The O-specific polysaccharide structure and gene cluster of serotype O:12 of the Yersinia pseudotuberculosis complex, and the identification of a novel L-quinovose biosynthesis gene

A major virulence factor for Yersinia pseudotuberculosis is lipopolysaccharide, including O-polysaccharide (OPS). Currently, the OPS based serotyping scheme for Y. pseudotuberculosis includes 21 known O-serotypes, with genetic and structural data available for 17 of them. The completion of the OPS structures and genetics of this species will enable the visualization of relationships between O-serotypes and allow for analysis of the evolutionary processes within the species that give rise to new serotypes. Here we present the OPS structure and gene cluster of serotype O:12, thus adding one more to the set of completed serotypes, and show that this serotype is present in both Y. pseudotuberculosis and the newly identified Y. similis species. The O:12 structure is shown to include two rare sugars: 4-C[(R)-1-hydroxyethyl]-3,6-dideoxy-d-xylo-hexose (d-yersiniose) and 6-deoxy-l-glucopyranose (l-quinovose). We have identified a novel putative guanine diphosphate (GDP)-l-fucose 4-epimerase gene and propose a pathway for the synthesis of GDP-l-quinovose, which extends the known GDP-l-fucose pathway.

A rare view: Barbara Hatley’s new book documents a career-long study of, and passion for performance in Central Java

Javanese Performances on an Indonesian Stage: Contesting Culture, Embracing Change, is Barbara Hatley’s first book about the performing arts in Indonesia, a topic that piqued her interest while undergoing a masters program at Yale University in the late 1960s. In this sense, it is a landmark study, for Hatley has since become very well known in Indonesianist circles, especially among those with an interest in matters of culture, popular and elite. Until recently, her writings on Indonesian performing arts have only been available in the form of journal articles and book chapters...

Beyond Moa's Ark and Wallace's Line: extralimital distribution of new species of Austronothrus (Acari, Oribatida, Crotoniidae) and the endemicity of the New Zealand oribatid mite fauna

The genus Austronothrus was previously known from three species recorded only from New Zealand. Austronothrus kinabalu sp. nov. is described from Sabah, Borneo and A. rostralis sp. nov. from Norfolk Island, south-west Pacific. A key to Austronothrus is included. These new species extend the distribution of Austronothrus beyond New Zealand and confirms that the subfamily Crotoniinae is not confined to former Gondwanan landmasses. The distribution pattern of Austronothrus spp., combining Oriental and Gondwanan localities, is indicative of a curved, linear track; consistent with the accretion of island arcs and volcanic terranes around the plate margins of the Pacific Ocean, with older taxa persisting on younger island though localised dispersal within island arc metapopulations. Phylogenetic analysis and an area cladogram are consistent with a broad ancestral distribution of Austronothrus in the Oriental region and on Gondwanan terranes, with subsequent divergence and distribution southward from the Sunda region to New Zealand. This pattern is more complex than might be expected if the New Zealand oribatid fauna was derived from dispersal following re-emergence of land after inundation during the Oligocene (25 mya), as well as if the fauna emanated from endemic, relictual taxa following separation of New Zealand from Gondwana during the Cretaceous (80 mya).

Anatomical studies of the flower, fruit and seeds of Myrceugenia rufa (Myrtaceae)

Myceugenia rufa is a rare and endemic species from the coast of central Chile. There are no published studies describing flower, fruit or seed anatomy. Forty-two accessions were collected from across the geographic range of the species. Reproductive structures were fixed, dehydrated, embedded in paraffin, sectioned and stained with Safranin O and Fast green. Anatomy of floral buds, mature flowers, fruits and seeds was described. Reproductive anatomy matches that of other Myrtaceae, such as presence of druses, internal phloem and schizogenous secretory cavities in buds, flowers, fruits and seeds. The anatomy and development of reproductive structures of M. rufa might enhance the understanding for future studies regarding natural reproduction and conservation programs.

A review of iron species for visible-light photocatalytic water purification

Iron species are one of the least toxic and least expensive substances that are photocatalytic in the visible region of the spectrum. Therefore, this article focuses on iron-based photocatalysts sensitive to visible light. Photo-Fenton reactions are considered with respect to those assisted by and involve the in situ production of H2O2. The possible role that photoactive iron species play by interacting with natural organic matter in water purification in the natural environment is considered. The review also considered photosensitization by phthalocyanines and the potential role that layered double hydroxides may have not only as catalyst supports but also as photosensitizers themselves. Finally, photocatalytic disinfection of water is discussed, and the desirability of standardized metrics and experimental conditions to assist in the comparative evaluation of photocatalysts is highlighted.

The characterisation of Ureaplasma species isolated from the Chorioamnion of women who deliver late Preterm

This thesis investigated, for the first time, the prevalence of Ureaplasma species infection within the placentae of women who delivered in the late preterm stages of pregnancy. The presence of these microorganisms was associated with either severe inflammation within the placenta or, for some women, there were no pregnancy complications and these women delivered at term. Ureaplasmas are able to vary their surface exposed lipoproteins and we demonstrated that different host immune responses were generated in vivo to different sized surface lipoproteins. This may explain why ureaplasma infections do not always result in adverse pregnancy and neonatal outcomes.

