School of Agriculture, Food and Ecosystem Sciences - Research Publications

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    Evaluation of Spectral Indices for Assessing Fire Severity in Australian Temperate Forests
    Tran, BN ; Tanase, MA ; Bennett, LT ; Aponte, C (MDPI AG, 2018)
    Spectral indices derived from optical remote sensing data have been widely used for fire-severity classification in forests from local to global scales. However, comparative analyses of multiple indices across diverse forest types are few. This represents an information gap for fire management agencies in areas like temperate south-eastern Australia, which is characterised by a diversity of natural forests that vary in structure, and in the fire-regeneration strategies of the dominant trees. We evaluate 10 spectral indices across eight areas burnt by wildfires in 1998, 2006, 2007, and 2009 in south-eastern Australia. These wildfire areas encompass 13 forest types, which represent 86% of the 7.9M ha region’s forest area. Forest types were aggregated into six forest groups based on their fire-regeneration strategies (seeders, resprouters) and structure (tree height and canopy cover). Index performance was evaluated for each forest type and forest group by examining its sensitivity to four fire-severity classes (unburnt, low, moderate, high) using three independent methods (anova, separability, and optimality). For the best-performing indices, we calculated index-specific thresholds (by forest types and groups) to separate between the four severity classes, and evaluated the accuracy of fire-severity classification on independent samples. Our results indicated that the best-performing indices of fire severity varied with forest type and group. Overall accuracy for the best-performing indices ranged from 0.50 to 0.78, and kappa values ranged from 0.33 (fair agreement) to 0.77 (substantial agreement), depending on the forest group and index. Fire severity in resprouter open forests and woodlands was most accurately mapped using the delta Normalised Burnt ratio (dNBR). In contrast, dNDVI (delta Normalised difference vegetation index) performed best for open forests with mixed fire responses (resprouters and seeders), and dNDWI (delta Normalised difference water index) was the most accurate for obligate seeder closed forests. Our analysis highlighted the low sensitivity of all indices to fire impacts in Rainforest. We conclude that the optimal spectral index for quantifying fire severity varies with forest type, but that there is scope to group forests by structure and fire-regeneration strategy to simplify fire-severity classification in heterogeneous forest landscapes.
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    Molecular Basis for Lysine Specificity in the Yeast Ubiquitin-Conjugating Enzyme Cdc34
    Sadowski, M ; Suryadinata, R ; Lai, X ; Heierhorst, J ; Sarcevic, B (AMER SOC MICROBIOLOGY, 2010-05-15)
    Ubiquitin (Ub)-conjugating enzymes (E2s) and ubiquitin ligases (E3s) catalyze the attachment of Ub to lysine residues in substrates and Ub during monoubiquitination and polyubiquitination. Lysine selection is important for the generation of diverse substrate-Ub structures, which provides versatility to this pathway in the targeting of proteins to different fates. The mechanisms of lysine selection remain poorly understood, with previous studies suggesting that the ubiquitination site(s) is selected by the E2/E3-mediated positioning of a lysine(s) toward the E2/E3 active site. By studying the polyubiquitination of Sic1 by the E2 protein Cdc34 and the RING E3 Skp1/Cul1/F-box (SCF) protein, we now demonstrate that in addition to E2/E3-mediated positioning, proximal amino acids surrounding the lysine residues in Sic1 and Ub are critical for ubiquitination. This mechanism is linked to key residues composing the catalytic core of Cdc34 and independent of SCF. Changes to these core residues altered the lysine preference of Cdc34 and specified whether this enzyme monoubiquitinated or polyubiquitinated Sic1. These new findings indicate that compatibility between amino acids surrounding acceptor lysine residues and key amino acids in the catalytic core of ubiquitin-conjugating enzymes is an important mechanism for lysine selection during ubiquitination.
