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  1. Article ; Online: Protocol to decode the role of transcriptionally active microbes in SARS-CoV-2-positive patients using an RNA-seq-based approach.

    Yadav, Aanchal / Devi, Priti / Kumari, Pallawi / Maurya, Ranjeet / Shamim, Uzma / Pandey, Rajesh

    STAR protocols

    2024  Volume 5, Issue 2, Page(s) 103071

    Abstract: The elucidation of the role of microorganisms in human infections has been hindered by difficulties using conventional culture-based techniques. Here, we present a protocol for the investigation of transcriptionally active microbes (TAMs) using an RNA ... ...

    Abstract The elucidation of the role of microorganisms in human infections has been hindered by difficulties using conventional culture-based techniques. Here, we present a protocol for the investigation of transcriptionally active microbes (TAMs) using an RNA sequencing (RNA-seq)-based approach. We describe the steps for RNA isolation, viral genome sequencing, RNA-seq library preparation, and metatranscriptomic and transcriptomic analysis. This protocol permits a comprehensive evaluation of TAMs' contributions to the differential severity of infectious diseases, with a particular focus on diseases such as COVID-19. For complete details on the use and execution of this protocol, please refer to Devi et al.
    Language English
    Publishing date 2024-05-19
    Publishing country United States
    Document type Journal Article
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2024.103071
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  2. Article ; Online: Characterization of

    Yadav, Monika / Kumar, Tarun / Maurya, Ranjeet / Pandey, Rajesh / Chauhan, Nar Singh

    Frontiers in cellular and infection microbiology

    2023  Volume 12, Page(s) 1082674

    Abstract: ... ...

    Abstract Cellulomonas
    MeSH term(s) Humans ; Cellulomonas/genetics ; Cellulomonas/chemistry ; Sequence Analysis, DNA ; Caco-2 Cells ; Ecosystem ; Probiotics ; Glutens ; RNA, Ribosomal, 16S/genetics
    Chemical Substances Glutens (8002-80-0) ; RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-01-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2022.1082674
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  3. Article: Isolation and Characterization of Human Intestinal Bacteria

    Yadav, Monika / Kumar, Tarun / Kanakan, Akshay / Maurya, Ranjeet / Pandey, Rajesh / Chauhan, Nar Singh

    Frontiers in microbiology

    2022  Volume 13, Page(s) 932795

    Abstract: Systemic characterization of the human gut microbiota highlighted its vast therapeutic potential. Despite having enormous potential, the non-availability of their culture representatives created a bottleneck to understand the concept of microbiome-based ... ...

    Abstract Systemic characterization of the human gut microbiota highlighted its vast therapeutic potential. Despite having enormous potential, the non-availability of their culture representatives created a bottleneck to understand the concept of microbiome-based therapeutics. The present study is aimed to isolate and evaluate the probiotic potential of a human gut isolate. Physiochemical, morphological, and phylogenetic characterization of a human gut isolate identifies it as a rod-shaped gram-negative microbe taxonomically affiliated with the
    Language English
    Publishing date 2022-07-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.932795
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  4. Article ; Online: Intertwined Dysregulation of Ribosomal Proteins and Immune Response Delineates SARS-CoV-2 Vaccination Breakthroughs.

    Maurya, Ranjeet / Shamim, Uzma / Mishra, Pallavi / Swaminathan, Aparna / Raina, Aakarshan / Tarai, Bansidhar / Budhiraja, Sandeep / Pandey, Rajesh

    Microbiology spectrum

    2023  Volume 11, Issue 3, Page(s) e0429222

    Abstract: Globally, COVID-19 vaccines have emerged as a boon, especially during the severe pandemic phases to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, saving millions of lives. However, mixed responses to ... ...

    Abstract Globally, COVID-19 vaccines have emerged as a boon, especially during the severe pandemic phases to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, saving millions of lives. However, mixed responses to vaccination with breakthrough challenges provided a rationale to explore the immune responses generated postvaccination, which plausibly alter the subsequent course of infection. In this regard, we comprehensively profiled the nasopharyngeal transcriptomic signature of double-dose-vaccinated individuals with breakthrough infections in comparison to unvaccinated infected persons. The vaccinated individuals demonstrated a gross downregulation of ribosomal proteins along with immune response genes and transcription/translational machinery that methodically modulated the entire innate immune landscape toward immune tolerance, a feature of innate immune memory. This coordinated response was orchestrated through 17 transcription factors captured as differentially expressed in the vaccination breakthroughs, including epigenetic modulators of
    MeSH term(s) Humans ; COVID-19 Vaccines ; SARS-CoV-2/genetics ; COVID-19/prevention & control ; Vaccination ; Immunity, Innate ; Breakthrough Infections
    Chemical Substances COVID-19 Vaccines
    Language English
    Publishing date 2023-04-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.04292-22
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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.

