell suspension was centrifuged at 1500 rpm for 5 min and pellets with protoplasts were washed and mixed in fresh PBS and stored at 4 °C until further use.
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4

Hexokinase and Pyruvate Kinase Assays

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The Hexokinase assay was performed as previously described87 (link). Briefly, 20 µg of fresh tissue lysate was added to 1 ml of reaction buffer for hexokinase (50 mM Tris HCl (Sigma-Aldrich), pH 7.5, 10 mM MgCl2 (Sigma-Aldrich), 0.6 mM ATP (Sigma-Aldrich), 100 mM glucose (Sigma-Aldrich), 0.2 mM NADP+ (Sigma-Aldrich), and 0.1 units of glucose-6-phosphate dehydrogenase (Sigma-Aldrich)). Ten units of glyceraldehyde-3-phosphate dehydrogenase (Sigma-Aldrich) per ml was used for analyzing the Hexokinase activity. The Pyruvate kinase assay was performed as previously described87 (link). Briefly, 20 µg of fresh tissue lysate was added to 1 ml of reaction buffer for pyruvate kinase (50 mM Tris HCl (Sigma-Aldrich), pH 7.5, 5 mM MgCl2 (Sigma-Aldrich), 5 mM ATP (Sigma-Aldrich), 0.2 mM NADH (Sigma-Aldrich) 100 mM KCl (Sigma-Aldrich), 5 mM Na2HPO4 (Sigma-Aldrich), 5 mM MgCl2 (Sigma-Aldrich), 0.01 mM AMP (Sigma-Aldrich)) 5 mM fructose-6-phosphate (Sigma-Aldrich), 5 units of triosephosphate isomerase (Sigma-Aldrich) per ml, 1 unit of aldolase (Sigma-Aldrich) per ml was added to check the pyruvate kinase activity. A negative and positive control has been included without tissue lysate and with 0.05 units of hexokinase and pyruvate kinase in both the assays. Enzyme activities were measured and represented as the change in absorbance/min, calculated using a linear portion of the obtained curve.
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5

Magnesium Modulation of Osteogenic Induction

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The basal medium used for osteogenic induction was high-glucose Dulbecco's modified Eagle's medium (HG-DMEM) for mMSCs and Iscove's modified Dulbecco's medium (IMDM) for hMSCs supplemented with the induction factors: 0.1 μM dexamethasone (Sigma-Aldrich), 10 mM β-glycerol phosphate (βGP; Sigma-Aldrich), and 0.2 mM ascorbic acid (ASA; Sigma-Aldrich) [31 (link)]. The cells were seeded at 4000 cells/cm2 and were maintained in culture medium (low-glucose DMEM supplemented with 10% FBS) for 24 hours before the induction. The induction medium was changed twice a week.
DMEM and IMDM contain 0.8 mM magnesium ion, and therefore 0.8 mM magnesium concentration is defined as normal magnesium concentration. The serum magnesium level in patients with renal disease is around 1 mM [32 (link)] and a serum magnesium level around 5 mM is associated with profound muscle weakness; on the other hand, physiological magnesium concentrations in soft tissue and bone are 8.5 and 43.2 mmol/kg wet weight respectively [15 (link)]. Therefore, for the induction medium with high concentration of magnesium, DMEM and IMDM were supplemented with 5 mM MgCl2 (Sigma-Aldrich) and we defined 5.8 mM MgCl2 as the experimental group of high magnesium concentration. A 1 M MgCl2 stock solution was prepared in double-distilled water (ddH2O) to make the final concentration of magnesium 5.8 mM.
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6

Hippocampal Slice Preparation for Electrophysiology

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Mice were briefly anesthetized with 3% sevoflurane before decapitation. Acute sagittal hippocampal slices (300 μm) were obtained using a VT1200S vibratome (Leica, Switzerland) in ice-cold dissection buffer (212 mM sucrose [Sigma-Aldrich, Cat# S5016], 25 mM NaHCO3 [Sigma-Aldrich, Cat# S6297], 5 mM KCl [Sigma-Aldrich, Cat# P3911], 1.25 mM NaH2PO4 [Sigma-Aldrich, Cat# S0751], 10 mM D-glucose [Sigma-Aldrich, Cat# G7578], 2 mM sodium pyruvate [Sigma-Aldrich, Cat# P2256], 1.2 mM sodium ascorbate [Sigma-Aldrich, Cat# A4034], 3.5 mM MgCl2 [Sigma-Aldrich, Cat# M0250], 0.5 mM CaCl2 [Sigma-Aldrich, Cat# C3881], continuously aerated with 95% O2/5% CO2). The slices were transferred to a chamber filled with warmed (32 °C) artificial cerebrospinal fluid (aCSF: 125 mM NaCl [Sigma-Aldrich, Cat# S7653], 25 mM NaHCO3, 2.5 mM KCl, 1.25 mM NaH2PO4, 10 mM D-glucose, 1.3 mM MgCl2, 2.5 mM CaCl2, aerated with 95% O2/5% CO2) for recovery (30 minutes), and then placed in room temperature prior to the experiments.
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7

