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18 protocols using mops buffer

1

Lignocellulose Enzyme Activity Assay

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The activities of four different enzymes were monitored at time points 0, 24, 48, and 72 h. Substrates for β-glucosidase (BG) (EC. 3.2.1.37), cellobiohydrolase (CBH) (EC. 3.2.1.91), β-mannosidase (BM) (3.2.1.25), and β-xylosidase (BX) (EC. 3.2.1.37) activities were used. The first two substrates report on the degradation of cellulose and the last two on that of the hemicellulose part of wheat straw. The activities were quantified on the basis of the (enzyme-specific) substrate label 4-methylumbelliferone (MUB): 4-MUB-β-glucosidase, 4-MUB-β-cellobiosidase, 4-MUB-β-mannosidase, and 4-MUB-β-xylosidase (Sigma–Aldrich, Darmstadt, Germany). The reaction mixtures consisted of 150 μL diluted supernatant (usually 1/4) in MOPS buffer (50 mM, pH 6.5; Sigma–Aldrich, Darmstadt, Germany) and 2 mM of MUB substrate in black 96-well plates. The reactions were incubated 1 h at 28°C in the dark, after which 30 μL of NaOH (1 M) was added. Fluorescence was measured at an excitation wave length of 365 nm with emission at 445 nm. The enzymatic activities were then calculated from the fluorescence units using a standard calibration curve. Supernatant recovered from the NC was also tested, and thus served as the NC. The enzymatic activities are reported as the rate of MUB production (nmol MUB per h at 28°C, pH 6.8). All assays were done in triplicate.
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2

Extraction and Characterization of Blueberry Anthocyanins

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The blueberry anthocyanins were extracted from Rabbiteye blueberries (Lishui Town, Nanjing, China) [53 (link)] and stored at −18 °C at the Institute of Agricultural Products Processing, Chinese Academy of Agricultural Sciences. High-performance liquid chromatography (HPLC) solvents potassium chloride and acetonitrile were acquired from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China) and TEDIA (Fairfield, OH, USA), respectively. Ferritin (from horse spleen), MOPS buffer, 2,2-bipyridine, and bovine serum protein (BSA) were procured from Sigma-Aldrich (Shanghai, China). The bicinchoninic acid (BCA) and protein-assay kits were purchased from Beijing Solarbio Company (Beijing, China). The reagents used in the experiment are all of analytical grade.
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3

Antifungal Activity of Plant Extracts

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The screening of plant extracts for antifungal activity was investigated using a modified broth microdilution method. The plant extract/fungal isolate microtiter trays were stored at 35°C and assessed for growth after 48 h. The antifungal agents were prepared for minimum inhibitory concentration (MIC), according to Clinical and Laboratory Standards Institute (CLSI-formerly NCCLS) [16 , 17 ] with RPMI-MOPS (RPMI 1640 medium containing l-glutamine, without sodium bicarbonate (Sigma-Aldrich Co., St. Louis, USA) buffered to pH 7.0 with 0.165 mol/L MOPS buffer-Sigma). The SDB media were used as negative control, and fluconazole (1 mg/mL) was used as positive control. MIC was represented as the lowest concentration of compounds at which the microorganism tested did not demonstrate visible growth. The experiments were carried out in triplicate. Inhibition (%) was calculated as follows:
Inhibition  (%)=[(DCDE)DC]×100,
where DE is the diameter of growth zone in experimental disc (cm) and DC is the diameter of the growth zone in the control disc (cm).
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4

Antifungal Susceptibility of Aspergillus Species

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The isolates that were identified as Aspergillus fumigatus species complex were screened for their susceptibility to itraconazole, posaconazole and itraconazole, using the microdilution method according to EUCAST [16 ]. Serial dilutions (0.03–32 mg/L) of the tested antifungals were prepared in the medium RPMI1640 2× buffered with MOPS and dispersed in 100 µL aliquots on sterile 96-well microplates. To prepare inoculum spores from 2–3 day old cultures of Aspergillus on Sabouraud agar, the slants were suspended in sterile distilled water supplemented with 0.1% Tween 20 to obtain a density of McFarland 0.5. After dilution 10 times, suspensions of densities 1–2.5 × 105 CFU/mL were dispersed on the microplates with antimycotics (100 µL per well). The plates were incubated for 48 hrs at 35 °C, and the MIC was read visually as the lowest drug concentration that resulted in 100% inhibition of fungal growth. The results were interpreted according to EUCAST breakpoint tables for interpretation of the MICs [17 ]. The strains with MIC values of >1 mg/L for ITR and VOR, and >0.25 mg/L for POS, were regarded as resistant, while values of ≤1 mg/L for ITR, VOR, and ≤0.125 mg/L for POS were regarded as susceptible. The antimycotics and reagents used (DMSO, RPMI 1640 medium, MOPS buffer) were obtained from Sigma-Aldrich.
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5

Characterization of Clinical C. glabrata Isolates

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Twelve C. glabrata strains, isolated from different patients and of different origins, seven from hemoculture (12, 20, 30, 42, 45, 52 and 62), one vaginal (64), one from sputum (63), two exudates (60, 61), and one from sample preservation liquid (65) at a tertiary care hospital (Hospital Universitario de Badajoz, Spain) were included in this study. The isolated C. glabrata strains were sent to us anonymized, in accordance with the protocol approved by the Ethical Committee of the Hospital, (Comité de Ética de la Investigación Clínica del CHUB), in order to maintain the confidentiality of the patients, and were included in our collection (MicromedBA). The clinical isolates were identified by sowing in chromogenic medium CHROMagar Candida® and with biochemical methods using the API Candida ID32C system (bioMèrieux, Marcy L’Étoile, France). Sensitivity to antifungals was assessed by means of the automatic system Sensititre YeastOneR (Trek Diagnostic Systems, United Kingdom). Yeasts were conserved in vials at − 80 °C (Microbanc, Prolab, Ontario, Canada). Later, the strains were cultivated on Sabouraud agar plates (OXOID LTD., Basingstoke, Hampshire, UK) and incubated at 37 °C for 24 h; two subcultures were made in RPMI-1640 (Sigma, St. Louis, MO, USA.) medium supplemented with 2% glucose, and at pH 7 in MOPS buffer (Sigma) for the different experiments.
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6

