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.

Evaluating automatic road detection across a large aerial imagery collection

The automated extraction of roads from aerial imagery can be of value for tasks including mapping, surveillance and change detection. Unfortunately, there are no public databases or standard evaluation protocols for evaluating these techniques. Many techniques are further hindered by a reliance on manual initialisation, making large scale application of the techniques impractical. In this paper, we present a public database and evaluation protocol for the evaluation of road extraction algorithms, and propose an improved automatic seed finding technique to initialise road extraction, based on a combination of geometric and colour features.

Immobilised anatase on clay mineral particles as a photocatalyst for herbicides degradation

Materials consisting of anatase linked to Laponite particles were synthesized by the reaction of TiOSO4 with Laponite, and were used for the degradation of pesticides. All these materials were characterized by XRD, FTIR, Raman, TEM, specific surface area and porosity determinations. Based on the amount of photoactive phase per unit mass of the clay mineral, not based on the total weight of the catalysts, these porous catalysts were displaying a high degradation rate than commercial P25. The TiO2 immobilized clay mineral catalysts can sediment in few minutes and could be readily separated out from a slurry system after the photocatalytic reaction. Settling properties of these catalysts are enormously high in aqueous media in contrast to P25.

An information accountability framework for shared eHealth policies

Privacy issues have hindered the evolution of e-health since its emergence. Patients demand better solutions for the protection of private information. Health professionals demand open access to patient health records. Existing e-health systems find it difficult to fulfill these competing requirements. In this paper, we present an information accountability framework (IAF) for e-health systems. The IAF is intended to address privacy issues and their competing concerns related to e-health. Capabilities of the IAF adhere to information accountability principles and e-health requirements. Policy representation and policy reasoning are key capabilities introduced in the IAF. We investigate how these capabilities are feasible using Semantic Web technologies. We discuss with the use of a case scenario, how we can represent the different types of policies in the IAF using the Open Digital Rights Language (ODRL).

Status of current research on the implication of climate change on built environment

The cycling interaction between climate change and building performance is of dynamic nature and both are essentially the cause and the effect of each other. On one hand, buildings contribute significantly to the global warming process. On the other hand, climate change is also expected to impact on many aspects of building performance. In this paper, the status of current research on the implication of climate change on built environment is reviewed. It is found that although the present research has covered broad areas of research, they are generally only limited to the qualitative analyses. It is also highlighted that although it is widely realized that reducing greenhouse gas emissions from the building sector is very important, the adoption of complementary adaptation strategy to prepare the building for a range of climate change scenarios is also necessary. Due to the lack of holistic approach to generate future hourly weather data, various approaches have been used to generate different key weather variables. This ad hoc situation has seriously hindered the application of building simulation technique to the climate change impact study, in particular, to provide quantitative information for policy and design development.

Insights to the Clarification of Sugar Cane Juice Expressed from Sugar Cane Stalk and Trash

Processing of juice expressed from green sugar cane containing all the trash (i.e., tops and leaves, the nonstalk component) of the sugar cane plant during sugar manufacture has been reported to lead to poor clarified juice (CJ) quality. Studies of different liming techniques have been conducted to identify which liming technique gives the best clarification performance from juice expressed from green cane containing half of all trash extracted (GE). Results have shown that lime saccharate addition to juice at 76 °C either continuous or batchwise gives satisfactory settling rates of calcium phosphate flocs(50−70 cm/min) and CJ with low turbidity and minimal amounts of mineral constituents. Surprisingly, the addition of phosphoric acid (≤300 mg/kg as P2O5), prior to liming to reduce juice turbidity (≤80%), increased the Mg (≤101%) and Si(≤148%) contents particularly for clarified GE juices. The increase was not proportional with increasing phosphoric acid dose. The nature of the flocs formed, including the zeta potential of the particles by the different liming techniques, has been used to account for the differences in clarification performance. Differences between the qualities of the CJ obtained with GE juice and that of burnt cane juices with all trash extracted (BE) have been discussed to provide further insights into GE processing.

Development of a transformation system for sorghum (Sorghum bicolor L.)

