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  1. Article ; Online: In silico approach for the identification of tRNA-derived small non-coding RNAs in SARS-CoV infection.

    Ajmeriya, Swati / Bharti, Deepak Ramkumar / Kumar, Amit / Rana, Shweta / Singh, Harpreet / Karmakar, Subhradip

    Journal of applied genetics

    2024  Volume 65, Issue 2, Page(s) 403–413

    Abstract: tsRNAs (tRNA-derived small non-coding RNAs), including tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been implicated in some viral infections, such as respiratory viral infections. However, their involvement in SARS-CoV infection is completely ... ...

    Abstract tsRNAs (tRNA-derived small non-coding RNAs), including tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been implicated in some viral infections, such as respiratory viral infections. However, their involvement in SARS-CoV infection is completely unknown. A comprehensive analysis was performed to determine tsRNA populations in a mouse model of SARS-CoV-infected samples containing the wild-type and attenuated viruses. Data from the Gene Expression Omnibus (GEO) dataset at NCBI (accession ID GSE90624 ) was used for this study. A count matrix was generated for the tRNAs. Differentially expressed tRNAs, followed by tsRNAs derived from each significant tRNAs at different conditions and time points between the two groups WT(SARS-CoV-MA15-WT) vs Mock and ΔE (SARS-CoV-MA15-ΔE) vs Mock were identified. Notably, significantly differentially expressed tRNAs at 2dpi but not at 4dpi. The tsRNAs originating from differentially expressed tRNAs across all the samples belonging to each condition (WT, ΔE, and Mock) were identified. Intriguingly, tRFs (tRNA-derived RNA fragments) exhibited higher levels compared to tiRNAs (tRNA-derived stress-induced RNAs) across all samples associated with WT SARS-CoV strain compared to ΔE and mock-infected samples. This discrepancy suggests a non-random formation of tsRNAs, hinting at a possible involvement of tsRNAs in SARS-CoV viral infection.
    MeSH term(s) Mice ; Animals ; Virus Diseases ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Severe acute respiratory syndrome-related coronavirus/genetics
    Chemical Substances RNA, Transfer (9014-25-9)
    Language English
    Publishing date 2024-03-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 1235302-4
    ISSN 2190-3883 ; 1234-1983
    ISSN (online) 2190-3883
    ISSN 1234-1983
    DOI 10.1007/s13353-024-00853-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Neutralizing Antibodies and Antibody-Dependent Enhancement in COVID-19: A Perspective.

    Ajmeriya, Swati / Kumar, Amit / Karmakar, Subhradip / Rana, Shweta / Singh, Harpreet

    Journal of the Indian Institute of Science

    2022  Volume 102, Issue 2, Page(s) 671–687

    Abstract: Antibody-dependent enhancement (ADE) is an alternative route of viral entry in the susceptible host cell. In this process, antiviral antibodies enhance the entry access of virus in the cells via interaction with the complement or Fc receptors leading to ... ...

    Abstract Antibody-dependent enhancement (ADE) is an alternative route of viral entry in the susceptible host cell. In this process, antiviral antibodies enhance the entry access of virus in the cells via interaction with the complement or Fc receptors leading to the worsening of infection. SARS-CoV-2 variants pose a general concern for the efficacy of neutralizing antibodies that may fail to neutralize infection, raising the possibility of a more severe form of COVID-19. Data from various studies on respiratory viruses raise the speculation that antibodies elicited against SARS-CoV-2 and during COVID-19 recovery could potentially exacerbate the infection through ADE at sub-neutralizing concentrations; this may contribute to disease pathogenesis. It is, therefore, of utmost importance to study the effectiveness of the anti-SARS-CoV-2 antibodies in COVID-19-infected subjects. Theoretically, ADE remains a general concern for the efficacy of antibodies elicited during infection, most notably in convalescent plasma therapy and in response to vaccines where it could be counterproductive.
    Language English
    Publishing date 2022-02-04
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2139553-6
    ISSN 0970-4140 ; 0970-4140 ; 0019-4964
    ISSN (online) 0970-4140
    ISSN 0970-4140 ; 0019-4964
    DOI 10.1007/s41745-021-00268-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Uncovering the role of aquaporin and chromobox family members as potential biomarkers in head and neck squamous cell carcinoma via integrative multiomics and in silico approach.