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

    iScience

    2023  Volume 26, Issue 12, Page(s) 108336

    Abstract: 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 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.
    Language English
    Publishing date 2023-10-27
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.108336
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  6. Article ; Online: Genome-Wide Identification and Characterization of Trihelix Gene Family in Asian and African Vigna Species

    Kumari, Shweta / Wankhede, Dhammaprakash Pandhari / Murmu, Sneha / Maurya, Ranjeet / Jaiswal, Sarika / Rai, Anil / Archak, Sunil

    Agriculture. 2022 Dec. 18, v. 12, no. 12

    2022  

    Abstract: Trihelix transcription factors play a crucial role in varied stress responses as well as in the growth and development of plants. The role of trihelix transcription factors in the non-shattering phenotype in domesticated rice is known. The Vigna group of ...

    Abstract Trihelix transcription factors play a crucial role in varied stress responses as well as in the growth and development of plants. The role of trihelix transcription factors in the non-shattering phenotype in domesticated rice is known. The Vigna group of crops has different degrees of shattering phenotypes in different species. To understand the evolutionary conservation or divergence of the trihelix gene family in important Vigna species here, the genome-wide identification and characterization of the trihelix gene family in four Vigna species including the cowpea (Vigna unguiculata), mung bean (V. radiata), adzuki bean (V. angularis) and rice bean (V. umbellata) was performed. A total of 39, 35, 41 and 50 trihelix genes were identified in the cowpea, mung bean, adzuki bean and rice bean, respectively. The trihelix genes in each of the four Vigna species were classified into five subgroups: GT, GTγ, SH4, S1P1 and GTδ. The members of each subgroup shared similar patterns of gene structure and motif across the four species. The cross-species positional relationships of the cowpea, adzuki bean and mung bean vis-a-vis rice trihelix genes were studied. Further, the Ka/Ks ratio for the trihelix genes in the four Vigna species indicated the purifying or stabilizing selection of the family. The gene expression analysis of the trihelix gene family in the cowpea showed that most of the genes express in at least some of the seed and/or pod developmental stages, although at varying degrees. Based on detailed bioinformatic analysis, a potential target for gene editing towards a possible non-shattering phenotype in the four important Vigna crops was discussed.
    Keywords Vigna angularis ; Vigna umbellata ; Vigna unguiculata ; agriculture ; bioinformatics ; cowpeas ; gene expression ; genes ; growth and development ; mung beans ; phenotype ; rice
    Language English
    Dates of publication 2022-1218
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2651678-0
    ISSN 2077-0472
    ISSN 2077-0472
    DOI 10.3390/agriculture12122172
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  7. Article: Centenary of Soil and Air Borne Wheat Karnal Bunt Disease Research: A Review

    Iquebal, Mir Asif / Mishra, Pallavi / Maurya, Ranjeet / Jaiswal, Sarika / Rai, Anil / Kumar, Dinesh

    Biology. 2021 Nov. 09, v. 10, no. 11

    2021  

    Abstract: Karnal bunt (KB) of wheat (Triticum aestivum L.), known as partial bunt has its origin in Karnal, India and is caused by Tilletia indica (Ti). Its incidence had grown drastically since late 1960s from northwestern India to northern India in early 1970s. ... ...

    Abstract Karnal bunt (KB) of wheat (Triticum aestivum L.), known as partial bunt has its origin in Karnal, India and is caused by Tilletia indica (Ti). Its incidence had grown drastically since late 1960s from northwestern India to northern India in early 1970s. It is a seed, air and soil borne pathogen mainly affecting common wheat, durum wheat, triticale and other related species. The seeds become inedible, inviable and infertile with the precedence of trimethylamine secreted by teliospores in the infected seeds. Initially the causal pathogen was named Tilletia indica but was later renamed Neovossia indica. The black powdered smelly spores remain viable for years in soil, wheat straw and farmyard manure as primary sources of inoculum. The losses reported were as high as 40% in India and also the cumulative reduction of national farm income in USA was USD 5.3 billion due to KB. The present review utilizes information from literature of the past 100 years, since 1909, to provide a comprehensive and updated understanding of KB, its causal pathogen, biology, epidemiology, pathogenesis, etc. Next generation sequencing (NGS) is gaining popularity in revolutionizing KB genomics for understanding and improving agronomic traits like yield, disease tolerance and disease resistance. Genetic resistance is the best way to manage KB, which may be achieved through detection of genes/quantitative trait loci (QTLs). The genome-wide association studies can be applied to reveal the association mapping panel for understanding and obtaining the KB resistance locus on the wheat genome, which can be crossed with elite wheat cultivars globally for a diverse wheat breeding program. The review discusses the current NGS-based genomic studies, assembly, annotations, resistant QTLs, GWAS, technology landscape of diagnostics and management of KB. The compiled exhaustive information can be beneficial to the wheat breeders for better understanding of incidence of disease in endeavor of quality production of the crop.
    Keywords Tilletia indica ; Triticum aestivum ; air ; animal manures ; cultivars ; diagnostic techniques ; disease incidence ; disease resistance ; durum wheat ; farm income ; genetic resistance ; genomics ; inoculum ; karnal bunt ; landscapes ; pathogenesis ; pathogens ; quantitative traits ; resistance genes ; soil ; teliospores ; trimethylamine ; triticale ; wheat straw ; India
    Language English
    Dates of publication 2021-1109
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology10111152
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  8. Article: Centenary of Soil and Air Borne Wheat Karnal Bunt Disease Research: A Review.

