School of BioSciences - Research Publications

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    Eliciting group judgements about replicability: A technical implementation of the IDEA Protocol
    Pearson, ER ; Fraser, H ; Bush, M ; Mody, F ; Widjaja, I ; Head, A ; Wilkinson, DP ; Wintle, B ; Sinnott, R ; Vesk, P ; Burgman, M ; Fidler, F (Hawaii International Conference on System Sciences, 2021-01-01)
    In recent years there has been increased interest in replicating prior research. One of the biggest challenges to assessing replicability is the cost in resources and time that it takes to repeat studies. Thus there is an impetus to develop rapid elicitation protocols that can, in a practical manner, estimate the likelihood that research findings will successfully replicate. We employ a novel implementation of the IDEA ('Investigate', 'Discuss', 'Estimate' and 'Aggregate) protocol, realised through the repliCATS platform. The repliCATS platform is designed to scalably elicit expert opinion about replicability of social and behavioural science research. The IDEA protocol provides a structured methodology for eliciting judgements and reasoning from groups. This paper describes the repliCATS platform as a multi-user cloud-based software platform featuring (1) a technical implementation of the IDEA protocol for eliciting expert opinion on research replicability, (2) capture of consent and demographic data, (3) on-line training on replication concepts, and (4) exporting of completed judgements. The platform has, to date, evaluated 3432 social and behavioural science research claims from 637 participants.
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    A portable fluorescence spectroscopy imaging system for automated root phenotyping in soil cores in the field
    Wasson, A ; Bischof, L ; Zwart, A ; Watt, M (OXFORD UNIV PRESS, 2016-02)
    Root architecture traits are a target for pre-breeders. Incorporation of root architecture traits into new cultivars requires phenotyping. It is attractive to rapidly and directly phenotype root architecture in the field, avoiding laboratory studies that may not translate to the field. A combination of soil coring with a hydraulic push press and manual core-break counting can directly phenotype root architecture traits of depth and distribution in the field through to grain development, but large teams of people are required and labour costs are high with this method. We developed a portable fluorescence imaging system (BlueBox) to automate root counting in soil cores with image analysis software directly in the field. The lighting system was optimized to produce high-contrast images of roots emerging from soil cores. The correlation of the measurements with the root length density of the soil cores exceeded the correlation achieved by human operator measurements (R (2)=0.68 versus 0.57, respectively). A BlueBox-equipped team processed 4.3 cores/hour/person, compared with 3.7 cores/hour/person for the manual method. The portable, automated in-field root architecture phenotyping system was 16% more labour efficient, 19% more accurate, and 12% cheaper than manual conventional coring, and presents an opportunity to directly phenotype root architecture in the field as part of pre-breeding programs. The platform has wide possibilities to capture more information about root health and other root traits in the field.
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    Simultaneous effects of leaf irradiance and soil moisture on growth and root system architecture of novel wheat genotypes: implications for phenotyping
    Nagel, KA ; Bonnett, D ; Furbank, R ; Walter, A ; Schurr, U ; Watt, M (OXFORD UNIV PRESS, 2015-09)
    Plants in the field are exposed to varying light and moisture. Agronomic improvement requires knowledge of whole-plant phenotypes expressed in response to simultaneous variation in these essential resources. Most phenotypes, however, have been described from experiments where resources are varied singularly. To test the importance of varying shoot and root resources for phenotyping studies, sister pre-breeding lines of wheat were phenotyped in response to independent or simultaneous exposure to two light levels and soil moisture profiles. The distribution and architecture of the root systems depended strongly on the moisture of the deeper soil layer. For one genotype, roots, specifically lateral roots, were stimulated to grow into moist soil when the upper zone was well-watered and were inhibited by drier deep zones. In contrast, the other genotype showed much less plasticity and responsiveness to upper moist soil, but maintained deeper penetration of roots into the dry layer. The sum of shoot and root responses was greater when treated simultaneously to low light and low soil water, compared to each treatment alone, suggesting the value of whole plant phenotyping in response to multiple conditions for agronomic improvement. The results suggest that canopy management for increased irradiation of leaves would encourage root growth into deeper drier soil, and that genetic variation within closely related breeding lines may exist to favour surface root growth in response to irrigation or in-season rainfall.
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    Soil coring at multiple field environments can directly quantify variation in deep root traits to select wheat genotypes for breeding
    Wasson, AP ; Rebetzke, GJ ; Kirkegaard, JA ; Christopher, J ; Richards, RA ; Watt, M (OXFORD UNIV PRESS, 2014-11)
    We aim to incorporate deep root traits into future wheat varieties to increase access to stored soil water during grain development, which is twice as valuable for yield as water captured at younger stages. Most root phenotyping efforts have been indirect studies in the laboratory, at young plant stages, or using indirect shoot measures. Here, soil coring to 2 m depth was used across three field environments to directly phenotype deep root traits on grain development (depth, descent rate, density, length, and distribution). Shoot phenotypes at coring included canopy temperature depression, chlorophyll reflectance, and green leaf scoring, with developmental stage, biomass, and yield. Current varieties, and genotypes with breeding histories and plant architectures expected to promote deep roots, were used to maximize identification of variation due to genetics. Variation was observed for deep root traits (e.g. 111.4-178.5cm (60%) for depth; 0.09-0.22cm/°C day (144%) for descent rate) using soil coring in the field environments. There was significant variation for root traits between sites, and variation in the relative performance of genotypes between sites. However, genotypes were identified that performed consistently well or poorly at both sites. Furthermore, high-performing genotypes were statistically superior in root traits than low-performing genotypes or commercial varieties. There was a weak but significant negative correlation between green leaf score (-0.5), CTD (0.45), and rooting depth and a positive correlation for chlorophyll reflectance (0.32). Shoot phenotypes did not predict other root traits. This study suggests that field coring can directly identify variation in deep root traits to speed up selection of genotypes for breeding programmes.
