To prepare emulsion samples, 3 % by volume of perfluorooctane (PFO) was introduced into DI water. A coarse PFO emulsion was synthesized by sonicating the sample using a tip sonicator (Digital Sonifier 450, Branson, Danbury, CT, USA) at 30% amplitude for 10 seconds with a 50% duty cycle (0.1 seconds on, 0.1 seconds off for a 5 second total sonication period). The PFO emulsion was loaded into the sample cell and exposed to varying pressures from 0 to 7.2 MPa while simultaneously acquiring USAXS measurements. At each pressure, the sample was exposed to 90 seconds of sonication with simultaneous USAXS data collection.
Digital sonifier 450
Manufactured by Emerson
Sourced in United States
The Digital Sonifier 450 is a laboratory instrument designed for sample preparation and homogenization. It utilizes ultrasonic energy to disrupt cells, emulsify samples, and mix solutions. The device features a digital control interface for adjusting parameters such as amplitude and processing time.
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Lab products found in correlation
Pierce bca protein assay kit, by Merck Group (4 mentions)
Fluo 5n, by AAT Bioquest (2 mentions)
Fluo 5n, by Cytiva (2 mentions)
Microspin g 50 columns, by Cytiva (2 mentions)
Poly d lysine, by Merck Group (2 mentions)
Thermomixer, by Eppendorf (2 mentions)
Sodium chloride (nacl), by Avantor (2 mentions)
Hydrochloric acid (hcl), by Avantor (2 mentions)
Miseq platform, by Illumina (2 mentions)
Meso quickplex sq 120 plate reader, by Mesoscale (2 mentions)
V plex plus mouse cytokine 19 plex elisa kit, by Mesoscale (2 mentions)
96 well plate, by Thermo Fisher Scientific (2 mentions)
Spectramax id5, by Molecular Devices (2 mentions)
Cyquant, by Thermo Fisher Scientific (1 mentions)
Collagenase 1 solution, by Merck Group (1 mentions)
Oil red o, by Merck Group (1 mentions)
Vhx digital microscope, by Keyence (1 mentions)
Oil red o, by Keyence (1 mentions)
Ix81 microscope, by Olympus (1 mentions)
H3k4me3 antibody, by Abcam (1 mentions)
76 protocols using digital sonifier 450
1
Emulsion Synthesis and USAXS Analysis
2
Liquid Metal Powder Preparation Protocol
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Example 2
Liquid Metal Powder (Field's Metal) Preparation Process
To a 150 mL beaker was added 250 mL of deionized water and a magnetic stir bar. The water was heated to 70° C. and stirred at 300 RPM. Next, 20 g of Field's metal (Roto144F from Rotometals, San Leandro, Calif.) was added as small centimeter-sized chunks until the material was molten. Next, 60 g of butylamine was added, and an ultrasonic probe mixer (Branson Digital Sonifier 450) was immersed into the suspension. The material was allowed to disperse, and the sonication was continued for 5 minutes. Finally, the dispersion was quenched by cooling to <60° C. to ‘freeze’ the Field's metal particle size by adding ice to the mixture. Isolation of the Field's metal particles was done by decantation and rinsing with water 4 times. Approximately 15.4 g of particles were recovered and 4.6 g of undispersed Field's metal. Average particle size was 1-30 μm, based on microscope analysis. A photograph of the Field's metal is depicted in
3
Traumatic Optic Neuropathy Induction in Mice
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Traumatic optic neuropathy (TON) was induced in 3-month-old C57BL/6 J mice with a Branson Digital Sonifier 450 (Branson) by a 3mm microtip probe (Branson) in an acoustic soundproof enclosure chamber (Branson). Before the experiment, the mice were anesthetized by inhaling vaporized isoflurane supplied with oxygen in an induction chamber. The fur adjacent to each mouse’s supraorbital rim was removed with a trimmer. The mice were then placed on the stage of a soundproof enclosure equipped with anesthesia mask. During the procedure, the mice were continually supplied with vaporized isoflurane with oxygen. The microtip probe was placed against each animal’s supraorbital rim above the insertion point of the optic nerve into the optic canal– 2mm medial, and 2mm caudal to the vertical mid-pupillary line. The stage was adjusted and raised so that the microtip probe was in direct contact with the supraorbital ridge, and its weight completely supported by the skull. The sonicator was then activated to deliver a 500msec shock at a 35% or 40% amplitude (resulting in a 230–250 micron oscillation according to manufacturers’ specifications). The contralateral eye was used as a control. Following sonication, the animals were removed from the enclosure and placed in a new cage with thermal support until fully recovered.
