Vibra cell sonicator, by Sonics - Product details - Pubcompare (2025)

Manufactured by Sonics

1

Cell Lysis and Protein Extraction

All procedures were conducted at 4°C. Cells (grown under aerobic, microaerobic or anaerobic conditions) were centrifuged at 5000×g for 10min, washed three times with distilled water and resuspended in 50mL 10mM HEPES, pH 7.4, supplemented with one tablet of protease-inhibitor cocktail (Complete) and 1mM PMSF. Cells were disrupted by sonication using a Sonics VibraCell sonicator (Sonics & materials, Inc., Newtown, CT) 7 × 20s with 20s intervals. To remove unbroken cells the suspension was centrifuged at 10,000×g for 10min and the supernatant was recovered.

Pedroza-Dávila U., Uribe-Alvarez C., Morales-García L., Espinoza-Simón E., Méndez-Romero O., Muhlia-Almazán A., Chiquete-Félix N, & Uribe-Carvajal S. (2020). Metabolism, ATP production and biofilm generation by Staphylococcus epidermidis in either respiratory or fermentative conditions. AMB Express, 10, 31.

2

Fragmentation of Human and Bacterial DNA

HuDNA or bacDNA preparations were purchased or extracted from PBMCs or Escherichia coli (E. Coli) cultures, respectively (as reported [12 (link)]) and were fragmented by sonication. Five milligrams of DNA in a volume of 300 µL were fragmented using the Sonics Vibra Cell sonicator (Sonics & Materials Inc., Newtown, CT, USA), with the following settings: 2, 4, and 10 sonication cycles (30 s on, 30 s off in ice) to obtain DNA fragment sizes between 100 and 1000 bp. The resulting size distribution was controlled by 2% agarose gel electrophoresis.
This digestion was done to mimic the degradation of DNA in an extracellular environment in vivo. Human RNA was extracted from PBMCs and bacterial RNA from E. coli cultures.

Lande R., Mennella A., Palazzo R., Pietraforte I., Stefanantoni K., Iannace N., Butera A., Boirivant M., Pica R., Conrad C., Chizzolini C., Riccieri V, & Frasca L. (2020). Anti-CXCL4 Antibody Reactivity Is Present in Systemic Sclerosis (SSc) and Correlates with the SSc Type I Interferon Signature. International Journal of Molecular Sciences, 21(14), 5102.

3

Preparation and Characterization of Liposomes

Liposomes were prepared as previously described (21 (link)), using six differentsynthetic lipid mixtures: 1) DOPE:DOPG:DOPC, 2) POPE:POPG:POPC, 3) 67% DOPE:DOPG:DOPC+ 33% POPE:POPG:POPC, 4) 33% DOPE:DOPG:DOPC+ 67% POPE:POPG:POP, 5) 67% POPE:POPG:POPC+ 33% DPPE:DPPG:DPPC, and 6) 33% POPE:POPG:POPC+ 67% DPPE:DPPG:DPPC. The lipids (25mg/mL in chloroform) were purchased from Avanti Polar Lipids and mixed in a 2:1:1 (PE/PG/PC) weight ratio. The exceptions are DPPE and DPPG, which were purchased as powder and dissolved in chloroform/methanol/water (65:35:8) and chloroform/methanol (5:1), respectively. The organic solvents (chloroform, mainly) were removed by evaporation with a rotary vaporizer (Rotovapor r-3; BUCHI, Flawil, Switzerland). Lipids were suspended in diethylether, followed by evaporation, and finally rehydrated in assay buffer (100mM KPi (pH 7.0)) to a concentration of 10mg/mL. The liposome solution was homogenized by tip sonication with a Sonics Vibra Cell sonicator (Sonics & Materials, Newton, CT) at 0°C for 30s with 5s pulses and 5s pause between every pulse. The amplitude was set to 100%. Subsequently, the liposomes were snap frozen and thawed at 30°C (65°C for mixtures containing DP lipids) for two times. The prepared liposomes were aliquoted (2mg/0.2mL) and stocked in liquid nitrogen to prevent oxidation.

Gabba M., Frallicciardi J., van ’t Klooster J., Henderson R., Syga Ł., Mans R., van Maris A.J, & Poolman B. (2019). Weak Acid Permeation in Synthetic Lipid Vesicles and Across the Yeast Plasma Membrane. Biophysical Journal, 118(2), 422-434.

