Prof. Tapash Chandra Ghosh: Recent submissions
Now showing items 21-40 of 45
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Temperature adaptation of synonymous codon usage in different functional categories of genes: A comparative study between homologous genes of Methanococcus jannaschii and Methanococcus maripaludis
(ELSEVIER SCIENCE, 2006-07-10)Synonymous codon usage of homologous sequences between Methanococcus jannaschii and Methanococcus maripaludis have been analyzed in three broad functional categories of genes namely: (i) information storage and processing; ... -
Nature of selective constraints on synonymous codon usage of rice differs in GC-poor and GC-rich genes
(ELSEVIER, 2007-10-01)Synonymous codon usage and cellular tRNA abundance are thought to be co-evolved in optimizing translational efficiencies in highly expressed genes. Here in this communication by taking the advantage of publicly available ... -
Synonymous codon usage in different protein secondary structural classes of human genes: Implication for increased non-randomness of GC(3) rich genes towards protein stability
(INDIAN ACAD SCIENCES, 2007-08)The relationship between the synonymous codon usage and different protein secondary structural classes were investigated using 401 Homo sapiens proteins extracted from Protein Data Bank (PDB). A simple Chi-square test was ... -
Structural insight into the functionality of the transcriptional regulator SoxR from Paracoccus pantotrophus in sulfur oxidation operon
(Academic Journals, 2007)The redox reactions involving inorganic sulfur compounds in the environment are one of the major reactions of the global sulfur cycle mediated by prokaryotes of different phylogenetic groups. The Sulfur oxidizing gene ... -
Homology modeling and molecular dynamics study of the interactions of SoxY and SoxZ: The central player of biochemical oxidation of sulfur anions in Pseudaminobacter salicylatoxidans
(Academic Journals, 2007)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 ... -
On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes
(ELSEVIER, 2007-12-22)Synonymous codon usage analysis between thermophilic and mesophilic prokaryotes has gained wide attention in recent years. Although it is known that thermophilic and mesophilic prokaryotes use different subset of synonymous ... -
Different functional classes of genes are characterized by different compositional properties
(ELSEVIER, 2007-12-22)A compositional analysis on a set of human genes classified in several functional classes was performed. We found out that the GC3, i.e. the GC level at the third codon positions, of the genes involved in cellular metabolism ... -
Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development
(SPRINGER, 2008-06)Cancer cells and tissues exhibit genome wide hypomethylation and regional hypermethylation. CpG-methylation of DNA ((Me)CpG-DNA) is defined as the formation of a C-C covalent bond between the 5'-C of cytosine and the -CH(3) ... -
Differential Selective Constraints Shaping Codon Usage Pattern of Housekeeping and Tissue-specific Homologous Genes of Rice and Arabidopsis
(OXFORD UNIV, 2008-12)Intra-genomic variation between housekeeping and tissue-specific genes has always been a study of interest in higher eukaryotes. To-date, however, no such investigation has been done in plants. Availability of whole genome ... -
Nucleotide Triplet Based Molecular Phylogeny of Class I and Class II Aminoacyl t-RNA Synthetase in Three Domain of Life Process: Bacteria, Archaea, and Eukarya
(ADENINE, 2008-12)The amoniacyl-tRNA synthetases are one of the major protein components in the translation machinery. These essential proteins are found in all forms of life and are responsible for charging their cognate tRNAs with the ... -
Delving deeper into the unexpected correlation between gene expressivity and codon usage bias of Escherichia coli genome
(ADENINE, 2008-06)Biased usage of synonymous codons has been elucidated under the perspective of cellular tRNA abundance and more recently by the mRNA secondary structure folding stability of the corresponding genes. Taking advantage of ... -
Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network
(ELSEVIER, 2009-01-15)Evolutionary rates of party hub and date hub proteins of Saccharomyces cerevisiae are analyzed under the perspective of ordered/disordered ness of proteins and the three dimensional structural context such as the solvent ... -
Structural interaction between DsrE-DsrF-DsrH proteins involved in the transport of electrons in the dsr operon.
(PubMed, 2008-04)Biological redox reactions of inorganic sulfur compounds are important for the proper maintenance of environmental sulfur balance. These reactions are mediated by phylogeneticaly diverse set of microorganisms. The protein ... -
Genomic adaptation of prokaryotic organisms at high temperature.
(Biomedical Informatics, 2010-02-28)One of the central issues of evolutionary genomics is to find out the adaptive strategies of microorganisms to stabilize nucleic acid molecules under high temperature. Thermal adaptation hypothesis gives a link between G+C ... -
Evolutionary constraints on hub and non-hub proteins in human protein interaction network: Insight from protein connectivity and intrinsic disorder
(ELSEVIER SCIENCE, 2009-04-01)It has been claimed that proteins with more interacting partners (hubs) are structurally more disordered and have a slow evolutionary rate. Here, in this paper we analyzed the evolutionary rate and structural disorderness ... -
Relationship between Gene Compactness and Base Composition in Rice and Human Genome
(ADENINE, 2010-02)In human, highly expressed genes contain shorter and fewer introns and these have been attributed to selection for economy in transcription and translation. On the other hand, in plants, it has been shown that highly ... -
Multifunctionality dominantly determines the rate of human housekeeping and tissue specific interacting protein evolution
(ELSEVIER SCIENCE, 2009-06-15)Elucidation of the determinants of the rate of protein sequence evolution is one of the great challenges in evolutionary biology. It has been proposed that housekeeping genes are evolutionarily slower than tissue specific ... -
Investigation of the molecular evolution of nitrogen fixation using nucleotide triplet based condensed matrix method
(IJIB, 2010)Evolutionary history of nitrogen fixation has been retraced by analyzing nif H, D and K genes, and whole genomes from cyanobacteria, proteobacteria, clostridia, actinobacteria, green sulfur bacteria and archaea using ... -
On nucleotide solvent accessibility in RNA structure
(ELSEVIER SCIENCE, 2010-09-01)Sequence dependence of solvent accessibility in globular and membrane proteins is well established. However, this important structural property has been poorly investigated in nucleic acids. On the other hand investigation ... -
Insights into the genomic features and evolutionary impact of the genes configuring duplicated pseudogenes in human
(ELSEVIER SCIENCE, 2010-09-24)Pseudogenes, regarded as 'genomic fossils', are DNA sequences resembling functional genes in perspective of sequence homology but completely non-functional. In this study, we explored the unique characteristic features of ...