Redding M.R.,AgriScience Queensland |
Lewis R.,AgriScience Queensland |
Waller J.,Agresearch Ltd. |
Phillips F.,University of Wollongong |
Griffith D.,University of Wollongong
Journal of Environmental Quality | Year: 2013
Measurement of individual emission sources (e.g., animals or pen manure) within intensive livestock enterprises is necessary to test emission calculation protocols and to identify targets for decreased emissions. In this study, a vented, fabric-covered large chamber (4.5 × 4.5 m, 1.5 m high; encompassing greater spatial variability than a smaller chamber) in combination with on-line analysis (nitrous oxide [N2O] and methane [CH4] via Fourier Transform Infrared Spectroscopy; 1 analysis min-1) was tested as a means to isolate and measure emissions from beef feedlot pen manure sources. An exponential model relating chamber concentrations to ambient gas concentrations, air exchange (e.g., due to poor sealing with the surface; model linear when ≈ 0 m3 s-1), and chamber dimensions allowed data to be fitted with high confidence. Alternating manure source emission measurements using the large-chamber and the backward Lagrangian stochastic (bLS) technique (5-mo period; bLS validated via tracer gas release, recovery 94-104%) produced comparable N2O and CH4 emission values (no significant difference at P < 0.05). Greater precision of individual measurements was achieved via the large chamber than for the bLS (mean ± standard error of variance components: bLS half-hour measurements, 99.5 ± 325 mg CH4 s-1 and 9.26 ± 20.6 mg N2O s-1; large-chamber measurements, 99.6 ± 64.2 mg CH4 s-1 and 8.18 ± 0.3 mg N2O s-1). The large-chamber design is suitable for measurement of emissions from manure on pen surfaces, isolating these emissions from surrounding emission sources, including enteric emissions. © © American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.
Taylor S.M.,Australian Department of Primary Industries and Fisheries |
Webley J.A.C.,Australian Department of Primary Industries and Fisheries |
Mayer D.G.,AgriScience Queensland
Fisheries Research | Year: 2011
As recreational fishing continues to expand, the need to obtain precise harvest estimates is becoming increasingly important for the sustainable management of fisheries. Recreational fishing data are frequently zero-inflated which can present problems for commonly used analyses that assume a normal distribution. In this study, we analysed zero-inflated recreational fishing data collected from a bus-route access point survey in southeastern Queensland, Australia. Using the Time Interval Count method, we compared estimates of the proportion of boats fishing, fishing effort, harvest per unit effort (HPUE) and harvest using sample mean values and mean values derived from a two-part conditional general linear model (CGLM). The CGLM gave more precise estimates of the proportion of boats fishing, fishing effort and HPUE, which formed the basis of the harvest calculations. Differences in harvest estimates using the two methods ranged from 3 to 28% for the five recreational species examined. Relative standard errors for harvest estimated by the CGLM were 65-84% smaller. The results suggest that CGLMs may deliver more precise outputs in other types of recreational fishing surveys that derive effort and catch from zero-inflated data. © 2011 Elsevier B.V.
Webley J.A.C.,Australian Department of Primary Industries and Fisheries |
Mayer D.G.,AgriScience Queensland |
Taylor S.M.,Australian Department of Primary Industries and Fisheries
Fisheries Research | Year: 2011
Many decisions and assessments made by fisheries managers and researchers use estimates. The confidence stakeholders have in these decisions is greater when those estimates are accurate and precise. Complex statistical models are often used in fisheries management and research to improve these estimates. The models usually assume the underlying data are distributed according to some theoretical distribution (e.g. Poisson, gamma) but in reality fishery data usually only approximate theoretical distributions, breaching them to varying degrees. If the models are not sufficiently robust, these breaches can produce biased and/or imprecise estimates leading to excessive Type I and Type II errors, both of which can lead to poor decisions. We examined the robustness of seven models used in fisheries research to varying degrees of breaches in their distribution assumptions. Using six different zero-inflated gamma and Poisson distributions and three different sample sizes we examined the mean bias, confidence interval width and actual Type I error rate (as opposed to the modeled α of 0.05) of these models by comparing the estimates to the known population parameters. We found that the more complex models tended to be less robust to breaches of their distribution assumptions than the simpler normal model (sample mean). We recommend that the robustness of a chosen statistical model be assessed a priori to provide stakeholders with some confidence in the accuracy and precision of the estimates and we present a simple iterative method to do this. © 2011.
