School of Ecosystem and Forest Sciences - Research Publications
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ItemIdentification of molecular genetic contributants to canine cutaneous mast cell tumour metastasis by global gene expression analysis.(Public Library of Science (PLoS), 2018)Cutaneous mast cell tumours are one of the most common canine cancers. Approximately 25% of the tumours metastasise. Activating c-kit mutations are present in about 20% of tumours, but metastases occur in the absence of mutations. Tumour metastasis is associated with significantly diminished survival in spite of adjuvant chemotherapy. Available prognostic tests do not reliably predict whether a tumour will metastasise. In this study we compared the global expression profiles of 20 primary cutaneous mast cell tumours that metastasised with those of 20 primary tumours that did not metastasise. The objective was to identify genes associated with mast cell tumour metastatic progression that may represent targets for therapeutic intervention and biomarkers for prediction of tumour metastasis. Canine Gene 1.1 ST Arrays were employed for genome-wide expression analysis of formalin-fixed, paraffin-embedded biopsies of mast cell tumours borne by dogs that either died due to confirmed mast cell tumour metastasis, or were still alive more than 1000 days post-surgery. Decreased gene expression in the metastasising tumours appears to be associated with a loss of cell polarity, reduced cell-cell and cell-ECM adhesion, and increased cell deformability and motility. Dysregulated gene expression may also promote extracellular matrix and base membrane degradation, suppression of cell cycle arrest and apoptosis, and angiogenesis. Down-regulation of gene expression in the metastasising tumours may be achieved at least in part by small nucleolar RNA-derived RNA and microRNA-effected gene silencing. Employing cross-validation, a linear discriminant analysis-based classifier featuring 19 genes that displayed two-fold differences in expression between metastasising and non-metastasising tumours was estimated to classify metastasising and non-metastasising tumours with accuracies of 90-100% and 70-100%, respectively. The differential expression of 9 of the discriminator genes was confirmed by quantitative reverse transcription-PCR.
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ItemA synonymous germline variant in a gene encoding a cell adhesion molecule is associated with cutaneous mast cell tumour development in Labrador and Golden Retrievers.(Public Library of Science (PLoS), 2019-03)Mast cell tumours are the most common type of skin cancer in dogs, representing a significant concern in canine health. The molecular pathogenesis is largely unknown, but breed-predisposition for mast cell tumour development suggests the involvement of inherited genetic risk factors in some breeds. In this study, we aimed to identify germline risk factors associated with the development of mast cell tumours in Labrador Retrievers, a breed with an elevated risk of mast cell tumour development. Using a methodological approach that combined a genome-wide association study, targeted next generation sequencing, and TaqMan genotyping, we identified a synonymous variant in the DSCAM gene on canine chromosome 31 that is associated with mast cell tumours in Labrador Retrievers. DSCAM encodes a cell-adhesion molecule. We showed that the variant has no effect on the DSCAM mRNA level but is associated with a significant reduction in the level of the DSCAM protein, suggesting that the variant affects the dynamics of DSCAM mRNA translation. Furthermore, we showed that the variant is also associated with mast cell tumours in Golden Retrievers, a breed that is closely related to Labrador Retrievers and that also has a predilection for mast cell tumour development. The variant is common in both Labradors and Golden Retrievers and consequently is likely to be a significant genetic contributor to the increased susceptibility of both breeds to develop mast cell tumours. The results presented here not only represent an important contribution to the understanding of mast cell tumour development in dogs, as they highlight the role of cell adhesion in mast cell tumour tumourigenesis, but they also emphasise the potential importance of the effects of synonymous variants in complex diseases such as cancer.
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ItemGenome-wide analysis of canine oral malignant melanoma metastasis-associated gene expression.(Springer Science and Business Media LLC, 2019-04-24)Oral malignant melanoma (OMM) is the most common canine melanocytic neoplasm. Overlap between the somatic mutation profiles of canine OMM and human mucosal melanomas suggest a shared UV-independent molecular aetiology. In common with human mucosal melanomas, most canine OMM metastasise. There is no reliable means of predicting canine OMM metastasis, and systemic therapies for metastatic disease are largely palliative. Herein, we employed exon microarrays for comparative expression profiling of FFPE biopsies of 18 primary canine OMM that metastasised and 10 primary OMM that did not metastasise. Genes displaying metastasis-associated expression may be targets for anti-metastasis treatments, and biomarkers of OMM metastasis. Reduced expression of CXCL12 in the metastasising OMMs implies that the CXCR4/CXCL12 axis may be involved in OMM metastasis. Increased expression of APOBEC3A in the metastasising OMMs may indicate APOBEC3A-induced double-strand DNA breaks and pro-metastatic hypermutation. DNA double strand breakage triggers the DNA damage response network and two Fanconi anaemia DNA repair pathway members showed elevated expression in the metastasising OMMs. Cross-validation was employed to test a Linear Discriminant Analysis classifier based upon the RT-qPCR-measured expression levels of CXCL12, APOBEC3A and RPL29. Classification accuracies of 94% (metastasising OMMs) and 86% (non-metastasising OMMs) were estimated.
