School of Agriculture, Food and Ecosystem Sciences - Research Publications
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ItemOrigin and Evolution of the Kiwifruit Canker Pandemic(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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ItemGenetic structure of Cercospora beticola populations on Beta vulgaris in New York and Hawaii(NATURE PORTFOLIO, 2017-05-11)Cercospora leaf spot (CLS), caused by Cercospora beticola, is a major disease of Beta vulgaris worldwide. No sexual stage is known for C. beticola but in its asexual form it overwinters on infected plant debris as pseudostromata, and travels short distances by rain splash-dispersed conidiospores. Cercospora beticola infects a broad range of host species and may be seedborne. The relative contribution of these inoculum sources to CLS epidemics on table beet is not well understood. Pathogen isolates collected from table beet, Swiss chard and common lambsquarters in mixed-cropping farms and monoculture fields in New York and Hawaii, USA, were genotyped (n = 600) using 12 microsatellite markers. All isolates from CLS symptoms on lambsquarters were identified as C. chenopodii. Sympatric populations of C. beticola derived from Swiss chard and table beet were not genetically differentiated. Results suggested that local (within field) inoculum sources may be responsible for the initiation of CLS epidemics in mixed-cropping farms, whereas external sources of inoculum may be contributing to CLS epidemics in the monoculture fields in New York. New multiplex PCR assays were developed for mating-type determination for C. beticola. Implications of these findings for disease management are discussed.
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ItemUsing multiple lines of evidence to assess the risk of ecosystem collapse(ROYAL SOC, 2017-09-27)Effective ecosystem risk assessment relies on a conceptual understanding of ecosystem dynamics and the synthesis of multiple lines of evidence. Risk assessment protocols and ecosystem models integrate limited observational data with threat scenarios, making them valuable tools for monitoring ecosystem status and diagnosing key mechanisms of decline to be addressed by management. We applied the IUCN Red List of Ecosystems criteria to quantify the risk of collapse of the Meso-American Reef, a unique ecosystem containing the second longest barrier reef in the world. We collated a wide array of empirical data (field and remotely sensed), and used a stochastic ecosystem model to backcast past ecosystem dynamics, as well as forecast future ecosystem dynamics under 11 scenarios of threat. The ecosystem is at high risk from mass bleaching in the coming decades, with compounding effects of ocean acidification, hurricanes, pollution and fishing. The overall status of the ecosystem is Critically Endangered (plausibly Vulnerable to Critically Endangered), with notable differences among Red List criteria and data types in detecting the most severe symptoms of risk. Our case study provides a template for assessing risks to coral reefs and for further application of ecosystem models in risk assessment.
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ItemDeguelin exerts potent nematocidal activity via the mitochondrial respiratory chain(WILEY, 2017-10)As a result of limited classes of anthelmintics and an over-reliance on chemical control, there is a great need to discover new compounds to combat drug resistance in parasitic nematodes. Here, we show that deguelin, a plant-derived rotenoid, selectively and potently inhibits the motility and development of nematodes, which supports its potential as a lead candidate for drug development. Furthermore, we demonstrate that deguelin treatment significantly increases gene transcription that is associated with energy metabolism, particularly oxidative phosphorylation and mitoribosomal protein production before inhibiting motility. Mitochondrial tracking confirmed enhanced oxidative phosphorylation. In accordance, real-time measurements of oxidative phosphorylation in response to deguelin treatment demonstrated an immediate decrease in oxygen consumption in both parasitic (Haemonchus contortus) and free-living (Caenorhabditis elegans) nematodes. Consequently, we hypothesize that deguelin is exerting its toxic effect on nematodes as a modulator of oxidative phosphorylation. This study highlights the dynamic biologic response of multicellular organisms to deguelin perturbation.-Preston, S., Korhonen, P. K., Mouchiroud, L., Cornaglia, M., McGee, S. L., Young, N. D., Davis, R. A., Crawford, S., Nowell, C., Ansell, B. R. E., Fisher, G. M., Andrews, K. T., Chang, B. C. H., Gijs, M. A. M., Sternberg, P. W., Auwerx, J., Baell, J., Hofmann, A., Jabbar, A., Gasser, R. B. Deguelin exerts potent nematocidal activity via the mitochondrial respiratory chain.
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ItemDOCUMENTATION OF ETHNOVETERINARY PRACTICES IN DISTRICT JHANG, PAKISTAN(PAKISTAN AGRICULTURAL SCIENTISTS FORUM, 2017-04)The study was conducted to document the plants used in the traditional veterinary practices in Jhang district of Pakistan. Rapid and participatory rural appraisal techniques were used for collection of information i.e. the interviews and focused group discussions were carried with 253 traditional veterinary healers for a period of one year. From the study area, 46 plant species representing 31 families were documented for the treatment of different infectious and non-infectious ailments. The most frequently reported (≥ 22% respondents) plants included: Trachyspermum ammi (L.) Sprague, Capsicum annuum Linn, Vernonia anthelmintica L., Foeniculum vulgare Mill, and Allium cepa Linn. Of 46 plants, 33 were indigenous. Materials other than plants are also used as adjunctive therapy for different ailments. A wide variation in the dose, vehicle, part of plant, mode of preparation and administration/application was observed. The efficacy claims and indications for different plants were quite conflicting. The traditional veterinary healers in the study area used diverse plant species in the veterinary practices with varying claims about their efficacies. Controlled studies for the validation of the plant usage are underway in the Department of Parasitology, University of Agriculture, Faisalabad, Pakistan.
