Bijaya Ketan Sarangi

Synthesis of Silver Nanoparticles from the Aqueous Extract of Leaves of Ocimum sanctum for Enhanced Antibacterial Activity

The field of nanotechnology is the most active area of research in modern materials science. Though there are many chemical as well as physical methods, green synthesis of nanomaterials is the most emerging method of synthesis. We report the synthesis of antibacterial silver nanoparticles (AgNPs) using leaf broth of medicinal herb, Ocimum sanctum (Tulsi). The synthesized AgNPs have been characterized by UV-Vis spectroscopy, transmission electron microscopy (TEM), and X-ray diffractometry. The mean particle of synthesized NPs was found to be 18 nm, as confirmed by TEM. The qualitative assessment of reducing potential of leaf extract has also been carried out which indicated presence of significant amount of reducing entities. FTIR analysis revealed that the AgNPs were stabilized by eugenols, terpenes, and other aromatic compounds present in the extract. Such AgNPs stabilized by Tulsi leaf extract were found to have enhanced antimicrobial activity against well-known pathogenic strains, namely Staphylococcus aureus and E. coli.

In Silico Characterization of Pectate Lyase Protein Sequences from Different Source Organisms

A total of 121 protein sequences of pectate lyases were subjected to homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis. The phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases. The multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity. The multiple sequence alignment of these pectate lyase protein sequences from different source organisms showed conserved regions at different stretches with maximum homology from amino acid residues 439–467, 715–816, and 829–910 which could be used for designing degenerate primers or probes specific for pectate lyases. The motif analysis revealed a conserved Pec_Lyase_C domain uniformly observed in all pectate lyases irrespective of variable sources suggesting its possible role in structural and enzymatic functions.

Analysis of genetic diversity in cowpea (Vigna unguiculata L.Walp.) cultivars with random amplified polymorphic DNA markers

The genetic diversity among ten Indian cultivars of cowpea was analyzed using 18 sets of RAPD markers. A total of 181 bands with an average of 15 bands per primer were obtained. Out of 181 bands, 148 showed polymorphism (81.7%). The variation in genetic diversity among these cultivars ranged from 0.1742 to 0.4054. Cluster analysis based on Jaccard’s similarity coefficient using UPGMA with high bootstrap values revealed two distinct clusters I and II comprised of two and seven cultivars, respectively. Cluster II was further differentiated into various subclusters. Cultivar IC-9883 was found to be unique based on its altogether distinct position in the dendrogram and two-dimensional space projections.

Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.)

The DNA binding with One Finger (Dof) protein is a plant specific transcription factor involved in the regulation of wide range of processes. The analysis of whole genome sequence of pigeonpea has identified 38 putative Dof genes (CcDof) distributed on 8 chromosomes. A total of 17 out of 38 CcDof genes were found to be intronless. A comprehensive in silico characterization of CcDof gene family including the gene structure, chromosome location, protein motif, phylogeny, gene duplication and functional divergence has been attempted. The phylogenetic analysis resulted in 3 major clusters with closely related members in phylogenetic tree revealed common motif distribution. The in silico cis-regulatory element analysis revealed functional diversity with predominance of light responsive and stress responsive elements indicating the possibility of these CcDof genes to be associated with photoperiodic control and biotic and abiotic stress. The duplication pattern showed that tandem duplication is predominant over segmental duplication events. The comparative phylogenetic analysis of these Dof proteins along with 78 soybean, 36 Arabidopsis and 30 rice Dof proteins revealed 7 major clusters. Several groups of orthologs and paralogs were identified based on phylogenetic tree constructed. Our study provides useful information for functional characterization of CcDof genes.

Cloning, In Silico Characterization and Prediction of Three Dimensional Structure of SbDof1, SbDof19, SbDof23 and SbDof24 Proteins from Sorghum [Sorghum bicolor (L.) Moench]

In the present study, four full-length Dof (DNA-binding with one finger) genes from Sorghum bicolor namely SbDof1, SbDof19, SbDof23, and SbDof24 were PCR amplified, gel eluted, cloned, and sequenced (accession number HQ540084, HQ540085, HQ540086, and HQ540087, respectively). These sequences were further characterized in silico by subjecting them to homology search, multiple sequence alignment, phylogenetic tree construction, and protein functional analysis, revealing their identity to Dof like proteins. Phylogenetic analysis of cloned SbDof genes along with other reported Dof proteins revealed existence of two major groups A and B, while group A was further bifurcated into two sub-groups (viz., I and II). Motif scan analysis of SbDof proteins revealed the presence of glycine- and alanine-rich profiles in SbDof1, while proline-rich profile was observed in SbDof23. Asparagines, methionine, and serine-rich profiles were common in case of both SbDof19 and SbDof24 proteins. The three dimensional structures of SbDof proteins were predicted by I-TASSER server based on multiple threading method. The modeled structures were refined by energy minimization and their stereo chemical qualities were validated by PROCHECK and QMEAN server indicating the acceptability of the predicted models. The final models were submitted to PMDB database with assigned PMDB IDs, i.e., PM0077395, PM0077396, PM0077397, PM0077398, and PM0076448 for SbDof1, SbDof19, SbDof23, SbDof24, and Dof domain, respectively. Based on gene ontology (GO) terms in I-TASSER server putative functions of modeled SbDof proteins were also predicted.

