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Brilliant qpcr master mix

Manufactured by Agilent Technologies
Sourced in Denmark

Brilliant QPCR Master Mix is a pre-formulated solution designed for quantitative real-time PCR (qPCR) applications. It contains all the necessary components, including a hot-start DNA polymerase, dNTPs, and optimized buffer, to facilitate efficient and accurate qPCR experiments.

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4 protocols using brilliant qpcr master mix

1

Quantitative Detection of Mycobacterium ulcerans

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Oligonucleotide primer and TaqMan probe sequences were used for detection of the IS2404 sequence and the ketoreductase B (KR) domain of the mycolactone polyketide synthase (mls) gene from the plasmid pMUM001 [13 (link),42 (link),43 (link)]. PCR mixtures contained 5 μl of template DNA, 0.3 μM of each primer, 0.25 μM probe, and Brilliant QPCR Master Mix (Agilent Technologies) in a total volume of 25 μl. Amplification and detection were performed with a Thermocycler StepOne (Applied Biosystems), using the following program: heating at 95°C for 10 min, followed by 40 cycles of 95°C for 15 s and 60°C for 1 min. DNA extracts were tested at least in duplicates, and negative controls were included in each assay. Quantitative readout assays were set up, based on an external standard curve generated with five tenfold serial dilutions of M. ulcerans (strain 1G897) DNA. Samples were considered positive only if both the IS2404 sequence and the gene sequence encoding the ketoreductase B domain (KR) were detected, with threshold cycle (Ct) values strictly < 35 cycles. An inhibition control was performed as previously described [44 ] and 10% negative controls (water alone) were included in each assay.
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2

Quantitative PCR for S. pyogenes and Bacteria

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Quantification of S. pyogenes [38 (link)] and 16S rRNA genes [39 (link)] was performed using hydrolysis probe chemistry. The S. pyogenes assay is commercially available from Biosearch Technologies (Novato, CA). For each sample duplicate 25 μL reactions were run, each containing: 12.5 μL Brilliant® qPCR Master mix (Agilent Technologies, Santa Clara, California), 25 μg BSA (Sigma-Aldrich, Brøndby, Denmark), appropriate concentration of primers and TaqMan® probes (S. pyogenes: 400 nM primers and 100 nM probe, 16S rRNA: 900 nM primers and 200 nM probe), 0.75 μM ROX reference dye (Agilent Technologies) and 2 μL of template DNA. Measurements were obtained by absolute quantification using genomic DNA isolated from S. pyogenes (DSM 20565) and P. aeruginosa (DSM 1253) for total bacteria quantification. The number of isolated genomes was calculated based on DNA concentration (Quant-iT™ dsDNA Assay Kit (Invitrogen)) and genome size estimated to be 1.8 Mbp for S. pyogenes and 6.5 Mbp for P. aeruginosa (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi). Dilution series of the genomic DNA covered a range of 106-100 genome copies. Reactions were run on an Mx3005P (Agilent Technologies) with the following program: 10 min at 95 °C, followed by 40 cycles of 30 s at 95 °C, 1 min at 60 °C.
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3

Quantification of Glyoxalase I Expression

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Glyoxalase I expression vs β-actin was evaluated by quantitative real-time TaqMan PCR analysis (qRT–PCR) on a MX3000P Real-Time PCR System (Agilent Technology). The sequences of oligonucleotide primers and TaqMan probes used for qRT–PCR were as follows: GI: 5′-CTCTCCAGAAAAGCTACACTTTGAG-3′ (sense, 400 nM), 5′-CGAGGGTCTGAATTGCCATTG-3′ (antisense, 400 nM), 5′-FAM-TGGGTCGCATCATCTTCAGTGCCC-TAMRA-3′ (TaqMan Probe, 200 nM); β-actin: 5′-CACTCTTCCAGCCTTCCTTCC-3′ (sense, 600 nM), 5′-ACAGCACTGTGTTGGCGTAC-3′ (antisense, 600 nM), 5′-TEXASRED-TGCGGATGTCCACGTCACACTTCA-BHQ-3′ (TaqMan Probe, 200 nM). All PCR primers and probes were designed using Beacon Designer 4 software (Stratagene, Santa Clara, CA, USA), starting from published sequence data supplied by the NCBI database. The PCR reactions were performed in a total volume of 25 μl, containing 250 ng of cDNA, 1 × Brilliant QPCR master mix (Agilent Technology), 0.5 μl of ROX Reference Dye (Agilent Technology) and a concentration of specific primers and probes. The thermal cycling conditions were as follows: 1 cycle at 95 °C for 10 min, followed by 45 cycles at 95 °C for 20 s and 55 °C for 1 min. Data for comparative analysis of gene expression were obtained using the ΔΔCt method (Livak and Schmittgen, 2001 (link)).
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4

NCAM mRNA Expression in Neurons

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After 12-days of culture on the different matrices, total RNA from the neurons was extracted using an RNAesy Extraction Kit (Qiagen) and quantified by UV absorbance at 260 nm. Aliquots of 5μg of RNA were treated with DNAase I (Sigma), and then reverse transcribed to cDNA using iScript Reverse Transcription Supermix (Bio-Rad). The level of NCAM mRNA expression was determined by real-time qPCR using Brilliant QPCR Master Mix (Agilent) and Rat Ncam1 TaqMan Probe and primers (cat#Rn00580526_m1, Applied Biosystems), according to the manufacturer's instructions. The final results were normalized with GAPDH (cat#Rn01775763_g1, Applied Biosystems) expression levels.
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