Ultrasonic processor

Manufactured by Qsonica

The Ultrasonic Processor is a versatile laboratory equipment used for a variety of applications. It generates high-frequency sound waves to disrupt and homogenize samples, including liquids, suspensions, and emulsions.

Automatically generated - may contain errors

Lab products found in correlation

X series 2 icp ms unit, by Thermo Fisher Scientific (2 mentions) Size exclusion column, by GE Healthcare (2 mentions) Kta pure system, by GE Healthcare (2 mentions) Nanodrop 1000 uv vis spectrometer, by Thermo Fisher Scientific (2 mentions) Histrap column, by GE Healthcare (2 mentions) Speedvac vacuum, by Thermo Fisher Scientific (1 mentions) Speedvac vacuum concentrator, by Thermo Fisher Scientific (1 mentions)

9 protocols using ultrasonic processor

Quantification of Cellular Rhodium and Platinum

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Example 12

HCT116O cells (1.0×10⁶) were seeded in 6-well plates containing 3 ml media and allowed 24 hours to adhere. The cells were treated with 2 μM of RhPt, Rh(Amal), Pt(Amal), cisplatin, or oxaliplatin and incubated for periods of 1, 3, 6, 12, or 24 hours. After the incubation period, the media was decanted and the wells were washed with 4×5 ml PBS. The cells were lysed with 1 ml of a 1% sodium dodecyl sulfate (SDS) solution and sonicated using a Qsonica Ultrasonic processor for 20 s at 20% amplitude. A 750 μl aliquot was diluted with 750 μl of a 2% HNO₃(v/v) solution and analyzed for rhodium and platinum content on a Thermo X Series II ICP-MS unit. ICP-MS measurements for platinum content were measured only for the three most abundant naturally occurring isotopes, ¹⁹⁴Pt (33%), ¹⁹⁵Pt (34%), and ¹⁹⁶Pt (25%). The remainder of the cell lysate was analyzed for protein content via a bicinchoninic assay (BCA), as described in Smith et al., Anal. Biochem. 1985, 150, 76-85, the entire contents of which are herein incorporated by reference. Rhodium and platinum counts were normalized to protein content to obtain ng [Rh/Pt]/mg [protein], and standard errors were calculated from three replicates.

US09969858B2. Metalloinsertor conjugates (2018-05-15). CALIFORNIA INSTITUTE OF TECHNOLOGY [US]. Inventors: Alyson Weidmann [US], Jacqueline K. Barton [US].

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LSD1 chromatin immunoprecipitation in Jurkat cells

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Half-ChIP assays were performed according to the manufacturer's instructions (Upstate Biotechnology, Millipore) and as previously described for Jurkat T cells (27 (link)). Fixation was performed as detailed, and fixed chromatin was sonicated with an Ultrasonic processor (Qsonica, Newtown, CT) under optimized conditions to produce average DNA fragments of approximately 500 bp. Prior to antibody addition, samples were pre-cleared with salmon sperm DNA-protein A-agarose, and the soluble chromatin fraction was incubated overnight at 4°C with a primary antibody to LSD1p (ABE1462) and Protein A magnetic beads. The beads were washed and incubated with immunoblot loading buffer containing beta-mercaptoethanol at 95°C and analyzed as above (immunoblot analysis) with a primary EOMES antibody (AB23345).

Tu W.J., McCuaig R.D., Tan A.H., Hardy K., Seddiki N., Ali S., Dahlstrom J.E., Bean E.G., Dunn J., Forwood J., Tsimbalyuk S., Smith K., Yip D., Malik L., Prasanna T., Milburn P, & Rao S. (2020). Targeting Nuclear LSD1 to Reprogram Cancer Cells and Reinvigorate Exhausted T Cells via a Novel LSD1-EOMES Switch. Frontiers in Immunology, 11, 1228.

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Rhodium Compound Uptake in Colorectal Cells

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HCT116O cells were
plated at 1 × 10⁶ cells/well in a 6-well plate. The
cells were allowed 24 h to adhere, then treated with 10 μM [Rh(HDPA)₂(chrysi)]Cl₃, 5 μM [Rh(chrysi)(phen)(DPE)]Cl₂, 1 μM [Rh(chrysi)(phen)(PPE)]Cl₂, or 0.5
μM [Rh(chrysi)(phen)(PPO)]Cl₂. After 24 h, the media
was decanted, the cell monolayer washed with 3 mL PBS, and the cells
lysed with 800 μL of 1% SDS. The cell lysate was sonicated on
a Qsonica Ultrasonic processor for 10 s at 20% amplitude. 750 μL
of the lysate was then combined with 750 μL of a 2% HNO₃ (v/v) solution, while the remainder of the lysate was quantified
for protein by a bicinchoninic assay (BCA).^{26 (link)} The 1% HNO₃ solution was analyzed for rhodium content
on a Thermo X Series II ICP-MS unit. Rhodium counts were normalized
to the amount of protein determined from the BCA analysis (to obtain
ng [Rhodium]/mg [protein] values). Standard errors for three independent
experiments are shown. The experiment was repeated with HCT116N cells
to verify similar uptake of rhodium by the two cell lines.

