Computational protocol: Chromium [Cr(VI)] biosorption property of the newly isolated actinobacterial probiont Streptomyces werraensis LD22

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Protocol publication

[…] The genomic DNA of the probiont LD22 was isolated by modified high salt method as described by Perry and Pasi (). PCR amplification of 16S rRNA gene of the isolate LD22 was performed in an automated Thermal Cycler (Applied Biosystems) using universal primers 27f (5′-AGAGTTTGATCMTGGCTCAG-3′) and 765r (5′-CTGTTTGCTCCCCACGCTTTC-3′) according to the amplification profile described by Coombs and Franco (). The PCR product was analyzed by agarose gel electrophoresis and DNA of the expected size was purified and then subjected to sequencing at Macrogen Inc., Korea. The 16S rRNA gene sequence obtained was searched through the NCBI database using the BLAST algorithm to identify the closest matches. The sequence was aligned with representative actinobacterial 16S rRNA gene sequences and a phylogenetic tree was constructed using the CLUSTALW and MEGA software version 5. Restriction enzyme site analysis and secondary structure prediction for 16S rRNA gene were carried out using NEBcutter program version 2.0 (http://tolls.neb.com/NEBCutter2/index.php) and GeneBee software (http://www.genebee.msu.su/services/rna2-reduced.html), respectively (Dhanasekaran et al. ). […]

Pipeline specifications

Software tools Clustal W, MEGA, NEBcutter
Application Phylogenetics
Organisms Gallus gallus, Capra hircus
Chemicals Amines, Chromium, Potassium Dichromate, Hydroxyl Radical