1,720,963 research outputs found
A Model for the Regulation of Lipopolysaccharide Synthesis during Outer Membrane Biogenesis in Escherichia Coli
Full text linkThe role of systems biology in the interpretation and analysis of important biological events is gaining rapid acceptance in a number of biological fields. Here a computational systems approach was applied to investigate the production and regulation of Escherichia coli’s (E. coli) outer membrane. The outer membrane comprises of phospholipids in the inner leaflet, and lipopolysaccharides (LPS) in the outer leaflet. LPS is an endotoxin that elicits a strong immune response from humans and its biosynthesis is in part, regulated via degradation of LpxC and WaaA enzymes by the protease FtsH. Despite a substantial amount of research conducted on LPS synthesis, there is remarkably little information on its regulation.The model of the outer membrane synthesis was completed in two phases; firstly a model of lipid A (representing the LPS pathway) was constructed followed by an integrated pathway model which incorporated fatty acids biosynthesis pathway (representing phospholipid production). The parameters used to construct the model were derived from published datasets where available, and estimated when necessary prior to model fitting. Model validation was carried out using a combination of published datasets alongside subsequent experimental data from this research.Model findings suggested that the FtsH-mediated LpxC degradation signal arises from levels of lipid A disaccharide, the substrate for LpxK. This was subsequently validated experimentally using an lpxK overexpression system. Analysis of the integrated model further refined this mechanism indicating the catalytic activity of LpxK appears to be dependent on the concentration of unsaturated fatty acids. This is biologically important because it assists in maintaining LPS/phospholipids homeostasis.Further crosstalk between the fatty acids and lipid A biosynthetic pathways was revealed by experimental observations that LpxC is additionally regulated by an unidentified protease whose activity is independent of lipid A disaccharide concentration, but could be induced in vitro by palmitic acid. The biological relevance of this acute mechanism is not obvious; however, experiments aimed at causing abrupt damage to the cell wall or membrane (by antimicrobials) suggest that under conditions which directly damage membrane structure, LPS regulation via this unidentified protease may be crucial.Computational analysis into the regulation of WaaA suggested that its proteolytic regulation does not affect the LPS synthetic rate. Subsequent experimental analysis provided evidence that WaaA regulation is aimed at controlling the quality of LPS synthesized by preventing glycosylation of undesirable lipid acceptors. Overexpression of waaA resulted in increased levels of 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) sugar whereas, levels of heptose were not elevated in comparison to non-overexpressed cells. This implies that an uncontrolled production of WaaA does not increase LPS level but rather re-glycosylates lipid A precursors. This is the first time experimental data has been produced attempting to explain the regulation of WaaA.Computation of flux coefficient indicates that LpxC is the rate-limiting step when pathway regulation is ignored, but LpxK becomes the limiting step if feedback regulation is included as it is in vivo. Thus, in contrast to LpxC, LpxK may represent a more appropriate target for novel drug development. Overall, the findings of this work provide novel insights into the complex biogenesis of the E. coli outer membrane
High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage.
No full textWe developed Growth Rate InDex (GRiD) for estimating in situ growth rates of ultra-low coverage (\u3e0.2×) and de novo-assembled metagenomes. Applying GRiD to human and environmental metagenomic datasets to demonstrate its versatility, we uncovered new associations with previously uncharacterized bacteria whose growth rates were associated with several disease characteristics or environmental interactions. In addition, with GRiD-MG (metagenomic), a high-throughput implementation of GRiD, we estimated growth dynamics of 1756 bacteria species from a healthy skin metagenomic dataset and identified a new Staphylococcus-Corynebacterium antagonism likely mediated by antimicrobial production in the skin. GRiD-MG significantly increases the ability to extract growth rate inferences from complex metagenomic data with minimal input from the user
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
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