Lal Bahadur Nagar, India
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Manivannan B.,Sri Sathya Sai Institute of Higher Learning | Mahalingam N.,Sri Sathya Sai Institute of Higher Medical science | Jadhao S.,Bionivid Technology Pvt. Ltd. | Mishra A.,Bionivid Technology Pvt. Ltd. | And 2 more authors.
Genome Announcements | Year: 2016

We present the draft genome assembly of an extensively drug-resistant (XDR) Pseudomonas aeruginosa strain isolated from a patient with a history of genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm formation, virulence, and antibiotic resistance. © 2016 Manivannan et al.


Kakumani P.K.,International Center for Genetic Engineering and Biotechnology | Shukla R.,Bionivid Technology Pvt. Ltd. | Todur V.N.,Bionivid Technology Pvt. Ltd. | Malhotra P.,International Center for Genetic Engineering and Biotechnology | And 3 more authors.
Biology Direct | Year: 2015

Spodoptera is an important polyphagous agricultural insect pest in the tropical world. The genomic details are limited to understand the pest biology at molecular level. In the present study, we sequenced and assembled the transcriptome from Sf21 cells into a non redundant set of 24,038 contigs of ~ 47.38 Mb in size. A total of 26,390 unigenes were identified from the assembled transcripts and their annotation revealed the prevalent protein domains in Sf21 cells. The present study would provide a resource for gene discovery and development of functional molecular markers to understand the biology of S. frugiperda. Reviewers: This article was reviewed by Dr. Thiago Motta Venancio and Prof. Michael Gray. © 2015 Kakumani et al.


PubMed | International Center for Genetic Engineering and Biotechnology and Bionivid Technology Pvt. Ltd.
Type: | Journal: Biology direct | Year: 2015

Spodoptera is an important polyphagous agricultural insect pest in the tropical world. The genomic details are limited to understand the pest biology at molecular level. In the present study, we sequenced and assembled the transcriptome from Sf21 cells into a non redundant set of 24,038 contigs of~47.38 Mb in size. A total of 26,390 unigenes were identified from the assembled transcripts and their annotation revealed the prevalent protein domains in Sf21 cells. The present study would provide a resource for gene discovery and development of functional molecular markers to understand the biology of S. frugiperda.


Banerjee A.,Saha Institute of Nuclear Physics | Sanyal S.,Saha Institute of Nuclear Physics | Kulkarni K.K.,Bionivid Technology Pvt Ltd | Jana K.,Bose Institute of India | And 3 more authors.
FEBS Open Bio | Year: 2014

Mithramycin (MTR) is a clinically approved DNA-binding antitumor antibiotic currently in Phase 2 clinical trials at National Institutes of Health for treatment of osteosarcoma. In view of the resurgence in the studies of this generic antibiotic as a human medicine, we have examined the binding properties of MTR with the integral component of chromatin - histone proteins - as a part of our broad objective to classify DNA-binding molecules in terms of their ability to bind chromosomal DNA alone (single binding mode) or both histones and chromosomal DNA (dual binding mode). The present report shows that besides DNA, MTR also binds to core histones present in chromatin and thus possesses the property of dual binding in the chromatin context. In contrast to the MTR-DNA interaction, association of MTR with histones does not require obligatory presence of bivalent metal ion like Mg2+. As a consequence of its ability to interact with core histones, MTR inhibits histone H3 acetylation at lysine 18, an important signature of active chromatin, in vitro and ex vivo. Reanalysis of microarray data of Ewing sarcoma cell lines shows that upon MTR treatment there is a significant down regulation of genes, possibly implicating a repression of H3K18Ac-enriched genes apart from DNA-binding transcription factors. Association of MTR with core histones and its ability to alter post-translational modification of histone H3 clearly indicates an additional mode of action of this anticancer drug that could be implicated in novel therapeutic strategies. © 2014 The Authors.


