Bead ruptor 4

Manufactured by Omni International

Sourced in United States

The Bead Ruptor 4 is a high-speed tissue homogenizer designed for efficient sample disruption. It utilizes oscillating bead motion to mechanically break down samples, facilitating the extraction of cellular contents for various analytical applications.

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Lab products found in correlation

Qiaseq mirna library kit, by Qiagen (1 mentions) Qiazol, by Qiagen (1 mentions) Mirneasy mini kit, by Qiagen (1 mentions) Qiazol, by Omni International (1 mentions) Fd8512, by IlShinBioBase (1 mentions) 2.8 mm ceramic beads, by Omni International (1 mentions) Bradford assay, by Thermo Fisher Scientific (1 mentions) Dnase 1, by Thermo Fisher Scientific (1 mentions) Anti flag monoclonal antibody, by Merck Group (1 mentions) Protein g sepharose, by Merck Group (1 mentions) Bioanalyzer, by Agilent Technologies (1 mentions) Qiaamp viral rna mini kit, by Qiagen (1 mentions) Rneasy plus mini kit, by Qiagen (1 mentions) Gsh gssg ratio detection assay kit, by Abcam (1 mentions) Vacuum rotator, by Eppendorf (1 mentions)

Spelling variants of this product

Bead Ruptor (36 citations) Bead Ruptor 4 Homogenizer (2 citations)

10 protocols using bead ruptor 4

Isolation and Sequencing of miRNA

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PrE and PrS cells were cultured to 70% confluency, conditioned media was collected and EVs were isolated by differential ultracentrifugation, as described above. PrE and PrS cells were lysed, and RNA was collected using QIAzol (Qiagen, Germany). Tissue slices were homogenized in QIAzol using the BeadRuptor 4 (OMNI International, Bedford, NH). RNA was isolated from all intracellular samples with the miRNeasy Mini Kit (Qiagen, Germany) and from EVs using the Serum/Plasma miRNeasy Kit (Qiagen, Germany). MiR quantification from all samples was completed with microRNA Qubit (Thermo Fisher Scientific, Waltham, MA).
MiR libraries were generated from 100 to 150 ng of cell using the QIAseq miRNA Library Kit according to the protocol (Qiagen, Germany). Library quality control and concentrations were determined using a High Sensitivity D1000 ScreenTape with TapeStation Analysis Software A.02.02 (Agilent Technologies, Santa Clara, CA) Libraries (10 µM) were submitted to the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana‐Champaign, where they were titrated for equal loading using the MiSeq followed by sequencing on a HiSeq 4000 with 100 nucleotide forward single reads.

Zenner M.L., Kirkpatrick B., Leonardo T.R., Schlicht M.J., Saldana A.C., Loitz C., Valyi‐Nagy K., Maienschein‐Cline M., Gann P.H., Abern M, & Nonn L. (2023). Prostate‐derived circulating microRNAs add prognostic value to prostate cancer risk calculators. Journal of Extracellular Biology, 2(11), e122.

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Freeze-Drying and Methanolic Extraction

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All leaves of three plants per treatment were sampled and lyophilized using a freeze dryer (FD8512, Ilshin Biobase Co., Yangju, Korea) at −80 °C under a vacuum of 0.007 mmHg for 120 h. The 50-mg freeze-dried samples were ground and extracted with 1 mL of 70% (v/v) methanol and 2.8-mm ceramic beads using a bead mill homogenizer (Beadruptor 4, Omni International, Kennesaw, GA, USA).

Yoon H.I., Kim H.Y., Kim J., Oh M.M, & Son J.E. (2021). Quantitative Analysis of UV-B Radiation Interception in 3D Plant Structures and Intraindividual Distribution of Phenolic Contents. International Journal of Molecular Sciences, 22(5), 2701.

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Microbial Spike-in for Tissue Samples

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On the day of spiking/DNA extraction, tissue pieces were defrosted on ice, pooled by 6 in a Microbial DNA Free 2-mL tube with 2.8 mm ceramic beads (Omni International, Kennesaw, GA, US) and ground on a Bead Ruptor 4 (Omni International) for 30 s at speed 3. Such obtained homogenates were pooled by two and then divided into 100-mg aliquots, which were spiked with the mock community containing 1.4 × 10⁶ of bacterial cells (3.5 × 10⁵ cells of each species). For that purpose, we used 140 µL of the fresh bacterial pool (Fresh), 154 µL of the glycerol-supplemented fresh bacterial pool (Fresh Gro), 140 µL of the frozen bacterial pool (−80°) and 154 µL of the glycerol-supplemented frozen bacterial pool (−80° Gro), respectively, per tissue homogenate aliquot. Each mock community stored under specified condition (Fresh, Fresh Gro, −80° or −80° Gro) was spiked onto 6 tissue aliquots (24 spiked samples in total).

