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Takagi W.,University of Tokyo | Kajimura M.,Wakayama University | Bell J.D.,Deakin University | Bell J.D.,Primary Industries Research Victoria | And 3 more authors.
Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology | Year: 2012

Cartilaginous fish comprise two subclasses, the Holocephali (chimaeras) and Elasmobranchii (sharks, skates and rays). Little is known about osmoregulatory mechanisms in holocephalan fishes except that they conduct urea-based osmoregulation, as in elasmobranchs. In the present study, we examined the ornithine urea cycle (OUC) enzymes that play a role in urea biosynthesis in the holocephalan elephant fish, Callorhinchus milii (cm). We obtained a single mRNA encoding carbamoyl phosphate synthetase III (cmCPSIII) and ornithine transcarbamylase (cmOTC), and two mRNAs encoding glutamine synthetases (cmGSs) and two arginases (cmARGs), respectively. The two cmGSs were structurally and functionally separated into two types: brain/liver/kidney-type cmGS1 and muscle-type cmGS2. Furthermore, two alternatively spliced transcripts with different sizes were found for cm. gs1 gene. The longer transcript has a putative mitochondrial targeting signal (MTS) and was predominantly expressed in the liver and kidney. MTS was not found in the short form of cmGS1 and cmGS2. A high mRNA expression and enzyme activities were found in the liver and muscle. Furthermore, in various tissues examined, mRNA levels of all the enzymes except cmCPSIII were significantly increased after hatching. The data show that the liver is the important organ for urea biosynthesis in elephant fish, but, extrahepatic tissues such as the kidney and muscle may also contribute to the urea production. In addition to the role of the extrahepatic tissues and nitrogen metabolism, the molecular and functional characteristics of multiple isoforms of GSs and ARGs are discussed. © 2011 Elsevier Inc.


Hayden M.J.,University of Adelaide | Hayden M.J.,Primary Industries Research Victoria | Tabone T.L.,University of Adelaide | Tabone T.L.,Royal Melbourne Hospital | And 7 more authors.
Crop and Pasture Science | Year: 2010

The identification of genetic variation using molecular markers is fundamental to modern plant breeding and research. The present study was undertaken to develop a resource of informative single nucleotide polymorphism (SNP) markers for molecular characterisation of Australian barley germplasm. In total, 190 SNP markers were developed and characterised using 88 elite barley lines and varieties, sampling genetic diversity relevant to Australian breeding programs, and a core set of 48 SNPs for distinguishing among the barley lines was identified. The utility of the core 48-SNP set for distinguishing barley lines and varieties using DNA extracted from grain samples was also assessed. Finally, the 48 SNPs in the core set were converted into simple PCR markers to enable co-dominant SNP genotyping on agarose gel. The SNP markers developed, and in particular the core 48-SNP set, provide a useful marker resource for assessing genetic relationships between individuals and populations of current Australian barley germplasm. They are also useful for identity and purity testing of inbred lines in research, breeding, and commercial applications. © CSIRO 2010.


Bernard M.B.,University of Melbourne | Cole P.,IPM Technologies Pty. Ltd. | Kobelt A.,Primary Industries Research Victoria | Horne P.A.,IPM Technologies Pty. Ltd. | And 3 more authors.
Journal of Economic Entomology | Year: 2010

Laboratory bioassays on detached soybean, Glycine max (L.) Merr., leaves were used to test 23 fungicides, five insecticides, two acaricides, one herbicide, and two adjuvants on a key Australian predatory mite species Euseius victoriensis (Womersley) in "worst-case scenario" direct overspray assays. Zero- to 48-h-old juveniles, their initial food, and water supply were sprayed to runoff with a Potter tower; spinosad and wettable sulfur residues also were tested. Tests were standardized to deliver a pesticide dose comparable with commercial application of highest label rates at 1,000 liter/ha. Cumulative mortality was assessed 48 h, 4 d, and 7 d after spraying. Fecundity was assessed for 7 d from start of oviposition. No significant mortality or fecundity effects were detected for the following compounds at single-use application at 1,000 liter/ha: azoxystrobin, Bacillus thuringiensis (Bt) subsp. kurstaki, captan, chlorothalonil, copper hydroxide, fenarimol, glyphosate, hexaconazole, indoxacarb, metalaxyl/copper hydroxide, myclobutanil, nonyl phenol ethylene oxide, phosphorous acid, potassium bicarbonate, pyraclostrobin, quinoxyfen, spiroxamine, synthetic latex, tebufenozide, triadimenol, and trifloxystrobin. Iprodione and penconazole had some detrimental effect on fecundity. Canola oil as acaricide (2 liter/100 liter) and wettable sulfur (200 g/100 liter) had some detrimental effect on survival and fecundity and cyprodinil/fludioxonil on survivor. The following compounds were highly toxic (high 48-h mortality): benomyl, carbendazim, emamectin benzoate, mancozeb, spinosad (direct overspray and residue), wettable sulfur (≥400 g/100 liter), and pyrimethanil; pyrimethanil had no significant effect on fecundity of surviving females. Indoxacarb safety to E. victoriensis contrasts with its toxicity to key parasitoids and chrysopid predators. Potential impact of findings is discussed. © 2010 Entomological Society of America.