Sorghum (Sorghum bicolor (L.) Moench) is the world’s fifth major cereal crop and holds importance as a construction material, food and fodder source. More recently, the potential of this plant as a biofuel source has been noted. Despite its agronomic importance, the use of sorghum production is being constrained by both biotic and abiotic factors. These challenges could be addressed by the use of genetic engineering strategies to complement conventional breeding techniques. However, sorghum is one of the most recalcitrant crops for genetic modification with the lack of an efficient tissue culture system being amongst the chief reasons. Therefore, the aim of this study was to develop an efficient tissue culture system for establishing regenerable embryogenic cell lines, micropropagation and acclimatisation for Sorghum bicolor and use this to optimise parameters for genetic transformation via Agrobacterium-mediated transformation and microprojectile bombardment. Using five different sorghum cultivars, SA281, 296B, SC49, Wray and Rio, numerous parameters were investigated in an attempt to establish an efficient and reproducible tissue culture and transformation system. Using immature embryos (IEs) as explants, regenerable embryogenic cell lines (ECLs) could only be established from cultivars SA281 and 296B. Large amounts of phenolics were produced from IEs of cultivars, SC49, Wary and Rio, and these compounds severely hindered callus formation and development. Cultivar SA281 also produced phenolics during regeneration. Attempts to suppress the production of these compounds in cultivars SA281 and SC49 using activated charcoal, PVP, ascorbic acid, citric acid and liquid filter paper bridge methods were either ineffective or had a detrimental effect on embryogenic callus formation, development and regeneration. Immature embryos sourced during summer were found to be far more responsive in vitro than those sourced during winter. In an attempt to overcome this problem, IEs were sourced from sorghum grown under summer conditions in either a temperature controlled glasshouse or a growth chamber. However, the performance of these explants was still inferior to that of natural summer-sourced explants. Leaf whorls, mature embryos, shoot tips and leaf primordia were found to be unsuitable as explants for establishing ECLs in sorghum cultivars SA281 and 296B. Using the florets of immature inflorescences (IFs) as explants, however, ECLs were established and regenerated for these cultivars, as well as for cultivar Tx430, using callus induction media, SCIM, and regeneration media, VWRM. The best in vitro responses, from the largest possible sized IFs, were obtained using plants at the FL-2 stage (where the last fully opened leaf was two leaves away from the flag leaf). Immature inflorescences could be stored at 25oC for up to three days without affecting their in vitro responses. Compared to IEs, the IFs were more robust in tissue culture and showed responses which were season and growth condition independent. A micropropagation protocol for sorghum was developed in this study. The optimum plant growth regulator (PGR) combination for the micropropagation of in vitro regenerated plantlets was found to be 1.0 mg/L BAP in combination with 0.5 mg/L NAA. With this protocol, cultivars 296B and SA281 produced an average of 57 and 13 off-shoots per plantlet, respectively. The plantlets were successfully acclimatised and developed into phenotypically normal plants that set seeds. A simplified acclimatisation protocol for in vitro regenerated plantlets was also developed. This protocol involved deflasking in vitro plantlets with at least 2 fully-opened healthy leaves and at least 3 roots longer than 1.5 cm, washing the media from the roots with running tap water, planting in 100 mm pots and placing in plastic trays covered with a clear plastic bag in a plant growth chamber. After seven days, the corners of the plastic cover were opened and the bags were completely removed after 10 days. All plantlets were successfully acclimatised regardless of whether 1:1 perlite:potting mix, potting mix, UC mix or vermiculite were used as potting substrates. Parameters were optimised for Agrobacterium-mediated transformation (AMT) of cultivars SA281, 296B and Tx430. The optimal conditions were the use of Agrobacterium strain LBA4404 at an inoculum density of 0.5 OD600nm, heat shock at 43oC for 3 min, use of the surfactant Pluronic F-68 (0.02% w/v) in the inoculation media with a pH of 5.2 and a 3 day co-cultivation period in dark at 22oC. Using these parameters, high frequencies of transient GFP expression was observed in IEs precultured on callus initiation media for 1-7 days as well as in four weeks old IE- and IF-derived callus. Cultivar SA281 appeared very sensitive to Agrobacterium since all tissue turned necrotic within two weeks post-exposure. For cultivar 296B, GFP expression was observed up to 20 days post co-cultivation but no stably transformed plants were regenerated. Using cultivar Tx430, GFP was expressed for up to 50 days post co-cultivation. Although no stably transformed plants of this cultivar were regenerated, this was most likely due to the use of unsuitable regeneration media. Parameters were optimised for transformation by particle bombardment (PB) of cultivars SA281, 296B and Tx430. The optimal conditions were use of 3-7 days old IEs and 4 weeks old IF callus, 4 hour pre- and post-bombardment osmoticum treatment, use of 0.6 µm gold microparticles, helium pressure of 1500 kPa and target distance of 15 cm. Using these parameters for PB, transient GFP expression was observed for up to 14, 30 and 50 days for cultivars SA281, 296B and Tx430, respectively. Further, the use of PB resulted in less tissue necrosis compared to AMT for the respective cultivars. Despite the presence of transient GFP expression, no stably transformed plants were regenerated. The establishment of regenerable ECLs and the optimization of AMT and PB parameters in this study provides a platform for future efforts to develop an efficient transformation protocol for sorghum. The development of GM sorghum will be an important step towards improving its agronomic properties as well as its exploitation for biofuel production.