Banerjee A.,Saha Institute of Nuclear Physics | Sanyal S.,Saha Institute of Nuclear Physics | Majumder P.,Saha Institute of Nuclear Physics | Chakraborty P.,Bionivid Technology Pvt Ltd | And 3 more authors.
Biochemical and Biophysical Research Communications | Year: 2015

Abstract Recognition of core histone components of chromatin along with chromosomal DNA by a class of small molecule modulators is worth examining to evaluate their intracellular mode of action. A plant alkaloid ellipticine (ELP) which is a putative anticancer agent has so far been reported to function via DNA intercalation, association with topoisomerase II and binding to telomere region. However, its effect upon the potential intracellular target, chromatin is hitherto unreported. Here we have characterized the biomolecular recognition between ELP and different hierarchical levels of chromatin. The significant result is that in addition to DNA, it binds to core histone(s) and can be categorized as a 'dual binder'. As a sequel to binding with histone(s) and core octamer, it alters post-translational histone acetylation marks. We have further demonstrated that it has the potential to modulate gene expression thereby regulating several key biological processes such as nuclear organization, transcription, translation and histone modifications. © 2015 Elsevier Inc.


PubMed | Bionivid Technology Pvt Ltd., Bose Institute of India and Saha Institute of Nuclear Physics
Type: | Journal: Journal of biomolecular structure & dynamics | Year: 2016

Chelerythrine (CHL), a plant alkaloid, possesses antimicrobial, anti-inflammatory, and antitumor properties. Although CHL influences several key signal transduction pathways, its ability to interact directly with nucleoprotein complex chromatin, in eukaryotic cells has so far not been looked into. Here we have demonstrated its association with hierarchically assembled chromatin components, viz. long chromatin, chromatosome, nucleosome, chromosomal DNA, and histone H3 and the consequent effect on chromatin structure. CHL was found to repress acetylation at H3K9. It is more target-specific in terms of gene expression alteration and less cytotoxic compared to its structural analog sanguinarine.


Kulkarni K.K.,Bionivid Technology Pvt Ltd. | Bankar K.G.,Bionivid Technology Pvt Ltd. | Shukla R.N.,Bionivid Technology Pvt Ltd. | Das C.,Saha Institute of Nuclear Physics | And 3 more authors.
Genomics Data | Year: 2015

The role of Mithramycin as an anticancer drug has been well studied. Sarcoma is a type of cancer arising from cells of mesenchymal origin. Though incidence of sarcoma is not of significant percentage, it becomes vital to understand the role of Mithramycin in controlling tumor progression of sarcoma. In this article, we have analyzed the global gene expression profile changes induced by Mithramycin in two different sarcoma lines from whole genome gene expression profiling microarray data. We have found that the primary mode of action of Mithramycin is by global repression of key cellular processes and gene families like phosphoproteins, kinases, alternative splicing, regulation of transcription, DNA binding, regulation of histone acetylation, negative regulation of gene expression, chromosome organization or chromatin assembly and cytoskeleton. © 2014.


Bankar K.G.,Bionivid Technology Pvt Ltd | Todur V.N.,Bionivid Technology Pvt Ltd | Shukla R.N.,Bionivid Technology Pvt Ltd | Vasudevan M.,Bionivid Technology Pvt Ltd
Genomics Data | Year: 2015

Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays. © 2015.


PubMed | Bionivid Technology Pvt Ltd. and Saha Institute of Nuclear Physics
Type: | Journal: Genomics data | Year: 2015

The role of Mithramycin as an anticancer drug has been well studied. Sarcoma is a type of cancer arising from cells of mesenchymal origin. Though incidence of sarcoma is not of significant percentage, it becomes vital to understand the role of Mithramycin in controlling tumor progression of sarcoma. In this article, we have analyzed the global gene expression profile changes induced by Mithramycin in two different sarcoma lines from whole genome gene expression profiling microarray data. We have found that the primary mode of action of Mithramycin is by global repression of key cellular processes and gene families like phosphoproteins, kinases, alternative splicing, regulation of transcription, DNA binding, regulation of histone acetylation, negative regulation of gene expression, chromosome organization or chromatin assembly and cytoskeleton.


PubMed | Bionivid Technology Pvt Ltd
Type: | Journal: Genomics data | Year: 2015

Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays.

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