Taylor S.,Australian Department of Primary Industries and Fisheries |
Sumpton W.,AgriScience Queensland |
Ham T.,Australian Department of Primary Industries and Fisheries
Marine and Freshwater Research | Year: 2011
Our understanding of the ecological role of larger elasmobranchs is limited by a lack of information on their spatial and seasonal abundance. Analysis of 14 years of gill-net catch data in south-eastern Queensland, Australia, revealed that the species composition of large sharks and other elasmobranchs significantly differed among beaches and seasons. Spinner sharks (Carcharhinus brevipinna) and hammerhead sharks (Sphyrna spp.) comprised nearly half the catch of all elasmobranchs. Although the distribution of these sharks overlapped, spatial variation existed in their abundance. Spinner sharks characterised the catch at Sunshine Coast beaches, whereas the catch at Gold Coast beaches was dominated by hammerhead sharks. Seasonal differences in elasmobranch community structure were also apparent, driven largely by a lower abundance of many species during the winter and the predominance of species such as spinner sharks and hammerheads in spring and summer. The present study provides the first quantitative data for numerous species of Carcharhiniformes in south-eastern Queensland and demonstrates that analysis of catch-rate data can improve our understanding of how larger sharks partition resources. © CSIRO 2011.
PubMed | AgriScience Queensland and Formerly AgriScience Queensland
Type: Journal Article | Journal: Veterinary parasitology | Year: 2013
The in vivo faecal egg count reduction test (FECRT) is the most commonly used test to detect anthelmintic resistance (AR) in gastrointestinal nematodes (GIN) of ruminants in pasture based systems. However, there are several variations on the method, some more appropriate than others in specific circumstances. While in some cases labour and time can be saved by just collecting post-drench faecal worm egg counts (FEC) of treatment groups with controls, or pre- and post-drench FEC of a treatment group with no controls, there are circumstances when pre- and post-drench FEC of an untreated control group as well as from the treatment groups are necessary. Computer simulation techniques were used to determine the most appropriate of several methods for calculating AR when there is continuing larval development during the testing period, as often occurs when anthelmintic treatments against genera of GIN with high biotic potential or high re-infection rates, such as Haemonchus contortus of sheep and Cooperia punctata of cattle, are less than 100% efficacious. Three field FECRT experimental designs were investigated: (I) post-drench FEC of treatment and controls groups, (II) pre- and post-drench FEC of a treatment group only and (III) pre- and post-drench FEC of treatment and control groups. To investigate the performance of methods of indicating AR for each of these designs, simulated animal FEC were generated from negative binominal distributions with subsequent sampling from the binomial distributions to account for drench effect, with varying parameters for worm burden, larval development and drench resistance. Calculations of percent reductions and confidence limits were based on those of the Standing Committee for Agriculture (SCA) guidelines. For the two field methods with pre-drench FEC, confidence limits were also determined from cumulative inverse Beta distributions of FEC, for eggs per gram (epg) and the number of eggs counted at detection levels of 50 and 25. Two rules for determining AR: (1) %reduction (%R)<95% and lower confidence limit <90%; and (2) upper confidence limit <95%, were also assessed. For each combination of worm burden, larval development and drench resistance parameters, 1000 simulations were run to determine the number of times the theoretical percent reduction fell within the estimated confidence limits and the number of times resistance would have been declared. When continuing larval development occurs during the testing period of the FECRT, the simulations showed AR should be calculated from pre- and post-drench worm egg counts of an untreated control group as well as from the treatment group. If the widely used resistance rule 1 is used to assess resistance, rule 2 should also be applied, especially when %R is in the range 90 to 95% and resistance is suspected.
