The complete mitochondrial genome of the flesh fly, Sarcophaga impatiens Walker (Diptera: Sarcophagidae)

Approximately 2500 fly species comprise the Sarcophagidae family worldwide. The complete mitochondrial genome of the carrion-breeding, forensically important Sarcophaga impatiens Walker (Diptera: Sarcophagidae) from Australia was sequenced. The 15,169 bp circular genome contains the 37 genes found in a typical Metazoan genome: 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. It also contains one non-coding A+T-rich region. The arrangement of the genes was the same as that found in the ancestral insect. All the protein initiation codons are ATN, except for cox1 that begins with TCG (encoding S). The 22 tRNA anticodons of S. impatiens are consistent with those observed in Drosophila yakuba, and all form the typical cloverleaf structure, except for tRNA-Ser(AGN) that lacks the DHU arm. The mitochondrial genome of Sarcophaga presented will be valuable for resolving phylogenetic relationships within the family Sarcophagidae and the order Diptera, and could be used to identify favourable genetic markers for species identifications for forensic purposes.

A strong quantitative trait locus for wing length on chromosome 2 in a wild population of great reed warblers

Wing length is a key character for essential behaviours related to bird flight such as migration and foraging. In the present study, we initiate the search for the genes underlying wing length in birds by studying a long-distance migrant, the great reed warbler (Acrocephalus arundinaceus). In this species wing length is an evolutionary interesting trait with pronounced latitudinal gradient and sex-specific selection regimes in local populations. We performed a quantitative trait locus (QTL) scan for wing length in great reed warblers using phenotypic, genotypic, pedigree and linkage map data from our long-term study population in Sweden. We applied the linkage analysis mapping method implemented in GRIDQTL (a new web-based software) and detected a genome-wide significant QTL for wing length on chromosome 2, to our knowledge, the first detected QTL in wild birds. The QTL extended over 25 cM and accounted for a substantial part (37%) of the phenotypic variance of the trait. A genome scan for tarsus length (a bodysize-related trait) did not show any signal, implying that the wing-length QTL on chromosome 2 was not associated with body size. Our results provide a first important step into understanding the genetic architecture of avian wing length, and give opportunities to study the evolutionary dynamics of wing length at the locus level. This journal is© 2010 The Royal Society.

Nature and genesis of clay minerals of the Rustler Formation in the vicinity of the Waste Isolation Pilot Plant in Souteastern New Mexico

Detailed mineralogical studies of the matrix and fracture-fill materials of a large number of samples from the Rustler Formation have been carried out using x-ray diffraction, high-resolution transmission electron microscopy, electron microprobe analysis, x-ray fluorescence, and atomic absorption spectrophotometry. These analyses indicate the presence of four clay minerals: interstratified chlorite/saponite, illite, chlorite, and serpentine. Corrensite (regularly stratified chlorite/saponite) is the dominant clay mineral in samples from the Culebra dolomite and two shale layers of the lower unnamed member of the Rustler Formation. Within other layers of the Rustler Formation, disordered mixed chlorite/saponite is usually the most abundant clay mineral. Studies of the morphology and composition of clay crystallites suggest that the corrensite was formed by the alteration of detrital dioctahedral smectite in magnesium-rich pore fluids during early diagenesis of the Rustler Formation. This study provides initial estimates of the abundance and nature of the clay minerals in the Culebra dolomite in the vicinity of the Waste Isolation Pilot Plant.

