Leaf samples (from each of the 5 grape species) were collected from the repository of the agronomic school SupAgro at Montpellier, France (Mediterranean). 18–20 fully developed asymptomatic leaves were randomly sampled from 3–4 plants of each grape species in the Spring season (mid of May 2017 and 2018, before fungicide spraying) to make three replicates. The sample washing procedure was adopted by our previously published protocol12 (link) and was performed with isotonic sodium chloride solution (0.15 M) with 0.01% Tween 20 in 50 ml propylene tubes using a horizontal shaker at 100 RPM for 1hr10 (link). To maximize the microbial recovery from the leaf surface, samples were given an ultrasonic bath for 7–10 minute using Ultrasonic Cleaner (Branson 5510). Afterward, the remaining solution was centrifuged at 4,000 g and microbial pellets were transferred in 2-ml Eppendorf tubes and stored at −20 °C. DNA was extracted from each sample using the ZymoBiomics DNA MicroPrep Kit (Zymo Research, USA).
Ultrasonic cleaner
Manufactured by Emerson
Sourced in United States
The Emerson Ultrasonic Cleaner is a device designed to clean various items using high-frequency sound waves. It generates ultrasonic vibrations that agitate the liquid solution, effectively removing contaminants from the objects placed inside.
Automatically generated - may contain errors
Lab products found in correlation
Zymobiomics dna microprep kit, by Zymo Research (1 mentions)
Prominence column oven, by Shimadzu (1 mentions)
Cto 20a column oven, by Shimadzu (1 mentions)
Speedvac high capacity concentrator, by Thermo Fisher Scientific (1 mentions)
Refrigerated vapor trap, by Thermo Fisher Scientific (1 mentions)
Dimethyl sulphoxide, by Merck Group (1 mentions)
Cremophor, by Merck Group (1 mentions)
Balance 0.01 g, by Sartorius (1 mentions)
Tsq quantum gc, by Thermo Fisher Scientific (1 mentions)
Chloral hydrate, by Merck Group (1 mentions)
Analytical balance, by Ohaus (1 mentions)
Nano2, by Merck Group (1 mentions)
Alcl3, by Merck Group (1 mentions)
Ch3co2k, by Merck Group (1 mentions)
Quercetin, by Merck Group (1 mentions)
Ethanol 96, by Merck Group (1 mentions)
Hydrochloric acid (hcl), by Merck Group (1 mentions)
Sodium hydroxide (naoh), by Merck Group (1 mentions)
H2so4, by Merck Group (1 mentions)
Chloroform, by Mallinckrodt (1 mentions)
19 protocols using ultrasonic cleaner
1
Grape Leaf Microbiome Sampling Protocol
2
Ultrasound-Assisted Tissue Decellularization
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Example 3
Ultrasound was used to aid in the process of decellularization and partial lipid removal. The first method involved treatment of tissue before decellularization in sodium deoxycholate solution. The tissue was exposed to high ultrasonic energy for 30 seconds (−95 Watts per square inch). Ultrasound-treated tissue was then decellularized in 1% (w/v) sodium deoxycholate solution.
The second method involved decellularization of tissue material in a lower energy ultrasonic water bath (Bransonic ultrasonic cleaner, 44 kilohertz, −1.0 Watt per square inch) for up to 8 hours. Porcine dermal tissue was decellularized in two different solutions: (a) 1% sodium deoxycholate +0.5% Triton X-100 in 10 mM HEPES buffer (pH 8.0) and (b) 1% sodium dodecyl sulfate 10 mM HEPES buffer (pH 8.0).
3
HPLC-MS/MS Analysis of Samples
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A Thermo Scientific Savant Speedvac high capacity concentrator in combination with a Thermo Scientific Savant Refrigerated Vapor Trap was used for evaporation under vacuum of the samples during sample pretreatment. An ultrasonic cleaner from Branson was used for reconstitution and homogenization of the residue.
The HPLC-MS/MS system consisted of an Ultimate 3000 autosampler and pump with inline degasser, all of Dionex (Sunnyvale, CA, USA), connected to a degasser from LC Packings. The autosampler with a 100 μL sample loop was coupled to an AB Sciex API4000 mass spectrometer (Framingham, MA, USA) via a Shimadzu Prominence Column Oven (type CTO-20A) which was kept at 35 °C. Separation was performed with an Agilent column 2.1 × 100mm packed with material of Zorbax Extend 3.5 μm C-18 and kept at 35 °C using a CTO-20A column oven (Shimadzu, Kyoto, Japan). Instrument control and data acquisition was done using Analyst v1.6.2 and DCMS-link v2.12 software (Dionex).
The HPLC-MS/MS system consisted of an Ultimate 3000 autosampler and pump with inline degasser, all of Dionex (Sunnyvale, CA, USA), connected to a degasser from LC Packings. The autosampler with a 100 μL sample loop was coupled to an AB Sciex API4000 mass spectrometer (Framingham, MA, USA) via a Shimadzu Prominence Column Oven (type CTO-20A) which was kept at 35 °C. Separation was performed with an Agilent column 2.1 × 100mm packed with material of Zorbax Extend 3.5 μm C-18 and kept at 35 °C using a CTO-20A column oven (Shimadzu, Kyoto, Japan). Instrument control and data acquisition was done using Analyst v1.6.2 and DCMS-link v2.12 software (Dionex).