Widana Gamage S.M.K.,University of Queensland |
McGrath D.J.,AgriScience Queensland |
Persley D.M.,AgriScience Queensland |
Dietzgen R.G.,University of Queensland
PLoS ONE | Year: 2016
Background: Capsicum chlorosis virus (CaCV) is an emerging pathogen of capsicum, tomato and peanut crops in Australia and South-East Asia. Commercial capsicum cultivars with CaCV resistance are not yet available, but CaCV resistance identified in Capsicum chinense is being introgressed into commercial Bell capsicum. However, our knowledge of the molecular mechanisms leading to the resistance response to CaCV infection is limited. Therefore, transcriptome and expression profiling data provide an important resource to better understand CaCV resistance mechanisms. Methodology/Principal Findings: We assembled capsicum transcriptomes and analysed gene expression using Illumina HiSeq platform combined with a tag-based digital gene expression system. Total RNA extracted from CaCV/mock inoculated CaCV resistant (R) and susceptible (S) capsicum at the time point when R line showed a strong hypersensitive response to CaCV infection was used in transcriptome assembly. Gene expression profiles of R and S capsicum in CaCV- and buffer-inoculated conditions were compared. None of the genes were differentially expressed (DE) between R and S cultivars when mock-inoculated, while 2484 genes were DE when inoculated with CaCV. Functional classification revealed that the most highly up-regulated DE genes in R capsicum included pathogenesis-related genes, cell death-associated genes, genes associated with hormone-mediated signalling pathways and genes encoding enzymes involved in synthesis of defense-related secondary metabolites. We selected 15 genes to confirm DE expression levels by real-time quantitative PCR. Conclusion/Significance: DE transcript profiling data provided comprehensive gene expression information to gain an understanding of the underlying CaCV resistance mechanisms. Further, we identified candidate CaCV resistance genes in the CaCV-resistant C. annuum x C. chinense breeding line. This knowledge will be useful in future for fine mapping of the CaCV resistance locus and potential genetic engineering of resistance into CaCV-susceptible crops. © 2016 Widana Gamage et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Etebari K.,University of Queensland |
Palfreyman R.W.,University of Queensland |
Schlipalius D.,AgriScience Queensland |
Nielsen L.K.,University of Queensland |
And 2 more authors.
BMC Genomics | Year: 2011
Background: Parasitoid insects manipulate their hosts' physiology by injecting various factors into their host upon parasitization. Transcriptomic approaches provide a powerful approach to study insect host-parasitoid interactions at the molecular level. In order to investigate the effects of parasitization by an ichneumonid wasp (Diadegma semiclausum) on the host (Plutella xylostella), the larval transcriptome profile was analyzed using a short-read deep sequencing method (Illumina). Symbiotic polydnaviruses (PDVs) associated with ichneumonid parasitoids, known as ichnoviruses, play significant roles in host immune suppression and developmental regulation. In the current study, D. semiclausum ichnovirus (DsIV) genes expressed in P. xylostella were identified and their sequences compared with other reported PDVs. Five of these genes encode proteins of unknown identity, that have not previously been reported.Results: De novo assembly of cDNA sequence data generated 172,660 contigs between 100 and 10000 bp in length; with 35% of > 200 bp in length. Parasitization had significant impacts on expression levels of 928 identified insect host transcripts. Gene ontology data illustrated that the majority of the differentially expressed genes are involved in binding, catalytic activity, and metabolic and cellular processes. In addition, the results show that transcription levels of antimicrobial peptides, such as gloverin, cecropin E and lysozyme, were up-regulated after parasitism. Expression of ichnovirus genes were detected in parasitized larvae with 19 unique sequences identified from five PDV gene families including vankyrin, viral innexin, repeat elements, a cysteine-rich motif, and polar residue rich protein. Vankyrin 1 and repeat element 1 genes showed the highest transcription levels among the DsIV genes.Conclusion: This study provides detailed information on differential expression of P. xylostella larval genes following parasitization, DsIV genes expressed in the host and also improves our current understanding of this host-parasitoid interaction. © 2011 Etebari et al; licensee BioMed Central Ltd.