    Iquebal, Mir Asif / Mishra, Pallavi / Maurya, Ranjeet / Jaiswal, Sarika / Rai, Anil / Kumar, Dinesh

    Biology

    2021  Volume 10, Issue 11

    Abstract: Karnal bunt (KB) of wheat ( ...

    Abstract Karnal bunt (KB) of wheat (
    Language English
    Publishing date 2021-11-09
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology10111152
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  9. Article ; Online: Infection outcome needs two to tango: human host and the pathogen.

    Maurya, Ranjeet / Kanakan, Akshay / Vasudevan, Janani Srinivasa / Chattopadhyay, Partha / Pandey, Rajesh

    Briefings in functional genomics

    2021  Volume 21, Issue 2, Page(s) 90–102

    Abstract: Infectious diseases are potential drivers for human evolution, through a complex, continuous and dynamic interaction between the host and the pathogen/s. It is this dynamic interaction that contributes toward the clinical outcome of a pathogenic disease. ...

    Abstract Infectious diseases are potential drivers for human evolution, through a complex, continuous and dynamic interaction between the host and the pathogen/s. It is this dynamic interaction that contributes toward the clinical outcome of a pathogenic disease. These are modulated by contributions from the human genetic variants, transcriptional response (including noncoding RNA) and the pathogen's genome architecture. Modern genomic tools and techniques have been crucial for the detection and genomic characterization of pathogens with respect to the emerging infectious diseases. Aided by next-generation sequencing (NGS), risk stratification of host population/s allows for the identification of susceptible subgroups and better disease management. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain. In this review, we elucidate how a better understanding of the human host-pathogen interplay can substantially enhance, and in turn benefit from, current and future applications of multi-omics based approaches in infectious and rare diseases. This includes the RNA-level response, which modulates the disease severity and outcome. The need to understand the role of human genetic variants in disease severity and clinical outcome has been further highlighted during the Coronavirus disease 2019 (COVID-19) pandemic. This would enhance and contribute toward our future pandemic preparedness.
    MeSH term(s) COVID-19/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/genetics ; Humans ; Pandemics
    Language English
    Publishing date 2021-07-07
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2540916-5
    ISSN 2041-2657 ; 2041-2649 ; 2041-2647
    ISSN (online) 2041-2657
    ISSN 2041-2649 ; 2041-2647
    DOI 10.1093/bfgp/elab037
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  10. Article ; Online: Draft genome sequence and functional analysis of Lysinibacillus

    Phazna, T A / Ngashangva, N G / Yentrembam, Randhir-Babu Singh / Maurya, Ranjeet / Mukherjee, Pulok / Sharma, Chandradev / Verma, Praveen K / Sarangthem, Indira

    Journal of biosciences

    2022  Volume 47

    Abstract: Capsicum chinense is the chilli species containing the highest amount of capsaicin, and is an important traditional spice crop of Northeast India. Capsaicinoids derived ... ...

    Abstract Capsicum chinense is the chilli species containing the highest amount of capsaicin, and is an important traditional spice crop of Northeast India. Capsaicinoids derived from
    MeSH term(s) Agrochemicals/metabolism ; Bacillaceae ; Bacteria/genetics ; Bacteriocins/metabolism ; Capsaicin/metabolism ; Capsicum/metabolism ; Humans ; Pesticides ; Plant Diseases/microbiology ; Plant Diseases/prevention & control ; Polyketides/metabolism ; Rhizosphere ; Siderophores ; Soil ; Soil Microbiology ; Terpenes/metabolism
    Chemical Substances Agrochemicals ; Bacteriocins ; Pesticides ; Polyketides ; Siderophores ; Soil ; Terpenes ; Capsaicin (S07O44R1ZM)
    Language English
    Publishing date 2022-10-12
    Publishing country India
    Document type Journal Article
    ZDB-ID 756157-x
    ISSN 0973-7138 ; 0250-5991
    ISSN (online) 0973-7138
    ISSN 0250-5991
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