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.

Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species

Background Chlamydia pneumoniae is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on four essentially clonal (> 99% identity) C. pneumoniae human genomes (AR39, CWL029, J138 and TW183), providing relatively little insight into strain diversity and evolution of this species. Results We performed individual gene-by-gene comparisons of the recently sequenced C. pneumoniae koala genome and four C. pneumoniae human genomes to identify species-specific genes, and more importantly, to gain an insight into the genetic diversity and evolution of the species. We selected genes dispersed throughout the chromosome, representing genes that were specific to C. pneumoniae, genes with a demonstrated role in chlamydial biology and/or pathogenicity (n = 49), genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6), and extrachromosomal elements (9 plasmid and 2 bacteriophage genes). Conclusions We have identified strain-specific differences and targets for detection of C. pneumoniae isolates from both human and animal origin. Such characterisation is necessary for an improved understanding of disease transmission and intervention.

Interaction in a Paired Speaking Test : the Rater's Perspective

Paired speaking tests are increasingly used in both low-and high-stakes second language assessment contexts. Until recently, very little was known about the way in which raters interpret and apply descriptors relating to interactional competence to a performance that is co-constructed. This book presents a study which explores the interactional features of a paired speaking test that were sailient to raters and the extent to which raters viewed the performance as separable. The study shows that raters use their own frames of reference to interpret descriptors and that they viewed certain features of the performance as mutual accomplishments. The book takes us 'beyond scores', and in doing so, contributes to the growing body of research on paired speaking tests.

Spectral–texture feature extraction using statistical moments with application to object-based vegetation species classification

The use of appropriate features to characterise an output class or object is critical for all classification problems. In order to find optimal feature descriptors for vegetation species classification in a power line corridor monitoring application, this article evaluates the capability of several spectral and texture features. A new idea of spectral–texture feature descriptor is proposed by incorporating spectral vegetation indices in statistical moment features. The proposed method is evaluated against several classic texture feature descriptors. Object-based classification method is used and a support vector machine is employed as the benchmark classifier. Individual tree crowns are first detected and segmented from aerial images and different feature vectors are extracted to represent each tree crown. The experimental results showed that the proposed spectral moment features outperform or can at least compare with the state-of-the-art texture descriptors in terms of classification accuracy. A comprehensive quantitative evaluation using receiver operating characteristic space analysis further demonstrates the strength of the proposed feature descriptors.

Innovation, interaction, and inclusion : heritage luxury brands in collusion with the consumer

Many luxury heritage brands operate on the misconception that heritage is interchangeable with history rather than representative of the emotional response they originally developed in their customer. This idea of heritage as static history inhibits innovation, prevents dynamic renewal and impedes their ability to redefine, strengthen and position their brand in current and emerging marketplaces. This paper examines a number of heritage luxury brands that have successfully identified the original emotional responses they developed in their customers and, through innovative approaches in design, marketing, branding and distribution evoke these responses in contemporary consumers. Using heritage and innovation hand-in-hand, these brands have continued to grow and develop a vision of heritage that incorporates both historical and contemporary ideas to meet emerging customer needs. While what constitutes a ‘luxury’ item is constantly challenged in this era of accessible luxury products, up scaling and aspirational spending, this paper sees consumers’ emotional needs as the key element in defining the concept of luxury. These emotional qualities consistently remain relevant due to their ability to enhance a positive sense of identity for the brand user. Luxury is about the ‘experience’ not just the product providing the consumer with a sense of enhanced status or identity through invoked feelings of exclusivity, authenticity, quality, uniqueness and culture. This paper will analyse luxury heritage brands that have successfully combined these emotional values with those of their ‘heritage’ to create an aura of authenticity and nostalgia that appeals to contemporary consumers. Like luxury, the line where clothing becomes fashion is blurred in the contemporary fashion industry; however, consumer emotion again plays an important role. For example, clothing becomes ‘fashion’ for consumers when it affects their self perception rather than fulfilling basic functions of shelter and protection. Successful luxury heritage brands can enhance consumers’ sense of self by involving them in the ‘experience’ and ‘personality’ of the brand so they see it as a reflection of their own exclusiveness, authentic uniqueness, belonging and cultural value. Innovation is a valuable tool for heritage luxury brands to successfully generate these desired emotional responses and meet the evolving needs of contemporary consumers. While traditionally fashion has been a monologue from brand to consumer, new technology has given consumers a voice to engage brands in a conversation to express their evolving needs, ideas and feedback. As a result, in this consumer-empowered era of information sharing, this paper defines innovation as the ability of heritage luxury brands to develop new design and branding strategies in response to this consumer feedback while retaining the emotional core values of their heritage. This paper analyses how luxury heritage brands can effectively position themselves in the contemporary marketplace by separating heritage from history to incorporate innovative strategies that will appeal to consumer needs of today and tomorrow.

Natural convection flow with combined buoyancy effects due to thermal and mass diffusion in a thermally stratified media

We present here a numerical study of laminar doubly diffusive free convection flows adjacent to a vertical surface in a stable thermally stratified medium. The governing equations of mass, momentum, energy and species are non-dimensionalized. These equations have been solved by using an implicit finite difference method and local non-similarity method. The results show many interesting aspects of complex interaction of the two buoyant mechanisms that have been shown in both the tabular as well as graphical form.