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13 protocols using fastprep 24 homogeniser

1

E. coli Protein Expression and Conjugation Protocol

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Escherichia coli cultures grown for 16 h were diluted into fresh 2YP media to an OD600 of 0.03. For protein expression and conjugation, after 4 h of growth the media was supplemented with 0.5 mM IPTG and incubated at 28 °C for 24 h. Cultures were pelleted by centrifugation at 4000×g for 10 min 4 °C. At this stage pellets were either lysed for immunoblot or lipid extraction and silver stained as described previously [25 (link), 84 (link)].
Pellets from strains expressing polysaccharide only were resuspended in PBS to OD600 nm of 10 with 1 mg ml-1 lysozyme and benzonase 40 U ml−1 and boiled for 10 min before SDS-PAGE analysis. Conjugate samples were resuspended in 1.5 ml lysis buffer (50 mM NaH2PO4, 0.3 M NaCl and 10 mM imidazole, pH 7.5) with lysozyme and benzonase as above, and lysed using 5 × 40 s bead-beating rounds at 6.5 m/sec using a FastPrep-24 homogeniser (MP Biomedicals, Belgium), before His purification.
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2

Western Blot Analysis of Streptococcus sanguinis Proteins

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Streptococcus sanguinis whole-cell protein extracts were prepared using a FastPrep-24 homogeniser (MP Biomedicals) and quantified as described elsewhere (6 (link)). Separation of the proteins by SDS-PAGE, subsequent blotting to Amersham Hybond ECL membranes (GE Healthcare) and blocking were carried out using standard molecular biology techniques. To detect PilE1 and PilE2, we used previously described (6 (link)) primary rabbit antibodies (1/2000 dilution), an ECL HRP-linked anti-rabbit antibody (GE Healthcare) (1/10 000 dilution), and Amersham ECL Prime (GE Healthcare). To detect His-tagged proteins, we used a commercial HRP-linked anti-6His antibody (Sigma) at 1/10 000 dilution.
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3

ONNV RNA Detection in Mosquitoes

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To analyse for ONNV RNA, the mosquito body parts were thawed at room temperature and homogenised in a FastPrep-24 homogeniser (Mpbiomedicals, USA) at 40 m/s for 20 s. The mosquito’s thorax and abdomen and the combined legs/wings/head samples were tested for ONNV RNA presence through RNA extraction using the QIAamp Viral RNA kit (Qiagen, Valencia, CA, USA) according to manufacturer’s protocol followed by q-RT-PCR. The mosquito saliva was tested for ONNV presence by cytopathogenic effect (CPE) on cell cultures followed by RNA extraction and qPCR. Vero B4 cells with a seeding density of 20,000 cells/well were seeded in a 96-well plate. When the wells had reached confluency, the cells were infected with 20 µl of saliva sample. The inoculated saliva samples were manually monitored for CPE daily for a week, and wells that showed CPE were harvested; RNA was extracted and q-RT-PCR performed. For the qPCR (Fisher Biosystems) we used Biosystems qPCRBIO Probe 1-step Go Lo-ROX kit and the following protocol: 1 cycle at 45 °C for 10 min, 1 cycle at 95 °C for 5 min and 40 cycles at 60 °C using primers targeting the ONNV Envelope genes E1 and E2 [24 (link)]. The specificity and sensitivity are shown elsewhere [24 (link)]. The probe was designed in close proximity to the forward and reverse primer and did not overlap with a primer binding site on the same site [24 (link)].
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4

Protein Expression Analysis in Avian Tissues

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Bursa of Fabricius, spleen and liver were taken from 6 week old birds (n = 2). Tissues were disrupted using lysing matrix D (MP Biomedical, Loughborough Leicester, UK) with lysis buffer (1% NP40/PBS) in a Fastprep 24 homogeniser (MP Biomedical); the lysates were centrifuged at 13,000× g for 5 min to remove any cell debris and DNA. 30 µg of lysate protein was separated in 4-15% SDS-PAGE (Bio-rad, Hertfordshire, UK). After trans-blotting protein onto PVDF membrane (Sigma-Aldrich), the membrane was probed with primary antibodies at 4°C overnight, followed by horse radish peroxidase (HRP)-conjugated secondary antibody for 2 h at room temperature. HRP activity was detected using Enhance Chemiluminescent (ECL) substrate (ThermoFisher).
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5

Isolation and Quantification of Bacterial RNA

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Pre-cultures were inoculated in TSB (1:10) and grown to an OD600 of 0.5. Total RNA was isolated with the High Pure RNA-Isolation Kit (Roche), according to the manufacturer’s instructions for bacterial RNA isolation, with an additional mechanical lysis step. The cell pellet was resuspended in 600 µL Tris-HCl pH 8, transferred to Lysing Matrix B tubes (MP Biomedicals™, Irvine, CA, USA) and homogenised at 5000 rpm 2 × 22 sec using a FastPrep-24 homogeniser (MP Biomedicals™). The RNA was quantified and the quality was assessed (Nanodrop 2000C) before cDNA was generated from total RNA using the First Strand cDNA Synthesis Kit as described by the manufacturer (Thermo Scientific). Quantitative Real Time PCR (RT-qPCR) was performed using the PowerUP SYBR Green Master Mix. DNA gyrase A was used as reference gene. The fold difference in transcription between mutants and WT was calculated using the ΔΔCq method.
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6