A snapshot of radiation therapy techniques and technology in Queensland : an aid to mapping undergraduate curriculum

Introduction: Undergraduate students studying the Bachelor of Radiation Therapy at Queensland University of Technology (QUT) attend clinical placements in a number of department sites across Queensland. To ensure that the curriculum prepares students for the most common treatments and current techniques in use in these departments, a curriculum matching exercise was performed. Methods: A cross-sectional census was performed on a pre-determined “Snapshot” date in 2012. This was undertaken by the clinical education staff in each department who used a standardized proforma to count the number of patients as well as prescription, equipment, and technique data for a list of tumour site categories. This information was combined into aggregate anonymized data. Results: All 12 Queensland radiation therapy clinical sites participated in the Snapshot data collection exercise to produce a comprehensive overview of clinical practice on the chosen day. A total of 59 different tumour sites were treated on the chosen day and as expected the most common treatment sites were prostate and breast, comprising 46% of patients treated. Data analysis also indicated that intensity-modulated radiotherapy (IMRT) use is relatively high with 19.6% of patients receiving IMRT treatment on the chosen day. Both IMRT and image-guided radiotherapy (IGRT) indications matched recommendations from the evidence. Conclusion: The Snapshot method proved to be a feasible and efficient method of gathering useful

Mapping quantitative trait loci in a wild population using linkage and linkage disequilibrium analyses

Historical information can be used, in addition to pedigree, traits and genotypes, to map quantitative trait locus (QTL) in general populations via maximum likelihood estimation of variance components. This analysis is known as linkage disequilibrium (LD) and linkage mapping, because it exploits both linkage in families and LD at the population level. The search for QTL in the wild population of Soay sheep on St. Kilda is a proof of principle. We analysed the data from a previous study and confirmed some of the QTLs reported. The most striking result was the confirmation of a QTL affecting birth weight that had been reported using association tests but not when using linkage-based analyses. Copyright © Cambridge University Press 2010.

Prediction of multilocus identity-by-descent

Previous studies have enabled exact prediction of probabilities of identity-by-descent (IBD) in randommating populations for a few loci (up to four or so), with extension to more using approximate regression methods. Here we present a precise predictor of multiple-locus IBD using simple formulas based on exact results for two loci. In particular, the probability of non-IBD X ABC at each of ordered loci A, B, and C can be well approximated by XABC = XABXBC/XB and generalizes to X123. . .k = X12X23. . .Xk-1,k/ Xk-2, where X is the probability of non-IBD at each locus. Predictions from this chain rule are very precise with population bottlenecks and migration, but are rather poorer in the presence of mutation. From these coefficients, the probabilities of multilocus IBD and non-IBD can also be computed for genomic regions as functions of population size, time, and map distances. An approximate but simple recurrence formula is also developed, which generally is less accurate than the chain rule but is more robust with mutation. Used together with the chain rule it leads to explicit equations for non-IBD in a region. The results can be applied to detection of quantitative trait loci (QTL) by computing the probability of IBD at candidate loci in terms of identity-by-state at neighboring markers.

Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.

From movie screens to moving screens : mapping qualities of new urban interactions

Next generation screens of diverse dimensions such as the Pebble e-paper watch, Google’s Project Glass, Microsoft’s Kinect and IllumiRoom, and large-scale multi-touch screen surface areas, increasingly saturate and diversify the urban mediascape. This paper seeks to contribute to media architecture and interaction design theory by starting to critically examine how these different screen formats are creating a ubiquitous screen mediascape across the city. We introduce next generation personal, domestic, and public screens. The paper critically challenges conventional dichotomies such as local / global, online / offline, private / public, large / small, mobile / static, that have been created in the past to describe some of the qualities and characteristics of interfaces and their usage. More and more scholars recognise that the black and white nature of these dichotomies does not adequately represent the fluid and agile capabilities of many new screen interfaces. With this paper, we hope to illustrate the more nuanced ‘trans-scalar’ qualities of these new urban interactions, that is, ways in which they provide a range functionality, without being locked into either end of a scale.

Genome-scale phylogeny and the detection of systematic biases

Phylogenetic inference from sequences can be misled by both sampling (stochastic) error and systematic error (nonhistorical signals where reality differs from our simplified models). A recent study of eight yeast species using 106 concatenated genes from complete genomes showed that even small internal edges of a tree received 100% bootstrap support. This effective negation of stochastic error from large data sets is important, but longer sequences exacerbate the potential for biases (systematic error) to be positively misleading. Indeed, when we analyzed the same data set using minimum evolution optimality criteria, an alternative tree received 100% bootstrap support. We identified a compositional bias as responsible for this inconsistency and showed that it is reduced effectively by coding the nucleotides as purines and pyrimidines (RY-coding), reinforcing the original tree. Thus, a comprehensive exploration of potential systematic biases is still required, even though genome-scale data sets greatly reduce sampling error.

