Sonicator 3000

Manufactured by Bioventus

Sourced in United States

The Sonicator 3000 is a laboratory instrument designed to generate high-frequency sound waves, which can be used for various applications in scientific research and analysis. The device utilizes piezoelectric transducers to convert electrical energy into mechanical vibrations, enabling the creation of ultrasonic waves. This equipment is commonly used for tasks such as cell disruption, sample homogenization, and nanoparticle dispersion in various fields of study.

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Lab products found in correlation

Chip assay kit, by Merck Group (4 mentions) Pierce bca protein assay kit, by Thermo Fisher Scientific (4 mentions) Mammalian cocktail protease inhibitors, by Merck Group (2 mentions) Protein g coupled magnetic beads, by Merck Group (2 mentions) Polyclonal goat anti human activin a antibody, by R&D Systems (2 mentions) Non reducing lithium dodecyl sulfate sample buffer, by Thermo Fisher Scientific (2 mentions) Ni nta affinity gel, by Qiagen (2 mentions) Ecl prime, by GE Healthcare (2 mentions) Imagequant las 4000, by Fujifilm (2 mentions) Lutrol f68, by BASF (2 mentions) Gst agarose beads, by Merck Group (2 mentions) Chemiluminescent substrate, by Thermo Fisher Scientific (2 mentions) Anti ctb antibody, by Aviva Systems Biology (2 mentions) Goat anti rabbit igg hrp secondary antibody, by Southern Biotech (2 mentions) Silent crusher m, by Heidolph (2 mentions) Fluorescein or dark red alexafluor647, by Thermo Fisher Scientific (2 mentions) Amicon ultra 4 centrifugal filter, by Merck Group (2 mentions) Talon metal affinity resin, by Takara Bio (2 mentions) Isopropyl β d 1 thiogalactopyranoside (iptg), by Merck Group (2 mentions) Optima tlx ultracentrifuge, by Beckman Coulter (2 mentions)

Close spelling variants of this product

Sonicator (21 citations) Misonix sonicator 3000 (11 citations) Ultrasonic Processors Sonicator 3000 (2 citations) Sonicator 3000 Homogenizer (2 citations)

101 protocols using sonicator 3000

Quantifying CTB-ACE2 Levels in Gum Tablets

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The total dose of CTB-ACE2 in the 2 g gum tablet was examined by western blot technique. 100 mg of the crushed gum powder was suspended in 500 μL of plant extraction buffer (PEB) (100 mM NaCl; 10 mM EDTA; 200 mM Tris-HCl, pH 8.0; 0.05% (v/v) Tween-20; 1 x protease inhibitor cocktail (PIC); 0.1% SDS; 14 mM β -Mercapto-ethanol; 400 mM sucrose; and 2 mM Phenyl-methylsulfonyl fluoride (PMSF)) and incubated for 1 h at 4 °C on a vortex. This was followed by sonication for 9 cycles at 80% amplitude for 10s on and 15s off using a sonicator 3000 (Misonix, Farmingdale, NY). Bradford assay for total protein quantitation followed by immunoblot analysis for total CTB-ACE2 dose quantitation were performed following protocols developed by Daniell lab [35 (link)].
For evaluation of the CTB-ACE2 release, 100 mg of the crushed gum tablet was suspended in 500 μL of PEB and incubated for 30 min while vortexing at 4 °C. This was followed by centrifugation at 750g for 5 min at 4 °C. The supernatant fraction was stored on ice until analysis. The remaining pellet fraction was resuspended in PEB and sonicated for 3 cycles at 80% amplitude for 5s on and 10s off using a sonicator 3000 (Misonix, Farmingdale, NY). Bradford assay for total protein quantitation followed by immunoblot analysis for CTB-ACE2 release were performed following protocols developed by Daniell lab [35 (link)].

Daniell H., Nair S.K., Guan H., Guo Y., Kulchar R.J., Torres M.D., Shahed-Al-Mahmud M., Wakade G., Liu Y.M., Marques A.D., Graham-Wooten J., Zhou W., Wang P., Molugu S.K., de Araujo W.R., de la Fuente-Nunez C., Ma C., Short W.R., Tebas P., Margulies K.B., Bushman F.D., Mante F.K., Ricciardi R.P., Collman R.G, & Wolff M.S. (2022). Debulking different Corona (SARS-CoV-2 delta, omicron, OC43) and Influenza (H1N1, H3N2) virus strains by plant viral trap proteins in chewing gums to decrease infection and transmission. Biomaterials, 288, 121671.

