Social water assessment protocol : a step towards connecting mining, water and human rights

The human right to water has recently been recognised by both the United Nations General Assembly and the Human Rights Council. As the mining industry interacts with water on multiple levels, it is important that these interactions respect the human right to water. Currently, a disconnect exists between mine site water management practices and the recognition of water from a human rights perspective. The Minerals Council of Australia (MCA) Water Accounting Framework (WAF) has previously been used to strengthen the connection between water management and human rights. This article extends this connection through the use of a Social Water Assessment Protocol (SWAP). The SWAP is scoping tool consisting of a set of questions classified into taxonomic themes under leading topics with suggested sources of data that enable mine sites to better understand the local water context in which they operate. Three of the themes contained in the SWAP – gender, Indigenous peoples and health – are discussed to demonstrate how the protocol may be useful in assisting mining companies to consider their impacts on the human right to water.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent

The relationship between N2O, NO, and N2 fluxes from fertilized and irrigated dryland soils of the Aral Sea Basin, Uzbekistan

Microbial respiratory reduction of nitrous oxide (N2O) to dinitrogen (N2) via denitrification plays a key role within the global N-cycle since it is the most important process for converting reactive nitrogen back into inert molecular N2. However, due to methodological constraints, we still lack a comprehensive, quantitative understanding of denitrification rates and controlling factors across various ecosystems. We investigated N2, N2O and NO emissions from irrigated cotton fields within the Aral Sera Basin using the He/O2 atmosphere gas flow soil core technique and an incubation assay. NH4NO3 fertilizer, equivalent to 75 kg ha−1 and irrigation water, adjusting the water holding capacity to 70, 100 and 130% were applied to the incubation vessels to assess its influence on gaseous N emissions. Under soil conditions as they are naturally found after concomitant irrigation and fertilization, denitrification was the dominant process and N2 the main end product of denitrification. The mean ratios of N2/N2O emissions increased with increasing soil moisture content. N2 emissions exceeded N2O emissions by a factor of 5 ± 2 at 70% soil water holding capacity (WHC) and a factor of 55 ± 27 at 130% WHC. The mean ratios of N2O/NO emissions varied between 1.5 ± 0.4 (70% WHC) and 644 ± 108 (130% WHC). The magnitude of N2 emissions for irrigated cotton was estimated to be in the range of 24 ± 9 to 175 ± 65 kg-N ha−1season−1, while emissions of NO were only of minor importance (between 0.1 to 0.7 kg-N ha−1 season−1). The findings demonstrate that for irrigated dryland soils in the Aral Sera Basin, denitrification is a major pathway of N-loss and that substantial amounts of N-fertilizer are lost as N2 to the atmosphere for irrigated dryland soils.

A large proportion of asymptomatic Plasmodium infections with low and sub-microscopic parasite densities in the low transmission setting of Temotu Province, Solomon Islands : challenges for malaria diagnostics in an elimination setting

Background Many countries are scaling up malaria interventions towards elimination. This transition changes demands on malaria diagnostics from diagnosing ill patients to detecting parasites in all carriers including asymptomatic infections and infections with low parasite densities. Detection methods suitable to local malaria epidemiology must be selected prior to transitioning a malaria control programme to elimination. A baseline malaria survey conducted in Temotu Province, Solomon Islands in late 2008, as the first step in a provincial malaria elimination programme, provided malaria epidemiology data and an opportunity to assess how well different diagnostic methods performed in this setting. Methods During the survey, 9,491 blood samples were collected and examined by microscopy for Plasmodium species and density, with a subset also examined by polymerase chain reaction (PCR) and rapid diagnostic tests (RDTs). The performances of these diagnostic methods were compared. Results A total of 256 samples were positive by microscopy, giving a point prevalence of 2.7%. The species distribution was 17.5% Plasmodium falciparum and 82.4% Plasmodium vivax. In this low transmission setting, only 17.8% of the P. falciparum and 2.9% of P. vivax infected subjects were febrile (≥38°C) at the time of the survey. A significant proportion of infections detected by microscopy, 40% and 65.6% for P. falciparum and P. vivax respectively, had parasite density below 100/μL. There was an age correlation for the proportion of parasite density below 100/μL for P. vivax infections, but not for P. falciparum infections. PCR detected substantially more infections than microscopy (point prevalence of 8.71%), indicating a large number of subjects had sub-microscopic parasitemia. The concordance between PCR and microscopy in detecting single species was greater for P. vivax (135/162) compared to P. falciparum (36/118). The malaria RDT detected the 12 microscopy and PCR positive P. falciparum, but failed to detect 12/13 microscopy and PCR positive P. vivax infections. Conclusion Asymptomatic malaria infections and infections with low and sub-microscopic parasite densities are highly prevalent in Temotu province where malaria transmission is low. This presents a challenge for elimination since the large proportion of the parasite reservoir will not be detected by standard active and passive case detection. Therefore effective mass screening and treatment campaigns will most likely need more sensitive assays such as a field deployable molecular based assay.