3D thermal mapping of building interiors using an RGB-D and thermal camera

The building sector is the dominant consumer of energy and therefore a major contributor to anthropomorphic climate change. The rapid generation of photorealistic, 3D environment models with incorporated surface temperature data has the potential to improve thermographic monitoring of building energy efficiency. In pursuit of this goal, we propose a system which combines a range sensor with a thermal-infrared camera. Our proposed system can generate dense 3D models of environments with both appearance and temperature information, and is the first such system to be developed using a low-cost RGB-D camera. The proposed pipeline processes depth maps successively, forming an ongoing pose estimate of the depth camera and optimizing a voxel occupancy map. Voxels are assigned 4 channels representing estimates of their true RGB and thermal-infrared intensity values. Poses corresponding to each RGB and thermal-infrared image are estimated through a combination of timestamp-based interpolation and a pre-determined knowledge of the extrinsic calibration of the system. Raycasting is then used to color the voxels to represent both visual appearance using RGB, and an estimate of the surface temperature. The output of the system is a dense 3D model which can simultaneously represent both RGB and thermal-infrared data using one of two alternative representation schemes. Experimental results demonstrate that the system is capable of accurately mapping difficult environments, even in complete darkness.

Mapping Multiple Literacies: An Introduction to Deleuzian Literacy Studies

Mapping Multiple Literacies brings together the latest theory and research in the fields of literacy study and European philosophy, Multiple Literacies Theory (MLT) and the philosophical work of Gilles Deleuze. It frames the process of becoming literate as a fluid process involving multiple modes of presentation, and explains these processes in terms of making maps of our social lives and ways of doing things together. For Deleuze, language acquisition is a social activity of which we are a part, but only one part amongst many others. Masny and Cole draw on Deleuze's thinking to expand the repertoires of literacy research and understanding. They outline how we can understand literacy as a social activity and map the ways in which becoming literate may take hold and transform communities. The chapters in this book weave together theory, data and practice to open up a creative new area of literacy studies and to provoke vigorous debate about the sociology of literacy.

Do RNA viruses require genome cyclisation for replication?

Complementary sequences at the 5′ and 3′ ends of the dengue virus RNA genome are essential for viral replication, and are believed to cyclise the genome through long-range base pairing in cis. Although consistent with evidence in the literature, this view neglects possible biologically active multimeric forms that are equally consistent with the data. Here, we propose alternative multimeric structures, and suggest that multigenome noncovalent concatemers are more likely to exist under cellular conditions than single cyclised monomers. Concatemers provide a plausible mechanism for the dengue virus to overcome the single-stranded (+)-sense RNA virus dilemma, and can potentially assist genome transport from the virus-induced vesicles into the cytosol.

A general model for host plant selection in phytophagous insects

We develop a general theoretical framework for exploring the host plant selection behaviour of herbivorous insects. This model can be used to address a number of questions, including the evolution of specialists, generalists, preference hierarchies, and learning. We use our model to: (i) demonstrate the consequences of the extent to which the reproductive success of a foraging female is limited by the rate at which they find host plants (host limitation) or the number of eggs they carry (egg limitation); (ii) emphasize the different consequences of variation in behaviour before and after landing on (locating) a host (termed pre- and post-alighting, respectively); (iii) show that, in contrast to previous predictions, learning can be favoured in post-alighting behaviour--in particular, individuals can be selected to concentrate oviposition on an abundant low-quality host, whilst ignoring a rare higher-quality host; (iv) emphasize the importance of interactions between mechanisms in favouring specialization or learning.