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Article ; Online: Evolutionary divergence of TLR9 through ancestral sequence reconstruction.

Ghosh, Manisha / Basak, Surajit / Dutta, Shanta

2024 Volume 76, Issue 3, Page(s) 203–211

Abstract: The transmembrane pattern recognition receptor, Toll-like receptor (TLR), are best known for their roles in innate immunity via recognition of pathogen and initiation of signaling response. Mammalian TLRs recognize molecular patterns associated with ... ...

Abstract	The transmembrane pattern recognition receptor, Toll-like receptor (TLR), are best known for their roles in innate immunity via recognition of pathogen and initiation of signaling response. Mammalian TLRs recognize molecular patterns associated with pathogens and initiate innate immune response. We have studied the evolutionary diversity of mammalian TLR genes for differences in immunological response. Reconstruction of ancestral sequences is a key aspect of the molecular evolution of TLR to track changes across the TLR genes. The comprehensive analysis of mammalian TLRs revealed a distinct pattern of evolution of TLR9. Various sequence-based features such as amino acid usage, hydrophobicity, GC content, and evolutionary constraints are found to influence the divergence of TLR9 from other TLRs. Ancestral sequence reconstruction analysis also revealed that the gradual evolution of TLR genes in several ancestral lineages leads to the distinct pattern of TLR9. It demonstrates evolutionary divergence with the progressive accumulation of mutations results in the distinct pattern of TLR9.
MeSH term(s)	Toll-Like Receptor 9/genetics ; Evolution, Molecular ; Animals ; Phylogeny ; Humans ; Genetic Variation ; Amino Acid Sequence ; Base Composition
Chemical Substances	Toll-Like Receptor 9 ; TLR9 protein, human
Language	English
Publishing date	2024-03-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186560-2
ISSN	1432-1211 ; 0093-7711
ISSN (online)	1432-1211
ISSN	0093-7711
DOI	10.1007/s00251-024-01338-8
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Article ; Online: Underlying selection for the diversity of Spike protein sequences of SARS-CoV-2

Basak, Surajit

bioRxiv

Abstract: The global spread of SARS-CoV-2 is fast moving and has caused a worldwide public health crisis. In the present manuscript we analyzed spike protein sequences of SARS-CoV-2 genomes to assess the impact of mutational diversity. We observed from amino acid ... ...

Abstract	The global spread of SARS-CoV-2 is fast moving and has caused a worldwide public health crisis. In the present manuscript we analyzed spike protein sequences of SARS-CoV-2 genomes to assess the impact of mutational diversity. We observed from amino acid usage patterns that spike proteins are associated with a diversity of mutational changes and most important underlying cause of variation of amino acid usage is the changes in hydrophobicity of spike proteins. The changing patterns of hydrophobicity of spike proteins over time and its influence on the receptor binding affinity provides crucial information on the SARS-CoV-2 interaction with human receptor. Our results also show that spike proteins have evolved to prefer more hydrophobic residues over time. The present study provides a comprehensive analysis of molecular sequence data to consider that mutational variants might play a crucial role in modulating the virulence and spread of the virus and has immediate implications for therapeutic strategies.
Keywords	covid19
Language	English
Publishing date	2021-10-22
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.10.22.465411
Database	COVID19

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Article ; Online: Emerging resistome diversity in clinical Vibrio cholerae strains revealing their role as potential reservoirs of antimicrobial resistance.

De, Rituparna / Mukhopadhyay, Asish K / Ghosh, Manisha / Basak, Surajit / Dutta, Shanta

Molecular biology reports

2024 Volume 51, Issue 1, Page(s) 409

Abstract: Background: This is a unique and novel study delineating the genotyping and subsequent prediction of AMR determinants of Vibrio cholerae revealing the potential of contemporary strains to serve as precursors of severe AMR crisis in cholera.: Methods ... ...

