Neeraj Kumar

Anomalous enhancement of the sheet carrier density beyond the classic limit on a SrTiO3 surface

Electrostatic carrier accumulation on an insulating (100) surface of SrTiO3 by fabricating a field effect transistor with Parylene-C (6u2009nm)/HfO2 (20u2009nm) bilayer gate insulator has revealed a mystifying phenomenon: sheet carrier density is about 10 times as large as ( is the sheet capacitance of the gate insulator, VG is the gate voltage, and e is the elementary charge). The channel is so clean to exhibit small subthreshod swing of 170u2009mV/decade and large mobility of 11u2009cm2/Vs for of 1u2009×u20091014u2009cm−2 at room temperature. Since does not depend on either VG nor time duration, beyond is solely ascribed to negative charge compressibility of the carriers, which was in general considered as due to exchange interactions among electrons in the small limit. However, the observed is too large to be naively understood by the framework. Alternative ideas are proposed in this work.

Draft Genome Sequence of Two Monosporidial Lines of the Karnal Bunt Fungus Tilletia indica Mitra (PSWKBGH-1 and PSWKBGH-2)

ABSTRACT Karnal bunt disease caused by the fungus Tilletia indica Mitra is a serious concern due to strict quarantines affecting international trade of wheat. We announce here the first draft assembly of two monosporidial lines, PSWKBGH-1 and -2, of this fungus, having approximate sizes of 37.46 and 37.21 Mbp, respectively.

Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence

Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25–80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73u2009Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.

Development of transcriptome based web genomic resources of yellow mosaic disease in Vigna mungo

Vigna mungo (Urdbean) is cultivated in the tropical and sub-tropical continental region of Asia. It is not only important source of dietary protein and nutritional elements, but also of immense value to human health due to medicinal properties. Yellow mosaic disease caused by Mungbean Yellow Mosaic India Virus is known to incur huge loss to crop, adversely affecting crop yield. Contrasting genotypes are ideal source for knowledge discovery of plant defence mechanism and associated candidate genes for varietal improvement. Whole genome sequence of this crop is yet to be completed. Moreover, genomic resources are also not freely accessible, thus available transcriptome data can be of immense use. V. mungo Transcriptome database, accessible at http://webtom.cabgrid.res.in/vmtdb/ has been developed using available data of two contrasting varieties viz., cv. VM84 (resistant) and cv. T9 (susceptible). De novo assembly was carried out using Trinity and CAP3. Out of total 240,945 unigenes, 165,894 (68.8%) showed similarity with known genes against NR database, and remaining 31.2% were found to be novel. We found 22,101 differentially expressed genes in all datasets, 44,335 putative genic SSR markers, 4105 SNPs and Indels, 64,964 transcriptional factor, 546 mature miRNA target prediction in 703 differentially expressed unigenes and 137 pathways. MAPK, salicylic acid-binding protein 2-like, pathogenesis-related protein and NBS-LRR domain were found which may play an important role in defencexa0against pathogens. This is the first web genomic resource of V. mungo for future genome annotation as well as ready to use markers for future variety improvement program.

Apoptotic efficacy of multifaceted biosynthesized silver nanoparticles on human adenocarcinoma cells

Metallic nanoparticles (NPs) especially silver (Ag) NPs have shown immense potential in medical applications due to their distinctive physio-chemical and biological properties. This article reports the conjugation of Ag NPs with Rubus fairholmianus extract. The modification of Ag NPs was confirmed using various physico-chemical characterization techniques. The cytotoxic effect of Rubus-conjugated Ag NPs (RAgNPs) was studied by LDH assay and proliferation by ATP assay. The apoptotic inducing ability of the NPs were investigated by Annexin V/PI staining, caspase 3/7 analysis, cytochrome c release, intracellular ROS analysis, Hoechst staining and mitochondrial membrane potential analysis using flow cytometry. The expression of apoptotic proteins caspase 3, Bax and P53 were analyzed using ELISA and caspase 3, Bax using western blotting. Cells treated with 10u2009µg/mL RAgNPs showed an increased number of cell death by microscopic analysis compared to untreated control cells. The RAgNPs induced a statistically significant dose-dependent decrease in proliferation (pu2009<u20090.001 for 5 and 10u2009µg/mL) and increased cytotoxicity in MCF-7 cells. A 1.83 fold increase in cytotoxicity was observed in cells treated with 10u2009µg/mL (pu2009<u20090.05) compared to the untreated cells. Nuclear damage and intracellular ROS production were observed upon treatment with all tested concentrations of RAgNPs and the highest concentrations (5 and 10u2009µg/mL) showed significant (pu2009<u20090.05, pu2009<u20090.01) expression of caspase 3, Bax and P53 proteins. The data strongly suggest that RAgNPs induces cell death in MCF-7 cells through the mitochondrial-mediated intrinsic apoptosis pathway. The present investigation supports the potential of RAgNPs in anticancer drug development.

MiSNPDb : a web-based genomic resources of tropical ecology fruit mango ( Mangifera indica L.) for phylogeography and varietal differentiation

Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world’s first web-based genomic resources for genetic improvement and germplasm management of mango.