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    Additive Genetic Variation in Schizophrenia Risk Is Shared by Populations of African and European Descent
    de Candia, TR ; Lee, SH ; Yang, J ; Browning, BL ; Gejman, PV ; Levinson, DF ; Mowry, BJ ; Hewitt, JK ; Goddard, ME ; O'Donovan, MC ; Purcell, SM ; Posthuma, D ; Visscher, PM ; Wray, NR ; Keller, MC (CELL PRESS, 2013-09-05)
    To investigate the extent to which the proportion of schizophrenia's additive genetic variation tagged by SNPs is shared by populations of European and African descent, we analyzed the largest combined African descent (AD [n = 2,142]) and European descent (ED [n = 4,990]) schizophrenia case-control genome-wide association study (GWAS) data set available, the Molecular Genetics of Schizophrenia (MGS) data set. We show how a method that uses genomic similarities at measured SNPs to estimate the additive genetic correlation (SNP correlation [SNP-rg]) between traits can be extended to estimate SNP-rg for the same trait between ethnicities. We estimated SNP-rg for schizophrenia between the MGS ED and MGS AD samples to be 0.66 (SE = 0.23), which is significantly different from 0 (p(SNP-rg = 0) = 0.0003), but not 1 (p(SNP-rg = 1) = 0.26). We re-estimated SNP-rg between an independent ED data set (n = 6,665) and the MGS AD sample to be 0.61 (SE = 0.21, p(SNP-rg = 0) = 0.0003, p(SNP-rg = 1) = 0.16). These results suggest that many schizophrenia risk alleles are shared across ethnic groups and predate African-European divergence.
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    Current and future adoption of leucaena-grass pastures in northern Australia
    Kenny, S ; Drysdale, G (CENTRO INT AGRICULTURA TROPICAL-CIAT, 2019-09)
    Keynote paper presented at the International Leucaena Conference, 1‒3 November 2018, Brisbane, Queensland, Australia.The leucaena-grass pastures and target markets for adoption project was commissioned by Meat & Livestock Australia (MLA) to examine the scope for further adoption of leucaena-grass pastures in northern Australia. Drawing upon stakeholder and producer interviews, focus groups, mapping of biophysical factors critical to growing leucaena and a review of existing literature, regional adoption profiles were developed using the ADOPT model. This work outlines the current and future potential for adoption of leucaena in northern Australia and recommends 5 interrelated strategic actions designed to support the ongoing adoption. These actions have been designed to address the complex technical, social and biophysical requirements for successful adoption and will require collaboration between investors, The Leucaena Network, producers, government agencies and the private sector to be effective.
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    Origin and Evolution of the Kiwifruit Canker Pandemic
    McCann, HC ; Li, L ; Liu, Y ; Li, D ; Pan, H ; Zhong, C ; Rikkerink, EHA ; Templeton, MD ; Straub, C ; Colombi, E ; Rainey, PB ; Huang, H (OXFORD UNIV PRESS, 2017-04)
    Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography, and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in China. Based on the analysis of 80 sequenced Psa genomes, we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single clade. In contrast, Korea and Japan harbor strains from multiple clades. Distinct independent transmission events marked introduction of the pandemic lineage into New Zealand, Chile, Europe, Korea, and Japan. Despite high similarity within the core genome and minimal impact of within-clade recombination, we observed extensive variation even within the single clade from which the global pandemic arose.
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    Microbial communities in top- and subsoil of repacked soil columns respond differently to amendments but their diversity is negatively correlated with plant productivity
    Celestina, C ; Wood, JL ; Manson, JB ; Wang, X ; Sale, PWG ; Tang, C ; Franks, AE (NATURE PUBLISHING GROUP, 2019-06-20)
    Organic and inorganic amendments with equivalent nutrient content may have comparable fertilizer effects on crop yield, but their effects on the soil microbial community and subsequent plant-soil-microbe interactions in this context are unknown. This experiment aimed to understand the relationship between soil microbial communities, soil physicochemical characteristics and crop performance after addition of amendments to soil. Poultry litter and synthetic fertilizer with balanced total nitrogen (N) content equivalent to 1,200 kg ha-1 were added to the topsoil (0-10 cm) or subsoil layer (20-30 cm) of repacked soil columns. Wheat plants were grown until maturity. Soil samples were taken at Zadoks 87-91 (76 days after sowing) for analysis of bacterial and fungal communities using 16S and ITS amplicon sequencing. The interaction between amendment type and placement depth had significant effects on bacterial and fungal community structure and diversity in the two soil layers. Addition of poultry litter and fertilizer stimulated or suppressed different taxa in the topsoil and subsoil leading to divergence of these layers from the untreated control. Both amendments reduced microbial community richness, diversity and evenness in the topsoil and subsoil compared to the nil-amendment control, with these reductions in diversity being consistently negatively correlated with plant biomass (root and shoot weight, root length, grain weight) and soil fertility (soil NH4+, shoot N). These results indicate that in this experimental system, the soil microbial diversity was correlated negatively with plant productivity.
