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.

The meaning of home for Karen and Chin refugees from Burma: An interpretative phenomenological approach

Loss of home is common to all people from a refugee background yet we have little understanding of the diversity of meaning associated with this important concept. A phenomenological approach was used to explore experiences of home amongst Karen and Chin refugees residing in Brisbane. In-depth, semi-structured interviews were conducted with nine participants from Karen and Chin backgrounds. The participants comprised five females and four males (mean age 40 years, median length of time in Australia 1.33 years). Participants described their migration stories, including pre- and post-migration history. Analysis was conducted using interpretative phenomenological analysis. Three superordinate themes, explicating the meaning of home for participants, were identified: home as the experience of a psychological space of safety and retreat; home as the socio-emotional space of relatedness to family; and home as geographical-emotional landscape. Loss of home was experienced as a multidimensional loss associated with emotional and physical disturbances. These findings, based upon a phenomenological paradigm, enhance understanding of the experience of being a refugee and of the suffering engendered by loss of home. They open up the possibility for conceptualizing refugee responses in terms of human suffering and meaning making.

A hybrid approach for resolving the electromagnetic fields inside a waveguide loaded with a lossy medium

In this work a novel hybrid approach is presented that uses a combination of both time domain and frequency domain solution strategies to predict the power distribution within a lossy medium loaded within a waveguide. The problem of determining the electromagnetic fields evolving within the waveguide and the lossy medium is decoupled into two components, one for computing the fields in the waveguide including a coarse representation of the medium (the exterior problem) and one for a detailed resolution of the lossy medium (the interior problem). A previously documented cell-centred Maxwell’s equations numerical solver can be used to resolve the exterior problem accurately in the time domain. Thereafter the discrete Fourier transform can be applied to the computed field data around the interface of the medium to estimate the frequency domain boundary condition in-formation that is needed for closure of the interior problem. Since only the electric fields are required to compute the power distribution generated within the lossy medium, the interior problem can be resolved efficiently using the Helmholtz equation. A consistent cell-centred finite-volume method is then used to discretise this equation on a fine mesh and the underlying large, sparse, complex matrix system is solved for the required electric field using the iterative Krylov subspace based GMRES iterative solver. It will be shown that the hybrid solution methodology works well when a single frequency is considered in the evaluation of the Helmholtz equation in a single mode waveguide. A restriction of the scheme is that the material needs to be sufficiently lossy, so that any penetrating waves in the material are absorbed.

IS-impact utility and intuitiveness : a rigorous approach to relevance

The study proposes to test the ‘IS-Impact’ index as Analytic Theory (AT). To (a) methodically evaluate the ‘relevance’ qualities of IS-Impact; namely, Utility & Intuitiveness. In so doing, to (b) document an exemplar of ‘a rigorous approach to relevance’, while (c) treating the overarching study as a higher-order case study having AT as the unit-of-analysis, and assessing adequacy of the 6 AT qualities, both for IS-Impact and for similar taxonomies. Also to (d) look beyond IS-Impact to other forms of Design Science, considering the generality of the AT qualities; and (e) further validating IS-Impact in new system organisation contexts taking account of contemporary understandings of construct theorisation, operationalization and validation.