Cryo-EM Structural Analysis of SUR2 Proteins

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Purified SUR2B proteins were further supplemented with 3 mM fluorinated Fos-Choline-8 (FFC), 8 mM MgCl2, 8 mM ATP (Sigma) and 200 μM P1075 (Tocris Bioscience) for Mg-nucleotides + P1075 state; 8 mM MgCl2 and 8 mM ADP (Sigma) for Mg-nucleotides state; 8 mM MgCl2, 8 mM ADP and 200 μM Lev (MedChemExpress) for Mg-nucleotides + Lev state. Purified SUR2A proteins were supplemented with 3 mM FFC, 8 mM MgCl2, 8 mM ADP and 200 μM P1075 for Mg-nucleotides + P1075 state. Cryo-EM sample was loaded on to glow-discharged Quantifoil 0.6/1 gold grids and frozen as described previously19 (link).
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8

X-gal Staining of Lgr4-LacZ Cochleae

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Staining was performed on cryosections. Tissues were washed with 2 mM MgCl2 in PBS twice for 5 min each at room temperature and incubated in X-gal (4%) mixed with X-gal mixer (1:40, v/v) at 37°C for 2–4 h. X-gal mixer comprises 5 mM K3Fe(CN)6, 5 mM K4Fe(CN)3H2O, 0.01% sodium deoxycholate, 0.2% Nonidet NP-40, 2 mM MgCl2 (all from Sigma–Aldrich) in PBS. Next, tissues were rinsed with PBS and mounted in Mowiol (Sigma–Aldrich). Cell nuclei were stained with Nuclear Fast Red (Vector laboratories) according to the manufacturer’s protocol. Using this protocol, we stained cochleae from 3 Lgr4-LacZ knock-out and heterozygous mice. Control experiments found no non-specific staining in cochleae harvested from 3 wild type littermates.
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9

Automated Patch-Clamp for Ion Channel Analysis

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An automated patch-clamp system (Patchliner Octo®, Nanion Technologies, Münich, Germany) was utilized as per standard procedure detailed by the manufacturer and as described previously (Haythornthwaite et al., 2012 (link)). Up to eight cells were measured simultaneously using the Patchliner Octo®, which is equipped with two EPC-10 Quadro patch-clamp amplifiers (HEKA Elektronik, Reutlingen, Germany). The external solution contained 4 mM KCl (Sigma), 140 mM NaCl (Sigma), 2 mM CaCl2 (Sigma), 1 mM MgCl2 (Sigma), 10 mM HEPES (Sigma), and 5 mM glucose (Sigma), at pH 7.4. The internal solution (60 mM KF, 50 mM KCl, 20 mM EGTA, 10 mM NaCl, 10 mM HEPES, and 1 mM MgCl2; Nanion) was supplemented with 3 mM MgCl2 (Sigma), 0.2 mM GTP (Sigma), and 3 mM ATP (Sigma), adjusted to pH 7.2. A seal-enhancer solution (3 mM KCl, 80 mM NaCl, 35 mM CaCl2, 10 mM MgCl2, and 10 mM HEPES [pH 7.4]; Nanion) was used and subsequently changed into external solution upon the establishment of the whole-cell configuration. Patch-ControlHT software (Nanion Technologies, version 12.0.1f9) and Patchmaster software (HEKA Elektronik, version 2×90.4 beta) were utilized for data acquisition. Data were recorded at a sampling rate of 20 kHz (at room temperature) and filtered at 5 kHz.
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10

Concentrating Endogenous Viruses from Wastewater

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Endogenous viruses were concentrated from the 18 wastewater samples using the AE concentration workflow. The AE workflow began with the addition of dissolved MgCl2 (Sigma-Aldrich, St. Louis, Missouri, USA) to a 10 mL wastewater sample to achieve a final concentration of 25 mM MgCl2. After amendment with MgCl2, wastewater samples were immediately filtered through 0.22, 0.45 and 0.80-μm pore-size, electronegative HA membranes (Merck Millipore Ltd., Tokyo, Japan) via a magnetic filter funnel (Pall Corporation, Port Washington, New York, USA) and filter flask (Merck Millipore Ltd.) (Ahmed et al., 2020b ). Following filtration, using aseptic technique, the membrane was immediately removed, rolled, and inserted into a 5-mL-bead-beating tube (Qiagen, Hilden, Germany) for nucleic acid extraction.
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