    Gurung, Rishabh / Masood, Mohammad / Singh, Prithvi / Jha, Prakash / Sinha, Anuradha / Ajmeriya, Swati / Sharma, Milin / Dohare, Ravins / Haque, Mohammad Mahfuzul

    Journal of applied genetics

    2024  

    Abstract: Head and neck squamous cell carcinoma (HNSC) is a diverse group of tumors arising from oral cavity, oropharynx, larynx, and hypopharynx squamous epithelium, posing significant morbidity. Aquaporins (AQPs) are membrane proteins forming water channels, ... ...

    Abstract Head and neck squamous cell carcinoma (HNSC) is a diverse group of tumors arising from oral cavity, oropharynx, larynx, and hypopharynx squamous epithelium, posing significant morbidity. Aquaporins (AQPs) are membrane proteins forming water channels, some associated with carcinomas. Chromobox (CBX) family is known to modulate physiological and oncological processes. In our study, we analyzed AQPs and CBXs having significant expression followed by their prognostic and mutational assessment. Next, we performed enrichment and tumor infiltration analysis followed by HPA validation. Lastly, we established a 3-node miRNA-TF-mRNA regulatory network and performed protein-protein docking of the highest-degree subnetwork motif between TF and mRNA. Significant upregulation of CBX3/2 and downregulation of AQP3/5/7 correlated with poor overall survival (OS) in HNSC patients. The most significant pathway, GO-BP, GO-MF, and GO-CC terms associated with AQP3 and CBX3 were passive transport by aquaporins, response to vitamin, glycerol channel activity, and condensed chromosome, centromeric region. AQP3 negatively correlated with [Formula: see text] T cells, positively with [Formula: see text] T cells and B cells, and negatively with tumor purity, whereas CBX3 positively correlated with [Formula: see text] T cells, negatively with [Formula: see text] T cells and B cells, and positively with tumor purity. Three-node miRNA-TF-mRNA regulatory network revealed a highest-degree subnetwork motif comprising one TF (SMAD3), one miRNA (miR-423-5p), and one mRNA (AQP3). Protein-protein interaction studies suggested a direct interaction between AQP3 and Smad3 proteins. We concluded that AQP3 and CBX3 hold potential as treatment strategies and individual prognostic biomarkers, while further protein-protein interaction studies of AQP3 could offer insights into its interactions with Smad3 proteins.
    Language English
    Publishing date 2024-02-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1235302-4
    ISSN 2190-3883 ; 1234-1983
    ISSN (online) 2190-3883
    ISSN 1234-1983
    DOI 10.1007/s13353-024-00843-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Unveiling the omicron B.1.1. 529

    Ruby Dhar / Joyeeta Talukdar / Arnab Nayek / Swati Ajmeriya / Arun Kumar / Subhradip Karmakar

    Asian Journal of Medical Sciences, Vol 13, Iss 1, Pp 166-

    The variant of concern that is rattling the globe

    2022  Volume 168

    Abstract: Most viruses–including SARS-CoV-2, seem to have evolved over time. The lack of stringent proofreading mechanisms makes viral DNA/RNA replication error-prone. When a virus replicates, it sometimes changes a little bit, which is called mutations. Any virus ...

    Abstract Most viruses–including SARS-CoV-2, seem to have evolved over time. The lack of stringent proofreading mechanisms makes viral DNA/RNA replication error-prone. When a virus replicates, it sometimes changes a little bit, which is called mutations. Any virus with one or more new mutations can be referred to as a “variant” of the original virus. The last 2 years have witnessed the emergence of a large number of variants. Since the pandemic’s beginning, the SARS-CoV-2 coronavirus has mutated extensively, resulting in the emergence of different variants of the virus. One of these is the delta variant (arising from Pango lineage B.1.617.2) that took the word in a storm this year (February-July). The current a variant of concern is the B.1.1.529 (Omicron) variant reported first from South Africa on November 24, 2021. In recent weeks, infections have been widely reported, along with the increased detection of the B.1.1.529 variant. We reviewed the emergence of the new variant (B1.1.529) and its possible outcomes.
    Keywords covid-19 ; sars-cov2 ; omicron ; pandemic ; variant of concern ; Medicine ; R
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Manipal College of Medical Sciences, Pokhara
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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