Satyabrata Sahoo - Academia.edu (original) (raw)

Papers by Satyabrata Sahoo

Genomics & Informatics, Dec 31, 2022

Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, whi... more Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, which are frequently utilized in therapeutic practice. In this study, bioinformatic methodologies were used to examine the pattern of coding sequences and the factors that might influence codon usage bias in the chloroplast genome of Atropa belladonna and other nightshade genomes. The chloroplast engineering being a promising field in modern biotechnology, the characterization of chloroplast genome is very important. The results revealed that the chloroplast genomes of Nicotiana tabacum, Solanum lycopersicum, Capsicum frutescens, Datura stramonium, Lyciumbarbarum, Solanum melongena, and Solanum tuberosum exhibited comparable codon usage patterns. In these chloroplast genomes, we observed a weak codon usage bias. According to the correspondence analysis, the genesis of the codon use bias in these chloroplast genes might be explained by natural selection, directed mutational pressure, and other factors. GC12 and GC3S were shown to have no meaningful relationship. Further research revealed that natural selection primarily shaped the codon usage in A. belladonna and other nightshade genomes for translational efficiency. The sequencing properties of these chloroplast genomes were also investigated by investing the occurrences of palindromes and inverted repeats, which would be useful for future research on medicinal plants.

The enzyme Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) catalyses the decomposition of glucos... more The enzyme Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) catalyses the decomposition of glucose. The gene that produces the GAPDH is therefore present in a wide class of organisms. We show that for this gene the average value of the fluctuations in nucleotide distribution in the codons, normalized to strand bias, provides a reasonable measure of how the gene has evolved in time.

International journal of pharma and bio sciences, 2021

The emergence of the 2019 novel coronavirus SARS-CoV-2, causing a highly contagious disease COVID... more The emergence of the 2019 novel coronavirus SARS-CoV-2, causing a highly contagious disease COVID-19 poses a tremendous global public health concern As the disease is quickly developing into a worldwide pandemic, a careful analysis of its origin, evolution, transmission, and cellular mechanism is urgently needed to combat the deadly virus Successful isolation of the 2019-nCoV has promoted some bioinformatic studies to understand the viral origin and the feature of its infectivity However, at this stage, much remains unclear about the origin of the novel virus and to be investigated to develop ways to control its spread The mechanisms associated with the infectiousness of SARS-CoV-2 are not entirely understood The current knowledge in 2019-nCoV pathogenicity and transmissibility along with several commonly known emerging viruses and information is very much important for better control of the disease So far, the treatment is only supportive Any antiviral agent is yet to emerge The sc...

Journal of Investigative Genomics

The complexity and diversity of genomic function can only be understood at the nucleotide level. ... more The complexity and diversity of genomic function can only be understood at the nucleotide level. The genetic code uses sixty one codons to translate twenty amino acids and three to stop translation. The genes in DNA sequence encode proteins, which perform all the functions necessary in the cell. Regulation of gene expression, thus, plays a central role in defining cell viability and is dominated by a number of genes that are involved in protein biosynthesis, mutation, and folding. The essential functions of many of the gene products strongly depend on codon usage bias that corresponds to abundant tRNAs and thus, biased amino acid composition of proteins indicating the high biological significance of these genes. Recently there has been considerable interest in finding the informational content in gene sequences. As automated sequencing techniques have started to produce a rapidly growing amount of raw DNA sequences, the extraction of information from these sequences becomes a scientific challenge. These sequences carry relevant biophysical information in the form of a one dimensional chain of four nucleotide bases. The availability of the complete genomic sequences has made it possible for researchers to develop approaches that focus on the systematic properties of regularatory and metabolic networks, and to investigate gene expression and regulation in the context of a global cellular work. Despite much effort spent, it is still an open question what kind of correlation exists in gene sequences which rule the tentative function of the particular gene. Hence, our basic task in this review is to search for correlation which accommodates the gene expression level for most situations of its habitat, energy sources and life style.

