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  1. Article: Biography of a scientist with strength, substance, sincerity and service: Late N. Srinivasan (1962-2021).

    Sowdhamini, R

    Bioinformation

    2022  Volume 18, Issue 6, Page(s) 600–603

    Abstract: Late N. Srinivasan belongs to the GN Ramachandran lineage of protein structural analysts. His role in the advancement of the structure based understanding of signal transduction, protein kinase analyses and host-pathogen interactions both developing and ... ...

    Abstract Late N. Srinivasan belongs to the GN Ramachandran lineage of protein structural analysts. His role in the advancement of the structure based understanding of signal transduction, protein kinase analyses and host-pathogen interactions both developing and using Bioinformatics tools for protein-protein interactions, protein dynamics, remote homology detection and polypeptide stereochemistry is well documented in the literature. Thus, his contribution to the understanding of protein function through structural analysis, using computational models and tools, is exceptional.
    Language English
    Publishing date 2022-06-30
    Publishing country Singapore
    Document type Editorial
    ZDB-ID 2203786-X
    ISSN 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630018600
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online ; E-Book: Bioinformatics for agriculture: high-throughput approaches

    Upadhyay, Atul Kumar / Sowdhamini, R. / Patil, Virupaksh U.

    2021  

    Author's details Atul Kumar Upadhyay, R Sowdhamini, Virupaksh U. Patil, editors
    Keywords Bioinformatics ; Human genetics ; Agriculture ; Plant genetics
    Subject code 570.285
    Language English
    Size 1 Online-Ressource (v, 160 Seiten)
    Publisher Springer
    Publishing place Singapore
    Publishing country Singapore
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    HBZ-ID HT021132946
    ISBN 978-981-33-4791-5 ; 9789813347908 ; 9789813347922 ; 9789813347939 ; 981-33-4791-0 ; 9813347902 ; 9813347929 ; 9813347937
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  3. Article: Structure modelling of odorant receptor from

    Tiwari, Vikas / Sowdhamini, R

    Computational and structural biotechnology journal

    2023  Volume 21, Page(s) 2204–2214

    Abstract: Odorant receptors (ORs) are important class of proteins involved in olfactory behaviour of insects. These are GPCR-like heptahelical transmembrane proteins with inverted topology compared to GPCR and require a co-receptor (ORco) for their function. OR ... ...

    Abstract Odorant receptors (ORs) are important class of proteins involved in olfactory behaviour of insects. These are GPCR-like heptahelical transmembrane proteins with inverted topology compared to GPCR and require a co-receptor (ORco) for their function. OR function can be modulated through small molecules and negative modulation can be beneficial in case of disease vectors like
    Language English
    Publishing date 2023-03-06
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2023.03.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Computational analysis of the flexibility in the disordered linker region connecting LIM domains in cysteine-glycine-rich protein.

    Chauhan, Pankaj Kumar / Sowdhamini, R

    Frontiers in genetics

    2023  Volume 14, Page(s) 1134509

    Abstract: One of the key proteins that are present in the Z-disc of cardiac tissues, CSRP3, has been implicated in dilated and hypertrophic cardiomyopathy leading to heart failure. Although multiple cardiomyopathy-related mutations have been reported to reside on ... ...

    Abstract One of the key proteins that are present in the Z-disc of cardiac tissues, CSRP3, has been implicated in dilated and hypertrophic cardiomyopathy leading to heart failure. Although multiple cardiomyopathy-related mutations have been reported to reside on the two LIM domains and the disordered regions connecting the domains in this protein, the exact role of the disordered linker region is not clear. The linker harbors a few post-translational modification sites and is expected to be a regulatory site. We have carried out evolutionary studies on 5614 homologs spanning across taxa. We also performed molecular dynamics simulations of full-length CSRP3 to show that the length variations and conformational flexibility of the disordered linker could provide additional levels of functional modulation. Finally, we show that the CSRP3 homologs with widely different lengths of the linker regions could display diversity in their functional specifications. The present study provides a useful perspective to our understanding of the evolution of the disordered region between CSRP3 LIM domains.
    Language English
    Publishing date 2023-03-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1134509
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Structural modelling and dynamics of full-length of TLR10 sheds light on possible modes of dimerization, ligand binding and mechanism of action.

    Tiwari, Vikas / Sowdhamini, R

    Current research in structural biology

    2023  Volume 5, Page(s) 100097

    Abstract: Toll like receptors (TLRs) play a pivotal role in innate and adaptive immunity. There are 10 TLRs in the human genome, of which TLR10 is the least characterized. Genetic polymorphism of TLR10 has been shown to be associated with multiple diseases ... ...