One-step macroscopic alignment of conjugated polymer systems by epitaxial crystallization during spin-coating

The one-step preparation of highly anisotropic polymer semiconductor thin films directly from solution is demonstrated. The conjugated polymer poly(3-hexylthiophene) (P3HT) as well as P3HT:fullerene bulk-heterojunction blends can be spin-coated from a mixture of the crystallizable solvent 1,3,5-trichlorobenzene (TCB) and a second carrier solvent such as chlorobenzene. Solidification is initiated by growth of macroscopic TCB spherulites followed by epitaxial crystallization of P3HT on TCB crystals. Subsequent sublimation of TCB leaves behind a replica of the original TCB spherulites. Thus, highly ordered thin films are obtained, which feature square-centimeter-sized domains that are composed of one spherulite-like structure each. A combination of optical microscopy and polarized photoluminescence spectroscopy reveals radial alignment of the polymer backbone in case of P3HT, whereas P3HT:fullerene blends display a tangential orientation with respect to the center of spherulite-like structures. Moreover, grazing-incidence wide-angle X-ray scattering reveals an increased relative degree of crystallinity and predominantly flat-on conformation of P3HT crystallites in the blend. The use of other processing methods such as dip-coating is also feasible and offers uniaxial orientation of the macromolecule. Finally, the applicability of this method to a variety of other semi-crystalline conjugated polymer systems is established. Those include other poly(3-alkylthiophene)s, two polyfluorenes, the low band-gap polymer PCPDTBT, a diketopyrrolopyrrole (DPP) small molecule as well as a number of polymer:fullerene and polymer:polymer blends. Macroscopic spherulite-like structures of the conjugated polymer poly(3-hexylthiophene) (P3HT) grow directly during spin-coating. This is achieved by processing P3HT or P3HT:fullerene bulk heterojunction blends from a mixture of the crystallizable solvent 1,3,5-trichlorobenzene and a second carrier solvent such as chlorobenzene. Epitaxial growth of the polymer on solidified solvent crystals gives rise to circular-symmetric, spherulite-like structures that feature a high degree of anisotropy.

High-mobility organic thin film transistors based on benzothiadiazole- sandwiched dihexylquaterthiophenes

We report here the synthesis, characterization, and organic thin-film transistor (OTFT) mobilities of 4,7-bis(5-(5-hexylthiophen-2-yl)thiophen-2-yl) benzo[1,2,5]thiadiazole (DH-BTZ-4T). DH-BTZ-4T was prepared in one high-yield step from commercially available materials using Suzuki chemistry and purified by column chromatography. OTFTs with hole mobilities of 0.17 cm2/(Vs) and on/off current ratios of 1 × 105 were prepared from DH-BTZ-4T active layers deposited by vacuum deposition. As DH-BTZ-4T is soluble in common solvents, solution processed devices were also prepared by spin coating yielding preliminary mobilities of 6.0 × 10-3 cm 2/(Vs). The promising mobilities and low band gap (1.90 eV) coupled with solution processability and ambient stability makes this material an excellent candidate for application in organic electronics.

Biodiesel production from non-edible beauty leaf (Calophyllum Inophyllum) oil : process optimization using response surface methodology (RSM)

In recent years, the beauty leaf plant (Calophyllum Inophyllum) is being considered as a potential 2nd generation biodiesel source due to high seed oil content, high fruit production rate, simple cultivation and ability to grow in a wide range of climate conditions. However, however, due to the high free fatty acid (FFA) content in this oil, the potential of this biodiesel feedstock is still unrealized, and little research has been undertaken on it. In this study, transesterification of beauty leaf oil to produce biodiesel has been investigated. A two-step biodiesel conversion method consisting of acid catalysed pre-esterification and alkali catalysed transesterification has been utilized. The three main factors that drive the biodiesel (fatty acid methyl ester (FAME)) conversion from vegetable oil (triglycerides) were studied using response surface methodology (RSM) based on a Box-Behnken experimental design. The factors considered in this study were catalyst concentration, methanol to oil molar ratio and reaction temperature. Linear and full quadratic regression models were developed to predict FFA and FAME concentration and to optimize the reaction conditions. The significance of these factors and their interaction in both stages was determined using analysis of variance (ANOVA). The reaction conditions for the largest reduction in FFA concentration for acid catalysed pre-esterification was 30:1 methanol to oil molar ratio, 10% (w/w) sulfuric acid catalyst loading and 75 °C reaction temperature. In the alkali catalysed transesterification process 7.5:1 methanol to oil molar ratio, 1% (w/w) sodium methoxide catalyst loading and 55 °C reaction temperature were found to result in the highest FAME conversion. The good agreement between model outputs and experimental results demonstrated that this methodology may be useful for industrial process optimization for biodiesel production from beauty leaf oil and possibly other industrial processes as well.