4

Preparation of Lipid Vesicles for Biochemical Assays

The lipids were purchased from Avanti Polar Lipids in powder and suspended in chloroform to a concentration of 25 mg/mL. After mixing the solubilized lipids in the desired ratio, a rotary vaporizer (rotavapor r-3 BUCHI, Flawil, Switzerland) was used to remove chloroform by evaporation. Next, the lipids were suspended in diethylether and subjected to a second of evaporation. Finally, the lipids were hydrated in the assay buffer (100 mM KPi, pH 7) and adjusted to a concentration of 10 mg/mL. The lipid solution was homogenized by tip (3.18 mm) sonication with a Sonics Vibra Cell sonicator (Sonics & Materials Inc. Newtown, CT, USA) at 4 °C (ice water) for 4 min with 15 s pulses and 15 s pause between every pulse. Amplitude of the sonicator was set to 100%. The prepared vesicles were stocked at 20 mg/mL in liquid nitrogen to prevent oxidation.

Frallicciardi J., Melcr J., Siginou P., Marrink S.J, & Poolman B. (2022). Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes. Nature Communications, 13, 1605.

5

ChIP Assay for Chromatin Immunoprecipitation

ChIP assays were performed as previously described. Briefly, 1 × 10⁷ to 3 × 10⁷ treated or untreated cells were cross-linked with 1% paraformaldehyde at room temperature for 10 min and quenched by glycine. Cells were sonicated or generate chromatin fragments of 200 to 600 bp with a Sonics Vibra-Cell sonicator (Sonics & Materials) followed by immunoprecipitation with the indicated antibodies. The resulting DNA was analyzed using SYBR Green Mix on the CFX connect Real-Time PCR detection System (Bio-Rad) and normalized to input.

Gao R., Bao J., Yan H., Xie L., Qin W., Ning H., Huang S., Cheng J., Zhi R., Li Z., Tucker B., Chen Y., Zhang K., Wu X., Liu Z., Gao X, & Hu D. (2020). Competition between PAF1 and MLL1/COMPASS confers the opposing function of LEDGF/p75 in HIV latency and proviral reactivation. Science Advances, 6(20), eaaz8411.

6

VPA Dose-Dependent Effects on TBI

Rats received either a single IP VPA injection of 30 mg/kg, 100 mg/kg, 200 mg/kg, or 400 mg/kg or a vehicle (0.9% sterile saline) 30 min after the TBI (n = 3 per group). Ipsilateral frontal cortical segments were obtained 24 h after the VPA or vehicle injection and homogenized. Brain tissue extracts were sonicated (five pulses per second) by using a Sonics Vibra-Cell sonicator (Sonics & Materials, Inc., Newtown, CT, USA) and a 0.4 mm diameter probe. The amount of protein in each sample was determined using a Bradford assay with bovine serum albumin as the standard. Equal amounts of protein were loaded, electrophoresed, and transferred to Immobilon-P membranes (Millipore, Billerica, MA, USA) by using the NOVEX X-Cell II system (Invitrogen, Burlingame, CA, USA). Membranes were then washed and incubated with antibodies at room temperature. A chemiluminescence system was used to detect immunoreactivity.

Tai Y.T., Lee W.Y., Lee F.P., Lin T.J., Shih C.L., Wang J.Y., Chiu W.T, & Hung K.S. (2014). Low Dose of Valproate Improves Motor Function after Traumatic Brain Injury. BioMed Research International, 2014, 980657.

7

DNA Fragmentation by Sonication

HuDNA or bacDNA preparations, purchased or extracted from PBMCs or E. coli cultures, respectively (as above), were fragmented by sonication. Five milligrams of DNA in a volume of 300 µl were fragmented by using the Sonics Vibra Cell sonicator (Sonics & Materials Inc.), with the following settings: 2, 4, and 10 sonication cycles (30 s ON, 30 s OFF in ice) to obtain the DNA fragment size between 100 and 1000 bp. The resulting size distribution was controlled by 2% agarose gel electrophoresis.

Lande R., Lee E.Y., Palazzo R., Marinari B., Pietraforte I., Santos G.S., Mattenberger Y., Spadaro F., Stefanantoni K., Iannace N., Dufour A.M., Falchi M., Bianco M., Botti E., Bianchi L., Alvarez M., Riccieri V., Truchetet M.E., C.L. Wong G., Chizzolini C, & Frasca L. (2019). CXCL4 assembles DNA into liquid crystalline complexes to amplify TLR9-mediated interferon-α production in systemic sclerosis. Nature Communications, 10, 1731.