    Abstract Toll like receptors (TLRs) play a pivotal role in innate and adaptive immunity. There are 10 TLRs in the human genome, of which TLR10 is the least characterized. Genetic polymorphism of TLR10 has been shown to be associated with multiple diseases including tuberculosis and rheumatoid arthritis. TLR10 consists of an extracellular domain (ECD), a single-pass transmembrane (TM) helix and intracellular TIR (Toll/Interleukin-1 receptor) domain. ECD is employed for ligand recognition and the intracellular domain interacts with other TIR domain-containing adapter proteins for signal transduction. Experimental structure of ECD or TM domain is not available for TLR10. In this study, we have modelled multiple forms of TLR10-ECD dimers, such as closed and open forms, starting from available structures of homologues. Subsequently, multiple full-length TLR10 homodimer models were generated by utilizing homology modelling and protein-protein docking. The dynamics of these models in membrane-aqueous environment revealed the global motion of ECD and TIR domain towards membrane bilayer. The TIR domain residues exhibited high root mean square fluctuation compared to ECD. The 'closed form' model was observed to be energetically more favorable than 'open form' model. The evaluation of persistent interchain interactions, along with their conservation score, unveiled critical residues for each model. Further, the binding of dsRNA to TLR10 was modelled by defined and blind docking approaches. Differential binding of dsRNA to the protomers of TLR10 was observed upon simulation that could provide clues on ligand disassociation. Dynamic network analysis revealed that the 'open form' model can be the functional form while 'closed form' model can be the apo form of TLR10.
    Language English
    Publishing date 2023-02-18
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2665-928X
    ISSN (online) 2665-928X
    DOI 10.1016/j.crstbi.2023.100097
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Transcriptome data analysis of primary cardiomyopathies reveals perturbations in arachidonic acid metabolism.

    Chauhan, Pankaj Kumar / Sowdhamini, Ramanathan

    Frontiers in cardiovascular medicine

    2023  Volume 10, Page(s) 1110119

    Abstract: Introduction: Cardiomyopathies are complex heart diseases with significant prevalence around the world. Among these, primary forms are the major contributors to heart failure and sudden cardiac death. As a high-energy demanding engine, the heart ... ...

    Abstract Introduction: Cardiomyopathies are complex heart diseases with significant prevalence around the world. Among these, primary forms are the major contributors to heart failure and sudden cardiac death. As a high-energy demanding engine, the heart utilizes fatty acids, glucose, amino acid, lactate and ketone bodies for energy to meet its requirement. However, continuous myocardial stress and cardiomyopathies drive towards metabolic impairment that advances heart failure (HF) pathogenesis. So far, metabolic profile correlation across different cardiomyopathies remains poorly understood.
    Methods: In this study, we systematically explore metabolic differences amongst primary cardiomyopathies. By assessing the metabolic gene expression of all primary cardiomyopathies, we highlight the significantly shared and distinct metabolic pathways that may represent specialized adaptations to unique cellular demands. We utilized publicly available RNA-seq datasets to profile global changes in the above diseases (|
    Results: Our analysis demonstrates that genes in arachidonic acid metabolism (AA) are significantly perturbed across cardiomyopathies. In particular, the arachidonic acid metabolism gene
    Conclusion: The profound significance of AA metabolism within the cardiovascular system renders it a key player in modulating the phenotypes of cardiomyopathies.
    Language English
    Publishing date 2023-05-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2781496-8
    ISSN 2297-055X
    ISSN 2297-055X
    DOI 10.3389/fcvm.2023.1110119
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Integrated approaches for the recognition of small molecule inhibitors for Toll-like receptor 4.

    Verma, Shailya / Reddy, Purushotham / Sowdhamini, R

    Computational and structural biotechnology journal

    2023  Volume 21, Page(s) 3680–3689

    Abstract: Toll-like receptors (TLRs) are pattern recognition receptors present on the surface of cells playing a crucial role in innate immunity. One of the TLRs, TLR4, recognizes LPS (Lipopolysaccharide) as its ligand leading to the release of anti-inflammatory ... ...

    Abstract Toll-like receptors (TLRs) are pattern recognition receptors present on the surface of cells playing a crucial role in innate immunity. One of the TLRs, TLR4, recognizes LPS (Lipopolysaccharide) as its ligand leading to the release of anti-inflammatory mediators as well as pro-inflammatory cytokines through signal transduction and domain recruitment. TLR4 homodimerizes at its intracellular TIR (Toll/interleukin-1 receptor) domain that helps in the recruitment of the TRAM/TICAM2 (TIR domain-containing adaptor molecule 2) molecule. TRAM also contains TIR domain which in turn, dimerizes and functions as an adapter protein to further recruit TRIF/TICAM1 (TIR domain-containing adaptor molecule 1) protein for mediating downstream signaling. Apart from LPS, TLR4 also recognizes endogenous ligands like fibrinogen, HMGB1, and hyaluronan in autoimmune conditions and sepsis. We employed computational approaches to target TRAM and recognize small molecule inhibitors from small molecules of natural origin, as contained in the Super Natural II database. Finally, cell reporter assays and NMR studies enabled the identification of promising lead compounds. Hence, this study aims to attenuate the signaling of the TLR4-TRAM-TRIF cascade in these auto-inflammatory conditions.
    Language English
    Publishing date 2023-07-22
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2023.07.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Integrative network analysis interweaves the missing links in cardiomyopathy diseasome.