Equally engaged : demystifying tertiary study in the creative arts to equity communities

The participation rate of students from low socio-economic (SES) backgrounds into Australian universities remains low. A nationwide initiative to raise participation rates aims to stimulate interest, highlight career possibilities and enhance understanding of university. The program also aims to improve retention and completion rates of those students. This paper provides a case study and preliminary evaluation of QUT’s Creative Industries Faculty’s (CIF) outreach programs to low SES school students, operating since 2012. Programs are conducted across the disciplines of Dance, Drama, Media, Digitalstorytelling, Music and Entertainment. Presenting the arts and creative industries as a viable study / career pathway is particularly challenging to low SES groups. However, the focus on the creative industries aims to broaden understanding of arts and creativity, emphasising the significance of digital technology in the transformation of the workforce, providing new career opportunities in the creative and non-creative sectors. CIF’s outreach programs have been delivered to hundreds of students and this paper presents a case study and evaluation of several programs.

Regulation of canonical Wnt signalling pathway during cementum regeneration

This project highlights the important role of cell signalling pathway during tooth regeneration. Biomaterials can be designed to activate relevant cell signals for the purpose of dental repair and tooth regeneration. Based on the results in the present project, strategies directly targeting cell signalling pathway may provide new approaches for periodontal regenerative tissue engineering.

A multicenter study on chronic cough in children : burden and etiologies based on a standardized management pathway

Background While the burden of chronic cough in children has been documented, etiologic factors across multiple settings and age have not been described. In children with chronic cough, we aimed (1) to evaluate the burden and etiologies using a standard management pathway in various settings, and (2) to determine the influence of age and setting on disease burden and etiologies and etiology on disease burden. We hypothesized that the etiology, but not the burden, of chronic cough in children is dependent on the clinical setting and age. Methods From five major hospitals and three rural-remote clinics, 346 children (mean age 4.5 years) newly referred with chronic cough (> 4 weeks) were prospectively managed in accordance with an evidence-based cough algorithm. We used a priori definitions, timeframes, and validated outcome measures (parent-proxy cough-specific quality of life [PC-QOL], a generic QOL [pediatric quality of life (PedsQL)], and cough diary). Results The burden of chronic cough (PC-QOL, cough duration) significantly differed between settings (P = .014, 0.021, respectively), but was not influenced by age or etiology. PC-QOL and PedsQL did not correlate with age. The frequency of etiologies was significantly different in dissimilar settings (P = .0001); 17.6% of children had a serious underlying diagnosis (bronchiectasis, aspiration, cystic fibrosis). Except for protracted bacterial bronchitis, the frequency of other common diagnoses (asthma, bronchiectasis, resolved without specific-diagnosis) was similar across age categories. Conclusions The high burden of cough is independent of children’s age and etiology but dependent on clinical setting. Irrespective of setting and age, children with chronic cough should be carefully evaluated and child-specific evidence-based algorithms used.

Transcriptional pathway signatures predict MEK addiction and response to selumetinib (AZD6244)

Selumetinib (AZD6244, ARRY-142886) is a selective, non-ATP-competitive inhibitor of mitogen-activated protein/extracellular signal-regulated kinase kinase (MEK)-1/2. The range of antitumor activity seen preclinically and in patients highlights the importance of identifying determinants of response to this drug. In large tumor cell panels of diverse lineage, we show that MEK inhibitor response does not have an absolute correlation with mutational or phospho-protein markers of BRAF/MEK, RAS, or phosphoinositide 3-kinase (PI3K) activity. We aimed to enhance predictivity by measuring pathway output through coregulated gene networks displaying differential mRNA expression exclusive to resistant cell subsets and correlated to mutational or dynamic pathway activity. We discovered an 18-gene signature enabling measurement of MEK functional output independent of tumor genotype. Where the MEK pathway is activated but the cells remain resistant to selumetinib, we identified a 13-gene signature that implicates the existence of compensatory signaling from RAS effectors other than PI3K. The ability of these signatures to stratify samples according to functional activation of MEK and/or selumetinib sensitivity was shown in multiple independent melanoma, colon, breast, and lung tumor cell lines and in xenograft models. Furthermore, we were able to measure these signatures in fixed archival melanoma tumor samples using a single RT-qPCR-based test and found intergene correlations and associations with genetic markers of pathway activity to be preserved. These signatures offer useful tools for the study of MEK biology and clinical application of MEK inhibitors, and the novel approaches taken may benefit other targeted therapies.

Transcription factories : gene expression in unions?

Transcription is a fundamental step in gene expression, yet it remains poorly understood at a cellular level. Visualization of transcription sites and active genes has led to the suggestion that transcription occurs at discrete sites in the nucleus, termed transcription factories, where multiple active RNA polymerases are concentrated and anchored to a nuclear substructure. However, this concept is not universally accepted. This Review discusses the experimental evidence in support of the transcription factory model and the evidence that argues against such a spatially structured view of transcription. The transcription factory model has implications for the regulation of transcription initiation and elongation, for the organization of genes in the genome, for the co-regulation of genes and for genome instability.

We need to talk : feminism and food (GOMA Harvest Picnic)

This collaborative, participatory work by feminist collective LEVEL took place at the Gallery of Modern Art (GOMA) as part of the official program of activities surrounding the exhibition 'Harvest', 2014. It took the form of a public picnic, where women and their friends were invited to share cooking recipes while also discussing the possible recipe for a gender revolution. Groups discussed their ideas, before a public reading of potential 'ingredients' and 'methods' outside the museum on the Maiwar Green.