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  1. Article: C. elegans

    Batachari, Lakshmi E / Dai, Alyssa Y / Troemel, Emily R

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Upon sensing viral RNA, mammalian RIG-I-like receptors activate downstream signals using caspase activation and recruitment domains (CARDs), which ultimately promote transcriptional immune responses that have been well-studied. In contrast, the ... ...

    Abstract Upon sensing viral RNA, mammalian RIG-I-like receptors activate downstream signals using caspase activation and recruitment domains (CARDs), which ultimately promote transcriptional immune responses that have been well-studied. In contrast, the downstream signaling mechanisms for invertebrate RIG-I-like receptors are much less clear. For example, the
    Language English
    Publishing date 2024-02-08
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.05.578694
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Similarities in the induction of the intracellular pathogen response in Caenorhabditis elegans and the type I interferon response in mammals.

    Lažetić, Vladimir / Batachari, Lakshmi E / Russell, Alistair B / Troemel, Emily R

    BioEssays : news and reviews in molecular, cellular and developmental biology

    2023  Volume 45, Issue 11, Page(s) e2300097

    Abstract: Although the type-I interferon (IFN-I) response is considered vertebrate-specific, recent findings about the Intracellular Pathogen Response (IPR) in nematode Caenorhabditis elegans indicate that there are similarities between these two transcriptional ... ...

    Abstract Although the type-I interferon (IFN-I) response is considered vertebrate-specific, recent findings about the Intracellular Pathogen Response (IPR) in nematode Caenorhabditis elegans indicate that there are similarities between these two transcriptional immunological programs. The IPR is induced during infection with natural intracellular fungal and viral pathogens of the intestine and promotes resistance against these pathogens. Similarly, the IFN-I response is induced by viruses and other intracellular pathogens and promotes resistance against infection. Whether the IPR and the IFN-I response evolved in a divergent or convergent manner is an unanswered and exciting question, which could be addressed by further studies of immunity against intracellular pathogens in C. elegans and other simple host organisms. Here we highlight similar roles played by RIG-I-like receptors, purine metabolism enzymes, proteotoxic stressors, and transcription factors to induce the IPR and IFN-I response, as well as the similar consequences of these defense programs on organismal development.
    MeSH term(s) Animals ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/metabolism ; Interferon Type I/metabolism ; Nematoda ; Mammals/metabolism
    Chemical Substances Caenorhabditis elegans Proteins ; Interferon Type I
    Language English
    Publishing date 2023-09-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.202300097
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Similarities in the induction of the intracellular pathogen response in Caenorhabditis elegans and the type I interferon response in mammals

    Lažetić, Vladimir / Batachari, Lakshmi E. / Russell, Alistair B. / Troemel, Emily R.

    BioEssays. 2023 Nov., v. 45, no. 11 p.e2300097-

    2023  

    Abstract: Although the type‐I interferon (IFN‐I) response is considered vertebrate‐specific, recent findings about the Intracellular Pathogen Response (IPR) in nematode Caenorhabditis elegans indicate that there are similarities between these two transcriptional ... ...

    Abstract Although the type‐I interferon (IFN‐I) response is considered vertebrate‐specific, recent findings about the Intracellular Pathogen Response (IPR) in nematode Caenorhabditis elegans indicate that there are similarities between these two transcriptional immunological programs. The IPR is induced during infection with natural intracellular fungal and viral pathogens of the intestine and promotes resistance against these pathogens. Similarly, the IFN‐I response is induced by viruses and other intracellular pathogens and promotes resistance against infection. Whether the IPR and the IFN‐I response evolved in a divergent or convergent manner is an unanswered and exciting question, which could be addressed by further studies of immunity against intracellular pathogens in C. elegans and other simple host organisms. Here we highlight similar roles played by RIG‐I‐like receptors, purine metabolism enzymes, proteotoxic stressors, and transcription factors to induce the IPR and IFN‐I response, as well as the similar consequences of these defense programs on organismal development.
    Keywords Caenorhabditis elegans ; fungi ; immunity ; interferons ; intestines ; metabolism ; pathogens ; transcription (genetics)
    Language English
    Dates of publication 2023-11
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.202300097
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  4. Article ; Online: Strain diversity in the microbiome: Lessons from Bacteroides fragilis.

    Carrow, Hannah C / Batachari, Lakshmi E / Chu, Hiutung

    PLoS pathogens

    2020  Volume 16, Issue 12, Page(s) e1009056

    MeSH term(s) Bacterial Infections/genetics ; Bacteroides fragilis/genetics ; Bacteroides fragilis/pathogenicity ; Genetic Variation/genetics ; Humans ; Microbiota/genetics
    Language English
    Publishing date 2020-12-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7374
    ISSN (online) 1553-7374
    ISSN 1553-7374
    DOI 10.1371/journal.ppat.1009056
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity.

    Mills, Robert H / Dulai, Parambir S / Vázquez-Baeza, Yoshiki / Sauceda, Consuelo / Daniel, Noëmie / Gerner, Romana R / Batachari, Lakshmi E / Malfavon, Mario / Zhu, Qiyun / Weldon, Kelly / Humphrey, Greg / Carrillo-Terrazas, Marvic / Goldasich, Lindsay DeRight / Bryant, MacKenzie / Raffatellu, Manuela / Quinn, Robert A / Gewirtz, Andrew T / Chassaing, Benoit / Chu, Hiutung /
    Sandborn, William J / Dorrestein, Pieter C / Knight, Rob / Gonzalez, David J

    Nature microbiology

    2022  Volume 7, Issue 2, Page(s) 262–276

    Abstract: Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six ... ...

    Abstract Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.
    MeSH term(s) Adult ; Animals ; Bacterial Proteins/classification ; Bacterial Proteins/genetics ; Bacteroides/enzymology ; Bacteroides/pathogenicity ; Cohort Studies ; Colitis, Ulcerative/microbiology ; Colitis, Ulcerative/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics ; Humans ; Longitudinal Studies ; Male ; Metagenome ; Metagenomics/methods ; Mice ; Middle Aged ; Peptide Hydrolases/classification ; Peptide Hydrolases/genetics ; Proteomics/methods ; Severity of Illness Index
    Chemical Substances Bacterial Proteins ; Peptide Hydrolases (EC 3.4.-)
    Language English
    Publishing date 2022-01-27
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-021-01050-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12.

    Wong, Garrett T / Bonocora, Richard P / Schep, Alicia N / Beeler, Suzannah M / Lee Fong, Anna J / Shull, Lauren M / Batachari, Lakshmi E / Dillon, Moira / Evans, Ciaran / Becker, Carla J / Bush, Eliot C / Hardin, Johanna / Wade, Joseph T / Stoebel, Daniel M

    Journal of bacteriology

    2017  Volume 199, Issue 7

    Abstract: The alternative sigma factor RpoS is a central regulator of many stress responses ... ...

    Abstract The alternative sigma factor RpoS is a central regulator of many stress responses in
    MeSH term(s) Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Blotting, Western ; Escherichia coli K12/metabolism ; Gene Expression Regulation, Bacterial/physiology ; Genome-Wide Association Study ; Mutation ; Promoter Regions, Genetic ; Sigma Factor/genetics ; Sigma Factor/metabolism ; Transcriptome
    Chemical Substances Bacterial Proteins ; Sigma Factor ; sigma factor KatF protein, Bacteria
    Language English
    Publishing date 2017-03-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.00755-16
    Database MEDical Literature Analysis and Retrieval System OnLINE

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