Lazarevic V., Gaïa N., Girard M., Mauffrey F., Ruppé E, & Schrenzel J. (2022). Effect of bacterial DNA enrichment on detection and quantification of bacteria in an infected tissue model by metagenomic next-generation sequencing. ISME Communications, 2, 122.

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Liver mRNA Extraction Protocol

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Total mRNA was prepared from liver samples using the RNA mini prep kit (Zymos Research, CA, USA) according to the manufacturer’s protocol. Liver tissue samples (~10 mg) were homogenized in 300 μl buffer containing 10 mM HEPES, pH 7.9, 25 mM Tris HCl, pH 8.0, 137 mM NaCl, 10% glycerol, 1 mM EDTA, 1mM PMSF and Roche EasyPack inhibitor cocktail, using a Bead Ruptor 4 (Omni International, GA, USA) (speed 4, 2 × 45 sec, rest 45 sec on ice in between). NP40 was added to the homogenates to a final concentration of 1% and incubated on ice for 10 min, followed by centrifugation at 12,000 × g for 10 min. The clear supernatant was transferred to a clean tube and total protein concentration was measured using the Bradford assay (ThermoFisher, CA, USA). Tissue lysates were aliquoted and stored at −80°C until use.

Collins J.M, & Wang D. (2021). Cytochrome P450 3A4 (CYP3A4) protein quantification using capillary western blot technology and total protein normalization. Journal of pharmacological and toxicological methods, 112, 107117.

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Quantification of Bacterial β-Glucuronidase Activity

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Fecal pellets were homogenized in phosphate-buffered saline (0.01 M, pH 7.0) using a Bead Ruptor 4 (Omni) and then sonicated using a Branson 3510 Water Bath Ultrasonicator. Activity of extracted bacterial GUS was measured by hydrolysis of phenolphthalein glucuronide (Sigma-Aldrich) to free phenolphthalein and quantified by spectrophotometry (39 (link)). GUS activity was calculated as mg of free phenolphthalein liberated/mg protein/hour of incubation.

Taylor M.R., Flannigan K.L., Rahim H., Mohamud A., Lewis I.A., Hirota S.A, & Greenway S.C. (2019). Vancomycin relieves mycophenolate mofetil–induced gastrointestinal toxicity by eliminating gut bacterial β-glucuronidase activity. Science Advances, 5(8), eaax2358.

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Coimmunoprecipitation of Hfq-associated RNAs in V. cholerae

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V. cholerae wild-type (KPS-0014) and hfq::3XFLAG-tagged strains (KPS-0995) were cultivated in LB medium to low (OD₆₀₀ of 0.2) and high cell densities (OD₆₀₀ of 2.0). Cells equivalent to 50 OD₆₀₀ units were collected and subjected to coimmunoprecipitation as described previously (9 (link)), with slight modifications. Briefly, cells were resuspended in lysis buffer (20 mM Tris⋅HCl [pH 8], 150 mM KCl, 1 mM MgCl₂, 1 mM DTT) and disrupted with 0.3-mL glass beads (Roth; 0.1 mm diameter) using a Bead Ruptor 4 (Omni). Cleared lysates were incubated with monoclonal anti-FLAG antibody (Sigma; F1804) and protein G Sepharose (Sigma; P3296). After stringent washing with lysis buffer, RNA and protein fractions were isolated by phenol-chloroform-isopropanol extraction. The RNA was subjected to DNase I (Thermo Fisher Scientific) digestion, and RNA integrity was confirmed using a Bioanalyzer (Agilent). cDNA libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina (NEB; E7300S) according to the manufacturer’s instructions.

Huber M., Fröhlich K.S., Radmer J, & Papenfort K. (2020). Switching fatty acid metabolism by an RNA-controlled feed forward loop. Proceedings of the National Academy of Sciences of the United States of America, 117(14), 8044-8054.

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Viral RNA Extraction from Oropharyngeal Swabs

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Oropharyngeal swabs were taken using fine tip Specimen collection swabs (TYPENEX Medical cat #SW0102) were placed in 500 μL of PBS and stored at −80°C until later use. Viral RNA was then isolated from the swab using the QIAamp Viral RNA Mini kit (Qiagen), as per the manufacturer’s instructions.
All tissues collected for protein extraction, RNA extraction, and TCID50 assay were homogenized using a bead mill homogenizer (Bead Ruptor4, OMNI). Homogenates for protein extraction were centrifuged for 15 min at 13,000 rpm at 4°C, and the proteins in the supernatant were collected and stored at −80°C for further analysis. For RNA extraction, total RNA from the homogenate was extracted using the RNeasy Plus mini kit (Qiagen) according to the manufacturer’s instructions and stored at −80°C until further analysis. For TCID50 assay, the homogenate was centrifuged for 5 min at 1500 g at 4°C, and the supernatant was collected and used for TCID50 assay. The virus titers (50% tissue culture infectious dose [TCID50]/mL) were determined from the supernatant using the Spearman and Karber method.