    Chauhan, Pankaj Kumar / Sowdhamini, Ramanathan

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 19670

    Abstract: Cardiomyopathies are progressive disease conditions that give rise to an abnormal heart phenotype and are a leading cause of heart failures in the general population. These are complex diseases that show co-morbidity with other diseases. The molecular ... ...

    Abstract Cardiomyopathies are progressive disease conditions that give rise to an abnormal heart phenotype and are a leading cause of heart failures in the general population. These are complex diseases that show co-morbidity with other diseases. The molecular interaction network in the localised disease neighbourhood is an important step toward deciphering molecular mechanisms underlying these complex conditions. In this pursuit, we employed network medicine techniques to systematically investigate cardiomyopathy's genetic interplay with other diseases and uncover the molecular players underlying these associations. We predicted a set of candidate genes in cardiomyopathy by exploring the DIAMOnD algorithm on the human interactome. We next revealed how these candidate genes form association across different diseases and highlighted the predominant association with brain, cancer and metabolic diseases. Through integrative systems analysis of molecular pathways, heart-specific mouse knockout data and disease tissue-specific transcriptomic data, we screened and ascertained prominent candidates that show abnormal heart phenotype, including NOS3, MMP2 and SIRT1. Our computational analysis broadens the understanding of the genetic associations of cardiomyopathies with other diseases and holds great potential in cardiomyopathy research.
    MeSH term(s) Humans ; Mice ; Animals ; Cardiomyopathies/genetics ; Phenotype ; Algorithms ; Heart
    Language English
    Publishing date 2022-11-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-24246-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members.

    Shafi, K Mohamed / Sowdhamini, Ramanathan

    BMC genomics

    2022  Volume 23, Issue 1, Page(s) 516

    Abstract: Background: Plant species from Rosaceae family are economically important. One of the major environmental factors impacting those species is cold stress. Although several Rosaceae plant genomes have recently been sequenced, there have been very few ... ...

    Abstract Background: Plant species from Rosaceae family are economically important. One of the major environmental factors impacting those species is cold stress. Although several Rosaceae plant genomes have recently been sequenced, there have been very few research conducted on cold upregulated genes and their promoter binding sites. In this study, we used computational approaches to identify and analyse potential cold stress response genes across ten Rosaceae family members.
    Results: Cold stress upregulated gene data from apple and strawberry were used to identify syntelogs in other Rosaceae species. Gene duplication analysis was carried out to better understand the distribution of these syntelog genes in different Rosaceae members. A total of 11,145 popular abiotic stress transcription factor-binding sites were identified in the upstream region of these potential cold-responsive genes, which were subsequently categorised into distinct transcription factor (TF) classes. MYB classes of transcription factor binding site (TFBS) were abundant, followed by bHLH, WRKY, and AP2/ERF. TFBS patterns in the promoter regions were compared among these species and gene families, found to be quite different even amongst functionally related syntelogs. A case study on important cold stress responsive transcription factor family, AP2/ERF showed less conservation in TFBS patterns in the promoter regions. This indicates that syntelogs from the same group may be comparable at the gene level but not at the level of cis-regulatory elements. Therefore, for such genes from the same family, different repertoire of TFs could be recruited for regulation and expression. Duplication events must have played a significant role in the similarity of TFBS patterns amongst few syntelogs of closely related species.
    Conclusions: Our study overall suggests that, despite being from the same gene family, different combinations of TFs may play a role in their regulation and expression. The findings of this study will provide information about potential genes involved in the cold stress response, which will aid future functional research of these gene families involved in many important biological processes.
    MeSH term(s) Cold-Shock Response/genetics ; Gene Expression Regulation, Plant ; Multigene Family ; Phylogeny ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Rosaceae/genetics ; Rosaceae/metabolism ; Stress, Physiological/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances Plant Proteins ; Transcription Factors
    Language English
    Publishing date 2022-07-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-022-08751-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Author Correction: LIM domain-wide comprehensive virtual mutagenesis provides structural rationale for cardiomyopathy mutations in CSRP3.

    Chauhan, Pankaj Kumar / Sowdhamini, Ramanathan

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 4363

    Language English
    Publishing date 2022-03-14
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-08526-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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