Journal of Pharmacogenomics & Pharmacoproteomics

In Archaea, previous studies have revealed the presence of multiple intron-containing tRNAs and s... more In Archaea, previous studies have revealed the presence of multiple intron-containing tRNAs and split tRNAs. The full unexpurgated analysis of archaeal tRNA genes remains a challenging task in the field of bioinformatics, because of the presence of various types of disrupted tRNA genes in archaea. Here we suggested a computational method that searched for widely separated genes encoding tRNA halves to generate suppressive variants of missing tRNAs. Considering the existence of split tRNA genes widely separated throughout the genome, we developed our tRNA search algorithm to predict such separated tRNA genes by searching both a conserved terminal 5ˈ-and 3ˈ-motif of tRNA in agreement with the split hypothesis on the basis of cloverleaf prediction and precise in silico determination of bulge-helix-bulge secondary structure at the splice sites. By a comprehensive search for missing tRNA genes, we characterized new variants of selenocysteine tRNA that had been found inserted in Methanopyrus kandleri AV19. Analysis of the complete genome sequence of M. kandleri AV19 revealed the multiple mode of transcription of a non-coding RNA decoding UGA to read selenocysteine (Sec) and suggested further study of the disrupted tRNA genes 002E.

Iranian Journal of Biotechnology

Background: In Archaea, previous studies have revealed the presence of multiple intron-containing... more Background: In Archaea, previous studies have revealed the presence of multiple intron-containing tRNAs and split tRNAs. The full unexpurgated analysis of archaeal tRNA genes remains a challenging task in the field of bioinformatics, because of the presence of various types of hidden tRNA genes in archaea. Here, we suggested a computational method that searched for widely separated genes encoding tRNA halves to generate suppressive variants of missing tRNAs. Objectives: The exploration of tRNA genes from a genome with varying hypotheses, among all three domain of life (eukaryotes, bacteria and archaea), has been rapidly identified in different ways in the field of bioinformatics. Like eukaryotic tRNA genes, it has been established that two separated regions of the coding sequence of a tRNA gene are essential and sufficient for promotion of transcription. Our objective is to find out the two essential regions in the genome sequence which comprises two halves of the hidden tRNAs. Material and Methods: Considering the existence of split tRNA genes widely separated throughout the genome, we developed our tRNA search algorithm to predict such separated tRNA genes by searching both a conserved terminal 5'-and 3'-motif of tRNA in agreement with the split hypothesis on the basis of cloverleaf prediction and precise insilico determination of bulge-helix-bulge secondary structure at the splice sites. Results: By a comprehensive search for all kinds of missing tRNA genes, we have constructed hybrid tRNA genes containing one essential region from tDNA (XYZ) and the other from tDNA (ABC), both from same species in the archaea. We have also found, this type of hybrid tRNA genes are identified in the different species of the archaea (XYZ: ASN, ARG and MET; ABC: ASP,SER, ARG and PRO).These hybrid split tRNA share a common structural motif called bulge-helix-bulge (BHB) a more relaxed bulge-helix loop (BHL), at the leader exon boundary and suggested to be evolutionary interrelated. Conclusions: Analysis of the complete genome sequences of Metallosphaera sedula DSM 5348, Desulfurococcus kamchatkensis 1221n and Ignicoccus hospitalis KIN4/I in archaea by our algorithm revealed that a number of hybrid tRNAs are constructed from different tDNAs. Asymmetric combination of 5' and 3' tRNA halves may have generated the diversity of tRNA molecules. Our study of hybrid tRNA genes will provide a new molecular basis for upcoming tRNA studies.

Gene: X

The extensive research for predicting highly expressed genes in plant genome sequences has been g... more The extensive research for predicting highly expressed genes in plant genome sequences has been going on for decades. The codon usage pattern of genes in Arabidopsis thaliana genome is a classical topic for plant biologists for its significance in the understanding of molecular plant biology. Here we have used a gene expression profiling methodology based on the score of modified relative codon bias (MRCBS) to elucidate expression pattern of genes in Arabidopsis thaliana. MRCBS relies exclusively on sequence features for identifying the highly expressed genes. In this study, a critical analysis of predicted highly expressed (PHE) genes in Arabidopsis thaliana has been performed using MRCBS as a numerical estimator of gene expression level. Consistent with previous other results, our study indicates that codon composition plays an important role in the regulation of gene expression. We found a systematic strong correlation between MRCBS and CAI (codon adaptation index) or other expression-measures. Additionally, MRCBS correlates well with experimental gene expression data. Our study highlights the relationship between gene expression and compositional signature in relation to codon usage bias and sets the ground for the further investigation of the evolution of the protein-coding genes in the plant genome.

