Attacking pathogens through their hosts.

Through understanding the intricacies of host-pathogen interactions, it is now possible to inhibit the growth of microbes, especially viruses, by targeting host-cell proteins and functions. This new antimicrobial strategy has proved effective in the laboratory and in the clinic, and it has great potential for the future

Can graph-cutting improve microarray gene expression reconstructions?

Microarrays produce high-resolution image data that are, unfortunately, permeated with a great deal of “noise” that must be removed for precision purposes. This paper presents a technique for such a removal process. On completion of this non-trivial task, a new surface (devoid of gene spots) is subtracted from the original to render more precise gene expressions. The graph-cutting technique as implemented has the benefits that only the most appropriate pixels are replaced and these replacements are replicates rather than estimates. This means the influence of outliers and other artifacts are handled more appropriately (than in previous methods) as well as the variability of the final gene expressions being considerably reduced. Experiments are carried out to test the technique against commercial and previously researched reconstruction methods. Final results show that the graph-cutting inspired identification mechanism has a positive significant impact on reconstruction accuracy

VIDA: a virus database system for the organization of animal virus genome open reading frames

VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on the basis of sequence similarity relationships, Conserved sequence regions of potential functional importance are identified and can be retrieved as sequence alignments. We use a controlled taxonomical and functional classification for all the proteins and protein families in the database. When available, protein structures that are related to the families have also been included. The database is available for online search and sequence information retrieval at http://www.biochem.ucl.ac.uk/bsm/virus-database/ VIDA.html

Consensus clustering and functional interpretation of gene-expression data

Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFκB and the unfolded protein response in certain B-cell lymphomas

Bat and pig IFN-induced transmembrane protein 3 restrict cell entry by influenza virus and lyssaviruses

IFN-induced transmembrane protein 3 (IFITM3) is a restriction factor that blocks cytosolic entry of numerous viruses that utilize acidic endosomal entry pathways. In humans and mice, IFITM3 limits influenza-induced morbidity and mortality. Although many IFITM3-sensitive viruses are zoonotic, whether IFITMs function as antiviral restriction factors in mammalian species other than humans and mice is unknown. Here, IFITM3 orthologues in the microbat (Myotis myotis) and pig (Sus scrofa domesticus) were identified using rapid amplification of cDNA ends. Amino acid residues known to be important for IFITM3 function were conserved in the pig and microbat orthologues. Ectopically expressed pig and microbat IFITM3 co-localized with transferrin (early endosomes) and CD63 (late endosomes/multivesicular bodies). Pig and microbat IFITM3 restricted cell entry mediated by multiple influenza haemagglutinin subtypes and lyssavirus glycoproteins. Expression of pig or microbat IFITM3 in A549 cells reduced influenza virus yields and nucleoprotein expression. Conversely, small interfering RNA knockdown of IFITM3 in pig NPTr cells and primary microbat cells enhanced virus replication, demonstrating that these genes are functional in their species of origin at endogenous levels. In summary, we showed that IFITMs function as potent broad-spectrum antiviral effectors in two mammals – pigs and bats – identified as major reservoirs for emerging viruses

Use of Recommended Laboratory Testing Methods Among Patients with Tuberculosis in California

This study assessed the extent to which laboratory methods recommended by the Centers for Disease Control and Prevention were used in tuberculosis testing of patients in California in 1998. While recommended methods were used for most patients, there was room for improvement by hospital and independent non-health maintenance organization laboratories

High-throughput pipeline for the de novo viral genome assembly and the identification of minority variants from Next-Generation Sequencing of residual diagnostic samples

Motivation: The underlying genomic variation of a large number of pathogenic viruses can give rise to drug resistant mutations resulting in treatment failure. Next generation sequencing (NGS) enables the identification of viral quasi-species and the quantification of minority variants in clinical samples; therefore, it can be of direct benefit by detecting drug resistant mutations and devising optimal treatment strategies for individual patients. / Results: The ICONIC (InfeCtion respONse through vIrus genomiCs) project has developed an automated, portable and customisable high-throughput computational pipeline to assemble de novo whole viral genomes, either segmented or non-segmented, and quantify minority variants using residual diagnostic samples. The pipeline has been benchmarked on a dedicated High-Performance Computing cluster using paired-end reads from RSV and Influenza clinical samples. The median length of generated genomes was 96% for the RSV dataset and 100% for each Influenza segment. The analysis of each set lasted less than 12 hours; each sample took around 3 hours and required a maximum memory of 10 GB. The pipeline can be easily ported to a dedicated server or cluster through either an installation script or a docker image. As it enables the subtyping of viral samples and the detection of relevant drug resistance mutations within three days of sample collection, our pipeline could operate within existing clinical reporting time frames and potentially be used as a decision support tool towards more effective personalised patient treatments. / Availability: The software and its documentation are available from https://github.com/ICONIC-UCL/pipeline / Contact: t.cassarino{at}ucl.ac.uk, pk5{at}sanger.ac.uk / Supplementary information: Supplementary data are available at Briefings in Bioinformatics online

Enabling Factors in Successful Product Development

The research literature and industry best-practices report a vast number of enabling factors that contribute to successful product development (PD). Collectively this body of work also establishes the causal linkages between these enabling factors and overall success in PD. But what specific factors will produce what specific outcomes are vague and ambiguous. To address this apparent void, we find distinct sets of PD enabling factors that are statistically accurate predictors of the specific project outcomes of profit, market share, customer satisfaction, organizational effectiveness, and product quality. We are also motivated to help organizations improve their PD. To that end, we develop a diagnostic tool using the factors that predict our five PD outcomes. The tool is used to pinpoint weaknesses and focus improvements to achieve specific desired outcomes. Results of in situ testing of the tool are reported in this article. The guiding principles of this work are specificity and actionability: specific enabling factors that can produce specific results, and an actionable diagnostic-tool that practitioners can use to improve the practice and results of their PD projects

An experimental evaluation of a loop versus a reference design for two-channel microarrays

Motivation: Despite theoretical arguments that socalled "loop designs" of two-channel DNA microarray experiments are more efficient, biologists keep on using "reference designs". We describe two sets of microarray experiments with RNA from two different biological systems (TPA-stimulated mammalian cells and Streptomyces coelicor). In each case, both a loop and a reference design were performed using the same RNA preparations with the aim to study their relative efficiency. Results: The results of these experiments show that (1) the loop design attains a much higher precision than the reference design, (2) multiplicative spot effects are a large source of variability, and if they are not accounted for in the mathematical model, for example by taking log-ratios or including spot-effects, then the model will perform poorly. The first result is reinforced by a simulation study. Practical recommendations are given on how simple loop designs can be extended to more realistic experimental designs and how standard statistical methods allow the experimentalist to use and interpret the results from loop designs in practice