Hernandez S.,Victoria University of Wellington | Hernandez S.,Católica del Norte University | Daley R.,CSIRO | Walker T.,Primary Industries Research Victoria | And 4 more authors.
Fisheries Research | Year: 2015

We used mitochondrial DNA (mtDNA) control region (CR) sequences and genotypes from eight microsatellite DNA (msatDNA) loci to determine the genetic structure of the school shark (Galeorhinus galeus) in New Zealand, Australia and Chile. The estimates of mtDNA haplotype and nucleotide diversity were very similar in New Zealand (h= 0.735 ± 0.032, π= 0.001 ± 0.001) and Australia (h= 0.729 ± 0.027, π= 0.001 ± 0.001), but in Chile they were higher (h= 0.800 ± 0.089, π= 0.002 ± 0.001). The haplotype genealogy showed evidence of two distinct clades, New Zealand and Australia combined (clade 1), and Chile (clade 2). A power analysis suggested that sample sizes were large enough to detect any significant differences within clade 1. Neutrality test, mismatch distribution, and demographic reconstructions based on a coalescence approach, suggested that the Oceania population (clade 1) went through a period of population expansion, whereas the population size of the Chile population (clade 2) has been relatively stable over the last 20,000 years. Data from microsatellite loci also supported the separation of the Oceania and Chile populations. Principal component analysis suggested that there might also be a separation of groups within clade 1, which was not statistically significant (P= 0.434). The genetic data reported in this study supported the model of a single G. galeus stock in New Zealand and Australia. Our findings were consistent with previous tagging data that showed individual G. galeus migrate across the Tasman Sea between Australia and New Zealand, and at least some of these migration events result in successful reproduction. © 2015 Elsevier B.V.


Kuske T.,Cooperative Research Center for Greenhouse Gas Technologies | Kuske T.,Geoscience Australia | Jenkins C.,Cooperative Research Center for Greenhouse Gas Technologies | Jenkins C.,CSIRO | And 5 more authors.
Energy Procedia | Year: 2013

Atmospheric tomography is a monitoring technique that uses an array of sampling sites and a Bayesian inversion technique to simultaneously solve for the location and magnitude of a gaseous emission. Application of the technique to date has relied on air samples being pumped over short distances to a high precision FTIR Spectrometer, which is impractical at larger scales. We have deployed a network of cheaper, less precise sensors during three recent large scale controlled CO2 release experiments; one at the CO 2CRC Ginninderra site, one at the CO2CRC Otway Site and another at the Australian Grains Free Air CO2 Enrichment (AGFACE) facility in Horsham, Victoria. The purpose of these deployments was to assess whether an array of independently powered, less precise, less accurate sensors could collect data of sufficient quality to enable application of the atmospheric tomography technique. With careful data manipulation a signal suitable for an inversion study can be seen. A signal processing workflow based on results obtained from the atmospheric array deployed at the CO2CRC Otway experiment is presented. © 2013 The Author.


Nordblom T.L.,Pine Gully Road | Nordblom T.L.,Future Farm Industries Cooperative Research Center | Christy B.P.,Primary Industries Research Victoria | Christy B.P.,Future Farm Industries Cooperative Research Center | And 6 more authors.
Agricultural Water Management | Year: 2010