Genome Wide In Silico Characterization of Dof Transcription Factor Gene Family of Sugarcane and Its Comparative Phylogenetic Analysis with Arabidopsis , Rice and Sorghum

A total of 25 Dof genes were retrieved from GRASSIUS grass regulatory information server. These sequences were in silico characterized for homology search, multiple sequence alignment for conserved Dof DNA binding domains, distribution of conserved motifs and phylogenetic relatedness with sorghum, rice and Arabidopsis. A highly conserved four cysteine residues associated with typical zinc finger of Dof family was observed on multiple sequence alignment of Dof domains. A highly conserved cysteine residue at positions 3 and 6 along with proline and sulfur at positions 4 and 8, respectively were observed. The phylogenetic tree of 119 Dof protein sequences of sugarcane, rice, sorghum and Arabidopsis revealed ten distinct clades with several orthologs and paralogs. The distributions of 25 conserved motifs were analyzed for Dof proteins of sugarcane. Dof proteins with closely related members in the phylogenetic tree shared common motif distribution revealing the possibility of functional similarities within the same subgroup. The motif 1 representing the conserved Dof domain of 50 amino acids was uniformly observed in all the Dof proteins of sugarcane except ScDof8 and ScDof14.

Determination of arsenic extraction by Vetiveria zizanioides (L.) Nash plant for phytoremediation application

ABSTRACT There is contradiction about Vetiveria zizanioides (L.) Nash as arsenic hyperaccumulator. The suitability of V. zizanioides plant for Arsenic (As) tolerance and accumulation in the plant biomass has been investigated for phytoremediation application. Plants were treated with 0, 25, 50, 75, 100 and 150 mg L−1 As levels in Hoagland nutrient solution. Arsenic accumulation in shoot and root biomass was determined after 14 days. Metal extraction competency from matrix and accumulation in the above ground plant part revealed that V. zizanioides accumulate As at a low level. Inefficiency of As accumulation by this plant relates to the absence of arsenate reductase activity, transcript of the arsC gene which is crucial for As detoxification. Though, the V. zizanioides system sustains low-level As stress, it is not suitable for As phytoextraction.

Implications of Nanotechnology on Plant Productivity and Its Rhizospheric Environment

Nanotechnology requires the ability to understand the materials and precisely manipulate it to nanoscale in a useful way. Nanotechnology emerged as a new broad science of diverse fields such as basic sciences, materials science, and engineering to assemble at the nanoscale. In contrast to conventional or other contaminants, nanoparticles are posing some new environmental challenges for scientists and environmentalists worldwide. Being a new area of science, nanotechnology will leave no field untouched including agriculture and allied sectors. So far, the use of nanotechnology in agriculture has been mostly theoretical, but it has begun to have a significant effect in the main areas of agrochemical industry. Nanoparticles finding great potential as delivery systems to specific targets in living organisms and is being used in medical sciences. In plants, the same principles can be applied for a broad range of uses, particularly to tackle phytopathological infections, nutrition supplement and as growth adjuvant. Nanoparticles can be tagged to agrochemicals or other substances as delivery agent to plant system and tissues for controlled release of chemicals. Doing so, the negative effects of nanomaterials on plant productivity and soil microbes and environment must not be overlooked, such as toxicity generated by free radicals leading to lipid peroxidation and DNA damage. Key focus of the chapter particularly relates the use of nanoparticles on agricultural crops and its toxic implications to plants and microbes naturally present in soil and generation of nanowaste in agroecosystem.

RNA-Seq analysis for indigo biosynthesis pathway genes in Indigofera tinctoria and Polygonum tinctorium.

Natural indigo is the most important blue dye for textile dyeing and valuable secondary metabolite biosynthesized in Indigofera tinctoria and Polygonum tinctorium plants. Present investigation is made to generation of gene resource for pathway enrichment and to understand possible gene expression involved in indigo biosynthesis. The data about raw reads and the transcriptome assembly project has been deposited at GenBank under the accessions SRA180766 and SRX692542 for I. tinctoria and P. tinctorium, respectively.

Transcriptome analysis for identification of indigo biosynthesis pathway genes in Polygonum tinctorium

Abstract Indigo is the most important blue dye for textile dyeing and is biosynthesized in Polygonum tinctorium. Some biochemical studies related to biosynthesis are available. However, genomic and transcriptome studies have not received sufficient attention. Here, we report de novo assembly of transcriptome datasets and its comprehensive analysis. A total of 60,395 unigenes were annotated using BLAST search against the different databases. At least 23,721 unigenes mapped onto different pathways using KEGG database. We found that 3,323 genes are involved in biosynthesis of secondary metabolites, 117 phenylalanine, tyrosine and tryptophan biosynthesis and 147 tryptophan metabolisms. Apart from this, indigo biosynthesis pathway genes viz., dioxygenase, monooxygenase, and glucosyltransferase have also been identified. Fourteen genes encoding cytochrome P450 monooxygenase, 26 glucoside dioxygenase, 9 UDP-glucose D-glucosyltransferase and 52 were β-D-glucosidase. These findings provide a foundation for further analysis of this pathway with potential to enhance the synthesis of indican in P. tinctorium