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  • 1
    Language: English
    In: Molecular Cell, 07 June 2018, Vol.70(5), pp.785-799
    Description: Bacteria are an exceedingly diverse group of organisms whose molecular exploration is experiencing a renaissance. While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, Hfq, and ProQ, as well as CRISPR/Cas systems that are programmed by RNAs. Moreover, increasing interest in members of the human microbiota and environmental microbial communities has highlighted the importance of understudied bacterial species with largely unknown transcriptome structures and RNA-based control mechanisms. Collectively, this creates a need for global RNA biology approaches that can rapidly and comprehensively analyze the RNA composition of a bacterium of interest. We review such approaches with a focus on RNA-seq as a versatile tool to investigate the different layers of gene expression in which RNA is made, processed, regulated, modified, translated, and turned over. RNA-seq-based approaches are revolutionizing how bacterial RNA biology can be studied. Hör, Gorski, and Vogel review the available global methods that can be used to chart the increasingly diverse number of RNA species and functions in any microbe of interest.
    Keywords: RNA-Seq ; Non-Coding RNA ; Small RNA ; Transcription ; RNA-Binding Protein ; Post-Transcriptional Control ; Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 2
    In: EMBO Journal, 01 February 2017, Vol.36(3), pp.245-247
    Description: While bacteria were long thought to rely primarily on transcriptional control, it is now well established that they also use numerous small s to regulate translation and stability. There has recently been a surge in studies, including one by Waters ([Waters SA, 2017]) in this issue of , that have used clever variations of the ‐seq technique to comprehensively map small –target networks. Several recent studies have used clever variations of RNA‐seq techniques to comprehensively map small RNA–target networks involved in controlling bacterial gene expression.
    Keywords: Biology ; Chemistry;
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 3
    Language: English
    In: EMBO journal: European Molecular Biology Organization, 2017, Issue 3, pp.245-247
    ISSN: 0261-4189
    Source: Fundación Dialnet
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  • 4
    Language: English
    In: Frontiers in Microbiology, 01 May 2017, Vol.8
    Description: Plant growth can be affected by soil bacteria. In turn, plants are known to influence soil bacteria through rhizodeposits and changes in abiotic conditions. We aimed to quantify the phylotype richness and relative abundance of rhizosphere bacteria that are actually influenced in a plant species-specific manner and to determine the role of the disproportionately large diversity of low-abundance bacteria belonging to the rare biosphere (〈0.1 relative abundance) in this process. In addition, we aimed to determine whether plant phylogeny has an influence on the plant species-specific rhizosphere bacterial community. For this purpose, 19 herbaceous plant species from five different plant orders were grown in a common soil substrate. Bacterial communities in the initial soil substrate and the established rhizosphere soils were compared by 16S rRNA gene amplicon sequencing. Only a small number of bacterial operational taxonomic units (OTUs, 97% sequence identity) responded either positively (ca. 1%) or negatively (ca. 1%) to a specific plant species. On average, 91% of plant-specific positive response OTUs comprised bacteria belonging to the rare biosphere, highlighting that low-abundance populations are metabolically active in the rhizosphere. In addition, low-abundance OTUs were in terms of their summed relative abundance major drivers of the bacterial phyla composition across the rhizosphere of all tested plant species. However, no effect of plant phylogeny could be observed on the established rhizosphere bacterial communities, neither when considering differences in the overall established rhizosphere communities nor when considering plant species-specific responders only. Our study provides a quantitative assessment of the effect of plants on their rhizosphere bacteria across multiple plant orders. Plant species-specific effects on soil bacterial communities involved only 18–111 bacterial OTUs out of several 1000s; this minority may potentially impact plant growth in plant–bacteria interactions.
    Keywords: Microbiome ; Next-Generation Amplicon Sequencing ; Rhizosphere ; 16s Rrna Gene ; Rare Biosphere ; Biology
    E-ISSN: 1664-302X
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  • 5
    Language: English
    In: Current Opinion in Microbiology, October 2017, Vol.39, pp.152-160
    Description: The identification of new RNA functions and the functional annotation of transcripts in genomes represent exciting yet challenging endeavours of modern biology. Crucial insights into the biological roles of RNA molecules can be gained from the identification of the proteins with which they form specific complexes. Modern interactome techniques permit to profile RNA–protein interactions in a genome-wide manner and identify new RNA classes associated with globally acting RNA-binding proteins. Applied to a variety of organisms, these methods are already revolutionising our understanding of RNA-mediated biological processes. Here, we focus on one such approach — Gradient sequencing or Grad-seq — which has recently guided the discovery of protein ProQ and its associated small RNAs as a new domain of post-transcriptional control in bacteria.
    Keywords: Biology
    ISSN: 1369-5274
    E-ISSN: 1879-0364
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  • 6
    Language: English
    In: Diabetes, 05/2018, Vol.67(Supplement 1), p.2057-P
    ISSN: 0012-1797
    E-ISSN: 1939-327X
    Source: CrossRef
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  • 7
    Language: English
    In: BMJ Open Diabetes Research & Care, 10 March 2017, Vol.5(1)
    Description: Youth onset type 2 diabetes mellitus (YT2DM) is a globally rising phenomenon with substantial Asians representation. The understanding of its pathophysiology is derived largely from studies in the obese African-American and Caucasian populations, while studies on incretin effect are scarce. We examined the insulin resistance, β-cell function (BC), glucagon-like peptide (GLP)-1 hormone and incretin effect in Asian YT2DM.
    Keywords: Youth ; Type 2 Diabetes ; Beta Cell Function ; Incretin Physiology
    E-ISSN: 2052-4897
    E-ISSN: 20524897
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