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Rāiganj, India

Mondal U.K.,Raiganj College | Sen A.,North Bengal University | Bothra A.K.,Raiganj College
International Journal of Integrative Biology

Helicobacter hepaticus is a naturally occurring pathogen of mice, has been used as a model for the study of hepatic carcinogenesis and gastrointestinal disease. H. hepaticus produces a soluble toxin known as cytolethal distending toxin (Cdt). The bacteria H. hepaticus is given increasing research effort and complete genome is sequenced but the structure of Cdt of H. hepticus is not solved yet. The 3D model of the CdtB of H. hepaticus ATCC 51449 is constructed by MODELLER 9v4 program using the templates CdtB from Actinobacillus actinomycetemcomitans. The model is validated by PROCHECK, ProSa, CASTp server, ProFunc server etc. After that molecular dynamics simulation is performed using GROMACS and the resulting trajectory is analyzed. © IJIB. Source

Sen A.,North Bengal University | Thakur S.,North Bengal University | Bothra A.K.,Raiganj College | Sur S.,North Bengal University | Tisa L.S.,University of New Hampshire
Archives of Microbiology

The TTA codon, one of the six available codons for the amino acid leucine, is the rarest codon among the high GC genomes of Actinobacteria including Frankia. This codon has been implicated in various regulatory mechanisms involving secondary metabolism and morphological development. TTA-mediated gene regulation is well documented in Streptomyces coelicolor, but that role has not been investigated in other Actinobacteria including Frankia. Among the various Actinomycetes with a GC content of more than 70%, Frankia genomes had the highest percentages of TTA-containing genes ranging from 5.2 to 10.68% of the genome. In contrast, TTA-bearing genes comprised 1.7, 3.4 and 4.1% of the Streptomyces coelicolor, S. avermitilis and Nocardia farcinia genomes, respectively. We analyzed their functional role, evolutionary significance, horizontal acquisition and the codon-anticodon interaction. The TTA-bearing genes were found to be well represented in metabolic genes involved in amino acid transport and secondary metabolism. A reciprocal Blast search reveal that many of the TTA-bearing genes have orthologs in the other Frankia genomes, and some of these orthologous genes also have a TTA codon in them. The gene expression level of TTA-containing genes was estimated by the use of the codon adaption index (CAI), and the CAI values were found to have a positive correlation with the GC3 (GC content at the 3rd codon position). A full-atomic 3D model of the leucine tRNA recognizing the TTA (UUA) codon was generated and utilized for in silico docking to determine binding affinity in codon-anticodon interaction. We found a proficient codon-anticodon interaction for this codon which is perhaps why so many genes hold on to this rare codon without compromising their translational efficiency. © 2011 Springer-Verlag. Source

Thakur S.,North Bengal University | Bothra A.K.,Raiganj College | Sen A.,North Bengal University
Journal of Biosciences

Biological nitrogen fixation is accomplished by prokaryotes through the catalytic action of complex metalloenzyme, nitrogenase. Nitrogenase is a two-protein component system comprising MoFe protein (NifD&K) and Fe protein (NifH). NifH shares structural and mechanistic similarities as well as evolutionary relationships with light-independent protochlorophyllide reductase (BchL), a photosynthesis-related metalloenzyme belonging to the same protein family. We performed a comprehensive bioinformatics analysis of the NifH/BchL family in order to elucidate the intrinsic functional diversity and the underlying evolutionary mechanism among the members. To analyse functional divergence in the NifH/BchL family, we have conducted pair-wise estimation in altered evolutionary rates between the member proteins. We identified a number of vital amino acid sites which contribute to predicted functional diversity. We have also made use of the maximum likelihood tests for detection of positive selection at the amino acid level followed by the structure-based phylogenetic approach to draw conclusion on the ancient lineage and novel characterization of the NifH/BchL protein family. Our investigation provides ample support to the fact that NifH protein and BchL share robust structural similarities and have probably deviated from a common ancestor followed by divergence in functional properties possibly due to gene duplication. © 2013 Indian Academy of Sciences. Source

Bandyopadhyay A.,University of Burdwan | Deb A.K.,Raiganj College | Kobayashi S.,Kyoto University | Yoshimura K.,Kyoto University | Chakrabarti P.K.,University of Burdwan
Journal of Alloys and Compounds

Nanoparticles of Fe-doped europium oxide (Eu1.90Fe 0.10O3- δ) are prepared by co-precipitation method. To obtain the desired nanocrystalline phase, the as prepared sample has been sintered at 700 °C for 6 h in an argon atmosphere. The crystallographic phase is confirmed by Rietveld analysis of the X-ray diffraction (XRD) pattern. The results of XRD analysis is also in agreement with those obtained from high resolution transmission electron microscopy (HRTEM) and Raman spectra of the sample. The results of XRD, HRTEM and Raman spectra confirmed that all Fe ions are successfully doped in the lattice of europium oxide. Also, no impurity phase has been formed in the sample. Hysteretic behavior in the magnetization versus applied field curve confirmed the presence of ferromagnetic ordering of Eu 1.90Fe0.10O3- δ at room temperature. The ferromagnetism is attributed to the substitution of Fe-ions in Eu 2O3, which is successfully explained by the bound-magnetic-polaron model. © 2014 Elsevier B.V. All rights reserved. Source

Kundu S.,North Bengal University | Bothra A.,Raiganj College | Tisa L.S.,University of New Hampshire | Sen A.,North Bengal University
Indian Journal of Biotechnology

The role of Xanthomonas spp. as phytopathogen has been well recognized in diseases of important crops like rice, canola, tomato, citrus, etc. The genomes of a number of Xanthomonas strains are also fully sequenced and they are made available in various data bases. In the present study, in silico analysis of six Xanthomonas genomes was carried out. Synonymous codon usage pattern study in these genomes revealed that pathogenicity related (PR)-horizontally transferred genes (HGTs) were, in general, expressed lowly and were less biased in comparison with average protein coding genes and ribosomal protein genes. Moreover, the correspondence analysis showed that the ribosomal genes were clustered at one end, while the HGTs and the PR-HGTs were all scattered. It has been also revealed that how the virulent HGTs, in spite of having low expression levels, did enhance the pathogenicity of the Xanthomonas strains to certain extent by targeting important cellular functions. Source

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