Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.

Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene list of interest, integrate contextual information, such as gene expression data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such contextual hubs are considerably more biologically relevant than degree-based hubs and that analyses which rely on the identification of hubs solely based on their connectivity may be biased towards nodes that are highly connected in general rather than in the specific context of interest. AVAILABILITY: CHAT is available for Cytoscape 3.0+ and can be installed via the Cytoscape App Store (http://apps.cytoscape.org/apps/chat).

A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23.

BACKGROUND: Bovine tuberculosis (bTB) infection in cattle is a significant economic concern in many countries, with annual costs to the UK and Irish governments of approximately €190 million and €63 million, respectively, for bTB control. The existence of host additive and non-additive genetic components to bTB susceptibility has been established. METHODS: Two approaches i.e. single-SNP (single nucleotide polymorphism) regression and a Bayesian method were applied to genome-wide association studies (GWAS) using high-density SNP genotypes (n = 597,144 SNPs) from 841 dairy artificial insemination (AI) sires. Deregressed estimated breeding values for bTB susceptibility were used as the quantitative dependent variable. Network analysis was performed using the quantitative trait loci (QTL) that were identified as significant in the single-SNP regression and Bayesian analyses separately. In addition, an identity-by-descent analysis was performed on a subset of the most prolific sires in the dataset that showed contrasting prevalences of bTB infection in daughters. RESULTS: A significant QTL region was identified on BTA23 (P value >1 × 10(-5), Bayes factor >10) across all analyses. Sires with the minor allele (minor allele frequency = 0.136) for this QTL on BTA23 had estimated breeding values that conferred a greater susceptibility to bTB infection than those that were homozygous for the major allele. Imputation of the regions that flank this QTL on BTA23 to full sequence indicated that the most significant associations were located within introns of the FKBP5 gene. CONCLUSIONS: A genomic region on BTA23 that is strongly associated with host susceptibility to bTB infection was identified. This region contained FKBP5, a gene involved in the TNFα/NFκ-B signalling pathway, which is a major biological pathway associated with immune response. Although there is no study that validates this region in the literature, our approach represents one of the most powerful studies for the analysis of bTB susceptibility to date.

Re-engineering cellular physiology by rewiring high-level global regulatory genes.

Knowledge of global regulatory networks has been exploited to rewire the gene control programmes of the model bacterium Salmonella enterica serovar Typhimurium. The product is an organism with competitive fitness that is superior to that of the wild type but tuneable under specific growth conditions. The paralogous hns and stpA global regulatory genes are located in distinct regions of the chromosome and control hundreds of target genes, many of which contribute to stress resistance. The locations of the hns and stpA open reading frames were exchanged reciprocally, each acquiring the transcription control signals of the other. The new strain had none of the compensatory mutations normally associated with alterations to hns expression in Salmonella; instead it displayed rescheduled expression of the stress and stationary phase sigma factor RpoS and its regulon. Thus the expression patterns of global regulators can be adjusted artificially to manipulate microbial physiology, creating a new and resilient organism.

A terminal Ni(III)-imide with diverse reactivity pathways.

The synthesis and structure of the beta-diketiminato Ni(I) lutidine adducts [MexNN]Ni(2,4-lutidine) (x = 2 (2); x = 3 (3)) are described which serve as synthons to the "naked" 13-electron [MexNN]Ni fragments in reactions with N3Ad to give Ni-imido complexes. The singly bridged imide {[Me2NN]Ni}2(mu-NAd) (4) possesses short Ni-Ni (2.506(1) A) and Ni-N(imido) distances (1.732(4)-1.752(4) A). Steric modification of the beta-diketiminate ligand to include an additional methyl group in the N-aryl 4-position affords the Ni(III) terminal imide [Me3NN]Ni=NAd (8) isolated in 52% yield. The X-ray structure of terminal imide 8 reveals a contracted Ni-N(imido) bond distance (1.662(2) A) and an only somewhat bent imido linkage (Ni-N-C = 164.5(2) degrees ) consistent with a significant degree of multiple bond character. Frozen glass EPR studies of 5 indicate a rhombic environment in which one of the signals exhibits strong hyperfine coupling (A = 22 G) to the imido 14N (I = 1) nucleus. The terminal imide 5 undergoes complete imido group transfer to CO and CNBut to give AdNCO and AdNCNBut, respectively, as well as with PMe3 to afford AdN=PMe3. Exemplifying the radical character at the imido N atom, 5 adds to cobaltocene and abstracts a H atom from 1,4-cyclohexadiene to give the Ni(II)-amides [Me3NN]Ni-NAd(eta4-C5H5)CoCp (7) and [Me3NN]Ni-NHAd (8).