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  • 1
    Online Resource
    Online Resource
    Cost-effectiveness of the adherence with recommendations for clinical monitoring of patients with diabetes
    Elsevier BV ; 2021
    In:  Nutrition, Metabolism and Cardiovascular Diseases Vol. 31, No. 11 ( 2021-10), p. 3111-3121
    Details
    In: Nutrition, Metabolism and Cardiovascular Diseases, Elsevier BV, Vol. 31, No. 11 ( 2021-10), p. 3111-3121
    Type of Medium: Online Resource
    ISSN: 0939-4753
    URL: Article
    DOI: 10.1016/j.numecd.2021.07.014
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
    detail.hit.zdb_id: 2050914-5
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  • 2
    Online Resource
    Online Resource
    An RNA-centric view on gut Bacteroidetes
    Walter de Gruyter GmbH ; 2020
    In:  Biological Chemistry Vol. 402, No. 1 ( 2020-11-18), p. 55-72
    Details
    In: Biological Chemistry, Walter de Gruyter GmbH, Vol. 402, No. 1 ( 2020-11-18), p. 55-72
    Abstract: Bacteria employ noncoding RNAs to maintain cellular physiology, adapt global gene expression to fluctuating environments, sense nutrients, coordinate their interaction with companion microbes and host cells, and protect themselves against bacteriophages. While bacterial RNA research has made fundamental contributions to biomedicine and biotechnology, the bulk of our knowledge of RNA biology stems from the study of a handful of aerobic model species. In comparison, RNA research is lagging in many medically relevant obligate anaerobic species, in particular the numerous commensal bacteria comprising our gut microbiota. This review presents a guide to RNA-based regulatory mechanisms in the phylum Bacteroidetes, focusing on the most abundant bacterial genus in the human gut, Bacteroides spp. This includes recent case reports on riboswitches, an mRNA leader, cis - and trans -encoded small RNAs (sRNAs) in Bacteroides spp., and a survey of CRISPR-Cas systems across Bacteroidetes. Recent work from our laboratory now suggests the existence of hundreds of noncoding RNA candidates in Bacteroides thetaiotaomicron , the emerging model organism for functional microbiota research. Based on these collective observations, we predict mechanistic and functional commonalities and differences between Bacteroides sRNAs and those of other model bacteria, and outline open questions and tools needed to boost Bacteroidetes RNA research.
    Type of Medium: Online Resource
    ISSN: 1437-4315 , 1431-6730
    URL: Article
    DOI: 10.1515/hsz-2020-0230
    Language: English
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2020
    detail.hit.zdb_id: 1466062-3
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads
    Cold Spring Harbor Laboratory ; 2020
    In:  RNA Vol. 26, No. 8 ( 2020-08), p. 1069-1078
    Details
    In: RNA, Cold Spring Harbor Laboratory, Vol. 26, No. 8 ( 2020-08), p. 1069-1078
    Abstract: A major challenge for RNA-seq analysis of gene expression is to achieve sufficient coverage of informative nonribosomal transcripts. In eukaryotic samples, this is typically achieved by selective oligo(dT)-priming of messenger RNAs to exclude ribosomal RNA (rRNA) during cDNA synthesis. However, this strategy is not compatible with prokaryotes in which functional transcripts are generally not polyadenylated. To overcome this, we adopted DASH ( d epletion of a bundant s equences by h ybridization), initially developed for eukaryotic cells, to improve both the sensitivity and depth of bacterial RNA-seq. DASH uses the Cas9 nuclease to remove unwanted cDNA sequences prior to library amplification. We report the design, evaluation, and optimization of DASH experiments for standard bacterial short-read sequencing approaches, including software for automated guide RNA (gRNA) design for Cas9-mediated cleavage in bacterial rDNA sequences. Using these gRNA pools, we effectively removed rRNA reads (56%–86%) in RNA-seq libraries from two different model bacteria, the Gram-negative pathogen Salmonella enterica and the anaerobic gut commensal Bacteroides thetaiotaomicron . DASH works robustly, even with subnanogram amounts of input RNA. Its efficiency, high sensitivity, ease of implementation, and low cost (∼$5 per sample) render DASH an attractive alternative to rRNA removal protocols, in particular for material-constrained studies where conventional ribodepletion techniques fail.