Abstract	Background: This is a unique and novel study delineating the genotyping and subsequent prediction of AMR determinants of Vibrio cholerae revealing the potential of contemporary strains to serve as precursors of severe AMR crisis in cholera. Methods and results: Genotyping of representative strains, VC1 and VC2 was undertaken to characterize antimicrobial resistance genes (ARGs) against chloramphenicol, SXT, nalidixic acid and streptomycin against which they were found to be resistant by antibiogram analysis in our previous investigation. strAB, sxt, sul2, qace∆1-sul1 were detected by PCR. Genome annotation and identification of ARGs with WGS helped to detect the presence of almG, varG, strA (APH(3'')-Ib), strB (APH(6)-Id), sul2, catB9, floR, CRP, dfrA1 genes. Signatures of resistance determinants and protein domains involved in antimicrobial resistance, primarily, efflux of antibiotics were identified on the basis of 30-100% homology to reference proteins. These domains were predicted to be involved in other metabolic functions on the basis of 100% identity with 100% coverage with reference protein and nucleotide sequences and were predicted to be of a diverse taxonomic origin accentuating the influence of the microbiota on AMR acquisition. Sequence analysis of QRDR (quinolone resistance-determining region) revealed SNPs. Cytoscape v3.8.2 was employed to analyse protein-protein interaction of MDR proteins, MdtA and EmrD-2, with nodes of vital AMR pathways. Vital nodes involved in efflux of different classes of antibiotics were found to be absent in VC1 and VC2 justifying the sensitivity of these strains to most antibiotics. Conclusions: The study helped to examine the resistome of VC isolated from recent outbreaks to understand the underlying reason of sensitivity to most antibiotics and also to characterize the ARGs in their genome. It revealed that VC is a reservoir of signatures of resistance determinants and serving as precursors for severe AMR crisis in cholera. This is the first study, to our knowledge, which has scrutinized and presented systematically, information on prospective domains which bear the potential of serving as AMR determinants in VC with the help of bioinformatic tools. This pioneering approach may help in the prediction of AMR landfalls and benefit epidemiological surveillance and early warning systems.
MeSH term(s)	Humans ; Vibrio cholerae/genetics ; Cholera/drug therapy ; Cholera/epidemiology ; Anti-Bacterial Agents/pharmacology ; Prospective Studies ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-03-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-024-09313-y
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Article ; Online: Emergence of Genomic Diversity in the Spike Protein of the "Omicron" Variant.

Basak, Surajit / Kayet, Pratanu / Ghosh, Manisha / Chatterjee, Joyeeta / Dutta, Shanta

Viruses

2023 Volume 15, Issue 10

Abstract: SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus) has constantly been evolving into different forms throughout its spread in the population. Emerging SARS-CoV-2 variants, predominantly the variants of concern (VOCs), could have an impact on the ... ...

Abstract	SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus) has constantly been evolving into different forms throughout its spread in the population. Emerging SARS-CoV-2 variants, predominantly the variants of concern (VOCs), could have an impact on the virus spread, pathogenicity, and diagnosis. The recently emerged "Omicron" variant has exhibited rapid transmission and divergence. The spike protein of SARS-CoV-2 has consistently been appearing as the mutational hotspot of all these VOCs. In order to determine a deeper understanding of the recently emerged and extremely divergent "Omicron", a study of amino acid usage patterns and their substitution patterns was performed and compared with those of the other four successful variants of concern ("Alpha", "Beta", "Gamma", and "Delta"). We observed that the amino acid usage of "Omicron" has a distinct pattern that distinguishes it from other VOCs and is significantly correlated with the increased hydrophobicity in spike proteins. We observed an increase in the non-synonymous substitution rate compared with the other four VOCs. Considering the phylogenetic relationship, we hypothesized about the functional interdependence between recombination and the mutation rate that might have resulted in a shift in the optimum of the mutation rate for the evolution of the "Omicron" variant. The results suggest that for improved disease prevention and control, more attention should be given to the significant genetic differentiation and diversity of newly emerging variants.
MeSH term(s)	Spike Glycoprotein, Coronavirus/genetics ; Phylogeny ; Genomics ; Amino Acids ; Genetic Drift
Chemical Substances	Spike Glycoprotein, Coronavirus ; Amino Acids
Language	English
Publishing date	2023-10-21
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15102132
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Article ; Online: Phylogeny and structural insights of lipase from Halopseudomonas maritima sp. nov., isolated from sea sand.