Intrinsic kinetics of titania photocatalysis : simplified models for their investigation

Even though titanium dioxide photocatalysis has been promoted as a leading green technology for water purification, many issues have hindered its application on a large commercial scale. For the materials scientist the main issues have centred the synthesis of more efficient materials and the investigation of degradation mechanisms; whereas for the engineers the main issues have been the development of appropriate models and the evaluation of intrinsic kinetics parameters that allow the scale up or re-design of efficient large-scale photocatalytic reactors. In order to obtain intrinsic kinetics parameters the reaction must be analysed and modelled considering the influence of the radiation field, pollutant concentrations and fluid dynamics. In this way, the obtained kinetic parameters are independent of the reactor size and configuration and can be subsequently used for scale-up purposes or for the development of entirely new reactor designs. This work investigates the intrinsic kinetics of phenol degradation over titania film due to the practicality of a fixed film configuration over a slurry. A flat plate reactor was designed in order to be able to control reaction parameters that include the UV irradiance, flow rates, pollutant concentration and temperature. Particular attention was paid to the investigation of the radiation field over the reactive surface and to the issue of mass transfer limited reactions. The ability of different emission models to describe the radiation field was investigated and compared to actinometric measurements. The RAD-LSI model was found to give the best predictions over the conditions tested. Mass transfer issues often limit fixed film reactors. The influence of this phenomenon was investigated with specifically planned sets of benzoic acid experiments and with the adoption of the stagnant film model. The phenol mass transfer coefficient in the system was calculated to be km,phenol=8.5815x10-7Re0.65(ms-1). The data obtained from a wide range of experimental conditions, together with an appropriate model of the system, has enabled determination of intrinsic kinetic parameters. The experiments were performed in four different irradiation levels (70.7, 57.9, 37.1 and 20.4 W m-2) and combined with three different initial phenol concentrations (20, 40 and 80 ppm) to give a wide range of final pollutant conversions (from 22% to 85%). The simple model adopted was able to fit the wide range of conditions with only four kinetic parameters; two reaction rate constants (one for phenol and one for the family of intermediates) and their corresponding adsorption constants. The intrinsic kinetic parameters values were defined as kph = 0.5226 mmol m-1 s-1 W-1, kI = 0.120 mmol m-1 s-1 W-1, Kph = 8.5 x 10-4 m3 mmol-1 and KI = 2.2 x 10-3 m3 mmol-1. The flat plate reactor allowed the investigation of the reaction under two different light configurations; liquid and substrate side illumination. The latter of particular interest for real world applications where light absorption due to turbidity and pollutants contained in the water stream to be treated could represent a significant issue. The two light configurations allowed the investigation of the effects of film thickness and the determination of the catalyst optimal thickness. The experimental investigation confirmed the predictions of a porous medium model developed to investigate the influence of diffusion, advection and photocatalytic phenomena inside the porous titania film, with the optimal thickness value individuated at 5 ìm. The model used the intrinsic kinetic parameters obtained from the flat plate reactor to predict the influence of thickness and transport phenomena on the final observed phenol conversion without using any correction factor; the excellent match between predictions and experimental results provided further proof of the quality of the parameters obtained with the proposed method.

The Waitangi Tribunal and the regulation of Maori protest

Much of the current academic and political discourse related the development and operations of the Waitangi Tribunal over its first twenty years portray it as a forum that provided Māori with a meaningful avenue for settling Treaty grievances compared to the formal legal systems performance in the preceding 100 years. In contrast, we argue that from its inception and throughout much of the 1980s, the Waitangi Tribunal functioned primarily as an informal justice forum that assisted the New Zealand state’s regulation of Māori Treaty activism during the transition from a Fordist to a Post-Fordist mode of capital accumulation.