    Type of Medium: Online Resource
    ISSN: 1355-8382 , 1469-9001
    URL: Article
    DOI: 10.1261/rna.075945.120
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2020
    detail.hit.zdb_id: 1475737-0
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Comparative genomics provides structural and functional insights into Bacteroides RNA biology
    Wiley ; 2022
    In:  Molecular Microbiology Vol. 117, No. 1 ( 2022-01), p. 67-85
    Details
    In: Molecular Microbiology, Wiley, Vol. 117, No. 1 ( 2022-01), p. 67-85
    Abstract: Bacteria employ noncoding RNA molecules for a wide range of biological processes, including scaffolding large molecular complexes, catalyzing chemical reactions, defending against phages, and controlling gene expression. Secondary structures, binding partners, and molecular mechanisms have been determined for numerous small noncoding RNAs (sRNAs) in model aerobic bacteria. However, technical hurdles have largely prevented analogous analyses in the anaerobic gut microbiota. While experimental techniques are being developed to investigate the sRNAs of gut commensals, computational tools and comparative genomics can provide immediate functional insight. Here, using Bacteroides thetaiotaomicron as a representative microbiota member, we illustrate how comparative genomics improves our understanding of RNA biology in an understudied gut bacterium. We investigate putative RNA‐binding proteins and predict a Bacteroides cold‐shock protein homolog to have an RNA‐related function. We apply an in silico protocol incorporating both sequence and structural analysis to determine the consensus structures and conservation of nine Bacteroides noncoding RNA families. Using structure probing, we validate and refine these predictions and deposit them in the Rfam database. Through synteny analyses, we illustrate how genomic coconservation can serve as a predictor of sRNA function. Altogether, this work showcases the power of RNA informatics for investigating the RNA biology of anaerobic microbiota members.
    Type of Medium: Online Resource
    ISSN: 0950-382X , 1365-2958
    URL: Issue
    URL: Article
    DOI: 10.1111/mmi.v117.1
    DOI: 10.1111/mmi.14793
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 1501537-3
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  • 5
    Online Resource
    Online Resource
    Cytosolic Ptbp2 modulates axon growth in motoneurons through axonal localization and translation of Hnrnpr
    Springer Science and Business Media LLC ; 2023
    In:  Nature Communications Vol. 14, No. 1 ( 2023-07-12)
    Details
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2023-07-12)
    Abstract: The neuronal RNA-binding protein Ptbp2 regulates neuronal differentiation by modulating alternative splicing programs in the nucleus. Such programs contribute to axonogenesis by adjusting the levels of protein isoforms involved in axon growth and branching. While its functions in alternative splicing have been described in detail, cytosolic roles of Ptbp2 for axon growth have remained elusive. Here, we show that Ptbp2 is located in the cytosol including axons and growth cones of motoneurons, and that depletion of cytosolic Ptbp2 affects axon growth. We identify Ptbp2 as a major interactor of the 3’ UTR of Hnrnpr mRNA encoding the RNA-binding protein hnRNP R. Axonal localization of Hnrnpr mRNA and local synthesis of hnRNP R protein are strongly reduced when Ptbp2 is depleted, leading to defective axon growth. Ptbp2 regulates hnRNP R translation by mediating the association of Hnrnpr with ribosomes in a manner dependent on the translation factor eIF5A2. Our data thus suggest a mechanism whereby cytosolic Ptbp2 modulates axon growth by fine-tuning the mRNA transport and local synthesis of an RNA-binding protein.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    URL: Article
    DOI: 10.1038/s41467-023-39787-6
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2553671-0
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