@article{WheelerBarquistKingsleyetal.2016,
  author    = {Wheeler, Nicole E. and Barquist, Lars and Kingsley, Robert A. and Gardner, Paul P.},
  title     = {A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes},
  series = {Bioinformatics},
  volume    = {32},
  journal   = {Bioinformatics},
  number    = {23},
  doi       = {10.1093/bioinformatics/btw518},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-186502},
  pages     = {3566-3574},
  year      = {2016},
  abstract  = {Motivation: Next generation sequencing technologies have provided us with a wealth of information on genetic variation, but predi cting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics. Results: We present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms.},
  language  = {en}
}
@article{BarquistMayhoCumminsetal.2016,
  author    = {Barquist, Lars and Mayho, Matthew and Cummins, Carla and Cain, Amy K. and Boinett, Christine J. and Page, Andrew J. and Langridge, Gemma C. and Quail, Michael A. and Keane, Jacqueline A. and Parkhill, Julian},
  title     = {The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries},
  series = {Bioinformatics},
  volume    = {32},
  journal   = {Bioinformatics},
  number    = {7},
  doi       = {10.1093/bioinformatics/btw022},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189667},
  pages     = {1109-1111},
  year      = {2016},
  abstract  = {Transposon insertion sequencing is a high-throughput technique for assaying large libraries of otherwise isogenic transposon mutants providing insight into gene essentiality, gene function and genetic interactions. We previously developed the Transposon Directed Insertion Sequencing (TraDIS) protocol for this purpose, which utilizes shearing of genomic DNA followed by specific PCR amplification of transposon-containing fragments and Illumina sequencing. Here we describe an optimized high-yield library preparation and sequencing protocol for TraDIS experiments and a novel software pipeline for analysis of the resulting data. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. This article can serve as a general reference for the application of the TraDIS methodology.},
  language  = {en}
}
@article{ReadMillsJohnsonetal.2016,
  author    = {Read, Hannah M. and Mills, Grant and Johnson, Sarah and Tsai, Peter and Dalton, James and Barquist, Lars and Print, Cristin G. and Patrick, Wayne M. and Wiles, Siouxsie},
  title     = {The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium},
  series = {PeerJ},
  volume    = {4},
  journal   = {PeerJ},
  number    = {e2130},
  doi       = {10.7717/peerj.2130},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166576},
  year      = {2016},
  abstract  = {Bioluminescent reporter genes, such as those from fireflies and bacteria, let researchers use light production as a non-invasive and non-destructive surrogate measure of microbial numbers in a wide variety of environments. As bioluminescence needs microbial metabolites, tagging microorganisms with luciferases means only live metabolically active cells are detected. Despite the wide use of bioluminescent reporter genes, very little is known about the impact of continuous (also called constitutive) light expression on tagged bacteria. We have previously made a bioluminescent strain of Citrobacter rodentium, a bacterium which infects laboratory mice in a similar way to how enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC) infect humans. In this study, we compared the growth of the bioluminescent C. rodentium strain ICC180 with its non-bioluminescent parent (strain ICC169) in a wide variety of environments. To understand more about the metabolic burden of expressing light, we also compared the growth profiles of the two strains under approximately 2,000 different conditions. We found that constitutive light expression in ICC180 was near-neutral in almost every non-toxic environment tested. However, we also found that the non-bioluminescent parent strain has a competitive advantage over ICC180 during infection of adult mice, although this was not enough for ICC180 to be completely outcompeted. In conclusion, our data suggest that constitutive light expression is not metabolically costly to C. rodentium and supports the view that bioluminescent versions of microbes can be used as a substitute for their non-bioluminescent parents to study bacterial behaviour in a wide variety of environments.},
  language  = {en}
}