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Synthesis of Sonogel-Carbon Electrodes

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Sonogel–carbon was synthesized by mixing 500 µL of trimethoxymethylsilane and 100 µL of HCl 0.2 M, as reported in [18 (link)]. The mixture was homogenized using a high-power ultrasound generator, Sonicator 3000, from Misonix (Misonix, Inc., Farmingdale, NY, USA) (equipped with a 13 mm titanium tip), which provides a maximum power of 600 W. In this case, the energy applied was between 90 and 100 joules. After sonication, 0.5 g of graphite powder was added to the mixture and well homogenized. Then the SNGCEs were prepared by inserting the material obtained into glass capillary tubes (internal diameter of 1.15 and external diameter of 1.55 mm) and connecting the ceramic material to a copper wire for electric contact.

Takele A., Palacios-Santander J.M, & Palma M. (2022). A New Electrochemical Method to Determine Tryptophan in Fruit Juices: Development and Validation. Foods, 11(14), 2149.

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Activin A Immunoprecipitation from Leukocytes

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Eosinophil or neutrophil cell pellets (from 15 million cells) were lysed in buffer containing 10mM Tris HCl (pH 7.48), 0.1 mM NaCl, 1mM EDTA, 1mM EGTA, 1mM NaF, 14mM Na₄P₂O₇, 2mM Na₃VO₄, 0.1% Triton X-100, 0.1% SDS, mammalian cocktail protease inhibitors (Sigma-Aldrich Corp, St. Louis, MO, USA) and 1mM PMSF.^{46 (link)} The suspension was sonicated five times with 5 second pulses (output setting 0.5, Sonicator 3000, Misonix, Farmingdale, NY, USA), repeatedly passed through a syringe (28 gauge needle), and clarified by centrifugation (12 000 x g/10 min/4 °C). The lysate was incubated at 4°C for 24–30 h with protein G-coupled magnetic beads (EMD Millipore Corp, Billerica, MA, USA) coated with polyclonal goat anti-human activin A antibody (R&D Systems). The beads were collected with a magnet and resuspended in 20 μl of non-reducing lithium dodecyl sulfate sample buffer (Thermo Fisher Scientific, Grand Island, NY, USA). Samples were heated to 90°C for 5 min and loaded onto a 13.5 % SDS-PAGE gel.

Kelly E.A., Esnault S., Johnson S.H., Liu L.Y., Malter J.S., Burnham M.E, & Jarjour N.N. (2016). Human eosinophil activin A synthesis and mRNA stabilization are induced by the combination of IL-3 plus TNF. Immunology and cell biology, 94(7), 701-708.

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Fecal Metabolite Extraction for Metabolomic Analysis

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Fresh fecal samples were taken from all participants for metabolites extraction. Metabolites extraction was performed by adding 1.2 ml of cold (-80°C) high performance liquid chromatography (HPLC)-grade methanol to fecal samples. Samples were vortex-mixed followed by sonicated for 30 s (Sonicator^® 3000; Misonix) on liquid nitrogen. This protocol was repeated five times with a 60-min storage period at -80°C between each cycle. The final pellet was removed by centrifugation at 16,000 rpm for 10 min at 4°C, and the supernatant was stored at -80°C. The methanolic extract was centrifuged at 13,000 rpm for 20 min at 4°C to precipitate any solid impurity. The supernatant was analyzed by high-performance liquid phase chromatography and gas chromatography coupled with tandem mass spectrometry (HPLC-GC/MS-MS, Metabolon, Inc., Durham, NC, USA) as described previously (Sha et al., 2010 (link)).

Wei X., Jiang S., Zhao X., Li H., Lin W., Li B., Lu J., Sun Y, & Yuan J. (2016). Community-Metabolome Correlations of Gut Microbiota from Child-Turcotte-Pugh of A and B Patients. Frontiers in Microbiology, 7, 1856.