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    Isolation and Functional Characterisation of a fads2 in Rainbow Trout (Oncorhynchus mykiss) with Δ5 Desaturase Activity
    Hamid, NKA ; Carmona-Antonanzas, G ; Monroig, O ; Tocher, DR ; Turchini, GM ; Donald, JA ; Virolle, M-J (PUBLIC LIBRARY SCIENCE, 2016-03-04)
    Rainbow trout, Oncorhynchus mykiss, are intensively cultured globally. Understanding their requirement for long-chain polyunsaturated fatty acids (LC-PUFA) and the biochemistry of the enzymes and biosynthetic pathways required for fatty acid synthesis is important and highly relevant in current aquaculture. Most gnathostome vertebrates have two fatty acid desaturase (fads) genes with known functions in LC-PUFA biosynthesis and termed fads1 and fads2. However, teleost fish have exclusively fads2 genes. In rainbow trout, a fads2 cDNA had been previously cloned and found to encode an enzyme with Δ6 desaturase activity. In the present study, a second fads2 cDNA was cloned from the liver of rainbow trout and termed fads2b. The full-length mRNA contained 1578 nucleotides with an open reading frame of 1365 nucleotides that encoded a 454 amino acid protein with a predicted molecular weight of 52.48 kDa. The predicted Fads2b protein had the characteristic traits of the microsomal Fads family, including an N-terminal cytochrome b5 domain containing the heme-binding motif (HPPG), histidine boxes (HDXGH, HFQHH and QIEHH) and three transmembrane regions. The fads2b was expressed predominantly in the brain, liver, intestine and pyloric caeca. Expression of the fasd2b in yeast generated a protein that was found to specifically convert eicosatetraenoic acid (20:4n-3) to eicosapentaenoic acid (20:5n-3), and therefore functioned as a Δ5 desaturase. Therefore, rainbow trout have two fads2 genes that encode proteins with Δ5 and Δ6 desaturase activities, respectively, which enable this species to perform all the desaturation steps required for the biosynthesis of LC-PUFA from C18 precursors.
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    Δ-6 Desaturase Substrate Competition: Dietary Linoleic Acid (18:2n-6) Has Only Trivial Effects on α-Linolenic Acid (18:3n-3) Bioconversion in the Teleost Rainbow Trout
    Emery, JA ; Hermon, K ; Hamid, NKA ; Donald, JA ; Turchini, GM ; Yoshikawa, T (PUBLIC LIBRARY SCIENCE, 2013-02-27)
    It is generally accepted that, in vertebrates, omega-3 (n-3) and omega-6 (n-6) poly-unsaturated fatty acids (PUFA) compete for Δ-6 desaturase enzyme in order to be bioconverted into long-chain PUFA (LC-PUFA). However, recent studies into teleost fatty acid metabolism suggest that these metabolic processes may not conform entirely to what has been previously observed in mammals and other animal models. Recent work on rainbow trout has led us to question specifically if linoleic acid (LA, 18∶2n-6) and α-linolenic acid (ALA, 18∶3n-3) (Δ-6 desaturase substrates) are in direct competition for access to Δ-6 desaturase. Two experimental diets were formulated with fixed levels of ALA, while LA levels were varied (high and low) to examine if increased availability of LA would result in decreased bioconversion of ALA to its LC-PUFA products through substrate competition. No significant difference in ALA metabolism towards n-3 LC-PUFA was exhibited between diets while significant differences were observed in LA metabolism towards n-6 LC-PUFA. These results are evidence for minor if any competition between substrates for Δ-6 desaturase, suggesting that, paradoxically, the activity of Δ-6 desaturase on n-3 and n-6 substrates is independent. These results call for a paradigm shift in the way we approach teleost fatty acid metabolism. The findings are also important with regard to diet formulation in the aquaculture industry as they indicate that there should be no concern for possible substrate competition between 18∶3n-3 and 18∶2n-6, when aiming at increased n-3 LC-PUFA bioconversion in vivo.
