Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

<p>Abstract</p> <p>Background</p> <p>In <it>Escherichia coli</it>, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. To provide a comprehensive overview of sRNAs, we analysed the low-molecular-weight RNAs (< 200 nt) of <it>E. coli </it>with deep sequencing, because the regulatory RNAs in bacteria are usually 50-200 nt in length.</p> <p>Results</p> <p>We discovered 229 novel candidate sRNAs (≥ 50 nt) with computational or experimental evidence of transcription initiation. Among them, the expression of seven intergenic sRNAs and three <it>cis</it>-antisense sRNAs was detected by northern blot analysis. Interestingly, five novel sRNAs are expressed from prophage regions and we note that these sRNAs have several specific characteristics. Furthermore, we conducted an evolutionary conservation analysis of the candidate sRNAs and summarised the data among closely related bacterial strains.</p> <p>Conclusions</p> <p>This comprehensive screen for <it>E. coli </it>sRNAs using a deep sequencing approach has shown that many as-yet-undiscovered sRNAs are potentially encoded in the <it>E. coli </it>genome. We constructed the <it>Escherichia coli </it>Small RNA Browser (ECSBrowser; <url>http://rna.iab.keio.ac.jp/</url>), which integrates the data for previously identified sRNAs and the novel sRNAs found in this study.</p

YvqE and CovRS of Group A <i>Streptococcus</i> Play a Pivotal Role in Viability and Phenotypic Adaptations to Multiple Environmental Stresses

<div><p><i>Streptococcus pyogenes</i> (group A <i>Streptococcus</i>, or GAS) is a human pathogen that causes a wide range of diseases. For successful colonization within a variety of host niches, GAS utilizes TCSs to sense and respond to environmental changes and adapts its pathogenic traits accordingly; however, many GAS TCSs and their interactions remain uncharacterized. Here, we elucidated the roles of a poorly characterized TCS, YvqEC, and a well-studied TCS, CovRS, in 2 different GAS strain SSI-1 and JRS4, respectively. Deletion of <i>yvqE</i> and <i>yvqC</i> in JRS4 resulted in lower cell viability and abnormality of cell division when compared to the wild-type strain under standard culture conditions, demonstrating an important role for YvqEC. Furthermore, a double-deletion of <i>yvqEC</i> and <i>covRS</i> in SSI-1 and JRS4 resulted in a significantly impaired ability to survive under various stress conditions, as well as an increased sensitivity to cell wall-targeting antibiotics compared to that observed in either single mutant or wild-type strains suggesting synergistic interactions. Our findings provide new insights into the impact of poorly characterized TCS (YvqEC) and potential synergistic interactions between YvqEC and CovRS and reveal their potential role as novel therapeutic targets against GAS infection.</p></div

Paleogeography and tectono-stratigraphy of carboniferous-Permian and Triassic "Karoo-like" sequences of the congo basin

International audienceThe Congo Basin is a large Phanerozoic sedimentary basin with up to 3–6 km of Carboniferous to Triassic sequences, comparable to those of the Karoo Basins of southern Gondwana. Here, we present a substantially revised stratigraphy for the Congo Basin, based on new field observations, seismic and borehole data, together with paleontology and new geochronology. In the center of the basin, the deepest boreholes intercept 3 to 4 km thick successions of conglomerates and red sandstones that overlie carbonate rocks, which correlate to deformed upper Neoproterozoic (Pan African) platform sequences extending beyond the Congo Basin into the Pan African orogenic zones (e.g. the West Congolian Group). The overlying sequences are dated biostratigraphically to be Carboniferous-Permian (the Lukuga Group) and Triassic (the Haute Lueki Group) in age. A regional erosion surface separates these two groups, possibly related to late Paleozoic intracontinental deformation associated with the Mauritanian-Variscan and Cape-de la Ventana orogens flanking the northwestern and southern margins of Gondwana, respectively. This change in basin paleogeography is consistent with detrital zircons dated from these sequences that suggest the ca. 1.4 Ga Kibaran Belt along the eastern margin of the Congo Basin stopped acting as a major source during the early Mesozoic

Scented grasses in Norway - Identity and uses

Published version. Source at http://doi.org/10.1186/s13002-015-0070-y.Background: Some grass species are richer in coumarin and thus more sweetly scented than others. These have been eagerly sought after in parts of Norway, but the tradition has been weakly documented, both in terms of the species collected, their vernacular names, and uses. Methods: Based on literature data and a substantial body of information collected during my own ethnobotanical field work, artefacts and voucher specimens, the grass species are identified, and their uses clarified. Results: In Norwegian literature, the tradition of collecting and using scented grasses has received little attention, and past authors largely refer it to Anthoxanthum spp. The tradition’s concentration to the Sámi strongholds of northernmost Norway, and most authors’ lacking knowledge of the Sámi language, have contributed to the weak and misleading coverage in previous publications. Coumarin-rich grass species are well known in folk tradition in northernmost Norway, as luktegress (Norwegian, “scent grass”), háissasuoidni (North Sámi, “scent grass”), hajuheinä (Finnish, “scent grass”), or similar terms. They have been (and still are) frequently collected, and used as perfume, for storing with clothes, and a number of other purposes. Despite literature records identifying the species used as Anthoxanthum odoratum coll. (including A. nipponicum), the main source utilized in North Norway is Hierochloë odorata, both ssp. arctica and ssp. odorata. Anthoxanthum nipponicum and Milium effusum are alternative, but infrequently used sources of material, depending on local tradition and availability. Conclusion: By far the most important grass species hiding behind the “scented grass” tradition in Norway is Hierochloë odorata. Anthoxanthum nipponicum is also used, but much less frequently, and only a single record confirms the use of Milium effusum. Only the foliage of Hierochloë provides suitable material for making traditional braids. The three major ethnic groups in Norway have all utilized scented grasses as perfume and for storing with clothes, but the tradition’s geographical concentration to the far north of Norway (Finnmark and NE Troms), suggests that it has originally mainly been a Sámi tradition, adopted by their neighbours