Onodera Y., Liang J., Li Y., Griffin B., Thanabalasingam T., Lu C., Zhu J., Liu M., Moraes T., Zheng W., Khateeb J., Khang J., Huang Y., Jerkic M., Nakane M., Baker A., Orser B., Chen Y.W., Wirnsberger G., Penninger J.M., Rotstein O.D., Slutsky A.S., Li Y., Mubareka S, & Zhang H. (2023). Inhalation of ACE2 as a therapeutic target on sex-bias differences in SARS-CoV-2 infection and variant of concern. iScience, 26(8), 107470.

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Bacterial Profiling of Murine Organs

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After decapitation euthanasia, the spleen and liver were removed aseptically and 0.5 g of each organ was homogenized in 0.5 mL of sterile PBS (Phosphate buffered saline) by using ceramic beads in Bead Ruptor 4 (Omni International) and 10 µL sample was plated onto blood agar plate and incubated at 37 °C for 48 h. For blood culture, the blood was obtained immediately after decapitation at 14 days of life. 10 µl blood was plated onto blood agar plate and incubated at 37 °C for 48 h. The bacterial load was expressed as the number of CFU per 10 mm of sample for blood and as the number of CFU per gram of organ. Blood agar colonies were enumerated and sub-cultured using nonselective medial (LB broth). The culture was allowed to grow for 24 h and 100 µL of this culture was inoculated again in LB broth. The culture was allowed to grow for a further 24 h followed by centrifugation for processing for 16s rRNA for next generation sequencing.

Niu X., Daniel S., Kumar D., Ding E.Y., Savani R.C., Koh A.Y, & Mirpuri J. (2020). Transient neonatal antibiotic exposure increases susceptibility to late-onset sepsis driven by microbiota-dependent suppression of type 3 innate lymphoid cells. Scientific Reports, 10, 12974.

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Quantifying Reduced Glutathione Levels

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2.4 million cells were incubated with DMSO, IKE, or β-mercaptoethanol (β-ME) at a density of 0.2 million cells/mL for 24 h. Cells were collected and washed with cold PBS once. Cell number was counted by Vi-Cell. Cells were resuspended in ice-cold RIPA buffer (Thermo Fisher Scientific, 89900) with 100 μL/one million cells. Samples were centrifuged for 15 min at 4°C at 17,000 × g. The resulting supernatant was deproteinized using a trichloroacetic acid and sodium bicarbonate solution and kept on ice. The sample was diluted with assay buffer provided in GSH/GSSG Ratio Detection Assay Kit (Abcam, ab13881) ten-fold. Reduced glutathione (GSH) levels were determined using Fluorometric-Green provided in the kit following the manufacture’s protocol. 384-well (Corning) low volume black flat bottom polystyrene non-treated microplates 1230F99 were used.
To perform reduced glutathione measurement in tumor tissue, 10 mg of tumor tissue was mixed with 400 μL RIPA buffer, homogenized at speed 5 for 30 sec using a Bead Ruptor 4 (OMNI International). The sample was centrifuged at 17,000 × g for 5 min, then the above deprotenization and measurement steps performed.

Zhang Y., Tan H., Daniels J.D., Zandkarimi F., Liu H., Brown L.M., Uchida K., O’Connor O.A, & Stockwell B.R. (2019). Imidazole ketone erastin induces ferroptosis and slows tumor growth in a mouse lymphoma model. Cell chemical biology, 26(5), 623-633.e9.

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Extraction and Reconstitution of CCE Additive

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The CCE additive was extracted with hexane: ethanol: acetone (2:1:1) at a raw material to solvent ratio of 1:10 (w/v). Extraction was performed by Bead milling on the Bead Ruptor 4 (Omni International, Kennesaw, GA, USA) using 2.8 mm ceramic beads. After overnight maceration, the resulting extract was centrifuged at 16,000× g at 4 °C for 10 min and filtered using 0.22 μm syringe filter (Millipore PES Membrane, Macherey-Nagel GmbH & Co. KG, Düren, Germany). Afterward, the solvent was evaporated by use of concentrator plus vacuum rotator (Eppendorf, Hamburg, Germany), and then the dried extract was reconstituted with pure dimethylsulfoxide (DMSO) to various concentrations at a 5% final concentration of DMSO.

Mavrommatis A., Zografaki M.E., Marka S., Myrtsi E.D., Giamouri E., Christodoulou C., Evergetis E., Iliopoulos V., Koulocheri S.D., Moschopoulou G., Simitzis P.E., Pappas A.C., Flemetakis E., Koutinas A., Haroutounian S.A, & Tsiplakou E. (2022). Effect of a Carotenoid Extract from Citrus reticulata By-Products on the Immune-Oxidative Status of Broilers. Antioxidants, 11(1), 144.

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