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  1. Article ; Online: Transcriptionally active nasopharyngeal commensals and opportunistic microbial dynamics define mild symptoms in the COVID 19 vaccination breakthroughs.

    Priti Devi / Pallawi Kumari / Aanchal Yadav / Bansidhar Tarai / Sandeep Budhiraja / Uzma Shamim / Rajesh Pandey

    PLoS Pathogens, Vol 19, Iss 2, p e

    2023  Volume 1011160

    Abstract: The development of COVID 19 vaccines as an effort to mitigate the outbreak, has saved millions of lives globally. However, vaccination breakthroughs have continuously challenged the vaccines' effectiveness and provided incentives to explore facets ... ...

    Abstract The development of COVID 19 vaccines as an effort to mitigate the outbreak, has saved millions of lives globally. However, vaccination breakthroughs have continuously challenged the vaccines' effectiveness and provided incentives to explore facets holding potential to alter vaccination-induced immunity and protection from subsequent infection, especially VOCs (Variants Of Concern). We explored the functional dynamics of nasopharyngeal transcriptionally active microbes (TAMs) between vaccination breakthroughs and unvaccinated SARS-CoV-2 infected individuals. Microbial taxonomic communities were differentially altered with skewed enrichment of bacterial class/genera of Firmicutes and Gammaproteobacteria with grossly reduced phylum Bacteroidetes in vaccination breakthrough individuals. The Bacillus genus was abundant in Firmicutes in vaccination breakthrough whereas Prevotella among Bacteroides dominated the unvaccinated. Also, Pseudomonas and Salmonella of Gammaproteobacteria were overrepresented in vaccination breakthrough, whilst unvaccinated showed presence of several genera, Achromobacter, Bordetella, Burkholderia, Neisseria, Hemophilus, Salmonella and Pseudomonas, belonging to Proteobacteria. At species level, the microbiota of vaccination breakthrough exhibited relatively higher abundance of unique commensals, in comparison to potential opportunistic microbes enrichment in unvaccinated patients' microbiota. Functional metabolic pathways like amino acid biosynthesis, sulphate assimilation, fatty acid and beta oxidation, associated with generation of SCFAs (short chain fatty acids), were enriched in vaccination breakthroughs. Majorly, metabolic pathways of LCFAs biosynthesis (long chain fatty acids; oleate, dodecenoate, palmitoleate, gondoate) were found associated with the unvaccinated. Our research highlights that vaccination decreases the microbial diversity in terms of depleting opportunistic pathogens and increasing the preponderance of commensals with respect to unvaccinated patients. Metabolic pathway ...
    Keywords Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Unraveling the genetic evolution of SARS-CoV-2 Recombinants using mutational dynamics across the different lineages

    Varsha Ravi / Uzma Shamim / Md Abuzar Khan / Aparna Swaminathan / Pallavi Mishra / Rajender Singh / Pankaj Bharali / Nar Singh Chauhan / Rajesh Pandey

    Frontiers in Medicine, Vol

    2024  Volume 10

    Abstract: IntroductionRecombination serves as a common strategy employed by RNA viruses for their genetic evolution. Extensive genomic surveillance during the COVID-19 pandemic has reported SARS-CoV-2 Recombinant strains indicating recombination events during the ... ...

    Abstract IntroductionRecombination serves as a common strategy employed by RNA viruses for their genetic evolution. Extensive genomic surveillance during the COVID-19 pandemic has reported SARS-CoV-2 Recombinant strains indicating recombination events during the viral evolution. This study introspects the phenomenon of genome recombination by tracing the footprint of prominent lineages of SARS-CoV-2 at different time points in the context of on-going evolution and emergence of Recombinants.MethodWhole genome sequencing was carried out for 2,516 SARS-CoV-2 (discovery cohort) and 1,126 (validation cohort) using nasopharyngeal samples collected between the time period of March 2020 to August 2022, as part of the genomic surveillance program. The sequences were classified according to the different lineages of SARS-CoV-2 prevailing in India at respective time points.ResultsMutational diversity and abundance evaluation across the 12 lineages identified 58 Recombinant sequences as harboring the least number of mutations (n = 111), with 14 low-frequency unique mutations with major chunk of mutations coming from the BA.2. The spontaneously/dynamically increasing and decreasing trends of mutations highlight the loss of mutations in the Recombinants that were associated with the SARS-CoV-2 replication efficiency, infectivity, and disease severity, rendering them functionally with low infectivity and pathogenicity. Linkage disequilibrium (LD) analysis revealed that mutations comprising the LD blocks of BA.1, BA.2, and Recombinants were found as minor alleles or as low-frequency alleles in the LD blocks from the previous SARS-CoV-2 variant samples, especially Pre-VOC. Moreover, a dissipation in the size of LD blocks as well as LD decay along with a high negative regression coefficient (R squared) value was demonstrated in the Omicron and BA.1 and BA.2 lineages, which corroborated with the breakpoint analysis.ConclusionTogether, the findings help to understand the evolution and emergence of Recombinants after the Omicron lineages, ...
    Keywords SARS-CoV-2 ; lineages ; mutations ; recombination ; linkage disequilibrium ; breakpoints ; Medicine (General) ; R5-920
    Subject code 590
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Effect of preoperative intravenous steroids on seroma formation after modified radical mastectomy.