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    The Third International Symposium on Fungal Stress - ISFUS
    Alder-Rangel, A ; Idnurm, A ; Brand, AC ; Brown, AJP ; Gorbushina, A ; Kelliher, CM ; Campos, CB ; Levin, DE ; Bell-Pedersen, D ; Dadachova, E ; Bauer, FF ; Gadd, GM ; Braus, GH ; Braga, GUL ; Brancini, GTP ; Walker, GM ; Druzhinina, I ; Pocsi, I ; Dijksterhuis, J ; Aguirre, J ; Hallsworth, JE ; Schumacher, J ; Wong, KH ; Selbmann, L ; Corrochano, LM ; Kupiec, M ; Momany, M ; Molin, M ; Requena, N ; Yarden, O ; Cordero, RJB ; Fischer, R ; Pascon, RC ; Mancinelli, RL ; Emri, T ; Basso, TO ; Rangel, DEN (ELSEVIER SCI LTD, 2020-05)
    Stress is a normal part of life for fungi, which can survive in environments considered inhospitable or hostile for other organisms. Due to the ability of fungi to respond to, survive in, and transform the environment, even under severe stresses, many researchers are exploring the mechanisms that enable fungi to adapt to stress. The International Symposium on Fungal Stress (ISFUS) brings together leading scientists from around the world who research fungal stress. This article discusses presentations given at the third ISFUS, held in São José dos Campos, São Paulo, Brazil in 2019, thereby summarizing the state-of-the-art knowledge on fungal stress, a field that includes microbiology, agriculture, ecology, biotechnology, medicine, and astrobiology.
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    Evolving proteins at Darwin's bicentenary.
    Pinney, JW ; Stumpf, MPH (Springer Science and Business Media LLC, 2009)
    A report of the Biochemical Society/Wellcome Trust meeting 'Protein Evolution - Sequences, Structures and Systems', Hinxton, UK, 26-27 January 2009.
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    Modelling the spread of transboundary animal disease in and between domestic and wild swine populations
    Bradhurst, R (EuFMD, 2020)
    The challenge of planning for transboundary animal disease outbreaks can be compounded by the complex epidemiological interplay between livestock, wild animals, and the environment. Wild boar populations can form direct and indirect spread pathways for contagious livestock diseases such as FMD, ASF and CSF, both within and between countries. In this poster we describe the enhancement of the EuFMDiS decision support tool to assist disease managers explore the sometimes unpredictable interface between domestic pigs and wild boar. A key modelling outcome was the fusion of an existing agent-based model of livestock disease transmission with a new geographic automata model of wildlife disease transmission.
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    On using 'Emerging Interest' in Scientific Literature to inform Chemical Risk Prioritisation
    Whyte, J ; van Griensven, A ; Nossent, J ; Ames, DP (Brigham Young Universtiy, 2020-09-18)
    Modern industrial practices employ a large and diverse collection of chemicals. This can challenge regulators charged with environmental protection. Typically, insufficient data is available for risk assessments. Thus, chemicals may find widespread use until adequate evidence of adverse environmental effects prompts regulatory action. Globally, regulators have seen that such ‘reactive’ risk management has disadvantages. Recently in Australia (and elsewhere), relatively rapidly, certain unrestricted, long-used per- and polyfluoroalkyl substances (PFAS) became subjects of concern, then regulation. Such events motivate us to support regulators’ ‘proactive’ risk management efforts. We aim to assist regulators in anticipating the emergence of potentially risky chemicals, enabling their timely actions. We hypothesise that a time series of research interest mined from a scientific publication database may reveal ‘emerging interest’ in a chemical that foreshadows its progress towards regulation. We investigate this for six PFAS by determining the associated research interest in Web of Science. For each chemical, we use R code to apply queries to an application programming interface, and count annual positive results across a publication year range. Inspection of these time series suggests two tests, each of which determines the first year in which some condition is satisfied. We propose classification rules to interpret test outcomes, and compare results against PFAS regulatory histories. For the regulated PFAS, we anticipate the historical progression of Australian regulatory concern. We also judge some unrestricted PFAS as being of concern, and this is validated by interest from other jurisdictions. These results demonstrate our system’s predictive ability, and encourage further development.
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    Precision Medicine: Dawn of Supercomputing in ‘omics Research
    Reumann, M ; Holt, KE ; Inouye, M ; Stinear, T ; Goudey, B ; Abraham, G ; WANG, Q ; Shi, F ; Kowalczyk, A ; Pearce, A ; Isaac, A ; Pope, BJ ; Butzkueven, H ; Wagner, J ; Moore, S ; Downton, M ; Church, PC ; Turner, SJ ; Field, J ; Southey, M ; Bowtell, D ; Schmidt, D ; Makalic, E ; Zobel, J ; Hopper, J ; Petrovski, S ; O'Brien, T (eResearch Australasia, 2011)