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Additional file 1: Figure S1. of Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe
No full textIdentification of Bacillus sp. NRRL B-14911 spores. Bacterial smear was stained with malachite green and safranin as described in the Methods section and examined under oil immersion microscope. Arrows indicate round and symmetrical endospores present both within and outside the bacteria. Original magnification: 100x. Figure S2. The genes encoded by the plasmid of Bacillus sp. NRRL B-14911. The plasmid sequence was generated from the sequence data obtained by sequencing of the genomic DNA from Bacillus sp. NRRL B-14911 in long-reads. The genes encoded by the plasmid were annotated as described for the bacterial chromosome (see methods).Figure S3. Alignment of contigs previously reported for Bacillus sp. NRRL B-14911 to the new long-read-based finished assembly. The inner ring (blue) represents contigs assembled from short-reads without any scaffolding (middle panel in Figure 1) as aligned to our de novo assembly based on long-reads. The outer ring (pink and black) represents alignment of contigs after scaffolding (top and bottom panels in Fig. 1). Note, white lines and blocks show large areas without any coverage in the prior assembly. Designations for each scaffold and contig are derived from GenBank accession numbers, which are abbreviated for convenience in display. Scaffolds are shown in pink and have full accessions with the format CH6723XX, where XX is the number shown on the figure following “CH”. Black- and blue-shaded regions represent un-scaffolded contigs, which have full accessions with the format AAOX01000XYY, where X is either 0 (for YY between 23 and 99) or 1 (for YY between 00 and 09). Only contigs with ≥ 99.900 % identity are shown. The scale in the middle of the circle is based on the finished de novo assembly, made using long-read sequencing. Figure S4. Circular genome map of Bacillus sp. NRRL B-14911 showing the location of genes for virulence factors that are unique to this bacterium in relation to other Bacillus. The circular map of Bacillus sp. NRRL B-14911 shows the locations of 18 virulence factor genes that are unique to this bacterium as determined by comparing the genomes of three pathogenic, and three non-pathogenic bacteria as described in the ‘Methods’ section. The two outer blue circles represent the genes for virulence factors present in forward and reverse directions. The innermost circle represents the GC skewness, and the second innermost circle represents the GC content of the Bacillus sp. NRRL B-14911 genome. The coordinates of each gene are listed in Additional file 1: Table S3. The start and end positions in Additional file 1: Table S3 match with the location of genes in Additional file 1: Figure S4. Figure S5. Circular genome map showing the location of virulence factor genes common to both Bacillus sp. NRRL B-14911 and other pathogenic bacilli. The circular map shows the locations of 225 virulence factor genes that are common to both Bacillus sp. NRRL B-14911 and three other pathogenic bacilli. Their genome comparisons were made as described in the ‘Methods’ section. The two outer blue circles represent the genes for virulence factors shown in forward and reverse directions. The innermost circle represents the GC skewness, and the second innermost circle represents the GC content of the Bacillus sp. NRRL B-14911 genome. The coordinates of each gene are listed in Additional file 1: Table S4. The start and end positions in Additional file 1: Table S4 match with the location of genes in Additional file 1: Figure S5. Table S1. Comparison of the issues with sequencing by scaffolds in the bioproject in relation to our method of sequencing by long-reads. Table S2. List of genes for virulence factor encoded in the genome of Bacillus sp. NRRL B-14911. Table S3. List of unique genes for virulence factor encoded in the genome of Bacillus sp. NRRL B-14911. Table S4. List of genes for virulence factor encoded in the genome of Bacillus sp. NRRL B-14911 that are in common with pathogenic Bacilli. Table S5. Comparative analysis of the presence or absence of common methyltransferases between Bacillussp. NRRL B-14911 and other Bacillus species. Table S6. Comparative analysis of the presence or absence of transporters between Bacillus sp. NRRL B-14911 and other Bacillus species. Table S7. Comparison of the nucleotide sequences and amino acid sequences corresponding to the epitope BAC 25-40 from Bacillus sp. NRRL B-14911and B. infantis JCM 13438 T. Table S8. Comparative analysis of the presence or absence of enzymes and biochemical pathways of Bacillus sp. NRRL B-14911 in relation to other Bacillus species. Table S9. Comparison of insertion sequence elements between Bacillus sp. NRRL B-14911 and other Bacillus species. (PDF 2089 kb
Whole genomic sequence analysis of \u3ci\u3eBacillus infantis\u3c/i\u3e: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe
Full text linkBackground: We recently reported the identification of Bacillus sp. NRRL B-14911 that induces heart autoimmunity by generating cardiac-reactive T cells through molecular mimicry. This marine bacterium was originally isolated from the Gulf of Mexico, but no associations with human diseases were reported. Therefore, to characterize its biological and medical significance, we sought to determine and analyze the complete genome sequence of Bacillus sp. NRRL B-14911.
Results: Based on the phylogenetic analysis of 16S ribosomal RNA (rRNA) genes, sequence analysis of the 16S-23S rDNA intergenic transcribed spacers, phenotypic microarray, and matrix-assisted laser desorption ionization time-offlight mass spectrometry, we propose that this organism belongs to the species Bacillus infantis, previously shown to be associated with sepsis in a newborn child. Analysis of the complete genome of Bacillus sp. NRRL B-14911 revealed several virulence factors including adhesins, invasins, colonization factors, siderophores and transporters. Likewise, the bacterial genome encodes a wide range of methyl transferases, transporters, enzymatic and biochemical pathways, and insertion sequence elements that are distinct from other closely related bacilli.
Conclusions: The complete genome sequence of Bacillus sp. NRRL B-14911 provided in this study may facilitate genetic manipulations to assess gene functions associated with bacterial survival and virulence. Additionally, this bacterium may serve as a useful tool to establish a disease model that permits systematic analysis of autoimmune events in various susceptible rodent strains
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
Full text linkWe 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
Identification and Characterization of a Novel Class of Extracellular Poly(3-Hydroxybutyrate) Depolymerase from Bacillus sp. Strain NRRL B-14911
No full textABSTRACT
The catalytic, linker, and denatured poly(3-hydroxybutyrate) (dPHB)-binding domains of bacterial extracellular PHB depolymerases (PhaZs) are classified into several different types. We now report a novel class of extracellular PHB depolymerase from
Bacillus
sp. strain NRRL B-14911. Its catalytic domain belongs to type 1, whereas its putative linker region neither possesses the sequence features of the three known types of linker domains nor exhibits significant amino acid sequence similarity to them. Instead, this putative linker region can be divided into two distinct linker domains of novel types: LD1 and LD2. LD1 shows significant amino acid sequence similarity to certain regions of a large group of PHB depolymerase-unrelated proteins. LD2 and its homologs are present in a small group of PhaZs. The remaining C-terminal portion of this PhaZ can be further divided into two distinct domains: SBD1 and SBD2. Each domain showed strong binding to dPHB, and there is no significant sequence similarity between them. Each domain neither possesses the sequence features of the two known types of dPHB-binding domains nor shows significant amino acid sequence similarity to them. These unique features indicate the presence of two novel and distinct types of dPHB-binding domains. Homologs of these novel domains also are present in the extracellular PhaZ of
Bacillus megaterium
and the putative extracellular PhaZs of
Bacillus pseudofirmus
and
Bacillus
sp. strain SG-1. The
Bacillus
sp. NRRL B-14911 PhaZ appears to be a representative of a novel class of extracellular PHB depolymerases.
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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
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