School of Agriculture, Food and Ecosystem Sciences - Research Publications

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    Towards a systems approach for river basin management-Lessons from Australia's largest river
    Thompson, RM ; Bond, N ; Poff, NL ; Byron, N (WILEY, 2019-06)
    Abstract Globally, large river systems have been extensively modified and are increasingly managed for a range of purposes including ecosystem services and ecological values. Key to managing rivers effectively are developing approaches that deal with uncertainty, are adaptive in nature, and can incorporate multiple stakeholders with dynamic feedbacks. Australia's largest river system, the Murray–Darling Basin (MDB), has been extensively developed for shipping passage, irrigation, hydroelectric development, and water supply. Water development in the MDB over the last century resulted in overallocation of water resources and large‐scale environmental degradation throughout the Basin. Under the pressure of a significant drought, there was insufficient water to supply critical human, environmental, and agricultural needs. In response, a massive programme of water reform was enacted that resulted in considerable institutional, social, and economic change. The underlying policy was required to be enacted in an absence of certainty around the scientific basis, with an adaptive management focus to incorporate new knowledge. The resulting institutional arrangements were challenged by a need to generate new governance arrangements within the constraints of existing state and national structures. The ongoing reform and management of the MDB continues to challenge all parties to achieve optimization for multiple outcomes, and to communicate that effectively. As large‐scale water reform gains pace globally, the MDB provides a window of insight into the types of systems that may emerge and the challenges in working within them. Most particularly, it illustrates the need for much more sophisticated systems thinking that runs counter to the much more linear approaches often adopted in government.
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    Assessment of environmental flow scenarios using state-and-transition models
    Bond, NR ; Grigg, N ; Roberts, J ; McGinness, H ; Nielsen, D ; O'Brien, M ; Overton, I ; Pollino, C ; Reid, JRW ; Stratford, D (WILEY, 2018-08)
    Abstract Numerous methods have been developed to support the assessment of environmental flow requirements for rivers. Most methods are based around models of hydrologic time series rather than models of the ecological endpoints of interest. Important limitations that arise from this include (1) an inability to represent the state dependency of response to future conditions (i.e. the effects of current ecosystem condition on future condition), (2) the inability to predict ecological states through time under alternative flow regimes and (3) limited sensitivity to compare the differences between flow regimes with similar return intervals of ecologically important events, but different sequencing of those events. Here we outline a simple state‐and‐transition modelling approach to assess differences in ecological responses to alternative sequences of floodplain inundation events in a lowland river system. Our approach explicitly incorporates the state dependency of biotic response to flooding, thereby representing the influences of both antecedent conditions and current condition (in this case population state; good > medium > poor > critical). Our approach thus captures the influence of the entire historical sequence of flow events via a first‐order Markov chain process. We use prior data and expert opinion to determine state transitions for a broad suite of ecological indicators. Despite being implemented with deterministic transitions, and drawing heavily on expert opinion, this approach greatly improves on existing methods used in environmental flows planning, particularly when comparing scenarios with the different sequencing of ecologically relevant flow events. The outputs from these models are testable, and the approach is readily extensible to incorporate probabilistic state transitions and uncertainty, mechanistic links (via increased model complexity) and quantitative measures of population state (e.g. measures of abundance or tree condition). Most importantly, the adoption of such a framework represents a fundamental shift to modelling ecological endpoints rather than relying on just quantifying hydrologic surrogates to compare environmental flow scenarios.
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    Copy number variation in the horse genome.