Alkyl radical geometry controls geminate cage recombination in alkylcobalamins

Abstract: The radical pair that results from photolysis of adenosylcob(II1)alamin (AdoCbl"') undergoes primary geminate recombination with a first-order rate constant of 1 x lo9 s-l. In contrast, methylcob(II1)alamin (CH3Cbl"') and aristeromicylcob(II1)alamin (AriCblII', the carbocyclic analogue of AdoCbl"' in which the ribofuranose ring oxygen has been replaced with a methylene group) does not undergo primary geminate recombination. The ribofwanose group enables a high rate of geminate recombination in the [Ado' Cbl"'] radical pair. This may be due to a stereoelectronic (p-anomeric) effect that maintains a pyramidal geometry at the 5'-carbon of the 5'-deoxyadenosyl radical, or it may be due to hindered rotation about the C4t-C5, bond such that /?-elimination to the olefin is prevented. Recombination in the geminate singlet radical pair is in competition with diffusive escape to form a solvent-separated radical pair. Hyperfine coupling from Co" promotes intersystem crossing to the triplet radical pair (Chagovetz, A. M.; Grissom, C. B. J. Am. Chem. SOC. 1993, 115, 12152). Recombination of the [CH3' Cbl"] radical pair is not prevented by a lack of intersystem crossing, as neither unlabeled or I3C-labeled CH3Cbl"' undergoes geminate recombination. There is only a small difference in the rate of diffusive recombination in the solvent cage for AdoCbl"', AriCbl"', and CH3Cbl"' following photolysis: 2.01 x 10" s-l, 2.20 x lo4 s-l, and 1.16 x lo4 s-l. The rate of diffusive recombination is limited by productive collisions and not by radical geometry or intersystem crossing. The CF3' radical that results from photolysis of (trifluoromethyl)cob(III)alamin (CF3Cbl"') maintains its pyramidal geometry and undergoes faster diffusive recombination in the solvent cage at 51 x lo4 s-l. The C-Co bond dissociation enthalpy in AriCbl"' is 37 f 1.4 kcaymol. The profound difference in geminate recombination rates for AdoCbl"' and CH3Cbl"' is consistent with their different biological roles as enzymatic cofactors: AdoCbl"' is an initiator of radical chain chemistry in the active site, whereas CH3Cbl"' is a methyl group donor in an S~2-type process.

Anatomy of a submarine pyroclastic flow and associated turbidity current : July 2003 dome collapse, Soufrière Hills volcano, Montserrat, West Indies

The 12 to 13 July 2003 andesite lava dome collapse at the Soufrière Hills volcano, Montserrat, provides the first opportunity to document comprehensively both the sub-aerial and submarine sequence of events for an eruption. Numerous pyroclastic flows entered the ocean during the collapse, depositing approximately 90% of the total material into the submarine environment. During peak collapse conditions, as the main flow penetrated the air–ocean interface, phreatic explosions were observed and a surge cloud decoupled from the main flow body to travel 2 to 3 km over the ocean surface before settling. The bulk of the flow was submerged and rapidly mixed with sea water forming a water-saturated mass flow. Efficient sorting and physical differentiation occurred within the flow before initial deposition at 500 m water depth. The coarsest components (∼60% of the total volume) were deposited proximally from a dense granular flow, while the finer components (∼40%) were efficiently elutriated into the overlying part of the flow, which evolved into a far-reaching turbidity current.

Preparation, characterisation and in vivo osteogenesis of mesoporous bioactive glasses