    Seth, Uzma Shamim / Perveen, Sughra / Khan, Imran / Ahmed, Tanwer / Kamal, Muhammad Taha / Khomusi, Munira Murtaza

    JPMA. The Journal of the Pakistan Medical Association

    2023  Volume 73, Issue 1, Page(s) 69–73

    Abstract: Objective: To analyse the efficacy of preoperative intravenous injection of 120mg of methylprednisolone acetate steroid on the formation of seroma after modified radical mastectomy in breast cancer patients.: Method: The case-control study was ... ...

    Abstract Objective: To analyse the efficacy of preoperative intravenous injection of 120mg of methylprednisolone acetate steroid on the formation of seroma after modified radical mastectomy in breast cancer patients.
    Method: The case-control study was conducted at Ward 3, Surgical Unit 1, Department of General Surgery, Jinnah Postgraduate Medical Centre, Karachi, from November 2020 to April 2021, and comprised female patients with biopsy-proven carcinoma of breast who were scheduled for elective definitive breast cancer surgery. The subjects were randomised into treatment group A and control group B. Group A was given a single dose of intravenous injection methylprednisolone acetate 120mg half-an-hour before surgery, while group B underwent similar surgery without the said injection. Seroma was graded using the Common Terminology Criteria for Adverse Events v3.0. The groups were compared for age, total drainage, duration of drainage, seroma grading and wound status. Data was analysed using SPSS 25.
    Results: Of the 60 patients, there were 30(50%) in each of the two groups. The age difference between groups was non-significant (p=0.346). There was a significant difference in the mean total drainage volume and mean duration of drainage between the groups (p=0.001). Seroma formation, seroma grading and wound status were not significantly different between the groups (p>0.05). The efficacy in treatment was high in group A (odds ratio: 2.78; 95% confidence interval: 0.65-13.94).
    Conclusions: A single preoperative dose of Injection methylprednisolone acetate was effective in terms of post-mastectomy outcomes.
    MeSH term(s) Female ; Humans ; Mastectomy, Modified Radical/adverse effects ; Mastectomy/adverse effects ; Seroma/etiology ; Breast Neoplasms/pathology ; Methylprednisolone Acetate ; Case-Control Studies ; Postoperative Complications/etiology ; Drainage ; Injections, Intravenous
    Chemical Substances Methylprednisolone Acetate (43502P7F0P)
    Language English
    Publishing date 2023-02-25
    Publishing country Pakistan
    Document type Randomized Controlled Trial ; Journal Article
    ZDB-ID 603873-6
    ISSN 0030-9982
    ISSN 0030-9982
    DOI 10.47391/JPMA.6112
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Response on U S Seth, et al. (J Pak Med Assoc. 73: 69 -73, 2022) Effect of preoperative intravenous steroids on seroma formation after modified radical mastectomy.

