1,720,983 research outputs found
Project PXD015051: "Identification of an RNA sponge that controls the levels, processing and efficacy of the RoxS riboregulator of central metabolism in B. subtilis"
No full textOnly a few small regulatory RNAs (sRNAs) have been characterized in B. subtilis, the paradigm of Gram-positive bacteria, and one of the major challenges is target identification. Here we use global in vivo RNA psoralen cross-linking to identify RNA-RNA partners in Bacillus subtilis. Two sRNAs, RoxS and FsrA, play key roles in balancing the metabolic state of the cell in response to carbon sources and iron limitation, respectively. In this study, we identify new mRNA targets for both RoxS and FsrA, and a small RNA (S345/RosA) that is able to interact with both sRNAs. We report that RosA controls the maturation and degradation of RoxS and acts as a sponge to limit the efficacy of RoxS on its targets. Expression of RosA is catabolically repressed by the transcription factor CcpA. We provide evidence that the RosA/RoxS interaction plays a key role in regulating metabolism in response to a switches in carbon source.Strains were grown to O.D. 600 nm 1.0 in LB. 20 O.D. units were harvested and washed 3 X with PBS to remove media components. Cells were resuspended in 200 µl urea buffer (8M urea, 50 mM Tris and 75 mM NaCl). 200 µl of urea buffer washed 0.1 µM beads were added to the cells before being disrupted using three rounds of bead beating for 40 seconds using a FastPrep. Cells were placed on ice between the three rounds of bead beating. The disrupted cells were then sonicated in a water bath for 15 minutes. Cell extracts were centrifuged at 15,000 x g, 5 min and supernatants used for protein quantification (Qubit protein assay kit). Protein reduction and alkylation was conducted by mixing 150 µg of total protein with 10 mM TCEP and 40 mM CAA, at 600 rpm, for 20 min at room temperature. After, proteins were predigested with 1.5 µg of rLysC (Promega) for 3 h at room temperature and samples diluted with 50 mM ammonium bicarbonate, 2 M urea final concentration. Protein digestion was performed with 1.5 µg of Trypsin (Promega) overnight at room temperature. The reaction was stopped by adding 1% TFA and 10 µg of peptides were desalted using StageTip (Rappsilber et al. Nat Protoc. 2007; DOI: 10.1038/nprot.2007.261). Reversed phase chromatography was used to separate 1 µg of tryptic peptides prior to mass spectrometric analysis. The cell proteomes were analysed with two columns, an Acclaim PepMap µ-precolumn cartridge 300 µm i.d. x 5 mm, 5 μm, 100 Å and an Acclaim PepMap RSLC 75 µm i.d. x 50 cm, 2 µm, 100 Å (Thermo Scientific). The columns were installed on an Ultimate 3000 RSLCnano system (Dionex) at 40ᵒC. Mobile phase buffer A was composed of 0.1% formic acid and mobile phase B was composed of acetonitrile containing 0.1% formic acid. Samples were loaded onto the µ-precolumn equilibrated in 2% aqueous acetonitrile containing 0.1% trifluoroacetic acid for 8 min at 10 µL min-1 after which peptides were eluted onto the analytical column at 250 nL min-1 by increasing the mobile phase B concentration from 8% B to 25% over 90 min, then to 35% B over 12 min, followed by a 3 min wash at 90% B and a 15 min re-equilibration at 4% B. Eluting peptides were converted to gas-phase ions by means of electrospray ionization and analysed on a Thermo Orbitrap Fusion (Thermo Scientific). Survey scans of peptide precursors from 375 to 1500 m/z were performed at 120K resolution (at 200 m/z) with a 2x105 ion count target. The maximum injection time was set to 150 ms. Tandem MS was performed by isolation at 1.2 Th using the quadrupole, HCD fragmentation with normalized collision energy of 33, and rapid scan MS analysis in the ion trap. The MS2 ion count target was set to 3x103 and maximum injection time was 200 ms. Precursors with charge state 2–6 were selected and sampled for MS2. The dynamic exclusion duration was set to 60 s with a 10 ppm tolerance around the selected precursor and its isotopes. Monoisotopic precursor selection was turned on and instrument was run in top speed mode.
Thermo-Scientific raw files were analysed using MaxQuant software v1.6.0.16 (Tyanova et al. 2016, The MaxQuant computational platform for mass-spectrometry based shotgun proteomics, Nature Protocols 11, 2301-2319; DOI: 10.1038/nprot.2016.136) against the UniProtKB B. subtilis database (UP000001570, 4,260 entries). Peptide sequences were assigned to MS/MS spectra using the following parameters: cysteine carbamidomethylation as a fixed modification and protein N-terminal acetylation and methionine oxidations as variable modifications. The FDR was set to 0.01 for both proteins and peptides with a minimum length of 7 amino acids and was determined by searching a reversed database. Enzyme specificity was trypsin with a maximum of two missed cleavages. Peptide identification was performed with an initial precursor mass deviation of 7 ppm and a fragment mass deviation of 20 ppm. The MaxQuant feature ‘match between runs’ was enabled. Label-free protein quantification (LFQ) was done with a minimum ratio count of 2. Data processing was performed using the Perseus module of MaxQuant v1.6.0.16 (Tyanova, S., Temu, T., Sinitcyn, P., Carlson, A., et al., The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods 2016, 13, 731-740). Proteins identified by the reverse, contaminant and only by site hits were discarded. Only protein groups identified with at least two assigned peptides were accepted and LFQ intensities were log2 transformed
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Author Under Sail The Imagination of Jack London, 1893-1902
No full textIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Intro -- Title Page -- Copyright Page -- Dedication -- Contents -- Acknowledgments -- Introduction -- 1. Spirit Truth -- 2. From Absorption to Theatricality and Back Again -- 3. "I Will Build a New Present" -- 4. Sons as Authors -- 5. Fathers as Publishers -- 6. The Daughter as Author -- 7. Lovers as Authors -- 8. At Sea with the Family -- 9. Yellow News, Yellow Stories -- 10. The Return Home -- Notes -- Bibliography -- Index -- About Jay WilliamsIn Author Under Sail, Jay Williams offers the first complete literary biography of Jack London as a professional writer engaged in the labor of writing. It examines the authorial imagination in London's work, the use of imagination in both his fiction and nonfiction, and the ways he defined imagination in the creative process in his business dealings with his publishers, editors, and agents. In this first volume of a two-volume biography, Williams traverses the years 1893 to 1902, from London's "Story of a Typhoon" to The People of the Abyss. The Jack London who emerges in the pages of Author Under Sail is a writer whose partnership with publishers, most notably his productive alliance with George Brett of Macmillan, was one of the most formative in American literary history. London pioneered many author models during the heyday of realism and naturalism, blurring the boundaries of these popular genres by focusing on absorption and theatricality and the representation of the seen and unseen. London created an impassioned, sincere, and extremely personal realism unlike that of other American writers of the time. Author Under Sail is a literary tour de force that reveals the full range of London as writer, creative citizen, and entrepreneur at the same time it sheds light on the maverick side of machine-age literature.Description based on publisher supplied metadata and other sources.Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, YYYY. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries
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