Computational protocol: Antimicrobial and immunomodulatory efficacy of extracellularly synthesized silver and gold nanoparticles by a novel phosphate solubilizing fungus Bipolaris tetramera

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Protocol publication

[…] The fungus was isolated from rhizospheric soil of Kukrail forest, Lucknow, India and screened by its phosphate solubilizing ability on Pikovskaya’s medium by plate assay []. The fungal colonies were subculture on fresh petriplates containing media and the plates were incubated in inverted position for 72 h at 28 ± 2°C and further screened by observing halo zones around the colony.Biochemical characteristics of the fungus were tested on the basis of lacto-colony morphology, microscopic analysis of conidia, phosphate solubilization index, starch hydrolysis test and cellulose hydrolysis test according to standard protocols [].The fungus was further characterized at molecular level by 18S rRNA sequencing. Genomic DNA was isolated from pure culture of the isolated fungus and subjected to high–fidelity PCR using universal primers i.e. forward primer (5’-GGAAGTAAAAGTCGTAACAAGG-3’) and reverse primer (5’-TCCTCCGCTTATTGATATGC-3’) and analyzed on 1% agarose gel. The PCR product was sequenced bi-directionally using the forward and reverse primers. Homology between this 18S rRNA sequence and the strains available at the public databases (Genbank, EMBL and DDBJ) was determined using BLASTN sequence match routines. The UPGMA (Unweighted Pair Group Mathematical Average) algorithm was used to perform hierarchical cluster analysis []. The sequences were aligned using CLUSTALW2 program and its phylogenetic and molecular evolutionary analysis were conducted. Sequences analysis was performed by alignment of the partial 18S rRNA gene sequences to those obtained from the GenBank database, using the program BLAST (NCBI BLAST® homepage). The nucleotide sequences of 18S rRNA gene segments, determined in this study have been deposited in GenBank database under accession number KF934408. […]

Pipeline specifications

Software tools BLASTN, Clustal W
Databases DDBJ
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Bacillus cereus, Staphylococcus aureus, Mus musculus
Diseases Drug-Related Side Effects and Adverse Reactions
Chemicals Phosphates, Silver