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Abi prism1 3100 avant genetic analyser

Manufactured by Thermo Fisher Scientific

The ABI Prism 3100-Avant Genetic Analyzer is a capillary electrophoresis (CE) system designed for high-throughput DNA analysis. It features 16 capillaries and can perform a variety of applications, including DNA sequencing, fragment analysis, and microsatellite analysis.

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2 protocols using abi prism1 3100 avant genetic analyser

1

Fungal DNA Extraction and Sequencing

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Molecular biology techniques were carried out as described elsewhere [13 (link)]. The B28 strain was cultivated on a Czapek medium at 30°C under continuous agitation at 200 rpm. Mycelia from 48-h cultures were harvested and DNA was extracted.
The internal transcribed spacer regions (ITS) were submitted to PCR amplification using fungus-specific primers, namely ITSl (5′-TCC GTA GGT GAA CCT GCG G-3′) and ITS4 (5′-TCC TCC GCT TAT TGA TAT G-3′). The amplification was initiated by incubating the PCR reaction mixture at 95°C for 5 min, followed by 35 cycles of denaturation for 30 s at 94°C. The reaction was annealed at 50°C for 30 s and terminated with extension consisting of 1 min at 72°C and final steps of 10 min at 72°C. The PCR products were analyzed on an agarose gel (1%) and purified by the Polyethylene Glycerol- (PEG-) NaCl method. The nucleotide sequences were determined using the Big-Dye Terminator v3.1 Cycle Sequencing Kit and the automated ABI Prism1 3100-Avant Genetic Analyser (Applied Biosystems). The sequence obtained for the intergenic region rRNA. The BLAST search program (http://www.ncbi.nlm.nih.gov/BLAST/) was used to look for nucleotide sequence homology.
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2

Molecular Identification of Fungal Strain

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The fungi strain was morphologically and physiologically characterized according to universally accepted keys for fungus identification [22, 23] . The identification was confirmed by molecular methods [20] . For the latter, the K38 strain was cultivated in 100 mL of liquid medium at 30 °C under continuous agitation at 150 rpm. Mycelia from 48-h cultures were harvested and DNA was extracted.
The partial sequence of the fungal rDNA ITS gene was submitted to PCR amplification via forward primer ITSl (5′-TCCGTAGGTGAACCTGCG-3′) and reverse primer ITS4 (5′-TCCTCCGCTTATTGATATG-3′).
The PCR was initiated by incubating the reaction mixture at 94 °C for 3 min, followed by 35 cycles of 1 min at 94 °C. The reaction was annealed at 55 °C for 1 min and terminated with extension and final steps consisting of 1 min at 72 °C and 10 min at 72 °C. The PCR products were analysed on an agarose gel and purified by the PEG-NaCl method. The nucleotide sequences were determined using the Big-Dye Terminator v3.1 Cycle Sequencing Kit and the automated ABI Prism1 3100-Avant Genetic Analyser (Applied Biosystems). The sequence obtained for the intergenic region rRNA ITS was deposited at the GenBank in NCBI under accession number KM594388.
Fungi were identified by searching the homology of ITS genes sequences of the isolate with the sequences using BLAST search algorithm.
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