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    Bioconversion of α-Linolenic Acid into n-3 Long-Chain Polyunsaturated Fatty Acid in Hepatocytes and Ad Hoc Cell Culture Optimisation
    Alhazzaa, R ; Sinclair, AJ ; Turchini, GM ; Vajreswari, A (PUBLIC LIBRARY SCIENCE, 2013-09-11)
    This study aimed to establish optimal conditions for a cell culture system that would allow the measurement of 18:3n-3 (ALA) bioconversion into n-3 long-chain polyunsaturated fatty acid (n-3 LC-PUFA), and to determine the overall pathway kinetics. Using rat hepatocytes (FaO) as model cells, it was established that a maximum 20:5n-3 (EPA) production from 50 µM ALA initial concentration was achieved after 3 days of incubation. Next, it was established that a gradual increase in the ALA concentration from 0 up to 125 µM lead to a proportional increase in EPA, without concomitant increase in further elongated or desaturated products, such as 22:5n-3 (DPA) and 22:6n-3 (DHA) in 3 day incubations. Of interest, ALA bioconversion products were observed in the culture medium. Therefore, in vitro experiments disregarding the medium fatty acid content are underestimating the metabolism efficiency. The novel application of the fatty acid mass balance (FAMB) method on cell culture system (cells with medium) enabled quantifying the apparent enzymatic activities for the biosynthesis of n-3 LC-PUFA. The activity of the key enzymes was estimated and showed that, under these conditions, 50% (Km) of the theoretical maximal (V max = 3654 µmol.g(-1) of cell protein.hour(-1)) Fads2 activity on ALA can be achieved with 81 µM initial ALA. Interestingly, the apparent activity of Elovl2 (20:5n-3 elongation) was the slowest amongst other biosynthesis steps. Therefore, the possible improvement of Elovl2 activity is suggested toward a more efficient DHA production from ALA. The present study proposed and described an ad hoc optimised cell culture conditions and methodology towards achieving a reliable experimental platform, using FAMB, to assist in studying the efficiency of ALA bioconversion into n-3 LC-PUFA in vitro. The FAMB proved to be a powerful and inexpensive method to generate a detailed description of the kinetics of n-3 LC-PUFA biosynthesis enzymes activities in vitro.
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    Fish Oil Replacement in Current Aquaculture Feed: Is Cholesterol a Hidden Treasure for Fish Nutrition?
    Norambuena, F ; Lewis, M ; Hamid, NKA ; Hermon, K ; Donald, JA ; Turchini, GM ; Gothilf, Y (PUBLIC LIBRARY SCIENCE, 2013-12-04)
    Teleost fish, as with all vertebrates, are capable of synthesizing cholesterol and as such have no dietary requirement for it. Thus, limited research has addressed the potential effects of dietary cholesterol in fish, even if fish meal and fish oil are increasingly replaced by vegetable alternatives in modern aquafeeds, resulting in progressively reduced dietary cholesterol content. The objective of this study was to determine if dietary cholesterol fortification in a vegetable oil-based diet can manifest any effects on growth and feed utilization performance in the salmonid fish, the rainbow trout. In addition, given a series of studies in mammals have shown that dietary cholesterol can directly affect the fatty acid metabolism, the apparent in vivo fatty acid metabolism of fish fed the experimental diets was assessed. Triplicate groups of juvenile fish were fed one of two identical vegetable oil-based diets, with additional cholesterol fortification (high cholesterol; H-Chol) or without (low cholesterol; L-Chol), for 12 weeks. No effects were observed on growth and feed efficiency, however, in fish fed H-Col no biosynthesis of cholesterol, and a remarkably decreased apparent in vivo fatty acid β-oxidation were recorded, whilst in L-Chol fed fish, cholesterol was abundantly biosynthesised and an increased apparent in vivo fatty acid β-oxidation was observed. Only minor effects were observed on the activity of stearyl-CoA desaturase, but a significant increase was observed for both the transcription rate in liver and the apparent in vivo activity of the fatty acid Δ-6 desaturase and elongase, with increasing dietary cholesterol. This study showed that the possible effects of reduced dietary cholesterol in current aquafeeds can be significant and warrant future investigations.