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ItemCaliciopsis pleomorpha sp. nov. (Ascomycota: Coryneliales) causing a severe canker disease of Eucalyptus cladocalyx and other eucalypt species in Australia.(Westerdijk Fungal Biodiversity Institute, 2018-12)Caliciopsis pleomorpha sp. nov. is described from a severe stem canker disease of cultivated Eucalyptus cladocalyx 'Nana' (dwarf sugar gum) in Australia. The fungus is a pleomorphic ascomycete (Coryneliales), with pycnidial (pleurophoma-like) and hyphomycetous (phaeoacremonium-like) morphs, and differs in these respects and in ITS sequences from other Caliciopsis spp. The fungus was also found associated with cankers on other Eucalyptus species growing in native habitats, and was successfully inoculated under glasshouse conditions into a wide range of Eucalyptus species on which it caused cankers of varying severity.
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ItemBack to the roots: protocol for the photoautotrophic micropropagation of medicinal Cannabis(SPRINGER, 2019-08-01)The aim of this protocol was to develop an alternative in vitro propagation system for Cannabis sativa L. by mimicking nursery-based vegetative propagation. Photoautotrophic micropropagation (PAM) was achieved on rockwool blocks as substrate combined with commercially available fertilizer suitable for cannabis cultivation. Stock plants were initiated after sterilisation in forced-ventilated glass jars which then provided a continuous supply of shoot tip and nodal cuttings. A 97.5% rooting rate of in vitro shoot tip cuttings and successful acclimatisation were achieved within 3 weeks in glass vessels with passive ventilation.
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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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ItemGenome-Wide Association Study of Golden Retrievers Identifies Germ-Line Risk Factors Predisposing to Mast Cell Tumours.(Public Library of Science (PLoS), 2015-11)Canine mast cell tumours (CMCT) are one of the most common skin tumours in dogs with a major impact on canine health. Certain breeds have a higher risk of developing mast cell tumours, suggesting that underlying predisposing germ-line genetic factors play a role in the development of this disease. The genetic risk factors are largely unknown, although somatic mutations in the oncogene C-KIT have been detected in a proportion of CMCT, making CMCT a comparative model for mastocytosis in humans where C-KIT mutations are frequent. We have performed a genome wide association study in golden retrievers from two continents and identified separate regions in the genome associated with risk of CMCT in the two populations. Sequence capture of associated regions and subsequent fine mapping in a larger cohort of dogs identified a SNP associated with development of CMCT in the GNAI2 gene (p = 2.2x10-16), introducing an alternative splice form of this gene resulting in a truncated protein. In addition, disease associated haplotypes harbouring the hyaluronidase genes HYAL1, HYAL2 and HYAL3 on cfa20 and HYAL4, SPAM1 and HYALP1 on cfa14 were identified as separate risk factors in European and US golden retrievers, respectively, suggesting that turnover of hyaluronan plays an important role in the development of CMCT.
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ItemDeguelin exerts potent nematocidal activity via the mitochondrial respiratory chain(WILEY, 2017-10-01)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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ItemPlastic weed matting is better than jute or woodchips for controlling the invasive wetland grass Phalaris arundinacea, but not Phragmites australis.(Polymeria Publishing, 2016)Woven polypropylene (plastic) weed matting, jute and eucalypt woodchips were trialled for controlling reed canary grass (Phalaris arundinacea L.) and common reed (Phragmites australis (Cav.) Trin. ex Steud.). At two sites, one dominated by reed canary grass and the other by common reed, 50 m x 20 m was mowed and sprayed and ten (10 m x 10 m) plots established, eight of which were fenced. Plots were covered with either plastic weed matting, jute or eucalypt woodchips, or were controls. All plots were planted with native trees and shrubs and understorey plants. Plastic weed matting was the most effective at reducing regrowth of reed canary grass (<5% cover after one year) and promoting the growth of native plantings (>60% cover). Both plastic weed and jute matting were similarly effective at reducing its regrowth (to 10%), but both matting types were compromised by common reed regrowth. While trees and shrubs grew well across all fenced treatments ( 100% survival), understorey plants only established and grew where weed regrowth was controlled. Unfenced unguarded trees and shrubs were virtually eliminated by browsing. Plastic weed matting (combined with other control measures, and protection from browsers where necessary) may provide the best opportunity to control reed canary grass and facilitate wetland restoration.
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ItemCounting the cost of revegetation: is direct seeding cheaper than planting tube-stock?(University of New England, Armidale, 2018)Direct seeding is often assumed to be cheaper than planting tube–stock, but limited data exist to compare the relative costs of the two techniques. At four riparian sites in Victoria, we assessed the number of plants established over time in the months after direct seeding or planting. The costs of surviving plants and of weed management were calculated. Plants were 11 times cheaper when established by seeding ($1.88/plant) than when planted ($21.03/plant). Incorporating weed management costs, direct seeding was 1.3–2.4 times more cost–effective than planting tube–stock, although costs were high for both techniques.