Redding M.R.,AgriScience Queensland |
Lewis R.,AgriScience Queensland |
Kearton T.,AgriScience Queensland |
Smith O.,AgriScience Queensland
Science of the Total Environment | Year: 2016
The key to better nutrient efficiency is to simultaneously improve uptake and decrease losses. This study sought to achieve this balance using sorbent additions and manure nutrients (spent poultry litter; SL) compared with results obtained using conventional sources (Conv; urea nitrogen, N; and phosphate–phosphorus; P). Two experiments were conducted. Firstly, a phosphorus pot trial involving two soils (sandy and clay) based on a factorial design (Digitaria eriantha/Pennisetum clandestinum). Subsequently, a factorial N and P field trial was conducted on the clay soil (D. eriantha/Lolium rigidum). In the pot trial, sorbent additions (26.2 g of hydrotalcite [HT] g P− 1) to the Conv treatment deferred P availability (both soils) as did SL in the sandy soil. In this soil, P delivery by the Conv treatments declined rapidly, and began to fall behind the HT and SL treatments. Addition of HT increased post-trial Colwell P. In the field trial low HT-rates (3.75 and 7.5 g of HT g P− 1) plus bentonite, allowed dry matter production and nutrient uptake to match that of Conv treatments, and increased residual mineral-N. The SL treatments performed similarly to (or better than) Conv treatments regarding nutrient uptake. With successive application, HT forms may provide better supply profiles than Conv treatments. Our findings, combined with previous studies, suggest it is possible to use manures and ion-exchangers to match conventional N and P source productivity with lower risk of nutrient losses. © 2016
Redding M.R.,AgriScience Queensland
Applied Clay Science | Year: 2011
Manure by-products of intensive livestock industries, such as spent poultry litter are a considerable nutrient resource. This study sought to improve the environmental characteristics of spent poultry litter, through the addition of hydrotalcite and bentonite, to decrease likely nutrient losses to the environment. Three experiments were conducted. An incubation trial sought to identify the effect of bentonite addition (0 to 158%. m/m of dry spent-litter mass) on exchangeable retention of ammonium-N in poultry litter. A column leaching trial (33 pore volumes over 11. days) sought to determine the effect of varied hydrotalcite additions (0 to 50%. m/m) and a fixed rate of bentonite (127%. m/m) on phosphorus release. Rainfall simulations were conducted on turf-applied spent poultry litter to determine the effect of alum (0 to 11%. m/m), bentonite (0 to 158%. m/m), and hydrotalcite (0 to 50%. m/m) addition on overland losses of phosphorus. The addition of bentonite (0 to 158%) increased the proportion of mineral N retained in exchangeable form from 19% to as much as 54%. The additions of hydrotalcite at 30% of the mass of dried litter resulted in 90% decreases in the quantity of phosphorus leached. However, under rainfall simulation, the 10% hydrotalcite addition combined with bentonite (127%) was sufficient to effectively eliminate run-off phosphorus losses that occurred with untreated spent litter. The combination of hydrotalcite (10%) and bentonite appeared to exceed the performance of conventional rates (2 to 11%. m/m) of alum addition. Only a small proportion of the decrease in phosphorus losses was attributable to bentonite addition. © 2011.
PubMed | University of Queensland and AgriScience Queensland
Type: Journal Article | Journal: PloS one | Year: 2016
Capsicum chlorosis virus (CaCV) is an emerging pathogen of capsicum, tomato and peanut crops in Australia and South-East Asia. Commercial capsicum cultivars with CaCV resistance are not yet available, but CaCV resistance identified in Capsicum chinense is being introgressed into commercial Bell capsicum. However, our knowledge of the molecular mechanisms leading to the resistance response to CaCV infection is limited. Therefore, transcriptome and expression profiling data provide an important resource to better understand CaCV resistance mechanisms.We assembled capsicum transcriptomes and analysed gene expression using Illumina HiSeq platform combined with a tag-based digital gene expression system. Total RNA extracted from CaCV/mock inoculated CaCV resistant (R) and susceptible (S) capsicum at the time point when R line showed a strong hypersensitive response to CaCV infection was used in transcriptome assembly. Gene expression profiles of R and S capsicum in CaCV- and buffer-inoculated conditions were compared. None of the genes were differentially expressed (DE) between R and S cultivars when mock-inoculated, while 2484 genes were DE when inoculated with CaCV. Functional classification revealed that the most highly up-regulated DE genes in R capsicum included pathogenesis-related genes, cell death-associated genes, genes associated with hormone-mediated signalling pathways and genes encoding enzymes involved in synthesis of defense-related secondary metabolites. We selected 15 genes to confirm DE expression levels by real-time quantitative PCR.DE transcript profiling data provided comprehensive gene expression information to gain an understanding of the underlying CaCV resistance mechanisms. Further, we identified candidate CaCV resistance genes in the CaCV-resistant C. annuum x C. chinense breeding line. This knowledge will be useful in future for fine mapping of the CaCV resistance locus and potential genetic engineering of resistance into CaCV-susceptible crops.