Evidence of unique genotypes of Beak and feather disease virus in Southern Africa

Psittacine beak and feather disease (PBFD), caused by Beak and feather disease virus (BFDV), is the most significant infectious disease in psittacines. PBFD is thought to have originated in Australia but is now found worldwide; in Africa, it threatens the survival of the indigenous endangered Cape parrot and the vulnerable black-cheeked lovebird. We investigated the genetic diversity of putative BFDVs from southern Africa. Feathers and heparinized blood samples were collected from 27 birds representing 9 psittacine species, all showing clinical signs of PBFD. DNA extracted from these samples was used for PCR amplification of the putative BFDV coat protein (CP) gene. The nucleotide sequences of the CP genes of 19 unique BFDV isolates were determined and compared with the 24 previously described sequences of BFDV isolates from Australasia and America. Phylogenetic analysis revealed eight BFDV lineages, with the southern African isolates representing at least three distinctly unique genotypes; 10 complete genome sequences were determined, representing at least one of every distinct lineage. The nucleotide diversity of the southern African isolates was calculated to be 6.4% and is comparable to that found in Australia and New Zealand. BFDVs in southern Africa have, however, diverged substantially from viruses found in other parts of the world, as the average distance between the southern African isolates and BFDV isolates from Australia ranged from 8.3 to 10.8%. In addition to point mutations, recombination was found to contribute substantially to the level of genetic variation among BFDVs, with evidence of recombination in all but one of the genomes analyzed.

Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa

Maize streak virus strain A (MSV-A), the causal agent of maize streak disease, is today one of the most serious biotic threats to African food security. Determining where MSV-A originated and how it spread transcontinentally could yield valuable insights into its historical emergence as a crop pathogen. Similarly, determining where the major extant MSV-A lineages arose could identify geographical hot spots of MSV evolution. Here, we use model-based phylogeographic analyses of 353 fully sequenced MSV-A isolates to reconstruct a plausible history of MSV-A movements over the past 150 years. We show that since the probable emergence of MSV-A in southern Africa around 1863, the virus spread transcontinentally at an average rate of 32.5 km/year (95% highest probability density interval, 15.6 to 51.6 km/year). Using distinctive patterns of nucleotide variation caused by 20 unique intra-MSV-A recombination events, we tentatively classified the MSV-A isolates into 24 easily discernible lineages. Despite many of these lineages displaying distinct geographical distributions, it is apparent that almost all have emerged within the past 4 decades from either southern or east-central Africa. Collectively, our results suggest that regular analysis of MSV-A genomes within these diversification hot spots could be used to monitor the emergence of future MSV-A lineages that could affect maize cultivation in Africa. © 2011, American Society for Microbiology.

The causes of sinuous crustal-scale deformation patterns in hot orogens: Evidence from scaled analogue experiments and the southern Central Andes

The cause of upper-crustal segmentation into rhomb-shaped, shear zone-bound domains associated with contractional sedimentary basins in hot, wide orogens is not well understood. Here we use scaled multilayered analogue experiments to investigate the role of an orogen-parallel crustal-strength gradient on the formation of such structures. We show that the aspect ratio and size of domains, the sinuous character and abundance of transpressional shear zones vary with the integrated mechanical strength of crust. Upper-crustal deformation patterns and the degree of strain localization in the experiments are controlled by the ratio between the brittle and ductile strength in the model crust as well as gradients in tectonic and buoyancy forces. The experimental results match the first-order kinematic and structural characteristics of the southern Central Andes and provide insight on the dynamics of underlying deformation patterns in hot, wide orogens.

Micrinite in Southern Hemisphere sub-bituminous and bituminous coals : redefined as fine grained kaolinite

A range of complementary analytical techniques including SEM/EDS, TEM/EDS and conventional optical microscopy has been rigorously applied to precisely defined areas of micrinite in polished coal samples from Australia and New Zealand. Elemental analyses of micrinite regions showed a high abundance of Al, Si and O and high resolution images of micrinite revealed a grain size < 1μm. Electron diffraction and elemental analyses from individual grains within the optically and electron-optically correlated micrinite regions are consistent with the occurence of fine-grained kaolinite. The optical properties of "dark clay" and "micrinite" (i.e. fine-grained kaolinite) can be understood in terms of the diffuse scattering of visible light from the surfaces of materials with different grain sizes in single-phase or multi-phase mixtures.

The story behind the stories: Qualitative criminology research in Australia

Qualitative Criminology: Stories from the Field brings to life the stories behind the research of both emerging and established scholars in Australian criminology. The book’s contributors provided honest, reflective, and decidedly unsanitised accounts of their qualitative research journeys - the lively tales of what really happens when conducting research of this nature, the stories that often make for parenthetical asides in conference papers but tend to be excised from journal articles. This book considers the gap between research methods and the realities of qualitative research. As such, it aims to help researchers and students who conduct qualitative criminological research reflect upon their role as researchers, and the practical, ideological and ethical issues which may arise in the course of their research. It is also a call to criminologists to make public the ‘failures’ and missteps of their research endeavours so that we can learn from one another and become better informed and more reflexive qualitative criminologists.

