Computational protocol: Comparative efficacy of locally isolated fungal strains for Pb(II) removal and recovery from water

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Protocol publication

[…] The selected fungal strains were initially identified on the basis of macro- and microscopic characteristics and further confirmed using molecular approach. For molecular typing of fungal isolates, the total genomic DNA of fungal isolates was extracted by cetyl trimethyl ammonium bromide (CTAB) method [] that was partially modified in our lab as per requirements. DNA samples were used to amplify internal transcribed spacer (ITS) regions through PCR using universal primers ITS1 (Forward Primer): TCC GTA GGT GAA CCT GCG G and ITS4 (Reverse Primer): TCC TCC GCT TAT TGA TAT GC []. The PCR followed conditions were; 94 °C for 3 min, 94 °C for 30 s, 56 °C for 1 min 30 Cycles, 72 °C for 1 min, 72 °C for 10 min [].The amplified ITS regions/18S rRNA genes of isolates were partially sequenced commercially (Macrogen, Korea). These sequences were compared with other sequences of fungi present in the GenBank databases using the NCBI BLAST tool (http://www.ncbi.nlm.nih.gov) and then aligned with them using CLUSTALX []. The aligned sequences were used to construct a distance matrix, after the generation of 100 bootstrap sets that was subsequently used to construct a phylogenetic tree, by neighbor-joining method, using TREECON software. The partial ITS/18S rRNA gene sequences of theses isolates were submitted to GenBank to get Accession Numbers. […]

Pipeline specifications

Software tools BLASTN, Clustal W, TREECON
Application Phylogenetics
Organisms Fungi, Aspergillus flavus