    Ghosh, S ; Qu, Z ; Das, PJ ; Fang, E ; Juras, R ; Cothran, EG ; McDonell, S ; Kenney, DG ; Lear, TL ; Adelson, DL ; Chowdhary, BP ; Raudsepp, T ; Barsh, GS (Public Library of Science (PLoS), 2014-10)
    We constructed a 400K WG tiling oligoarray for the horse and applied it for the discovery of copy number variations (CNVs) in 38 normal horses of 16 diverse breeds, and the Przewalski horse. Probes on the array represented 18,763 autosomal and X-linked genes, and intergenic, sub-telomeric and chrY sequences. We identified 258 CNV regions (CNVRs) across all autosomes, chrX and chrUn, but not in chrY. CNVs comprised 1.3% of the horse genome with chr12 being most enriched. American Miniature horses had the highest and American Quarter Horses the lowest number of CNVs in relation to Thoroughbred reference. The Przewalski horse was similar to native ponies and draft breeds. The majority of CNVRs involved genes, while 20% were located in intergenic regions. Similar to previous studies in horses and other mammals, molecular functions of CNV-associated genes were predominantly in sensory perception, immunity and reproduction. The findings were integrated with previous studies to generate a composite genome-wide dataset of 1476 CNVRs. Of these, 301 CNVRs were shared between studies, while 1174 were novel and require further validation. Integrated data revealed that to date, 41 out of over 400 breeds of the domestic horse have been analyzed for CNVs, of which 11 new breeds were added in this study. Finally, the composite CNV dataset was applied in a pilot study for the discovery of CNVs in 6 horses with XY disorders of sexual development. A homozygous deletion involving AKR1C gene cluster in chr29 in two affected horses was considered possibly causative because of the known role of AKR1C genes in testicular androgen synthesis and sexual development. While the findings improve and integrate the knowledge of CNVs in horses, they also show that for effective discovery of variants of biomedical importance, more breeds and individuals need to be analyzed using comparable methodological approaches.
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    Short-term heat stress and vitamin E supplementation affect carcass weight, mucle omega-6 fatty acid and meat quality in lambs
    PONNAMPALAM, EN ; Chauhan, SS ; Kerr, M ; Hopkins, DL ; Plozza, T ; Dunshea, F (Elsevier, 2016)
    The effect of short term-heat stress and -vitamin E supplementation on carcass traits and muscle quality – vitamin E, nutritional value and retail colour of lambs was investigated. Forty-eight lambs (crossbred; 42 ± 2 kg body weight, 7 mo age) were randomly allocated by body weight to one of three groups (n = 16) and fed 3 different doses of Vitamin E and Se. The doses of Vitamin E and Se for control (CON), moderate (MOD), and supranutritional (SUP) diets were 28, 130, 228 mg/kg DM as α-tocopherol acetate and 0.16, 0.66, 1.16 mg Se as SelPlex™ kg/DM, respectively. Lambs were fed for 4 weeks followed by a week of exposure to heat treatment. After 4 weeks feeding in individual pens, including 1 week of adaptation, lambs were moved to metabolism cages for 1 week and allocated to one of 2 heat regimes (8 per feeding group): thermoneutral (TN) (18–21◦C and 40–50% relative humidity) or heat stress (HS) (28–40◦C and 30–40% relative humidity) conditions. Final body weight (P = 0.05, 44.1 vs 46.6 kg) and hot carcass weight (P = 0.01, 21.1 vs 22.5 kg) were significantly affected by diet such that lambs supplemented with SUP levels of antioxidants had a higher FBW and HCW as compared with lambs fed MOD and CON antioxidant diets, respectively. Vitamin E concentration in the longissimus lumborum (LL) muscle tended to be higher in lambs fed moderate or supranutritional levels of antioxidants compared with control lambs and values from all treatments were below the threshold (3.2 mg/kg muscle) for optimal maintenance of retail colour. Vitamin E supplementation also reduced lipid oxidation of aged meat, as assessed by thiobarbituric acid reactive substances (TBARS) formation after 72 h of display. One week of heat stress to lambs significantly increased muscle linoleic acid concentration, which in turn increased total n-6 concentration compared with the control group. Results demonstrate that 4 weeks of vitamin E supplementation or 1 week heat stress might not have been adequate to make significant changes in muscle vitamin E concentration and fatty acid composition, which in turn can influence retail colour stability of meat.