This study reports an analysis of the economics of options for strategic land-use change to attain future catchment level target combinations of salt load and water yield. Farm level survey information on land use, productivity, prices and costs of production were integrated with spatially specific soil, rainfall, topography, hydrology and salinity results of the simulation model CAT (Catchment Analysis Tool). This information was used to populate a two stage economic optimization model in which subcatchment economic results were combined for catchment level analyses. This study is the first to exploit CAT results in an economic framework and the first in which economic results are mapped using CAT. The 64,000 ha Bet Bet Catchment in Victoria, Australia, once deemed among the highest priority areas in the Murray Darling Basin for dryland salinity reduction, is the focus of this study. The calculated current net present value (NPV) of agricultural production in the catchment is AU$ 78 million 33AU$ 1 = US$ 0.9 December 2009. while providing 42 GL of water yield 441 GL = 1 gigalitre = 10 6 m 3 = 10 9 L. annually for use downstream with a salt load of 22,600 t. Results show that salt loads may be reduced to 18,600 t (reduction of 4000 t) through expansion of tree plantations and lucerne production, reducing water yield to 31 GL (11 GL reduction) and NPV to AU$ 63 million (AU$ 15 million reduction). Water yields could be increased from current levels by 2 GL while maintaining current salt loads. Alternatively, catchment NPV could be increased by approximately AU$ 7 million with little or no reduction in water yield; but there may be reasons (small farm size) why this is unlikely. For this catchment, the maximum reduction in salt load appears insufficient to justify public investment in tree planting and perennial pasture establishment, particularly when the reduced NPV and reduced water yields are taken into account. The results for this catchment do not support regulation of land use for the sake of lowering river salinity. However, the capacity of tree plantations to reduce water yields may support a regulation requiring purchase of water entitlements from downstream entitlement holders for new plantations. Despite millions of dollars of past public investment, it is now clear that Bet Bet Catchment was never one where land-use changes could benefit downstream water users. The approach described in this paper enables catchment management authorities to weigh costs of land-use change against downstream benefits and natural resource management (NRM) options elsewhere. © 2010 Elsevier B.V. All rights reserved.


Qanbari S.,University of Gottingen | Gianola D.,University of Wisconsin - Madison | Hayes B.,Primary Industries Research Victoria | Schenkel F.,University of Guelph | And 4 more authors.
BMC Genomics | Year: 2011

Background: 'Selection signatures' delimit regions of the genome that are, or have been, functionally important and have therefore been under either natural or artificial selection. In this study, two different and complementary methods--integrated Haplotype Homozygosity Score (|iHS|) and population differentiation index (FST)--were applied to identify traces of decades of intensive artificial selection for traits of economic importance in modern cattle.Results: We scanned the genome of a diverse set of dairy and beef breeds from Germany, Canada and Australia genotyped with a 50 K SNP panel. Across breeds, a total of 109 extreme |iHS| values exceeded the empirical threshold level of 5% with 19, 27, 9, 10 and 17 outliers in Holstein, Brown Swiss, Australian Angus, Hereford and Simmental, respectively. Annotating the regions harboring clustered |iHS| signals revealed a panel of interesting candidate genes like SPATA17, MGAT1, PGRMC2 and ACTC1, COL23A1, MATN2, respectively, in the context of reproduction and muscle formation. In a further step, a new Bayesian FST-based approach was applied with a set of geographically separated populations including Holstein, Brown Swiss, Simmental, North American Angus and Piedmontese for detecting differentiated loci. In total, 127 regions exceeding the 2.5 per cent threshold of the empirical posterior distribution were identified as extremely differentiated. In a substantial number (56 out of 127 cases) the extreme FSTvalues were found to be positioned in poor gene content regions which deviated significantly (p < 0.05) from the expectation assuming a random distribution. However, significant FSTvalues were found in regions of some relevant genes such as SMCP and FGF1.Conclusions: Overall, 236 regions putatively subject to recent positive selection in the cattle genome were detected. Both |iHS| and FSTsuggested selection in the vicinity of the Sialic acid binding Ig-like lectin 5 gene on BTA18. This region was recently reported to be a major QTL with strong effects on productive life and fertility traits in Holstein cattle. We conclude that high-resolution genome scans of selection signatures can be used to identify genomic regions contributing to within- and inter-breed phenotypic variation. © 2011 Qanbari et al; licensee BioMed Central Ltd.