    Seth, Uzma Shamim / Perveen, Sughra / Khan, Imran / Ahmed, Tanwer / Kamal, Muhammad Taha / Khomusi, Munira Murtaza

    JPMA. The Journal of the Pakistan Medical Association

    2023  Volume 73, Issue 5, Page(s) 1153

    MeSH term(s) Humans ; Female ; Mastectomy, Modified Radical ; Seroma/etiology ; Breast Neoplasms/surgery ; Mastectomy/adverse effects ; Steroids
    Chemical Substances Steroids
    Language English
    Publishing date 2023-05-12
    Publishing country Pakistan
    Document type Letter ; Comment
    ZDB-ID 603873-6
    ISSN 0030-9982
    ISSN 0030-9982
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  5. Article ; Online: Co-evolution of SARS-CoV-2 variants and host immune response trajectories underlie COVID-19 pandemic to epidemic transition

    Ranjeet Maurya / Aparna Swaminathan / Uzma Shamim / Smriti Arora / Pallavi Mishra / Aakarshan Raina / Varsha Ravi / Bansidhar Tarai / Sandeep Budhiraja / Rajesh Pandey

    iScience, Vol 26, Iss 12, Pp 108336- (2023)

    2023  

    Abstract: Summary: COVID-19 pandemic saw emergence of multiple SAR-CoV-2 variants. Exacerbated risk of severe outcome and hospital admissions led us to comprehend differential host-immune kinetics associated with SARS-CoV-2 variants. Longitudinal investigation was ...

    Abstract Summary: COVID-19 pandemic saw emergence of multiple SAR-CoV-2 variants. Exacerbated risk of severe outcome and hospital admissions led us to comprehend differential host-immune kinetics associated with SARS-CoV-2 variants. Longitudinal investigation was conducted through different time periods of Pre-VOC and VOCs (Delta & Omicron) mapping host transcriptome features. Robust antiviral type-1 interferon response marked Omicron infection, which was largely missing during Pre-VOC and Delta waves. SARS-CoV-2-host protein-protein interactions and docking complexes highlighted N protein to interact with HNRNPA1 in Pre-VOC, demonstrating its functional role for enhanced viral replication. Omicron revealed enhanced binding efficiency of LARP1 to N protein, probably potentiating antiviral effects of LARP1. Differential expression of zinc finger protein genes, especially in Omicron, mechanistically support induction of strong IFN (Interferon) response, thereby strengthening early viral clearance. Study highlights eventual adaptation of host to immune activation patterns that interrupt virus evolution with enhanced immune-evasion mutations and counteraction mechanisms, delimiting the next phase of COVID-19 pandemic.
    Keywords Health sciences ; Medicine ; Virology ; Science ; Q
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Human‐host transcriptomic analysis reveals unique early innate immune responses in different sub‐phenotypes of COVID‐19

    Ranjeet Maurya / Uzma Shamim / Partha Chattopadhyay / Priyanka Mehta / Pallavi Mishra / Priti Devi / Aparna Swaminathan / Sheeba Saifi / Kriti Khare / Aanchal Yadav / Shaista Parveen / Pooja Sharma / Vivekanand A / Akansha Tyagi / Vinita Jha / Bansidhar Tarai / Sujeet Jha / Mohd Faruq / Sandeep Budhiraja /
    Rajesh Pandey

    Clinical and Translational Medicine, Vol 12, Iss 6, Pp n/a-n/a (2022)

    2022  

    Keywords Medicine (General) ; R5-920
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Generation of induced pluripotent stem cell line (IGIBi007-A) from a patient with a novel acromesomelic dysplasia, PRKG2 type (AMDP)

    Manish Kumar / Saruchi Wadhwa / Nishu Tyagi / Istaq Ahmad / Somesh Kumar / Shakti Sagar / Sana Zahra / Asangla Kamai / Uzma Shamim / Seema Kapoor / Mohammed Faruq

    Stem Cell Research, Vol 53, Iss , Pp 102340- (2021)

    2021  

    Abstract: Biallelic PRKG2 (Protein Kinase, cGMP dependent Type-2) mutations cause a novel acromesomelic dysplasia PRKG2 type. We report generation of induced pluripotent stem cell line from lymphoblastoid cell lines of the patient carrying the reported frameshift ... ...

    Abstract Biallelic PRKG2 (Protein Kinase, cGMP dependent Type-2) mutations cause a novel acromesomelic dysplasia PRKG2 type. We report generation of induced pluripotent stem cell line from lymphoblastoid cell lines of the patient carrying the reported frameshift mutation (p.Asn164Lysfs*2). The derived iPSC line exhibits all the features of pluripotency, free of major genetic alterations due to reprogramming process and has the capability to differentiate into three germ layers. This iPSC cell line may provide an opportunity to investigate the effect of PRKG2 mutations upon FGF (fibroblast-growth-factor) induced MAPK signalling involved in chondrocyte proliferation in-vitro and may aid in possible therapeutic screening of novel biomolecules.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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