Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.

Expression of PSA-RP2, an alternatively spliced variant from the PSA gene, is increased in prostate cancer tissues but the protein is not secreted from prostate cancer cells

PSA-RP2 is a variant transcript expressed from the PSA gene that is conserved in gorillas, chimpanzees and humans suggesting a particular relevance for this transcript in these primates. We demonstrated by qRT-PCR that PSA-RP2 is upregulated in prostate cancer compared with benign prostatic hyperplasia tissues. The PSA-RP2 protein was not detected in seminal fluid and was cytoplasmically localised but not secreted from LNCaP or transfected PC3 prostate cells, despite secretion from transfected Cos-7 and HEK293 kidney cell lines. PSA-RP2-transfected PC3 cells showed slightly decreased proliferation and increased migration towards PC3-conditioned medium that could suggest a functional role in prostate cancer.

Court-provided trial technology : efficiency and fairness for criminal trials

In Australia, trials conducted as 'electronic trials' have ordinarily run with the assistance of commercial service providers, with the associated costs being borne by the parties. However, an innovative approach has been taken by the courts in Queensland. In October 2007 Queensland became the first Australian jurisdiction to develop its own court-provided technology, to facilitate the conduct of an electronic trial. This technology was first used in the conduct of civil trials. The use of the technology in the civil sphere highlighted its benefits and, more significantly, demonstrated the potential to achieve much greater efficiencies. The Queensland courts have now gone further, using the court-provided technology in the high proffle criminal trial of R v Hargraves, Hargraves and Stoten, in which the three accused were tried for conspiracy to defraud the Commonwealth of Australia of about $3.7 million in tax. This paper explains the technology employed in this case and reports on the perspectives of all of the participants in the process. The representatives for all parties involved in this trial acknowledged, without reservation, that the use of the technology at trial produced considerable overall efficiencies and costs savings. The experience in this trial also demonstrates that the benefits of trial technology for the criminal justice process are greater than those for civil litigation. It shows that, when skilfully employed, trial technology presents opportunities to enhance the fairness of trials for accused persons. The paper urges governments, courts and the judiciary in all jurisdictions to continue their efforts to promote change, and to introduce mechanisms to facilitate more broadly a shift from the entrenched paper-based approach to both criminal and civil procedure to one which embraces more broadly the enormous benefits trial technology has to offer.