Newman D.M.,Deakin University | Jones P.L.,Deakin University | Ingram B.A.,Primary Industries Research Victoria
Aquaculture | Year: 2010

The timing and characteristics of reproductive development in adult female Murray cod exposed to a simulated seasonal photothermal cycle (14:45 to 09:45 daylight h; 12-26°C) (CONTROL) were compared to the development of females exposed to a three month phase-shifted (advanced) seasonal photothermal cycle (PHOTOTHERMAL) and to females exposed to a three month phase-shifted (advanced) photoperiod cycle in combination with constant temperature (19.5°C) (PHOTOPERIOD). Females in PHOTOTHERMAL and PHOTOPERIOD treatments reached maturity up to three (June) and four (May) months in advance of CONTROL fish (October), respectively. Biannual maturation was also observed in four PHOTOPERIOD females (13%). Mean ovary diameter and relative fecundity of mature females were similar between treatments (p>0.05), and viable eggs were produced in all groups (100% ovulated; 14.02%-39.12% mean survival to hatching). Ovary diameters and plasma levels of E2 and T in phase-shifted females remained at basal levels and/or were significantly reduced (p<0.05) relative to CONTROL fish throughout the early to mid phases of the maturation period. However, rapid increases in plasma T (0.54-4.39ngml-1) and ovary diameter (20.0-42.4mm) in the 60 to 90days preceding the onset of maturity in phase-shifted females revealed a capacity of Murray cod to accelerate development processes to compensate for earlier delays in photo-responsiveness. Low levels of E2 that persisted throughout the maturation period of PHOTOTHERMAL and PHOTOPERIOD females did not appear to greatly affect ovarian growth. The successful maturation of photoperiodically-manipulated females under constant temperature demonstrates an alternative approach for influencing maturation patterns in Murray cod that may improve the versatility and cost-effectiveness of broodstock conditioning procedures. © 2010.


Robinson N.,Nofima Marine | Robinson N.,South Australian Research And Development Institute | Robinson N.,Flinders University | Li X.,South Australian Research And Development Institute | And 2 more authors.
Aquaculture Research | Year: 2010

The genetic response and economic benefit from alternative breeding programme designs for blacklip and greenlip abalone (Haliotis rubra and Haliotis laevigata, respectively) were evaluated using a computer simulation model. Two selection criteria were investigated, one used family breeding values for liability to disease challenge test infection and the other used a direct selection of the best performing individuals across families for growth rate. Five scales of breeding programme were tested and the model predicted that if growth rate is the only selection criterion, breeding programmes of a scale using 150 families of each species each generation would result in 12-13% genetic improvement in initial generations and have the greatest beneficial economic impact on the Australian abalone industry of the options tested. The model predicts an average discounted benefit-cost ratio of 48:1, total added discounted benefit of AU$4.90 for each kilogram of abalone produced and nominal economic effect on operating income of over AU$16 million per year after 10 years. If disease resistance is the only selective breeding criterion, 100 families of each species would result in the highest benefit-cost ratio of the options tested, although some genetic gain would need to be sacrificed to reduce inbreeding to acceptable levels in this scenario. A strategy for a stand-alone abalone selective breeding cooperative was also modelled. For a farm of current tank area yielding 100 t year-1, participation is expected to yield over AU$0.7 million in discounted total added production value and annual discounted returns of over AU$0.4 million per annum by year 10. © 2010 The Authors. Journal Compilation © 2010 Blackwell Publishing Ltd.


Tovar-Avila J.,University of Melbourne | Tovar-Avila J.,Primary Industries Research Victoria | Tovar-Avila J.,Instituto Nacional Of Pesca | Day R.W.,University of Melbourne | And 2 more authors.
Journal of Fish Biology | Year: 2010

A rapid semi-quantitative ecological risk assessment method (productivity and susceptibility analysis) indicated that, despite its low biological productivity, the Port Jackson shark Heterodontus portusjacksoni is at low risk to all fishing methods in far-eastern Victoria, Australia, under the present fishing practices, because of its low catch susceptibility. The risk to this population, however, would increase if the shark gillnet fishery operating in the region were to retain the species as a by-product. Demographic analysis indicated that the species has medium intrinsic population growth rate and potential rebound in comparison with other chondrichthyan species, juveniles have higher elasticity than mature females and both juvenile and mature females have higher elasticities than hatchlings. Because of its low biological productivity and moderate resilience to the effects of fishing, cautious management measures will be necessary to ensure the sustainable use of H. portusjacksoni if its marketing increases in the future. Information on the dynamics of a population that is valuable to provide management advice can be obtained through demographic methods, but rapid assessment methods can also provide complementary information on the effects of fishing by considering the catch susceptibility of the population to each fishing method. © 2010 The Authors. Journal of Fish Biology © 2010 The Fisheries Society of the British Isles.

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