The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.

The thermophilic bacterium, Bacillus licheniformis U1 is used for the optimization of bacterial growth (R1), laccase production (R2) and synthetic disperse blue DBR textile dye decolorization (R3) in the present study. Preliminary optimization has been performed by one variable at time (OVAT) approach using four media components viz., dye concentration, copper sulphate concentration, pH, and inoculum size. Based on OVAT result further statistical optimization of R1, R2 and R3 performed by Box–Behnken design (BBD) using response surface methodology (RSM) in R software with R Commander package. The total 29 experimental runs conducted in the experimental design study towards the construction of a quadratic model. The model indicated that dye concentration 110 ppm, copper sulphate 0.2 mM, pH 7.5 and inoculum size 6% v/v were found to be optimum to maximize the laccase production and bacterial growth. Whereas, maximum dye decolorization achieved in media containing dye concentration 110 ppm, copper sulphate 0.6 mM, pH 6 and inoculum size 6% v/v. R package predicted R² of R1, R2 and R3 were 0.9917, 0.9831 and 0.9703 respectively; likened to Design-Expert (Stat-Ease) (DOE) predicted R² of R1, R2, and R3 were 0.9893, 0.9822 and 0.8442 respectively. The values obtained by R software were more precise, reliable and reproducible, compared to the DOE model. The laccase production was 1.80 fold increased, and 2.24 fold enhancement in dye decolorization was achieved using optimized medium than initial experiments. Moreover, the laccase-treated sample demonstrated the less cytotoxic effect on L132 and MCF-7 cell lines compared to untreated sample using MTT assay. Higher cell viability and lower cytotoxicity observed in a laccase-treated sample suggest the impending application of bacterial laccase in the reduction of toxicity of dye to design rapid biodegradation process.

Protease is the largest selling enzyme in the world due to its various applications in the making of detergent, food and leather, meat tenderisation and pharmaceutical industries. The aim of the study is to isolate and identify thermophilic Bacillus licheniformis U1 strains for thermostable protease production. The partial purified enzyme was characterized under different conditions using Anson-Hagihara’s method. Casein as a substrate in the concentration of 0.6 % w/v optimum for enzyme activity and tolerant up to 2.0% casein concentration. An optimum enzyme activity was reported at pH 7 and decreased with increasing in pH, while temperature optimum was found at 50 °C. The enzyme was stable at 40 °C to 50 °C for half an hour and nearly 50% residual activity was indicated at 60 °C. NaCl was not required for catalysis. Stability of enzymes in the presence of various organic solvents and different detergents was remarkable. The enzyme was stable up to 3 days into various solvents and slowly denatured with prolonged incubation. The result of the washing performance with detergent was clearly indicated. Moreover the removal of blood stains and dehairing in goat skin suggests the crucial application in the commercial production at large scale.DOI: http://dx.doi.org/10.3126/ijasbt.v2i1.9519Int J Appl Sci Biotechnol, Vol. 2(1): 75-82

The data in this article contains the sequences of fungal Internal Transcribed Spacer (ITS) and 18S rRNA gene from a metagenome of Lonar soda lake, India. Sequences were amplified using fungal specific primers, which amplified the amplicon lined between the 18S and 28S rRNA genes. Data were obtained using Fungal tag-encoded FLX amplicon pyrosequencing (fTEFAP) technique and used to analyze fungal profile by the culture-independent method. Primary analysis using PlutoF 454 pipeline suggests the Lonar lake mycobiome contained the 29 different fungal species. The raw sequencing data used to perform this analysis along with FASTQ file are located in the NCBI Sequence Read Archive (SRA) under accession No. SRX889598 (http://www.ncbi.nlm.nih.gov/sra/SRX889598).

Textile industry effluents contain several hazardous substances, such as dye-containing effluents, which pose environmental and aesthetic challenges. Presently, the microbial-based remediation process is in use. This study investigated the application of ferrous–ferric oxide (Fe₃O₄) nanoparticles, a readily formulated nanoadsorbent, to remove scattered dye molecules from industrial effluents. The ferrous–ferric oxide nanoparticles were prepared using a chemical co-precipitation method. The nanoparticles had 26.93 emu g⁻¹ magnetization, with sizes smaller than 20 nm, and possessed a highly purified cubic spinel crystallite structure. The catalytic activity of the iron oxide depended on the dose, photocatalytic enhancer, i.e., H₂O₂ level, pH of the reaction medium, and dye concentration. We optimized the Fenton-like reaction to work best using 1.0 g/L of ferrous–ferric oxide nanoparticles, 60 mM oxalic acid at pH 7.0, and 60 ppm of dye. Iron oxides act as photocatalysts, and oxalic acid generates electron–hole pairs. Consequently, higher amounts of super-radicals cause the rapid degradation of dye and pseudo-first-order reactions. Liquid chromatography–mass spectrometry (LC-MS) analysis revealed the ferrous–ferric oxide nanoparticles decolorized and destroyed Disperse Red 277 in 180 min under visible light. Hence, complete demineralization is observed using a photo-Fenton-like reaction within 3 h under visible light. These high-capacity, easy-to-separate next-generation adsorption systems are suggested to be suitable for industrial-scale use. Ferrous–ferric oxide nanoparticles with increased adsorption and magnetic properties could be utilized to clean environmental pollution.

Assessment of Genetic Purity of Parental Lines of Hybrid Rice Using DNA-Based Markers