Kujur, Ritu Rani Archana / Ghosh, Manisha / Basak, Surajit / Das, Subrata K

International microbiology : the official journal of the Spanish Society for Microbiology

2023 Volume 26, Issue 4, Page(s) 1021–1031

Abstract: A Gram-negative, aerobic bacterial strain ... ...

Abstract	A Gram-negative, aerobic bacterial strain RR6
MeSH term(s)	Sand/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Lipase/genetics ; Phospholipids/chemistry ; DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Sequence Analysis, DNA
Chemical Substances	Sand ; RNA, Ribosomal, 16S ; Lipase (EC 3.1.1.3) ; Phospholipids ; DNA (9007-49-2) ; DNA, Bacterial
Language	English
Publishing date	2023-04-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1454951-7
ISSN	1618-1905 ; 1139-6709
ISSN (online)	1618-1905
ISSN	1139-6709
DOI	10.1007/s10123-023-00362-0
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Article ; Online: Natural selection shaped the evolution of amino acid usage in mammalian toll like receptor genes.

Ghosh, Manisha / Basak, Surajit / Dutta, Shanta

Computational biology and chemistry

2022 Volume 97, Page(s) 107637

Abstract: Toll-like receptors (TLRs) are important as they are able to sense diverse set of pathogens associated molecular patterns (PAMPs) as ligands. These receptors are involved in functions such as immune response, development of signaling process and cell ... ...

Abstract	Toll-like receptors (TLRs) are important as they are able to sense diverse set of pathogens associated molecular patterns (PAMPs) as ligands. These receptors are involved in functions such as immune response, development of signaling process and cell adhesion. In the present study we are interested to analyze the influence of evolutionary selection pressure on the mutational diversity of mammalian TLR genes. We observed differential patterns of amino acid usage between primate and non-primate mammalian TLR genes. GC-content of TLR genes and hydrophobicity of the encoded proteins are the most influential factors correlated with the differential pattern of amino acid usage.The influence of the subcellular location on the amino acid usage pattern of TLRs is evident in present study. Purifying selection is uniformly present on TLR genes, positively selected sites are mostly located over the ligand binding domain. Our study clearly demonstrates that natural selection has shaped the evolution of primate and non-primate mammalian TLR genes.
MeSH term(s)	Amino Acids/genetics ; Animals ; Evolution, Molecular ; Phylogeny ; Selection, Genetic ; Toll-Like Receptors/genetics
Chemical Substances	Amino Acids ; Toll-Like Receptors
Language	English
Publishing date	2022-02-02
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2022.107637
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Book ; Online: Majorana bound states in the presence of the half-smeared potential

Basak, Surajit / Ptok, Andrzej

2022

Abstract: The Majorana bound state can be realized in one dimensional chain, in form of two well localized and separated states at both ends of the chain. In this paper, we discuss the case when the potential is smeared at one end of the system. In our ... ...

Abstract	The Majorana bound state can be realized in one dimensional chain, in form of two well localized and separated states at both ends of the chain. In this paper, we discuss the case when the potential is smeared at one end of the system. In our investigation, we assume the smearing in form of a quadratic function of position. We show that the smearing potential lead to the emergence of extra in-gap states, and effectively decrease the local gap (around the smeared potential). The Majorana states are still preserved in the system, however, their localization depend on the smearing. Moreover, the symmetric localization of the Majorana states from both side of the system is no longer preserved in the presence of the smearing potential. Comment: 6 pages, 4 figures
Keywords	Condensed Matter - Superconductivity ; Condensed Matter - Materials Science
Publishing date	2022-08-17
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Termination dependence of the surface states in Pb$_{2}$Pd

Basak, Surajit / Ptok, Andrzej

2022

Abstract: Topological properties of systems lead to the emergence of surface states which can be observed experimentally within the angle-resolved photoemission spectroscopy (ARPES) measurements. Recently, the topological properties of Pb$_{2}$Pd were reported. In ...