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ItemHabitat characteristics of a threatened arboreal marsupial and its resource use in a degraded landscape: the brush-tailed phascogale (Phascogale tapoatafa tapoatafa) in central Victoria, Australia(CSIRO PUBLISHING, 2017-06)Context Habitat loss and degradation has contributed significantly to the decline of many species worldwide. To address this loss, we first require a comprehensive understanding of habitat requirements and resource-use patterns of the species under threat. Aims The study aimed to quantify variation in the habitat of a species threatened by habitat loss and degradation, the brush-tailed phascogale (Phascogale tapoatafa tapoatafa), by measuring several physical characteristics of trees and ground cover, as well as to determine potential foraging resource preferences using abundance data from a long-term monitoring study. Methods Phascogale monitoring surveys were conducted over a 13-year period from 2000 to 2012. Habitat variables characterising tree communities, ground cover and coarse woody debris were used to develop explanatory models of phascogale abundance at the site scale. Tree species preference by foraging phascogales was evaluated by comparing usage (trees on which they were captured) and availability. Key results The highest overall animal abundance was at sites characterised by associations of red stringybark, red box, grey box and broad-leaved and narrow-leaved peppermints. At these sites, red stringybark and grey box trees were of small diameter and tended to have small hollows. These sites also had low average tree height, low grass and/or herb and shrub cover and low volumes of coarse woody debris. From a resource-use perspective, phascogales foraged preferentially on certain species of Eucalyptus. Conclusions Our study suggests that phascogale abundance is highly spatially and temporally variable, most likely as a response to heterogeneity in habitat and foraging resources operating at a range of spatial scales. Implications This study has provided new information concerning spatial patterns of phascogale abundance and resource use within a forested area in central Victoria that has been subjected to multiple disturbances. Currently, the composition and age structure of tree communities and ground habitats are a response to severe disturbance due to past mining and harvesting activities. Successful conservation of this threatened species could be enhanced through active management of this forest to maintain the ongoing supply of nesting hollows and foraging resources.
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ItemNew approaches to learning for facilitating resilience in the built environment(Planning Institute of Australia, Victoria Division, 2017)
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ItemPopulation Structure Analysis of Bull Genomes of European and Western Ancestry.(Springer Science and Business Media LLC, 2017-01-13)Since domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics of Bos taurus. In turn, characterization of population structure among diverse bull (males of Bos taurus) genomes enables detailed assessment of genetic resources and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the European/Western cattle population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models for individual-specific allele frequencies that directly capture a wide range of complex structure from genome-wide genotypes. As measured by magnitude of differentiation, selection pressure on SNPs within genes is substantially greater than that on intergenic regions. Additionally, broad regions of chromosome 6 harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our population structure analysis of bull genomes can support genetic management strategies that capture structural complexity and promote sustainable genetic breadth.
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ItemThe effect of training on the temporal dominance of sensations method: A study with milk protein hydrolysates(WILEY, 2017-12)Abstract The Temporal Dominance of Sensations (TDS) method could be an alternative approach to time‐consuming trained panels for the sensory analysis of protein hydrolysates. However, the amount of training required for accurate TDS results with hydrolysates is unclear. In addition, the masking of unpleasant aftertastes in protein hydrolysates using sweeteners is often only partially successful. The aim of this study was: (a) To examine changes in TDS results with hydrolysates as a group of panelists progress through different levels of training: as untrained panelists, familiarized panelists, and trained panelists. (b) To examine the effect of increasing sweetness on the temporal suppression of sensory attributes in hydrolysates. Four products were assessed: a casein hydrolysate at 10% wt/wt with 4 levels of sucralose (0%, 1.5, 3, and 6% equivalent sweetness). Similar TDS results were obtained for all three levels of training for each product, however consensus of selection and product discrimination increased with training. As sweetness increased bitterness was suppressed however cheesiness increased. Sweetness tended to peak before bitterness and cheesiness, however temporal changes were small and subtle. Practical applications Running traditional descriptive trained panels is expensive and time‐consuming. It is particularly difficult with protein hydrolysates, as their unpleasant sensory properties mean that panelists are hard to recruit, and will often leave panels during training. This work attempted to understand if the Temporal Dominance of Sensations (TDS) method could be used with untrained panelists for protein hydrolysates. Results suggest a TDS panel of untrained panelists may be suitable for the assessment of hydrolysates, however TDS training still provided the best quality data. This work also represents a first attempt to understand the aftertaste profile of a protein hydrolysate (and attempts to mask aftertaste with a sweet masking agent) using a temporal sensory method. Results showed most sensory attributes dominating during tasting in the mouth declined very slowly after swallowing.