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Immobilizing Hexafluoroisopropanol Selector on SWCNTs

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This process immobilized a hexafluoroisopropanol group-containing chemoselective compound (selector), which has been shown to bind the target analyte DEEP^{4 (link)}, to semiconducting SWCNTs. A small sheet (15 mm × 15 mm) of semiconducting SWCNTs (IsoNanotubes-S. NanoIntegris Technologies, Inc., Boisbriand, Quebec, Canada) was immersed in dimethylformamide (DMF) and then sonicated slightly (10 seconds at power level 10) with a probe sonicator (Sonicator 3000, Misonix, Farmingdale, NY, USA). After a short centrifugation (4, 500 × g, 1 min) (5804R centrifuge, Eppendorf North America, Hauppauge, NY, USA), the resulting SWCNT particle suspension was incubated with a 5 mg/ml DMF-based solution of 2-(2-hydroxy-1, 1, 1, 3, 3, 3-hexafluoropropyl)-1-naphthol (Synquest Laboratories, Inc., Alachua, FL, USA) for 2 hours in an incubator shaker (25 °C, 90 rpm). After a centrifugation (4,500 × g, 5 min) to remove the unbound selector, the resulting SWCNT pellets were washed 3 times with DMF with a centrifugation (4,500 × g, 5 min) between each wash, and re-suspended in DMF. The suspension was further sonicated with the probe sonicator until a homogeneous DMF-based solution of SWCNT-selector complexes was obtained.

Fang Y., Akbari M., Hester J.G., Sydänheimo L., Ukkonen L, & Tentzeris M.M. (2017). Sensitivity enhancement of flexible gas sensors via conversion of inkjet-printed silver electrodes into porous gold counterparts. Scientific Reports, 7, 8988.

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Purification of His-tagged Nitrogenase Proteins

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His-tagged NITs in pET-21b(+) (Novagen) were expressed at 37 °C in E. coli BL21-CodonPlus (DE3)-RIL (Agilent Technologies) for 4 h in LB containing 100 μg ml⁻¹ ampicillin and 1 mM IPTG. The cells were pelleted at 4 °C and resuspended in 50 mM Tris–Hcl pH 8.0, 100 mM NaCl with cOmplete^TM protease inhibitor (Roche) and sonicated on ice for 4 min (at 15 s intervals) (Sonicator^® 3000, Misonix). The clarified supernatant was loaded onto a Ni²⁺-NTA-agarose (Qiagen) column and washed with 50 mM Tris–Hcl pH 8.0, 500 mM NaCl, 20 mM imidazole and eluted over a gradient up to 500 mM imidazole. The NIT-containing peak was pooled and loaded onto a TSKgel PWXL4000 HPLC size exclusion column (Tosoh Corp), equilibrated with 50 mM Tris–Hcl pH 8.0, 100 mM NaCl and the leading edge of the NIT-containing peak was collected. Cryo-EM grids were immediately prepared using this material and aliquots destined for long-term storage were flash frozen in liquid nitrogen and stored at −80 °C after addition of 1 mM DTT. Activity assays were performed after buffer exchange into 50 mM potassium phosphate pH 8.0, 1 mM DTT.

Mulelu A.E., Kirykowicz A.M, & Woodward J.D. (2019). Cryo-EM and directed evolution reveal how Arabidopsis nitrilase specificity is influenced by its quaternary structure. Communications Biology, 2, 260.

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Purification of PorX-c-His6 Protein from E. coli

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E. coli BL21-Gold (DE3) harboring plasmid pYS15493 (pET15b-porX-His₆) was grown in 500 ml of LB medium by shaking at 37 °C to OD_{600 nm} 0.5; then IPTG was added to a final concentration of 0.4 mM, and bacterial cells were cultured for another 2 h. Bacterial cells were harvested by centrifuging at 10,000g for 15 min and washed with 50 ml of PBS once, suspended in 10 ml of PBS, and opened by sonication (Misonix Sonicator 3000). The cell lysate was used for purification of the PorX-c-His₆ protein with a Ni-NTA Affinity Gel (QIAGEN) by following the instructions from the manufacturer. The purity and concentrations of protein samples were tested using Silver Staining Kit (Pierce) and BCA Protein Assay Kit (Pierce) by following the instructions from the manufacturer.

Yang D., Jiang C., Ning B., Kong W, & Shi Y. (2021). The PorX/PorY system is a virulence factor of Porphyromonas gingivalis and mediates the activation of the type IX secretion system. The Journal of Biological Chemistry, 296, 100574.

