https://repository.auw.edu.bd/handle/123456789/678 2026-06-09T23:49:09Z 2026-06-09T23:49:09Z Roy, Ayan https://repository.auw.edu.bd/handle/123456789/745 2026-02-18T06:15:14Z 2015-01-01T00:00:00Z

Molecular characterization influencing metal resistance in the Cupriavidus/Ralstonia genomes Roy, Ayan Our environment is stressed with a load of heavy and toxic metals. Microbes, abundant in our environment are found to adapt well to this metal stressed condition. A comparative study among five Cupriavidus/Ralstonia genomes, can offer a better perception of their evolutionary mechanisms to adapt to these conditions. We have studied codon usage among 1051 genes common to all these organisms and identified 15 optimal codons frequently used in highly expressed genes present within 1051 genes. We found, the core genes of Cupriavidus metallidurans CH34 have a different optimal codon choice for Arginine, Glycine and Alanine in comparison to the other four bacteria. We also found that the synonymous codon-usage bias within these 1051 core genes is highly correlated with their gene expression. This supports that translational selection drives synonymous codon usage in the core genes of these genomes. Synonymous Codon usage is highly conserved in the core genes of these five genomes. The only exception among them is Cupriavidus metallidurans CH34. This genome-wide shift in synonymous codon choice in C. metallidurans CH34 may have taken place due to the insertion of new genes in its genomes facilitating them to survive in heavy-metal containing environment and the co-evolution of the other genes in its genome to achieve a balance in gene expression. Structural studies indicated the presence of a longer N-terminal region containing a copper binding domain in the cupC proteins of C. metallidurans CH3 that helps it to attain higher binding efficacy with copper in comparison to its orthologs.

2015-01-01T00:00:00Z Roy, Ayan https://repository.auw.edu.bd/handle/123456789/742 2026-02-18T06:14:57Z 2015-01-01T00:00:00Z

Comparative investigation of the various determinants that influence the codon and amino acid usage patterns in the genus Bifidobacterium Roy, Ayan Various strains of the genus Bifidobacterium are crucial members of the human, animal and insect gut, associated with beneficial probiotic activities. An extensive analysis on codon and amino acid usage of the GC rich genus Bifidobacterium has been executed in the present study. Multivariate statistical analysis revealed a coupled effect of GC compositional constraint and natural selection for translational efficiency to be operative in producing the observed codon usage variations. Gene expression level was inferred to be the most crucial factor governing the codon usage patterns. Amino acid usage was found to be influenced significantly by hydrophobic and aromatic character of the encoded proteins. Gene expressivity and protein energetic cost also had considerable impact on the differential mode of amino acid usage. The genus was found to strictly obey the cost-minimization hypothesis as was reflected from the amino acid usage patterns of the potential highly expressed gene products. Evolutionary analysis revealed that the highly expressed genes were candidates to extreme evolutionary selection pressure and indicated a high degree of conservation at the proteomic level. Interestingly, the complimentary strands of replica- tion appeared to evolve under similar evolutionary constraints which might be addressed as a consequence of absence of replicational selection and lack of strand- specific asymmetry among the members of the genus. Thus, the present endeavor confers considerable know-how pertaining to the codon and amino acid usage intricacies in Bifidobacterium and might prove handy for further scien- tific investigations associated with the concerned domain.

2015-01-01T00:00:00Z Roy, Ayan https://repository.auw.edu.bd/handle/123456789/726 2026-02-18T06:14:59Z 2015-01-01T00:00:00Z

Similarity of currently circulating H1N1 virus with the 2009 pandemic clone: Viability of an imminent pandemic Roy, Ayan The first influenza pandemic in the 21st century commenced in March, 2009 causing nearly 300,000 deaths globally within the first year of the pandemic. In late 2013 and in early 2014, there was gradual increase in the reported case of H1N1 infection and according to World Health Organization (WHO) report, influenza activity increased in several areas of the Southern Hemisphere and was dominated by the H1N1 pandemic strain of 2009. In the present study, a comprehensive comparison of the global amino acid composition and the structural features of all HA gene sequences of H1N1, available in the Flu Database (NCBI), from 1918 to December, 2014 has been performed to trace out the possibility of a further H1N1 pandemic in near future. The results suggest that the increased potential to enhance pathogenicity for the H1N1 samples of 2013 (latter part) and 2014 could lead to a more severe outbreak in the near future.

2015-01-01T00:00:00Z