Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior

Contains fulltext : 95738.pdf (publisher's version ) (Open Access)BACKGROUND: Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme. RESULTS: We have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan. CONCLUSION: Our analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm

Harry Potter and the meat-filled freezer:a case study of spontaneous usage of visualization tools

This paper is a report on early user activity in Many Eyes, a public web site where users may upload data, create visualizations, and carry on discussions. Since the site launched, users have uploaded data and created graphics on everything from DNA microarray data to co-occurrences of names in the New Testament to personal gift-giving networks. Our results show that in addition to traditional data analysis, Many Eyes is used for goals ranging from journalism and advocacy to personal expression and social interaction. We propose several implications of this usage for visualization designers and contend that these findings suggest a role for visualization as an expressive medium

Visualising a Text with a Tree Cloud

International audienceTag clouds have gained popularity over the internet to provide a quick overview of the content of a website or a text. We introduce a new visualisation which displays more information: the tree cloud. Like a word cloud, it shows the most frequent words of the text, where the size reflects the frequency, but the words are arranged on a tree to reflect their semantic proximity according to the text. Such tree clouds help identify the main topics of a document, and even be used for text analysis. We also provide methods to evaluate the quality of the obtained tree cloud, and some key steps of its construction. Our algorithms are implemented in the free software TreeCloud available at http://www.treecloud.or

Improved Approximation Algorithms for Box Contact Representations

We study the following geometric representation problem: Given a graph whose vertices correspond to axis-aligned rectangles with fixed dimensions, arrange the rectangles without overlaps in the plane such that two rectangles touch if the graph contains an edge between them. This problem is called Contact Representation of Word Networks (Crown) since it formalizes the geometric problem behind drawing word clouds in which semantically related words are close to each other. Crown is known to be NP-hard, and there are approximation algorithms for certain graph classes for the optimization version, Max-Crown, in which realizing each desired adjacency yields a certain profit. We present the first O(1)-approximation algorithm for the general case, when the input is a complete weighted graph, and for the bipartite case. Since the subgraph of realized adjacencies is necessarily planar, we also consider several planar graph classes (namely stars, trees, outerplanar, and planar graphs), improving upon the known results. For some graph classes, we also describe improvements in the unweighted case, where each adjacency yields the same profit. Finally, we show that the problem is APX-complete on bipartite graphs of bounded maximum degree.ESF EuroGIGA project GraDR; NSF [CCF-1115971, DEB 1053573]12 month embargo; First Online: 27 January 2016This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]