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Isolation of S. coelicolor Membrane Fractions

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S. coelicolor membrane fractions were isolated as previously described [7, 8, 25 (link)]. Briefly, mycelium from Streptomyces liquid cultures were grown at 30 °C in Difco nutrient broth (DNB) for 48 h, centrifuged (2 min, 3500 g), washed (20 mM Tris-HCl pH 8, 4 °C) and stored at −80 °C. Mycelial pellets were resuspended in two volumes of lysis buffer (20 mM Tris-HCl pH 8, 4 mM MgCl₂, 4 mM DTT containing a protease inhibitor tablet (Roche)). Mycelium was lysed by sonication using a Sonicator 3000 (Misonix) (10 cycles of 30 s pulse and 60 s cooling). Debris was removed by centrifugation (30 min, 5525 g followed by 30 min at 13 500 g, 4 °C). Membranes were finally pelleted by ultracentrifugation (1 h at 100 000 g, 4 °C) The membrane pellet was resuspended in 20 mM Tris-HCl pH 8 to yield the membrane fraction while the supernatant constituted the soluble fraction.

Holman N.D., Wilkinson A.J, & Smith M.C. (2021). Alanine-scanning mutagenesis of protein mannosyl-transferase from Streptomyces coelicolor reveals strong activity-stability correlation. Microbiology, 167(10), 001103.

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ChIP-qPCR for SOX2 Occupancy

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Chromatin immunoprecipitation was performed according to the protocols of chromatin immunoprecipitation (ChIP) Assay Kit (Cat No.16-157; EMD Millipore, NY, USA). Briefly, 1% formaldehyde cross‐linked 1.0 × 10⁶ HIOEC cells were collected and suspended in lysis buffer, and the cross‐linked DNA were sonicated into 200–1 000 bp fragments using Sonicator 3000 (Misonix, Farmingdale, NY, USA). Chromatin immunoprecipitation was performed using 60 μL of Protein A agarose and 4 μL of anti-SOX2 (Cat No. sc−365964, SantaCruz) or IgG (Abclonal). Immunoprecipitated DNA were then purified by treatment with RNase A, proteinase K, and multiple extractions with phenol/chloroform/isoamyl alcohol. Purified DNA was used as a template for qPCR analysis, The primer sequences for enhancer with rs560789 were: forward, 5′-CTGGCTTGCACTGGTTCTCT-3′ and reverse, 5′-GCTATGCGTGGAGTTGTCCT-3′; for Offtarget (chr10:17276056-17276160, located in VIMENTIN locus): forward, 5′-ATTGTGTTTGCCACCACAGC-3′ and reverse, 5′-CCTGGGCAGTAGAGCAAGAC-3′.

Xiao Y., Jiao S., He M., Lin D., Zuo H., Han J., Sun Y., Cao G., Chen Z, & Liu H. (2022). Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants. International Journal of Oral Science, 14, 43.

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BaP Metabolism in Mouse Liver Microsomes

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C57BL/6 mice were i.p. injected with 200 mg/kg body weight BaP. After 20 h, mice were sacrificed and the liver was isolated, transferred in ice-cold microsome buffer (25 mM Sucrose, 1 mM EDTA, 1 mM NADPH; 1:5, w/v) and homogenized for 3 min at 4 °C at maximum power (Ultra-Turrax^®, IKA^®-Werke). Unsolved compartments were spun down (12,000× g, 20 min, 4 °C) and the supernatant was transferred into a fresh vial; 100 µL BaP stock solution (10 mg/mL) was added to 5 mL supernatant (final conc. [0.2 mg/mL) and incubated at 37 °C on a conventional shaking incubator at 220 rpm (Innova40, New Brunswick Scientific, Edison, NJ, USA). After 2, 4, 6 and 8 h, 1 mL sample per reaction was harvested, aliquoted into two Eppendorf vials and shock-frozen in liquid nitrogen. Microsome fraction was released by 3 freeze/thaw cycles and subsequent sonication 5 times for 3 s on ice at half-maximum power (Sonicator 3000, Misonix, Farmingdale, NY, USA). Then, the sample was added to 1.5 parts (v/v) ethyl acetate, mixed and spun down (9300× g, 1 min, 4 °C). The organic phase was harvested using a Hamilton microliter syringe and transferred into a GC glass vial. After removing ethyl acetate using a vacuum centrifuge, BaP metabolites were dissolved in DMSO at a final concentration of 5 µg/mL.

Fueldner C., Riemschneider S., Haupt J., Jungnickel H., Schulze F., Zoldan K., Esser C., Hauschildt S., Knauer J., Luch A., Kalkhof S, & Lehmann J. (2022). Aryl Hydrocarbon Receptor Activation by Benzo[a]pyrene Prevents Development of Septic Shock and Fatal Outcome in a Mouse Model of Systemic Salmonella enterica Infection. Cells, 11(4), 737.

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