Bone defects, especially large bone defects, remain a major challenge in orthopaedic surgery. Autologous bone transplantation is considered the most effective treatment, but insufficient donor tissue, coupled with concerns about donor site morbidity, has hindered this approach in large-scale applications. Alternative approaches include implanting biomaterials such as bioactive glass (BG), which has been widely used for bone defect healing, due to having generally good biocompatibility, and can be gradually biodegraded during the process of new bone formation. Mesoporous bioactive glass (MBG) is a newly developed bioactive glass which has been proven to have enhanced in-vitro bioactivity; however the in-vivo osteogenesis has not been studied. A critical problem in using the bone tissue engineering approach to restore large bone defects is that the nutrient supply and cell viability at the centre of the scaffold is severely hampered since the diffusion distance of nutrients and oxygen for cell survival is limited to 150-200µm. Cobalt ions has been shown to mimic hypoxia, which plays a pivotal role in coupling angiogenesis with osteogenesis in-vivo by activating hypoxia inducing factor-1α (HIF-1α) transcription factor, subsequently initiating the expression of genes associated with tissue regeneration. Therefore, one aim of this study is to investigate the in-vivo osteogenesis of MBG by comparison with BG and β-TCP, which are widely used clinically. The other aim is to explore hypoxia-mimicking biomaterials by incorporating Cobalt into MBG and β-TCP. MBG and β-TCP incorporated with 5% cobalt (5Co-MBG and 5CCP) have also been studied in-vivo to determine whether the hypoxic effect has a beneficial effect on the bone formation. The composition and microstructure of synthesised materials (BG, MBG, 5Co-MBG, 5CCP) were characterised, along with the mesopore properties of the MBG materials. Dissolution and cytotoxicity of the Co-containing materials were also investigated. Femoral samples with defects harvested at 4 and 8 weeks were scanned using micro-CT followed by processing for histology (H&E staining) to determine bone formation. Histology of MBG showed a slower rate of bone formation at 4 weeks than BG, however at 8 weeks it could be clearly seen that MBG had more bone formation. The in-vivo results show that the osteogenesis of MBG reciprocates the enhanced performance shown in-vitro compared to BG. Dissolution study showed that Co ions can be efficiently released from MBG and β-TCP in a controllable way. Low amounts of Co incorporated into the MBG and β-TCP showed no significant cytotoxicity and the Co-MBG powders maintained a mesopore structure although not as highly ordered as pure MBG. Preliminary study has shown that Co incorporated samples showed little to no bone formation, instead incurring high lymphocyte activity. Further studies need to be done on Co incorporated materials to determine the cause for high lymphocyte activity in-vivo, which appear to hinder bone formation. In conclusion, this study demonstrated the osteogenic activity of MBG and provided some valuable information of tissue reaction to Co-incorporated MBG and TCP materials.

Unpacking the micro-macro nexus: narratives of suffering and hope among refugees from Burma recently settled in Australia

Narratives of forced migration are open to a variety of interpretations. In mental health, refugee narratives of arduous journeys in the face of systemic macro socio-political forces are often transformed from this context into a medicalized micro context of inner individual worlds. Both the dominant pathogenic lens of trauma studies and the growing salutogenic lens embodied in resilience research, often reflect a western cultural idiom of focusing on the individualized nature of these phenomena. Using qualitative data collected from refugees from Burma now settling in Australia, the article emphasizes the need for a more reflexive and expansive account of both suffering and hope within refugee narratives. It recounts these narratives within a conceptual framework which acknowledges the importance of the connections between the micro individual experience and the macro, socio-political context. This is not only a question of political principle, but also a matter of listening to the voice of those who know most about the relationship between macro forces of human rights violations and their impact on individual, family and community trajectories.

Producing solidarity : a settlement strategy of the Karen refugee community in Brisbane, Australia

This paper explores the link between experience and context. It places the lived experiences of Karen refugees during settlement in Brisbane, Australia within the socio-political context of Burma, or particularly the historical context of persecution. Two key events – the Wrist-tying Ceremony and the Karen New Year – provide a link between experience and context. The findings of this study show a community strategically at work in a new and ongoing settlement process. This process pays respect to the complexities of cultural integrity whilst also engaging with the challenges of integration. The complexities are local (in terms of cultural, linguistic and religious diversity), national (maintaining a broader sense of community that includes linkages across Australia, as well as an engagement with the Australian socio-political context), and transnational (participating in a global Karen community). This transnational community encompasses Karen settling elsewhere in the world, Karen in refugee camps neighbouring Burma, and Karen living inside Burma. This paper argues that substantial “identity work” is involved in Karen settlement. The two key community events are useful vignettes of this identity work. Both events demonstrate how Karen cultural practices can meaningfully negotiate deeply historical ideas of Karen identity with contemporary challenges of settlement. In addition, they set out a version of settlement that departs from traditional settlement constructs; they show how the lived experience of settlement is messy, complex and dynamic, and not reflective of the neat, idealistic models that immigration policy and settlement theory project.