25 million years to break a continent : early to middle Miocene rifting and syn-extensional magmatism in the southern Gulf of California

Cenozoic extension in western Mexico has been divided into two episodes separated by the change from convergence to oblique divergence at the plate boundary. The Gulf Extensional Province is thought to have started once subduction ended at ~12.5 Ma whereas early extension is classified as Basin and Range. Mid-Miocene volcanism of the Comondú group has been considered as a subduction-related arc, whereas post ~12.5 Ma volcanism would be extension-related. Our new integration of the continental onshore and offshore geology of the south-east Gulf region, backed by tens of Ar-Ar and U-Pb ages and geochemical studies, document an early-mid Miocene rifting and extension-related bimodal to andesitic magmatism prior to subduction termination. Between ~21 and 11 Ma a system of NNW-SSE high-angle extensional faults rifted the western side of the Sierra Madre Occidental (SMO) ignimbrite plateau. In Nayarit, rhyolitic domes and some basalts were emplaced along this extensional belt at 18-17 Ma. These rocks show strong antecrystic inheritance but an absence of Mesozoic and older xenocrysts, suggesting a genesis in the mid-upper crust triggered by extension-induced basaltic influx. In Sinaloa, large grabens were floored by huge dome complexes at ~21-17 Ma and filled by continental sediments with interlayered basalts dated at 15 Ma. Mid-Miocene volcanism, including the largely volcaniclastic Comondú strata in Baja California, was thus emplaced in rift basins and appears associated to decompression melting rather than subduction. Along the coast, flat-lying basaltic lava flows dated at 11-10 Ma are exposed just above the present sea level. Here crustal thickness is 25-20 Km, almost half that in the core of the SMO, implying significant lithosphere stretching before ~11 Ma. This mafic pulse, with relatively high Ti but still clear Nb-Ta negative spikes, may be related to the detachment of the lower part of the subducted slab, allowing asthenosphere to flow into parts of the mantle previously fluxed by subduction fluids. Very uniform OIB-like lavas appear in late Pliocene and Pleistocene, only 18 m.y. after the onset of rifting and ~9 m.y. after the end of subduction. Our study shows that rifting began much earlier than Late Miocene and progressively overwhelmed subduction in generating magmatism.

Consequences of extensional tectonics on volcanic eruption style, compositions and source regions : new insights from the southern Sierra Madre Occidental and Gulf of California regions, western Mexico

Understanding the link between tectonic-driven extensional faulting and volcanism is crucial from a hazard perspective in active volcanic environments, while ancient volcanic successions provide records on how volcanic eruption styles, compositions, magnitudes and frequencies can change in response to extension timing, distribution and intensity. This study draws on intimate relationships of volcanism and extension preserved in the Sierra Madre Occidental (SMO) and Gulf of California (GoC) regions of western Mexico. Here, a major Oligocene rhyolitic ignimbrite “flare-up” (>300,000 km3) switched to a dominantly bimodal and mixed effusive-explosive volcanic phase in the Early Miocene (~100,000 km3), associated with distributed extension and opening of numerous grabens. Rhyolitic dome fields were emplaced along graben edges and at intersections of cross-graben and graben-parallel structures during early stages of graben development. Concomitant with this change in rhyolite eruption style was a change in crustal source as revealed by zircon chronochemistry with rapid rates of rhyolite magma generation due to remelting of mid- to upper crustal, highly differentiated igneous rocks emplaced during earlier SMO magmatism. Extension became more focused ~18 Ma resulting in volcanic activity being localised along the site of GoC opening. This localised volcanism (known as the Comondú “arc”) was dominantly effusive and andesite-dacite in composition. This compositional change resulted from increased mixing of basaltic and rhyolitic magmas rather than fluid flux melting of the mantle wedge above the subducting Guadalupe Plate. A poor understanding of space-time relationships of volcanism and extension has thus led to incorrect past tectonic interpretations of Comondú-age volcanism.

Logan Basin Water Resource Plan : environmental assessment of the southern Moreton Bay islands. Technical Advisory Panel Report: Stage 1.

