Prof. Tapash Chandra Ghosh
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Recent Submissions
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Studies On The Relative Contribution Of Different Factors That Influence Codon Usage Patterns In Different Organisms
(Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 2019)Codon usage bias (CUB) and mRNA structural stability are important intrinsic features of mRNA that correlate positively with mRNA expression level. However, it remains unclear whether the mRNA expression level can be ... -
Synonymous Codon Usage in Lactococcus lactis: Mutational Bias Versus Translational Selection
(ADENINE PRESS, 2004-02)In this study codon usage bias of all experimentally known genes of Lactococcus lactis has been analyzed. Since Lactococcus lactis is an AT rich organism, it is expected to occur A and/or T at the third position of codons ... -
Correlations between genomic GC levels and optimal growth temperatures: some comments
(ACADEMIC PRESS, 2005-02-25)Regarding the existence of any specific correlation between optimal growth temperature and genomic GC levels, Musto et al. [FEBS Lett. 573 (2004) 73] have recently performed analysis on 20 prokaryotic families and showed ... -
The compositional transition of vertebrate genomes: an analysis of the secondary structure of the proteins encoded by human genes
(ELSEVIER SCIENCE, 2005-01-17)Fluctuations and increments of both C-3 and G(3) levels along the human coding sequences were investigated comparing two sets of Xenopus/human orthologous genes. The first set of genes shows minor differences of the GC(3) ... -
Investigation on the causes of codon and amino acid usages variation between thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis
(ADENINE PRESS,, 2004-10)Base composition, codon usages and amino acid usages have been analyzed by taking 529 orthologous sequences of Aquifex aeolicus and Bacillus subtilis, having different optimal growth temperatures. These two bacteria do not ... -
Evolutionary forces in shaping the codon and amino acid usages in Bochmannia floridanus
(ADENINE PRESS,, 2004-08)Endosymbiotic relationship has great effect on ecological system. Codon and amino acid usages bias of endosymbiotic bacteria Blochmannia floridanus (whose host is an ant Camponotus floridanus) was investigated using ... -
Shannon's uncertainty principle and gene expression levels
(CURRENT SCIENCE, 2004-04-25)Shannon's uncertainty principle has been applied to measure the degree of constraints in codon bias in the coding sequences of Escherichia coli, Saccharomyces cerevisiae and Haemophilus influenzae. Our study shows a high ... -
Structural Identification of the interactions of SoxA and SoxX during the oxidation of sulfur anions via the novel global sulfur oxidizing (Sox) operon
(Academic Journals, 2010)In this study, we have tried to elucidate the structural basis of the involvements of SoxA and SoxX in the binding and in electron transport during oxidation of sulfur anions via the novel global sulfur oxidation cycle. ... -
Compositional transitions between Oryza sativa and Arabidopsis thaliana genes are linked to the functional change of encoded proteins
(ELSEVIER SCIENCE, 2006-02)Compositional transition was previously reported between homologous pairs of Oryza sativa and Arabidopsis thaliana. We analysed 2041 homologous gene pairs of O. sativa and A. thaliana and found that the genes that underwent ... -
Synonymous codon usage analysis of the mycobacteriophage Bxz1 and its plating bacteria M-smegmatis: Identification of highly and lowly expressed genes of Bxz1 and the possible function of its tRNA species
(SPRINGER SINGAPORE PTE LTD, 2004-07-31)The extent of codon usage in the protein coding genes of the mycobacteriophage, Bxz1, and its plating bacteria, M. smegmatis, were determined, and it was observed that the codons ending with either G and / or C were ... -
Structural identification of a novel thioredoxin SoxS: Prediction of the function in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle
(ELSEVIER SCIENCE, 2006-01-31)Microbial redox reactions involving inorganic Sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically ... -
Structural insight into the interactions of SoxV, SoxW and SoxS in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle
(ELSEVIER SCIENCE, 2006-01-01)Microbial redox reactions involving inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically ... -
A structural study towards the understanding of the interactions of SoxY, SoxZ, and SoxB, leading to the oxidation of sulfur anions via the novel global sulfur oxidizing (sox) operon
(ACADEMIC PRESS, 2005-09-23)Microbial redox reactions of inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically diverse ... -
Role of mutational bias and natural selection on genome-wide nucleotide bias in prokaryotic organisms
(ELSEVIER SCI, 2005-07)Correlations between genomic GC contents and amino acid frequencies were studied in the homologous sequences of 12 eubacterial genomes. Results show that amino acids encoded by GC-rich codons increases significantly with ... -
On the origin of genomic adaptation at high temperature for prokaryotic organisms
(ELSEVIER SCIENCE, 2005-05-13)For a long time, the central issue of evolutionary genomics was to find out the adaptive strategy of nucleic acid molecules of various microorganisms having different optimal growth temperatures (T-opt). Long-standing ... -
Towards a resolution on the inherent methodological weakness of the "effective number of codons used by a gene"
(ELSEVIER SCIENCE, 2005-05-20)Recently Anders Fuglsang provided a modified way for calculating N-c when biased discrepancy is present in a gene [Biochem. Biophys. Res. Commun. 317 (2004) 957]. Instead of taking the average codon homozygosity for each ... -
Compositional correlations in canine genome reflects similarity with human genes
(SPRINGER, 2006-05-31)The base compositional correlations that hold among various coding and noncoding regions of the canine genome have been analysed. The distribution pattern of genes, on the basis of GC 3 composition, shows a wide range ... -
Structural and functional characterization of soxW-a thioredoxin involved in the transport of reductants during sulfur oxidation by the global sulfur oxidation reaction cycle
(Research Journal of Microbiology, 2010)Microbial oxidation-reduction reactions involving inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are carried out by ... -
Reinvestigating the codon and amino acid usage of S. cerevisiae genome: A new insight from protein secondary structure analysis
(ELSEVIER SCIENCE, 2003-03-28)Genomic GC (overall G + C content of the coding sequences) variations were reinvestigated between the orthologous genes of Mycobacterium tuberculosis and Mycobacterium leprae species. It was observed that overall genomic ... -
Structural study of two proteins SigE and ORF1 to predict their roles in the biochemical oxidation of sulfur anions via the global sulfur oxidation operon (sox)
(ELSEVIER SCIENCE, 2006-06)Microbial redox reactions involving inorganic sulfur compounds in the environment are one of the major reactions of the global sulfur cycle. These reactions are mediated by phylogenetically diverse prokaryotes containing ...
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