Abstract	Topological properties of systems lead to the emergence of surface states which can be observed experimentally within the angle-resolved photoemission spectroscopy (ARPES) measurements. Recently, the topological properties of Pb$_{2}$Pd were reported. In this paper, we discuss the role of the surface termination on the realized surface states. We discuss the termination dependence of the surface state for (001) and (110) surface. We demonstrate that the Pd terminated (001) surface allow realization of the Dirac cone-like surface state. In the case (110) we observe well visible surface states with parabolic-like dispersion relation in close vicinity of the Fermi level. Comment: 6 pages, 5 figures
Keywords	Condensed Matter - Materials Science ; Condensed Matter - Superconductivity
Publishing date	2022-08-17
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Shiba states in systems with density of states singularities

Basak, Surajit / Ptok, Andrzej

2022

Abstract: Magnetic impurities placed in the superconductor can lead to emergence of the Yu-Shiba-Rusinov bound states. Coupling between the impurity and the substrate depends on density of states (DOS) at the Fermi level and can be tuned by DOS singularities. In ... ...

Abstract	Magnetic impurities placed in the superconductor can lead to emergence of the Yu-Shiba-Rusinov bound states. Coupling between the impurity and the substrate depends on density of states (DOS) at the Fermi level and can be tuned by DOS singularities. In this paper, we study the role of DOS singularities using the real space Bogoliubov-de Gennes equations for chosen lattice models. To uncover the role of these singularities (Dirac point, van Hove singularity, or the flat band), we study honeycomb, kagome, and Lieb lattices. We show that the properties of the Shiba state strongly depends on the type of lattice. Nevertheless some behaviors are generic, e.g. dependence of the critical magnetic coupling on the DOS at the Fermi level. However, the Shiba states realized in the Lieb lattice exhibit extraordinary properties, which can be explained by the presence of a few nonequivalent sublattices. Depending on the location of the magnetic impurity in the chosen sublattice, the value of critical magnetic coupling $J_\text{c}$ can be reduced or enhanced when the flat band is located at the Fermi level. In this context, we also present differences in the local DOS and coherence lengths for different sublattices in the Lieb lattice. Comment: 8 pages, 5 figures
Keywords	Condensed Matter - Superconductivity ; Condensed Matter - Materials Science
Subject code	530
Publishing date	2022-03-31
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Theoretical study of dynamical and electronic properties of noncentrosymmetric superconductor NbReSi

Basak, Surajit / Ptok, Andrzej

2022

Abstract: The noncentrosymmetric NbReSi superconductor with $T_{c} \simeq 6.5$ K is characterized by the relatively large upper critical magnetic field. Its multigap features were observed experimentally. Recent studies suggested realization of P$\bar{6}$2m or ... ...

Abstract	The noncentrosymmetric NbReSi superconductor with $T_{c} \simeq 6.5$ K is characterized by the relatively large upper critical magnetic field. Its multigap features were observed experimentally. Recent studies suggested realization of P$\bar{6}$2m or Ima2 symmetry. We discuss the dynamical properties of both symmetries (e.g., phonon spectra). In this paper, using the ab initio techniques, we clarify this ambiguity, and conclude that the Ima2 symmetry is unstable, and P$\bar{6}$2m should be realized. The P$\bar{6}$2m symmetry is also stable in the presence of external hydrostatic pressure. We show that NbReSi with the P$\bar{6}$2m symmetry should host phonon surface states for (100) and (110) surfaces. Additionally, we discuss the main electronic properties of the system with the stable symmetry. Comment: 10 pages, 7 figures
Keywords	Condensed Matter - Superconductivity ; Condensed Matter - Materials Science ; Condensed Matter - Strongly Correlated Electrons
Subject code	539
Publishing date	2022-12-15
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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