Open Access Highly Accessed Research article

Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens

Chris J Stubben1†, Melanie L Duffield2†, Ian A Cooper2, Donna C Ford2, Jason D Gans1, Andrey V Karlyshev3, Bryan Lingard2, Petra CF Oyston2, Anna de Rochefort2, Jian Song1, Brendan W Wren4, Rick W Titball5 and Murray Wolinsky1*

  • * Corresponding author: Murray Wolinsky murray@lanl.gov

  • † Equal contributors

1 Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM

2 Biomedical Sciences, Dstl, Porton Down, Salisbury, UK

3 School of Life Sciences, Kingston University, Kingston-upon-Thames, Surrey, UK

4 Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK

5 School of Biosciences, University of Exeter, Stocker Road, Exeter, UK

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BMC Genomics 2009, 10:501 doi:10.1186/1471-2164-10-501

Published: 29 October 2009

Additional files

Additional file 1:

Non-pathogen species in profile searches. Species assigned to non-pathogen group in profile searches. The numbers of strains (if different than one) are listed in parentheses after the species name. The habitat and temperature range are taken from the NCBI organism information table http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi webcite.

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Additional file 2:

Growth curves. Growth curve for wild type and mutants over 24 hours measured by optical density (600 nm). Curve shown is a sigmoidal dose response model that best describes the data in its integrity; no significant differences were seen between individual models (p > 0.05 using an ANCOVA, comparing sigmoidal dose models, fitted to the data). Plot symbols in the key correspond to Y. pseudotuberculosis locus tags listed in Table 3.

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Additional file 3:

Overview of methodology. Each of the first three computational (or semi-computational) steps results in a large reduction of the potential search space (which can not be usefully shown to scale). Clustering provides an operational definition of the "same" protein in different organisms. Profiling determines which clusters are overrepresented in pathogens. Filtering selects those clusters which meet experimental criteria. The resulting candidates are then screened experimentally.

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Additional file 4:

Bacterial strains and plasmids. Characteristics and source of bacterial plasmids used in experimental work.

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Additional file 5:

Mutagenesis primers. A list of all primers used in the mutagenesis of Y. pseudotuberucosis

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Additional file 6:

Screening primers. A list of all primers used for screening and confirmation of this work

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