8

Proteomic Analysis of Organ Tissues

The animals (n = 6 per group) were anesthetized before being sacrificed 7 days after the last injection and the different organs brain, liver and lung were extracted, from each of the 6 animals per group, to be analyzed using proteomic approach. The organs were washed with a 0.9% solution of sodium chloride and immediately soaked in liquid nitrogen before storing them at −80 °C.
From each organ of the 6 rats per group, 100 mg were ground in lysis buffer using Tissue Lyser II at a frequency of 25 Hz for a period of 25 min. Then, additional 30 min of sonication were added using the Sonics Vibracell^® sonicator to lyse well the tissues until a total grinding. The brain, liver and lung tissues were lysed in a lysis buffer (4% SDS, 0.1M DTT in 0.1M Tris-HCl, pH 7.6) at a ratio of 100 mg organ per 1mL lysis buffer. The organs were vortexed and incubated for 5 min at 95 °C before being lysed for 20 s with 1 sec OFF 1 sec ON at 20% amplitude using Sonics Vibracell^® sonicator probe. Then, the lysate was centrifuged at 14,000× g for 10 min at 4 °C to get rid of the cell debris.

Askri D., Cunin V., Ouni S., Béal D., Rachidi W., Sakly M., Amara S., Lehmann S.G, & Sève M. (2019). Effects of Iron Oxide Nanoparticles (γ-Fe2O3) on Liver, Lung and Brain Proteomes following Sub-Acute Intranasal Exposure: A New Toxicological Assessment in Rat Model Using iTRAQ-Based Quantitative Proteomics. International Journal of Molecular Sciences, 20(20), 5186.

9

Assessing mRNA-Upf2 Association in HeLa Cells

To confirm the association between mRNA and Upf2, HeLa cells were collected using a cell scraper and suspended in cold NET-2 buffer [50 mM Tris-HCl (pH 7.4), 300 mM NaCl, 0.05% Igepal-CA630; Sigma-Aldrich]. For nuclear fractions, cells were treated with cNE-PER nuclear and cytoplasmic extraction reagent (Thermo Fisher Scientific, Inc.) and nuclear fractions were collected. Subsequently, nuclear fractions were suspended in cold NET-2 buffer. The samples were sonicated using the Vibra cell sonicator (Sonics & Materials, Inc., Newtown, CT, USA), and the sonicated samples were centrifuged for 15 min at 15,000 × g. The supernatant was treated with anti-Upf2 antiserum and normal rabbit serum as the control. Following an incubation with agitation in a cold room, Protein G-conjugated agarose beads (Invitrogen™; Thermo Fisher Scientific) were added to the samples, and the samples thus obtained were again incubated in a cold room. Following sufficient washing with NET-2 buffer, the beads were resuspended in Laemmli sample buffer (Bio-Rad Laboratories, Inc.) with 2-mercaptoethanol (Sigma-Aldrich). The sample was boiled, and the resultant sample buffer solution was processed for western blotting, which was performed as described above.

TATSUNO T., NAKAMURA Y., MA S., TOMOSUGI N, & ISHIGAKI Y. (2016). Nonsense-mediated mRNA decay factor Upf2 exists in both the nucleoplasm and the cytoplasm. Molecular Medicine Reports, 14(1), 655-660.

10

Aggregation of Fluorescent Aβ42 Fibrils

Fluorescent HiLyte™ Fluor 555 labeled human Aβ₄₂ monomers (Aβ₄₂-555; #60480-01, AnaSpec, CA, USA) were aggregated into insoluble fibrils according to a well-established protocol. Briefly, the synthetic Aβ₄₂ monomers were dissolved in a 10mM NaOH and 10× PBS (#11530486, Thermo Fisher Scientific) solution to a final concentration of 2mg/ml. The Aβ₄₂ samples were incubated on a shaker at 1500rpm, 37°C for 4days. Finally, theresulting Αβ-F were diluted in sterile 1× PBS to the final concentration of 0.5mg/ml and sonicated at 20% amplitude, 1s on/off pulses for 1min (#VCX130, Vibra Cell sonicator, Sonics, CT, USA).

Konstantinidis E., Portal B., Mothes T., Beretta C., Lindskog M, & Erlandsson A. (2023). Intracellular deposits of amyloid-beta influence the ability of human iPSC-derived astrocytes to support neuronal function. Journal of Neuroinflammation, 20, 3.