This report is a technical assessment of the hydrological environment of the southern Moreton Bay islands and follows the terms of reference supplied by the then Queensland Department of Natural Resources and Water. The terms of reference describe stage 1 as a condition assessment and stage 2 as an assessment of the implications of water planning scenarios on future condition. This report is the first stage of a two-stage investigation whose primary purpose is to identify and assess groundwater dependent ecosystems (GDEs) and the groundwater flow regimes necessary to support them. Within this context, the groundwaters themselves are also considered and comment made on their condition. Information provided in this report will inform an amendment to the Logan Basin Water Resource Plan to incorporate the southern Moreton Bay islands. The study area is the water resource plan amendment area, which includes North and South Stradbroke islands and the smaller islands between these and the mainland, including the inhabited smaller rocky islands—namely, Macleay, Russell, Karragarra, Lamb and Coochiemudlo islands. This assessment is largely a desktop study based on existing information, but incorporates some field observations, input from experts in specific areas and community representatives, and the professional experience and knowledge of the authors. This report reviews existing research and information on the southern Moreton Bay area with an emphasis on North Stradbroke Island, as it represents the largest and most regionally significant groundwater resource in southern Moreton Bay. The report provides an assessment of key waterrelated environmental features, their condition and their degree of dependence on groundwater. This report also assesses the condition and status of ecosystems within this region. In addition, the report identifies information gaps, uncertainties and potential impacts; reviews groundwater models that have been developed for North Stradbroke Island; and makes recommendations on monitoring and research needs.

Emerging Issues in Green Criminology : Exploring Power, Justice and Harm

This edited collection brings together internationally recognized scholars to explore Green Criminology through interdisciplinary lenses of power, justice and harm. The chapters provide innovative case study analyses from North America, Europe and Australia that seek to advance theoretical, policy and practice discourses about environmental harm. This book brings together transnational debates in environmental law, policy and justice. In doing so, it examines international agreements and policy within diverse environmental discourses of sociology, criminology and political economy.

Community-based control of Aedes aegypti by using Mesocyclops in southern Vietnam

We previously reported a new community-based mosquito control strategy that resulted in elimination of Aedes aegypti (Linn.) in 40 of 46 communes in northern and central Vietnam, and with annual recurrent total costs (direct and indirect) of only $0.28-$0.89 international dollars per person. This control strategy was extended to four provinces in southern Vietnam in Long An and Hau Giang (2004-2007) and to Long An, Ben Tre, and Vinh Long (2005-2010). In a total of 14 communes with 124,743 residents, the mean ± SD of adult female Ae. aegypti was reduced from 0.93 ± 0.62 to 0.06 ± 0.09, and the reduction of immature Ae. aegypti averaged 98.8%. By the final survey, no adults could be collected in 6 of 14 communes, and one commune, Binh Thanh, also had no immature forms. Although the community-based programs also involved community education and clean-up campaigns, the prevalence of Mesocyclops in large water storage containers > 50 liters increased from 12.77 ± 8.39 to 75.69 ± 9.17% over periods of 15-45 months. At the conclusion of the study, no confirmed dengue cases were detected in four of the five communes for which diagnostic serologic analysis was performed. The rate of progress was faster in communes that were added in stages to the program but the reason for this finding was unclear. At the completion of the formal project, sustainability funds were set up to provide each commune with the financial means to ensure that community-based dengue control activities continued.

Qualitative criminology : Stories from the field

Qualitative researchers in the discipline of criminology perform a wide range of challenging tasks. They interview prisoners, police officers, magistrates and judges. They speak with survivors of domestic violence, and drink tea with the mothers of murdered children. They observe courts and communities, investigate the decision-making processes of juries and immerse themselves in the data they collect. They ask ‘big’ questions – ‘how do we criminalise the producers of toxic toys?’ – as well as ‘little’ questions – ‘what should I wear to conduct this interview?’ Qualitative Criminology: Stories from the Field brings to life the stories behind the research of both emerging and established scholars in Australian criminology. The book’s contributors provided honest, reflective, and decidedly unsanitised accounts of their qualitative research journeys - the lively tales of what really happens when conducting research of this nature, the stories that often make for parenthetical asides in conference papers but tend to be excised from journal articles. This book considers the gap between research methods and the realities of qualitative research. As such, it aims to help researchers and students who conduct qualitative criminological research reflect upon their role as researchers, and the practical, ideological and ethical issues which may arise in the course of their research. It is also a call to criminologists to make public the ‘failures’ and missteps of their research endeavours so that we can learn from one another and become better informed and more reflexive qualitative criminologists.

First measurements of source apportionment of organic aerosols in the Southern Hemisphere

An Aerodyne Aerosol Mass Spectrometer was deployed at five urban schools to examine spatial and temporal variability of organic aerosols (OA) and positive matrix factorization (PMF) used for the first time in the Southern Hemisphere to apportion the sources of the OA across an urban area. The sources identified included hydrocarbon-like OA (HOA), biomass burning OA (BBOA) and oxygenated OA (OOA). At all sites, the main source was OOA, which accounted for 62–73% of the total OA mass and was generally more oxidized compared to those reported in the Northern Hemisphere. This suggests that there are differences in aging processes or regional sources in the two hemispheres. Unlike HOA and BBOA, OOA demonstrated instructive temporal variations but not spatial variation across the urban area. Application of cluster analysis to the PMF-derived sources offered a simple and effective method for qualitative comparison of PMF sources that can be used in other studies.