4
Sterilization and Callus Formation in Gracilaria lichenoides
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Healthy thalli of G. lichenoides were examined under a microscope, and those with the least contamination of epiphytes were selected and sterilized according to the methodology described by Shen et al39 . Briefly, thalli were washed three times in autoclaved seawater with a writing brush, three times in an ultrasonic cleaner (Branson, Beijing, China) and three times in 0.7% potassium iodide (KI).
The sterilized thalli were cut into short explants (5–7 mm) using a sterile surgical blade and inoculated in a 200-mL culture vessel for liquid media with f/2 medium (21 ± 1 °C, 30 μmol photons m−2 s−1 irradiance, 14-h: 10-h, light-dark cycle), which was replaced every 3 days. The effect of auxins (indole-3-acetic acid, IAA) and NPA (1 and 100 μM, respectively) and their combination on callus formation or AB induction in G. lichenoides explants was determined. A treatment control (without IAA or NPA) was prepared simultaneously. After exposure to the different conditions, the samples were subjected to extraction of RNA.
The sterilized thalli were cut into short explants (5–7 mm) using a sterile surgical blade and inoculated in a 200-mL culture vessel for liquid media with f/2 medium (21 ± 1 °C, 30 μmol photons m−2 s−1 irradiance, 14-h: 10-h, light-dark cycle), which was replaced every 3 days. The effect of auxins (indole-3-acetic acid, IAA) and NPA (1 and 100 μM, respectively) and their combination on callus formation or AB induction in G. lichenoides explants was determined. A treatment control (without IAA or NPA) was prepared simultaneously. After exposure to the different conditions, the samples were subjected to extraction of RNA.
5
Extracting Seagrass Metabolites
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One leaf sample (2nd youngest leaf) was collected monthly at random from each plastic container (three plastic containers for SBV and one for DBW in every aquarium). Epiphytes were removed by gently scraping each leaf with a clean razor blade, followed by a brief rinse in 0.2 μm-filtered seawater. The clean leaves were patted dry with a tissue, flash frozen in liquid nitrogen and stored at −80 °C. Samples collected in May 2014 used for the metabolomics analyses performed here were lyophilized for at least 48 h and powdered using a ball mill. The powdered samples were incubated in methanol/deionized water (4/1 v/v) at 10 °C on an orbital shaker (1 h), followed by gentle sonication for 2 min using a Branson ultrasonic cleaner (40 kHz). The extracts were centrifuged and the supernatants transferred to pre-combusted (450 °C for 8 h) amber glass vials for metabolite analysis. Three solvent-only vials were prepared using only methanol/deionized water (no plant material) processed as above.
6
Measuring Superoxide Dismutase Activity
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Superoxide dismutase activity was estimated by measuring the inhibition of autoxidation of pyrogallol by the enzyme [36] (link). NE treated cells were harvested at different time points and lysed in 20 mM Tris (pH 8.2) using Branson ultrasonic cleaner (US). Total SOD activity in the cell extract was measured in 50 mM Tris, pH 8.2; 100 mM EDTA; 8 mM pyrogallol (prepared in 1 mM HCl) and ~300 µg protein. Autoxidation of pyrogallol was monitored for 5 min at room temperature using a UV–visible spectrophotometer (Ultrospec 21000pro, GE Healthcare Life Sciences, UK) at 420 nm. To calculate SOD activity, percentage of inhibition was determined using the following formula: % inhibition=[(control rate−sample rate)/(control rate)] ⁎100.
7
Powdered MOHE Extraction and Analysis
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Samples were prepared according to the method described by Aliyu et al.25
About 1000 mg of powdered MOHE was dissolved into 1 mL of LC-MS-grade methanol and sonicated for 5 min at 25°C by Bransonic Ultra sonic cleaner (2510E-DTH, USA). The samples were later filtered using N Nylon (NY) 0.45 µm filter paper (Sartorius, Germany) into LCMS vials for further analyses.
About 1000 mg of powdered MOHE was dissolved into 1 mL of LC-MS-grade methanol and sonicated for 5 min at 25°C by Bransonic Ultra sonic cleaner (2510E-DTH, USA). The samples were later filtered using N Nylon (NY) 0.45 µm filter paper (Sartorius, Germany) into LCMS vials for further analyses.
8
Measuring Vaccinia Virus Titers
9
Catalase Activity Measurement Protocol
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Following treatment with 2 and 100 µM NE, cells were washed with ice-cold PBS and lysed in 50 mM potassium phosphate buffer (pH 7.8) using Branson ultrasonic cleaner (USA). The supernatant was then used as the source of catalase and the activity was measured by the method originally described by Beers and Sizer [34] (link). The assay reaction contained 50 mM potassium phosphate buffer (pH 7.8), 30 mM H2O2 and ~300 µg of protein in a total volume of 1.0 ml which measured the removal of hydrogen peroxide at 25 °C in a spectrophotometer (Cary 100 BIO UV Spectrophotometer, Sunnyvale, CA) at 240 nm wavelength. Activity was calculated using the formula described by Weydert and Cullen [35] and it was expressed as mU/mg protein. One unit is the amount of catalase necessary to decompose 1.0 µM of H2O2 per minute at pH 7.8 at 25 °C.
10
Quantification of CIP-HCL in Ocular Inserts
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