Protein Extraction and Immunoblotting Analysis

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Tumors were homogenized using the FastPrep-24 homogeniser (MP Biomedicals, CA, USA) and lysed in 1% (v/v) Triton X-100, 50 mM HEPES (pH 7.4) 150 mM NaCl, 1.5 mM MgCl2, 1 mM EGTA, 100 mM NaF, 10 mM Na4P2O7, 1 mM Na3VO4, 10% (v/v) glycerol, cOmpleteTM, EDTA-free Protease Inhibitor Cocktail and PhosSTOPTM (Roche) at 4 °C. Cells were washed twice in ice cold PBS and lysed in RIPA buffer (50 mM Tris pH 8.0, 150 mM NaCl, 1% TritonX-100, 0.5% sodium deoxycholate, 0.1% SDS) containing cOmpleteTM, EDTA-free Protease Inhibitor Cocktail and PhosSTOPTM (Roche) at 4 °C prior to SDS-PAGE. Proteins were transferred to nitrocellulose and membranes incubated with antibodies to HO-1 (catalogue number 5853; 1:1000), p62 (catalogue number 5114; 1:1000), pErk1/2 (Thr202/Tyr204) (catalogue number 4370; 1:1000), Erk1/2 (catalogue number 4696; 1:1000), pJNK (Thr183/Tyr185) (catalogue number 9251; 1:1000), JNK (catalogue number 9252; 1:1000) (all Cell Signaling, MA, USA) or LC3B (catalogue number L7543; 1:3000; Sigma Aldrich, MO, USA) overnight at 4 °C. Membranes were washed thrice with TBST before incubation with HRP-conjugated secondary antibodies (Cell Signaling, MA, USA1:1000). Washes were repeated in TBST and bound antibodies detected by chemiluminescence using Clarity ECL Substrate (BioRad, Germany) on the BioRad Gel Dox XR+.
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7

Triglyceride Analysis in Drosophila

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For triglyceride analysis, frozen Drosophila were placed in FastPrep tubes containing Lysis Beads and Matrix D (MP Biomedicals) and 350 μl cold PBST (PBS + 0.05% Tween-20) and then homogenised by using a FastPrep-24 homogeniser (MP Biomedicals) for 60 s at 6 m/s. Solutions were centrifuged (16,100 rcf, 4 °C, 3 min) to pellet debris, and 300 μl of supernatant pipetted into a fresh Eppendorf on ice. Homogenates were heat-inactivated (5 min, 70 °C). Triglyceride levels were analysed by using enzymatic assays by the Cambridge Core Biochemical Assay Laboratory. Triglyceride amount was normalised to the number of Drosophila.
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8

Leptin-induced Hypothalamic Gene Expression

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One hour after leptin injection, mice were euthanized by terminal anaesthesia (Dolethal, Vetoquinol UK Ltd) and hypothalami rapidly removed and flash frozen in liquid nitrogen and stored at −80 °C until further analysed.
Total RNA from the tissue of interest was purified with TRIsure (Bioline) using a FastPrep 24 homogeniser (MP Biomedicals) according to the manufacturer's instructions. The RNA was reverse transcribed and amplified using TaqMan Universal PCR Master Mix with TaqMan Assay on demand kit (Applied Biosystems). Quantitative PCR reactions were performed in duplicate and relative expression was determined for target mRNA and adjusted for total mRNA content by hypoxanthine-phosphoribosyl transferase (Hprt), TATA – binding protein (Tbp) and β2 – macroglobulin (B2M). Quantitative PCR statistical analysis was performed using Microsoft Excel. P-value was calculated using a two-tailed distribution unpaired Student's t-test and data expressed as mean ± SEM.
For the NFκB signalling pathway profiler PCR array (Mouse NFκB Signalling Pathway, Qiagen), total RNA was reverse transcribed according to the manufacturer's instructions using 400 ng starting material. Arithmetic mean of B2M, Heat shock protein 90 KDa alpha class B member 1 (Hsp90ab1) and B-glucuronidase (Gusb) expression level was used as loading controls.
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9

SARS-CoV-2 Inhibition in K18-hACE2 Mice

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Mouse experiments were approved by the Institutional Animal Care and Use Committee (IACUC) of the Korea Research Institute of Chemical Technology (approval number 2020-8B-07-01). Nine K18-hACE2 transgenic mice (8 weeks old) were evenly divided into three groups and housed in the ABSL-3 facility. Mice from each group were lightly euthanized with isoflurane and intranasally inoculated with SARS-CoV-2 (2 × 103 pfu/head, clade S). Mice were orally administered vehicle (PBS with 1% Tween 80) or vandetanib (25 mg/kg per mouse) once daily. Mouse lung samples were washed with PBS and harvested to determine the inhibition of SARS-CoV-2. Tissue samples from the lung were homogenised in cold PBS solution with a FastPrep-24 homogeniser (MP Biomedicals) for five cycles (20 s on/20 s off), followed by three additional freeze–thaw cycles were performed at −80 °C. Cell debris was removed by centrifugation at 13,000 rpm for 1 min to measure the viral RNA and proteins in the lung.
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10

Homogenization and RNA Extraction

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Homogenisation of each tumour and of the margin sample was the first step preceding RNA extraction and use of ceramic beads Lysing Matrix D (MP Biomedicals, Irvine, CA, USA) in FastPrep®-24 homogeniser (MP Biomedicals, Irvine, CA, USA). RNA extraction was performed with the use of an RNA isolation kit (BioVendor, Brno, Czech Republic) according to the manufacturer’s protocol. Estimation of the quality and quantity of the extracted RNA was performed on a NanoPhotometer® Pearl spectrophotometer (IMPLEN, Munich, Germany).
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