Measuring Branchial H+ Gradients in Fish

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The SIET was performed at room temperature (26–28 °C) in an agar chamber filled with FW-recording medium (0.2 mM NaCl, 0.05 mM KH2PO4, 0.05 mM K2HPO4, 0.2 mM CaSO4, 0.2 mM MgSO4, 300 µM MOPS buffer (Sigma-Aldrich, Taipei City, Taiwan), 0.3 mg/L ethyl 3-aminobenzoate (Sigma-Aldrich, Taipei City, Taiwan), pH 7.0). Anesthetized fish were laid out in the agar chamber with the belly facing upward (Figure 2a). To measure the H+ gradients (represented as Δ[H+]) between the target spot and background, a H+-selective microelectrode was prepared to record the H+ activities with ASET software, following the previous study [16 (link)]. The background H+ activities were first recorded before the fish were placed in the chamber. Once the fish were set on the chamber, the H+ activities at three target spots between each pair of gills (the middle part of the gills) were then detected (Figure 2b). Branchial Δ[H+] was then calculated.
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7

Controlled Release of NecroX-5 from Alginate Hydrogels

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NecroX-5 NPs were dispersed in 45 µL of 1% alginate (SLM100, FMC BioPolymers, NovaMatrix™, Sandvika, Norway) solution in 3-(n-morpholino)propanesulfonic acid, 4-morpholinepropanesulfonic acid (MOPS buffer) (M3183; Sigma-Aldrich, Darmstadt, Germany), prepared as previously described [30 (link)], and 5 µL of CaCl2 (50 mM solution in MOPS) was added to initiate gelation.
Hydrogels were placed in 96-well plates, covered with 250 µL of 40 mM CaCl2 PBS, and incubated at 37 °C. Release media were collected at different timings (4 h, and 1, 2, 4, 10, 15, 21 days). Samples were centrifuged, and NecroX-5 was quantified by fluorimetry after a 2-times dilution in PBS. Results were expressed as the percentage of released NecroX-5 compared to the total amount of NecroX-5 added in the hydrogel.
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8

Enzymatic Determination of Total Starch

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The enzyme assay was performed using commercial enzymes adopted from the total assay procedure method (AOAC Method 996.11/ AACC Method 76.13) from Megazyme (Megazyme Inc., Bray, Ireland). Thermostable α-amylase (3,000 U/mL) was diluted in MOPS buffer (Sigma-Aldrich, St. Louis, MO) at pH 7.0 followed by an incubation in C2H3NaO2 buffer (200 mM) at pH 4.5 and amyloglucosidase concentrate (3,300 U/mL). Total starch content was determined by the enzymatic hydrolysis of 100 mg of fine powder from each sampled stem core. The samples were hydrolysed using 3 mL of thermostable α-amylase to extract maltodextrin from starch at 100 °C over 6 min (vortex at 2, 4 and 6 min intervals). The slurry samples were incubated at 50 °C in a water bath with 4 mL of C2H3NaO2 buffer, followed by 0.1 mL of amyloglucosidase for 30 min to hydrolyse maltodextrin to glucose. The amount of glucose present was measured using an UV-VIS spectrophotometer at 510 nm (Perkin Elmer Lamda 35 UV/VIS Spectrophotometer, Perkin Elmer, MA, USA).
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9

Synthesis of Gold Nanoparticles

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The Good’s buffer used
was 3-(N-morpholino)propanesulfonic acid (MOPS buffer,
Sigma Aldrich). The 1 M stock MOPS solution was made by dissolving
the buffer salt in Millipore water (18.2 MΩ cm) using a medium-sized
stir bar to ensure thorough mixing. The pH of the MOPS solution was
measured using a Thermo Scientific pH meter and was adjusted using
the concentrated solutions of NaOH. For fine pH adjustments, HCl was
added dropwise.
AuNS were synthesized by adding 0.2 mM (final
concentration) gold(III) chloride trihydrate (HAuCl4; Sigma
Aldrich) to 150 mM of MOPS buffer. Each solution was vortexed in a
50 mL Falcon tube for 1 min before the addition of HAuCl4 and for 1–5 min afterward. After vortexing, the growth solution
was left undisturbed at room temperature for 24 h. The 0 min time
point indicates an unstirred growth solution after the addition of
HAuCl4.
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10

High-Quality RNA Extraction and cDNA Synthesis

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Total RNA was isolated from rice and Arabidopsis tissues using Tri-reagent (Sigma, USA) according to manufacturer’s instructions. To nullify any genomic DNA contamination, isolated RNA was treated with RNase free DNAse I (NEB) and subsequently purified using NucleoSpin RNA clean-up kit (Macherey-Nagel, Germany). Quality and quantity of purified RNA was confirmed by reading absorption at 260nm, 230nm and 280nm at nano-spectrophotometer (Eppendorf). Ratio of 1.8–2.0 for A260:A280 and 2.0–2.3 for A260:A230 confirmed the high quality of RNA. Integrity of purified RNA was verified on MOPS buffer (Sigma, USA) RNA denaturing gel. cDNA was prepared from 1μg purified RNA in a 20μl reaction volume using high-capacity cDNA Archive kit (Applied Biosystems, USA) according to manufacturer’s instruction.
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