Endangered species and the precautionary principle

This discussion paper is intended to provide background material for the workshop organised by Queensland University Technology (QUT) on 17 October 2014. The overall purpose of the workshop is to better understand the relationship between the precautionary principle and endangered species management in Australia. In particular, we are looking for real life examples (or hypotheticals) of where the principle is (or is not) being applied in relation to Australia’s endangered species. A wide variety of participants have been invited to the workshop including scientists, representatives of NGOs, lawyers and academics. Whilst some very general information is outlined below, we encourage all participants to bring their own thoughts on how the precautionary principle should operate and to reflect on examples of where you have seen it work (or not work) in Australia. The sharing of your own case studies is thus encouraged.

What is the available evidence concerning relative performance of different designs of mixed-species plantings for smallholder and community forestry in the tropics? A systematic map protocol

Background There has been growing interest in mixed species plantation systems because of their potential to provide a range of socio-economic and bio-physical benefits which can be matched to the diverse needs of smallholders and communities. Potential benefits include the production of a range of forest products for home and commercial use; improved soil fertility especially when nitrogen fixing species are included; improved survival rates and greater productivity of species; a reduction in the amount of damage from pests or disease; and improved biodiversity and wildlife habitats. Despite these documented services and growing interest in mixed species plantation systems, the actual planting areas in the tropics are low, and monocultures are still preferred for industrial plantings and many reforestation programs because of perceived higher economic returns and readily available information about the species and their silviculture. In contrast, there are few guidelines for the design and management of mixed-species systems, including the social and ecological factors of successful mixed species plantings. Methods This protocol explains the methodology used to investigate the following question: What is the available evidence for the relative performance of different designs of mixed-species plantings for smallholder and community forestry in the tropics? This study will systematically search, identify and describe studies related to mixed species plantings across tropical and temperate zones to identify the social and ecological factors that affect polyculture systems. The objectives of this study are first to identify the evidence of biophysical or socio-economic factors that have been considered when designing mixed species systems for community and smallholder forestry in the tropics; and second, to identify gaps in research of mixed species plantations. Results of the study will help create guidelines that can assist practitioners, scientists and farmers to better design mixed species plantation systems for smallholders in the tropics.

Uncertain species distribution: From interpolation to extrapolation

Species distribution models (SDMs) are considered to exemplify Pattern rather than Process based models of a species' response to its environment. Hence when used to map species distribution, the purpose of SDMs can be viewed as interpolation, since species response is measured at a few sites in the study region, and the aim is to interpolate species response at intermediate sites. Increasingly, however, SDMs are also being used to also extrapolate species-environment relationships beyond the limits of the study region as represented by the training data. Regardless of whether SDMs are to be used for interpolation or extrapolation, the debate over how to implement SDMs focusses on evaluating the quality of the SDM, both ecologically and mathematically. This paper proposes a framework that includes useful tools previously employed to address uncertainty in habitat modelling. Together with existing frameworks for addressing uncertainty more generally when modelling, we then outline how these existing tools help inform development of a broader framework for addressing uncertainty, specifically when building habitat models. As discussed earlier we focus on extrapolation rather than interpolation, where the emphasis on predictive performance is diluted by the concerns for robustness and ecological relevance. We are cognisant of the dangers of excessively propagating uncertainty. Thus, although the framework provides a smorgasbord of approaches, it is intended that the exact menu selected for a particular application, is small in size and targets the most important sources of uncertainty. We conclude with some guidance on a strategic approach to identifying these important sources of uncertainty. Whilst various aspects of uncertainty in SDMs have previously been addressed, either as the main aim of a study or as a necessary element of constructing SDMs, this is the first paper to provide a more holistic view.

Plant species’ origin predicts dominance and response to nutrient enrichment and herbivores in global grasslands

Exotic species dominate many communities; however the functional significance of species’ biogeographic origin remains highly contentious. This debate is fuelled in part by the lack of globally replicated, systematic data assessing the relationship between species provenance, function and response to perturbations. We examined the abundance of native and exotic plant species at 64 grasslands in 13 countries, and at a subset of the sites we experimentally tested native and exotic species responses to two fundamental drivers of invasion, mineral nutrient supplies and vertebrate herbivory. Exotic species are six times more likely to dominate communities than native species. Furthermore, while experimental nutrient addition increases the cover and richness of exotic species, nutrients decrease native diversity and cover. Native and exotic species also differ in their response to vertebrate consumer exclusion. These results suggest that species origin has functional significance, and that eutrophication will lead to increased exotic dominance in grasslands.