4
Quantifying Cellular Oil and DNA Content
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DNA content (Cyquant, ThermoFisher Scientific, Waltham, MA, USA) and Oil Red O (Sigma, St. Louis, MO, USA) assays were preformed according to manufacturers’ protocols (n = 3). Cells were imaged using an IX-81 microscope (Olympus, Center Valley, PA, USA). Cells stained with Oil Red O were imaged using a VHX digital microscope (Keyence Corp., Osaka, Japan). For quantitative determination of Oil Red O staining, the stain was extracted using isopropanol and absorbance was measured at 405 nm using ELX-800 absorbance plate reader (Winooski, VT, USA). To measure DNA content, cells were first removed from the scaffolds using a collagenase I solution (Sigma) and then lysed using a Branson Digital Sonifier 450 (Danbury, CT, USA).
5
Epigenetic Profiling of Neonatal Immune Cells
6
Optimized POS Phagocytosis Assay
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For all experiments, cells were primed with the different treatments for 1 h before the addition of POS. POS particles were sonicated in 500 μL of RPE media containing the different treatments (MFGE8, GAS6) for 5 s at 10% power with BRANSON Digital Sonifier 450 before addition to the cells to prevent aggregation. The composition of RPE media has been described previously (Zhu et al., 2013 (link)). Before seeding, POS were quantified using the Neubauer chamber combined with fluorescence microscopy imaging and CellProfiler analysis. In all phagocytosis experiments, unbound POS were washed away before fixation, at various time points after POS addition, depending on the purpose of the experiment, using PBS containing 1 mM MgCl2 and 0.2 mM CaCl2 (PBS-MC). GraphPad Prism was used for statistical significance calculations as indicated in the figure legend and final graph presentation.
7
Optimized Sonication Protocol
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The Branson Digital Sonifier 450 was equipped with a sonication chamber so that the sonication power from the horn is directed into a water flushable chamber (cup). The sonicator was inverted and the sonication cup is placed on top of the horn of the sonicator. The cup itself is attached to a cooling water supply. Via a three pipe system the water flow can be adjusted so that a constant temperature can be maintained during sonication.
8
Synthesis of Ag2S and Li-doped Ag2S Nanoparticles
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The Ag2S and Li-doped Ag2S NPs were synthesized using a Digital Sonifier 450 ultrasonication from Branson. For the synthesis of Ag2S NPs, Ag(NO)3 was added to a 20 mL vial containing 10 mL of DDT. The solution was treated by ultrasound irradiation for 10 min in an air atmosphere. The resulting suspension was centrifuged with ethyl acetate several times to remove any by-products and dried in an electric oven at 80 ℃. The Li-doped Ag2S NPs were synthesized with the same method upon the addition of the appropriate amount of lithium to the reaction bottle.
9
Chromatin Immunoprecipitation of Myc-tagged Proteins
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Yeast strains were grown to log phase (OD600 ≈ 1.8), and one-half of the culture was treated with CPZ at a final concentration of 500 μM for 1 h. ChIP was performed on both treated and untreated cells as previously described (Muddukrishna et al, 2017 (link)), with the exception of the sonication conditions (Branson Digital Sonifier 450, 3 mm tapered microtip, 20% amplitude, 20 s pulse/55 s pause/15× cycles). For each IP, anti-Myc (MS127P; Thermo Fisher Scientific) or anti-IgG (209-005-082; Jackson ImmunoResearch) antibodies were precoupled to protein A-Sepharose beads. qPCR was performed as previously described (Muddukrishna et al, 2017 (link)).
10
Purification of GST-tagged Kinase Protein
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The plasmid pGEX-4T-1-GST-KIN-EC-ter was transformed into E. coli strain BL21. Bacteria grown in 1-l lysogeny broth (LB) with 100-µg/ml ampicillin were induced with 1-mM isopropyl-β-d -thio-galactoside (IPTG) for 2.5–4 h at 37°C. Bacteria were centrifuged (4000 × g for 20 min at 4°C) and resuspended in cold lysis buffer (50-mM Tris, pH 8, 50-mM NaCl, 5-mM EDTA, 0.2% Triton-X 100, 1-mM β-mercaptoethanol, 150-μM PMSF, and 1-μg/ml final volume each of leupeptin, pepstatin, and chymostatin (LPC) protease inhibitor mix). Cells were lysed on ice using a Branson Digital Sonifier 450 (at level 6 for 1 min [10-s on, 10-s off, × 3] + 30 min rest, × 3–4 cycles). Cell lysate supernatant was loaded on a Glutathione Sepharose 4B column (GE Healthcare). The column was washed with TBS (20-mM Tris, pH 7.5, 150-mM NaCl) with 5-mM EDTA, 0.1% Triton-X 100, 1-mM β-mercaptoethanol, 150-μM PMSF, and LPC. Washed bound protein was then eluted with elution buffer, 50-mM Tris pH 8.0, plus 10-mM reduced glutathione, into 10 fractions. The column fraction with the greatest protein concentration were then subjected to gel-filtration chromatography on a Superdex 75 column equilibrated with 50-mM Tris, pH 8.0, plus 150-mM NaCl. Fractions containing GST-KIN-E were collected and stored at −80˚C.
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