Komor A.C, & Barton J.K. (2014). An Unusual Ligand Coordination Gives Rise to a New Family of Rhodium Metalloinsertors with Improved Selectivity and Potency. Journal of the American Chemical Society, 136(40), 14160-14172.

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Recombinant Protein Purification Protocol

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Protein expression was induced by adding 1 mM β-d-1-thiogalactopyranoside (IPTG) at an OD600 of 0.8. Cell pellets were resuspended in 20 mL lysis buffer, followed by sonication (QSONICA Ultrasonic Processor; 12 min, 50% amplitude, 1 s on/off) for cell lysis. Centrifugation at 12 000 rpm for 45 min at 4 °C (Sorvall LYNX 6000) and filtration (0.45 μm cellulose acetate syringe filters) was used to clear the lysates. 5 mL HisTrap columns (GE Healthcare, Vienna, Austria) for immobilized metal affinity chromatography on an ÄKTA pure system (GE Healthcare, Vienna, Austria) were used to purify the proteins. HisTrap columns were equilibrated using lysis buffer. Cleared E. coli lysates were applied to the columns at a flow rate of 2 mL min⁻¹ and contaminants were removed using washing buffer. Finally, proteins were eluted with purification buffer. Proteins were further purified at room temperature using size exclusion columns (10/300 200 pg, GE Healthcare) on an ÄKTA pure system (GE Healthcare) with SEC buffer. Finally, protein concentration was calculated using absorbance at 280 nm, determined by NanoDrop 1000 UV/vis spectrometer (Thermo Fisher Scientific, Vienna, Austria).

Burgstaller S., Bischof H., Gensch T., Stryeck S., Gottschalk B., Ramadani-Muja J., Eroglu E., Rost R., Balfanz S., Baumann A., Waldeck-Weiermair M., Hay J.C., Madl T., Graier W.F, & Malli R. (2019). pH-Lemon, a Fluorescent Protein-Based pH Reporter for Acidic Compartments. ACS Sensors, 4(4), 883-891.

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Metabolite Extraction and Purification

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To extract metabolites from samples, 1 ml of methanol was added to the dried materials for all the samples of metabolomic analysis. Additionally, 1.5 μl of 20 μM sphinganine-d7 (Avanti Lipids, Alabaster, AL) was added to samples for targeted metabolomics as an internal standard. Samples were sonicated for 3 min with on/off cycles of three seconds on and two seconds off at 100% power on a Qsonica’s Ultrasonic Processor with the Cup Horn water bath attachment maintained at 20°C. The samples were then placed on an end-over-end rotator for overnight extraction. Samples were then centrifuged at 18,000 g at 4°C for 30 min. The clarified supernatant was collected and transferred to a fresh 1.7 ml centrifuge tube, dried using a SpeedVac vacuum concentrator (Thermo Fisher Scientific, Waltham, MA), and then reconstituted in 200 μl of methanol. Samples were sonicated again and then centrifuged at 18,000 g at 4°C for 30 min. One hundred and fifty microliters of clarified concentrated extracted metabolome was transferred to an HPLC vial utilizing an insert (Thermo Fisher Scientific, Waltham, MA) and stored at 4°C until LC-MS analysis.

Lee M.T., Le H.H., Besler K.R, & Johnson E.L. (2022). Identification and characterization of 3-ketosphinganine reductase activity encoded at the BT_0972 locus in Bacteroides thetaiotaomicron. Journal of Lipid Research, 63(7), 100236.