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    AMP is a more potent activator of phosphofructokinase-1 activity than fructose 2,6-bisphospate in porcine skeletal muscle under simulated postmortem conditions
    Chauhan, SS ; LeMaster, M ; England, EM ; Troy, D ; Ciara, M ; Laura, H ; Kerry, J (Wageningen Academic Publishers, 2017)
    Phosphofructokinase-1 (PFK-1) is a key regulatory enzyme of postmortem glycolysis. PFK-1’s activity is regulated antemortem by a number of compounds including adenosine monophosphate (AMP) and fructose 2,6-bisphosphate (F-2,6-BP). However, PFK-1’s postmortem regulation by AMP and F-2,6-BP is still unclear. Therefore, a study was conducted where porcine longissimus lumborum samples were collected to determine PFK-1 activity as affected by various concentrations of AMP and F-2,6-BP at buffered pH. Both compounds increased PFK-1 activity. However, at physiological concentrations, 50 and 150 μM AMP increased PFK-1 activity compared to 1 and 2 μM F-2,6-BP. Thus, AMP may play a greater role in dictating the rate and extent of postmortem glycolysis and pH decline than F-2,6-BP.
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    Impacts Of Heat Stress On Retail Meat Quality Of 2ND Cross And Dorper Lambs
    Zhang, MH ; Warner, RD ; Dunshea, FR ; DiGiacomo, K ; Hopkins, DL ; Ha, M ; Joy, A ; Payyanakkal, APR ; Osei-Amponsah, R ; Chauhan, SS (ICoMST 2019, 2019)
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    Making “middle managers”: workforce development for agricultural industries in transition
    Santhanam-Martin, M ; Cowan, L (International Farming Systems Association, 2018)
    The availability of suitably skilled people is being increasingly recognised as a critical element for success in agriculture, yet this can be challenging to achieve. The perennial fruit industry in Australia’s Goulburn-Murray region is an example of this. In 2015, employers in this industry identified a shortage of people for ‘middle management’ roles as a particular current concern. This paper outlines the findings of a scoping study focused on developing a better understanding of the issues affecting the ability of fruit growers in this region to attract, retain and develop appropriately skilled ‘middle managers’. The study was informed by a ‘systemic’ approach to workforce development, according to which the availability of suitably-skilled workers arises from the dynamic interactions of elements in the workforce system. Based on structured interviews with the managers of twenty fruit growing businesses, we developed a typology of four typical workforce structures that are found in businesses of different sizes, including identification of the most common job titles and typical duties for these jobs. We discuss the approaches that employers used to recruit workers, including both internal and external recruitment pathways. The findings of this study allow us to begin identifying the range of entry points to jobs, and the career progression pathways, that currently exist for workers in the perennial fruit industry, and to identify opportunities for industry collective action to address current workforce challenges. As employed workers come to play increasingly important roles in family farm businesses, systemic understandings of workforce development will become increasingly important within the field of farming systems research.
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    The grass is greener on the other side: understanding the effects of green spaces on Twitter user sentiments
    Lim, KH ; Lee, K ; Kendal, D ; Rashidi, L ; Naghi Zadeh Kakhki, E ; Winter, S ; Vasardani, M (ACM Press, 2018)
    Green spaces are believed to improve the well-being of users in urban areas. While there are urban research exploring the emotional benefits of green spaces, these works are based on user surveys and case studies, which are typically small in scale, intrusive, time-intensive and costly. In contrast to earlier works, we utilize a non-intrusive methodology to understand green space effects at large-scale and in greater detail, via digital traces left by Twitter users. Using this methodology, we perform an empirical study on the effects of green spaces on user sentiments and emotions in Melbourne, Australia and our main findings are: (i) tweets in green spaces evoke more positive and less negative emotions, compared to those in urban areas; (ii) each season affects various emotion types differently; (iii) there are interesting changes in sentiments based on the hour, day and month that a tweet was posted; and (iv) negative sentiments are typically associated with large transport infrastructures such as train interchanges, major road junctions and railway tracks. The novelty of our study is the combination of psychological theory, alongside data collection and analysis techniques on a large-scale Twitter dataset, which overcomes the limitations of traditional methods in urban research.
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    Trees provide energy saving benefits to adjacent buildings for a small water cost
    Livesley, SJ ; Aye, L ; Hes, D ; DAWKINS, A ; LHENDUP, T ; CAFFIN, M ; Williams, NS (Australian Sustainable Cities and Regions Network, 2011)
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    Can digital infrared thermography help with prediction of ovulation in a pasture-based dairy system?
    Talukder, S ; Kerrisk, K ; Ingenhoff, L ; Garcia, S ; Celi, P (The University of Sydney, 2013)