To sonicate or not to sonicate PM filters: Reactive Oxygen Species generation upon ultrasonic irradiation

In aerosol research, a common approach for the collection of particulate matter (PM) is the use of filters in order to obtain sufficient material to undertake analysis. For subsequent chemical and toxicological analyses, in most of cases the PM needs to be extracted from the filters. Sonication is commonly used to most efficiently extract the PM from the filters. Extraction protocols generally involve 10 - 60 min of sonication. The energy of ultrasonic waves causes the formation and collapse of cavitation bubbles in the solution. Inside the collapsing cavities the localised temperatures and pressures can reach extraordinary values. Although fleeting, such conditions can lead to pyrolysis of the molecules present inside the cavitation bubbles (gases dissolved in the liquid and solvent vapours), which results in the production of free radicals and the generation of new compounds formed by reactions with these free radicals. For example, simple sonication of pure water will result in the formation of detectable levels of hydroxyl radicals. As hydroxyl radicals are recognised as playing key roles as oxidants in the atmosphere the extraction of PM from filters using sonication is therefore problematic. Sonication can result in significant chemical and physical changes to PM through thermal degradation and other reactions. In this article, an overview of sonication technique as used in aerosol research is provided, the capacity for radical generation under these conditions is described and an analysis is given of the impact of sonication-derived free radicals on three molecular probes commonly used by researchers in this field to detect Reactive Oxygen Species in PM.

Strain- and host species-specific inflammasome activation, IL-1β release, and cell death in macrophages infected with uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infections (UTIs). Little is known about interactions between UPEC and the inflammasome, a key innate immune pathway. Here we show that UPEC strains CFT073 and UTI89 trigger inflammasome activation and lytic cell death in human macrophages. Several other UPEC strains, including two multidrug-resistant ST131 isolates, did not kill macrophages. In mouse macrophages, UTI89 triggered cell death only at a high multiplicity of infection, and CFT073-mediated inflammasome responses were completely NLRP3-dependent. Surprisingly, CFT073- and UTI89-mediated responses only partially depended on NLRP3 in human macrophages. In these cells, NLRP3 was required for interleukin-1β (IL-1β) maturation, but contributed only marginally to cell death. Similarly, caspase-1 inhibition did not block cell death in human macrophages. In keeping with such differences, the pore-forming toxin α-hemolysin mediated a substantial proportion of CFT073-triggered IL-1β secretion in mouse but not human macrophages. There was also a more substantial α-hemolysin-independent cell death response in human vs. mouse macrophages. Thus, in mouse macrophages, CFT073-triggered inflammasome responses are completely NLRP3-dependent, and largely α-hemolysin-dependent. In contrast, UPEC activates an NLRP3-independent cell death pathway and an α-hemolysin-independent IL-1β secretion pathway in human macrophages. This has important implications for understanding UTI in humans.

Phylogeography of two freshwater prawn species from far-northern Queensland

The distribution of a freshwater species is often dependent on its ability to disperse within the riverine system. Species with high dispersal abilities tend to be widespread, whereas those with restricted dispersal tend to be geographically restricted and are usually given higher conservation priority. Population structure was compared between a widespread freshwater prawn species, Macrobrachium australiense, and a narrow-range endemic freshwater prawn, Macrobrachium koombooloomba. The distribution of M. australiense and M. koombooloomba did not overlap, although suggested historical river-boundary rearrangements indicate that there has been the potential for dispersal into neighbouring catchments. A fragment of the mtDNA CO1 gene was analysed and a Mantel test revealed a significant isolation by distance effect for both species. Significant overall FST values confirmed that both species exhibited low levels of dispersal, a prediction for populations inhabiting a fragmented upland environment. The level of structure in M. australiense is surprising for a widely distributed species. Not all M. australiense populations conformed to the stream-hierarchy model, with results being best explained by historical river realignment or cross-catchment dispersal. The fact that both species show limited dispersal highlights the importance of conservation in highland areas for both endemic and widely spread species.

A taxonomic assessment of the Australian Dusky Antechinus Complex: A new species, the Tasman Peninsula Dusky Antechinus (Antechinus vandycki sp. nov.) and an elevation to species of the Mainland Dusky Antechinus (Antechinus swainsonii mimetes (Thomas))

In 2014, the northern outlying population of carnivorous marsupial Dusky Antechinus (Antechinus swainsonii) was nominated a new species, A. arktos. Here, we describe a further new species in the dasyurid A. swainsonii complex, which now contains five taxa. We recognise two distinct species from Tasmania, formerly represented by A. swainsonii swainsonii (Waterhouse); one species (and 2 subspecies) from mainland south-eastern Australia, formerly known as A. swainsonii mimetes (Thomas) and A. swainsonii insulanus Davison; and one species from the Tweed Caldera in mid-eastern Australia, formerly known as A. s. mimetes but recently described as A. arktos Baker, Mutton, Hines and Van Dyck. Primacy of discovery dictates the Tasmanian Dusky Antechinus A. swainsonii (Waterhouse) is nominate; the Mainland Dusky Antechinus taxa, one raised from subspecies within A. swainsonii mimetes (Thomas) is elevated to species (now A. mimetes mimetes) and the other, A. swainsonii insulanus Davison is transferred as a subspecies of A. mimetes (now A. mimetes insulanus); a species from Tasmania, the Tasman Peninsula Dusky Antechinus, is named A. vandycki sp. nov. These taxa are strongly differentiated: geographically (in allopatry), morphologically (in coat colour and craniodental features) and genetically (in mtDNA, 7.5-12.5% between species pairs).