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ChIP Assay for PKC-θ and SC35

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Half-ChIP assays were performed according to the manufacturer’s instructions (Upstate Biotechnology) and as previously described for Jurkat T cells (31 (link)). Fixation was performed as detailed, and fixed chromatin was sonicated with an Ultrasonic processor (Qsonica) under optimized conditions to produce average DNA fragments of ~500 bp. Prior to antibody addition, samples were pre-cleared with salmon sperm DNA-protein A-agarose, and the soluble chromatin fraction was incubated overnight at 4°C with a primary antibody to PKC-θ and Protein A magnetic beads. The beads were washed and incubated with immunoblot loading buffer containing beta-mercaptoethanol at 95°C and analyzed as above (Immunoblot analysis) with a primary SC35 antibody.

McCuaig R.D., Dunn J., Li J., Masch A., Knaute T., Schutkowski M., Zerweck J, & Rao S. (2015). PKC-Theta is a Novel SC35 Splicing Factor Regulator in Response to T Cell Activation. Frontiers in Immunology, 6, 562.

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Extraction and Concentration of Metabolites

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One millilitre of methanol was added to the dried material and sonicated for 3 min, with on/off cycles of 3 s on, 2 s off, at 100% power on a Qsonica Ultrasonic Processor with the Cup Horn water bath attachment maintained at 20 °C. The samples were then placed on an end-over-end rotator and metabolites were extracted overnight. Samples were then centrifuged at 18,000g at 4 °C for 30 min. The clarified supernatant was collected and transferred to a fresh 1.7 ml centrifuge tube. The collected extracts were evaporated to dryness using a SpeedVac vacuum concentrator (Thermo Fisher Scientific) and reconstituted in 200 µl of methanol. Samples were sonicated again and centrifuged at 18,000g at 4 °C for 30 min. In total, 150 µl of clarified concentrated extracted metabolome was transferred to an HPLC vial utilizing an insert (Thermo Fisher Scientific) and stored at 4 °C until LC–MS analysis.

Le H.H., Lee M.T., Besler K.R., Comrie J.M, & Johnson E.L. (2022). Characterization of interactions of dietary cholesterol with the murine and human gut microbiome. Nature Microbiology, 7(9), 1390-1403.

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Chromatin Immunoprecipitation (ChIP) Protocol

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Half-ChIP assays were performed according to the manufacturer’s instructions (Upstate Biotechnology) and as previously described for Jurkat T cells [32 (link)]. Fixation was performed as detailed, and fixed chromatin was sonicated with an Ultrasonic processor (Qsonica) under optimised conditions to produce average DNA fragments of approximately 500 base pairs (bp). Soluble chromatin fraction was incubated overnight at 4°C with a primary antibody to DUSP4 (sc-17821) and Protein A magnetic beads or a no antibody negative control. The beads were washed and incubated with immunoblot loading buffer containing beta-mercaptoethanol at 95°C and analysed as above (immunoblot analysis) with a primary antibodies targeting p300-1834p (PA5-12735), RNA-Pol-II-serine2 (ab5095), or a RNA-Pol-II-serine5 (ab5131).

Boulding T., Wu F., McCuaig R., Dunn J., Sutton C.R., Hardy K., Tu W., Bullman A., Yip D., Dahlstrom J.E, & Rao S. (2016). Differential Roles for DUSP Family Members in Epithelial-to-Mesenchymal Transition and Cancer Stem Cell Regulation in Breast Cancer. PLoS ONE, 11(2), e0148065.

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Protein Purification by Affinity and Size Exclusion Chromatography

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Protein
expression was induced by adding 1 mM β-d-1-thiogalactopyranoside
(IPTG) at an OD600 of 0.8. Cell pellets were resuspended in 20 mL
lysis buffer, followed by sonication (QSONICA Ultrasonic Processor;
12 min, 50% amplitude, 1 s on/off) for cell lysis. Centrifugation
at 12 000 rpm for 45 min at 4 °C (Sorvall LYNX 6000) and
filtration (0.45 μm cellulose acetate syringe filters) was used
to clear the lysates. 5 mL HisTrap columns (GE Healthcare, Vienna,
Austria) for immobilized metal affinity chromatography on an ÄKTA
pure system (GE Healthcare, Vienna, Austria) were used to purify the
proteins. HisTrap columns were equilibrated using lysis buffer. Cleared E. coli lysates were applied to the columns at a flow rate
of 2 mL min^–1 and contaminants were removed using
washing buffer. Finally, proteins were eluted with purification buffer.
Proteins were further purified at room temperature using size exclusion
columns (10/300 200 pg, GE Healthcare) on an ÄKTA pure system
(GE Healthcare) with SEC buffer. Finally, protein concentration was
calculated using absorbance at 280 nm, determined by NanoDrop 1000
UV/vis spectrometer (Thermo Fisher Scientific, Vienna, Austria).

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