Genomics & informatics, 2017

Research into new methods for identifying highly expressed genes in anonymous genome sequences ha... more Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level. We found a systematic strong correlation between Codon Adaptation Index and MRCBS. Additionally, MRCBS correlated well with other expression measures. Our study indicates that MRCBS can consistently capture the highly expressed genes.

We precisely position a noncanonical intron in the odd second copy of tRNAAsp(GTC) gene in the ne... more We precisely position a noncanonical intron in the odd second copy of tRNAAsp(GTC) gene in the newly sequenced crenarchaea S.acidocaldarius. The uniform assortment of some features from normal aspartate tDNA and some from those corresponding to non-standard amino acids conduce us to conjecture it to be a novel tRNA gene, probably coding for a modified aspartate residue. Further we reposition intron in tRNAHis(GUG) gene in P.aerophilum.The BHB motif at the exon-intron boundaries are re-analyzed and found to support our conjectures.

The recent algorithm for five split tRNA-genes in N.equitans is new . It locates missing tRNA-trp... more The recent algorithm for five split tRNA-genes in N.equitans is new . It locates missing tRNA-trp, tRNA-imet, tRNA-glu and tRNA-his . But the split tRNA-trp(CCA) solution is anomalous ; the tRNA-imet lacks cognition elements for aminoacylation . In view therefore we present here alternate non-split composite solutions for tRNA-trp, tRNA-imet, tRNA-glu and tRNA-his .

Chinese Journal of Physics, 2005

The recently developed computational technique, the complex absorbing potential (CAP) method for ... more The recently developed computational technique, the complex absorbing potential (CAP) method for locating complex poles of resonance states, is applied to calculate the fieldinduced energy shifts and widths for the polyelectronic Na atom. The problem is formulated as an effective one-particle atomic system in external fields. In this regard we discuss the pertinence of using the model potential to simulate the multi-electron core interaction with the single valance electron. Results are presented for the 3S and 3P autoionizing states of Na (1s 2 2s 2 2p 6 nl) under the influence of electric and magnetic fields in parallel directions.

Advances in Bioscience and Biotechnology, 2011

Amongst endonuclease, the homodimeric variety is found in many prokaryotes for processing of the ... more Amongst endonuclease, the homodimeric variety is found in many prokaryotes for processing of the introns out from pre-RNAs. But as the variety and the complexity of introns rise with evolution, do the homodimeric endonuclease adapt to the changes? The correlations between evolving pre-RNAs and adapting homodimeric endonuclease in lower prokaryotes is investigated in this paper. First, we construct and observe the appearance of a long branch in the phylogeny based on homodimeric endonuclease. To appreciate the finer aspects of accelerating evolution near this long branch, we delve deeper into the pre-RNA substrates of the endonuclease. Computational evidence of an as-yet-unreported noncoding RNA gene then emerges from this study. The capabilities of homodimeric endonuclease and the complexities of its pre-RNA substrates appear to evolve in steps together.

Journal of Bioinformatics and Intelligent Control, 2014

Comparative and Functional Genomics, 2003

Our studies on the bases of codons from 11 completely sequenced archaeal genomes show that, as we... more Our studies on the bases of codons from 11 completely sequenced archaeal genomes show that, as we move from GC-rich to AT-rich protein-coding gene-containing species, the differences between G and C and between A and T, the purine load (AG content), and also the overall persistence (i.e. the tendency of a base to be followed by the same base) within codons, all increase almost simultaneously, although the extent of increase is different over the three positions within codons. These findings suggest that the deviations from the second parity rule (through the increasing differences between complementary base contents) and the increasing purine load hinder the chance of formation of the intra-strand Watson–Crick base-paired secondary structures in mRNAs (synonymous with the protein-coding genes we dealt with), thereby increasing the translational efficiency. We hypothesize that the ATrich protein-coding gene-containing archaeal species might have better translational efficiency than t...