• Saumitra Das

      Articles written in Journal of Biosciences

    • Organization and chromosomal localization ofβ-tubulin genes inLeishmania donovani

      Saumitra Das Samit Adhya

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      The genomic organization and chromosomal location of theβ-tubulin isogenes inLeishmania donovani promastigotes has been studied by nucleic acid hybridization techniques using a cloned β-tubulin gene. We have cloned aβ-tubulin gene fragment, 3.3 kbp long, from genomic DNA ofLeishmania donovani using a heterologousβ-tubulin DNA as probe. Restriction maps of this clone have been prepared. It has been estimated that there are approximately 11–15 copies of theβ-tubulin genes per haploid genome. The majority of these isogenes are arranged in a tandem repeat with a length of 3.5 kbp on a single chromosome. In addition a few dispersed gene copies at different chromosomal loci were detected by pulse field gradient gel electrophoresis. Part of the internal coding region of the gene has been sequenced to confirm the identity of theβ-tubulin clone and is found to be nearly identical to that ofLeishmania mexicana amazonensis.

    • Transcription and processing ofβ-tubulin messenger RNA inLeishmania donovani promastigotes

      Samit Adhya Saumitra Das Mantu Bhaumik

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      Transcription of the multicopyβ-tubulin locus inLeishmania donovani promastigotes was examined by nucleic acid hybridization techniques. By northern analysis of promastigote RNA multipleβ-tubulin mRNAs were detected. The major species of 2.2 kb RNA is derived from the tandem repeat cluster ofβ-tubulin genes, the other two (2.4 and 2.6 kb) are presumably derived from dispersed genomic loci. Combined S1-nuclease and primer extension mapping experiments demonstrated the presence of a single 5′-terminus with a 35 nucleotide spliced-leader sequence. The 3′-termini are heterogeneous. The development of a nuclear run-on system inLeishmania for studying transcription of individual genes is reported. Active but transient RNA polymerase II activity was observed in this system. Using specific DNA probes for labelled run-on RNA it was shown thatβ-tubulin transcription occurs asymmetrically (i.e., on one strand of the DNA template) in anα-amanitin sensitive manner. The significance of these results for the life cycle of the parasite is discussed.

    • Mini-exon derived RNA gene ofLeishmania donovani: structure, organization and expression

      Md Quamarul Hassan Saumitra Das Samit Adhya

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      Mini-exon derived RNA is a small nuclear RNA of trypanosomatid protozoa such asLeishmania which donates its 5′-terminal 39 nucleotides to the 5’-ends of cellular messenger RNAs by trans-splicing. We have cloned a mini-exon derived RNA gene fromLeishmania donovani and studied its organization and expression. About 200 copies of the gene per haploid genome are organized as a tandem repeat on a single chromosome. The gene is transcribed as a 95-nucleotide RNA. The first 39 nucleotides of mini-exon derived RNA is also found at the 5′-terminus of a cellular mRNA (Β-tubulin), thus confirming its identity. Sequence analysis of the gene and its flanking regions showed that while classical RNA polymerase II promoter elements such as TATA and CAAT are absent from the 5′-upstream region, intragenic sequence motifs resembling RNA polymerase III promoter elements are present. The implications of this finding for mini-exon derived RNA expression are discussed.

    • Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility

      ARINDAM MAITRA MAMTA CHAWLA SARKAR HARSHA RAHEJA NIDHAN K BISWAS SOHINI CHAKRABORTI ANIMESH KUMAR SINGH SHEKHAR GHOSH SUMANTA SARKAR SUBRATA PATRA RAJIV KUMAR MONDAL TRINATH GHOSH ANANYA CHATTERJEE HASINA BANU AGNIVA MAJUMDAR SREEDHAR CHINNASWAMY NARAYANASWAMY SRINIVASAN SHANTA DUTTA SAUMITRA DAS

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      Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal andoropharyngeal swab samples of infected individuals in Eastern India. Seven of the isolates belonged to the A2aclade, while one belonged to the B4 clade. Specific mutations, characteristic of the A2a clade, were alsodetected, which included the P323L in RNA-dependent RNA polymerase and D614G in the Spike glycoprotein.Further, our data revealed emergence of novel subclones harbouring nonsynonymous mutations, viz.G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein. The N protein mutationsreside in the SR-rich region involved in viral capsid formation and the S protein mutation is in the S2 domain,which is involved in triggering viral fusion with the host cell membrane. Interesting correlation was observedbetween these mutations and travel or contact history of COVID-19 positive cases. Consequent alterations ofmiRNA binding and structure were also predicted for these mutations. More importantly, the possibleimplications of mutation D614G (in SD domain) and G1124V (in S2 subunit) on the structural stability of Sprotein have also been discussed. Results report for the first time a bird’s eye view on the accumulation ofmutations in SARS-CoV-2 genome in Eastern India.

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