Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing

The sequence diversity of viral populations within individual hosts is the starting material for selection and subsequent evolution of RNA viruses such as foot-and-mouth disease virus (FMDV). Using next-generation sequencing (NGS) performed on a Genome Analyzer platform (Illumina), this study compared the viral populations within two bovine epithelial samples (foot lesions) from a single animal with the Inoculum used to initiate experimental infection. Genomic sequences were determined in duplicate sequencing runs, and the consensus sequence determined by NGS, for the Inoculum, was identical to that previously determined using the Sanger method. However, NGS reveals the fine polymorphic sub-structure of the viral population, from nucleotide variants present at just below 50% frequency to those present at fractions of 1%. Some of the higher frequency polymorphisms identified encoded changes within codons associated with heparan sulphate binding and were present in both feet lesions revealing intermediate stages in the evolution of a tissue-culture adapted virus replicating within a mammalian host. We identified 2,622, 1,434 and 1,703 polymorphisms in the Inoculum, and in the two foot lesions respectively: most of the substitutions occurred only in a small fraction of the population and represent the progeny from recent cellular replication prior to onset of any selective pressures. We estimated an upper limit for the genome-wide mutation rate of the virus within a cell to be 7.8 x 10-4 per nt. The greater depth of detection, achieved by NGS, demonstrates that this method is a powerful and valuable tool for the dissection of FMDV populations within-hosts

Project BRAHSS: behavioural response of Australian humpback whales to seismic surveys.

BRAHSS is a major project aimed at understanding how humpback whales respond to noise, particularly from seismic air gun arrays. It also aims to infer the longer term biological significance of the responses from the results and knowledge of normal behaviour. The aim is to provide the information that will allow seismic surveys to be conducted efficiently with minimal impact on whales. It also includes a study of the response to ramp-up in sound level. Ramp-up is widely used at the start of operations as a mitigation measure intended to cause whales to move away, but there is little information to show that it is effective. BRAHSS involves four experiments with migrating humpback whales off the east and west coasts of Australia with noise exposures ranging from a single air gun to a full seismic array. Two major experiments have been completed off the east coast, the second involving 70 scientists. Whale movements were tracked using theodolites on two high points ashore and behavioural observations were made from these points and from three small vessels and the source vessel. Vocalising whales were tracked underwater with an array of hydrophones. These and other moored acoustic receivers recorded the sound field at several points throughout the area. Tags (DTAGs) were attached to whales with suction caps for periods of several hours. Observations and measurements during the experiments include the wide range of variables likely to affect whale response and sufficient acoustic measurements to characterise the sound field throughout the area. The remaining two experiments will be conducted further off shore off the west coast in 2013 and 2014

Foot-and-Mouth Disease Virus Serotype A in Egypt

We describe the characterization of a foot-and-mouth disease (FMD) serotype A virus responsible for recent outbreaks of disease in Egypt. Phylogenetic analysis of VP1 nucleotide sequences demonstrated a close relationship to recent FMD virus isolates from East Africa, rather than to viruses currently circulating in the Middle East

Multiple Origins of Foot-and-Mouth Disease Virus Serotype Asia 1 Outbreaks, 2003–2007

Viruses in 6 genetic groups have caused recent outbreaks in Asia

Crop Updates 2000 - Oilseeds

This session covers seventeen papers from different authors: Introduction, Paul Carmody, Centre for Cropping Systems CANOLA AGRONOMY 2. Genotype, location and year influence the quality of canola grown across southern Australia, PingSi1, Rodney Mailer2, Nick Galwey1 and David Turner1, 1Plant Sciences, Faculty of Agriculture, The University of Western Australia, 2Agricultural Research Institute, New South Wales Agriculture 3. Development of Pioneer® Canola varieties for Australian market,Kevin Morthorpe, StephenAddenbrooke, Pioneer Hi-Bred Australia Pty Ltd 4. Canola, Erucic Acid, Markets and Agronomic Implications, Peter Nelson, The Grain Pool of Western Australia 5. The control of Capeweed in Clearfield Production System for Canola, Mike Jackson and ScottPaton, Cyanamid Agriculture Pty Ltd 6. Responsiveness of Canola to Soil Potassium Levels: How Low Do We Have To Go? Ross Brennan, Noeleen Edwards, Mike Bolland and Bill Bowden,Agriculture Western Australia 7. Adaption of Indian Mustard (Brassica juncea) in the Mediterranean Environment of South Western Australia, C.P. Gunasekera1, L.D. Martin1, G.H. Walton2 and K.H.M. Siddique2 1Muresk Institute of Agriculture, Curtin University of Technology, Northam, 2Agriculture Western Australia 8. Physiological Aspects of Drought Tolerance in Brassica napus and B.juncea, Sharon R. Niknam and David W. Turner, Plant Sciences, Faculty of Agriculture, The University of Western Australia 9. Cross resistance of chlorsulfuron-resistant wild radish to imidazolinones, Abul Hashem, Harmohinder Dhammu and David Bowran, Agriculture Western Australia 10. Canola Variety and PBR Update 2000, From The Canola Association of Western Australia 11. Development of a canola ideotype for the low rainfall areas of the western Australian wheat belt, Syed H. Zaheer, Nick W. Galwey and David W. Turner, Faculty of Agriculture, The University of Western Australia DISEASE MANAGEMENT 12. Evaluation of fungicides for the management of blackleg in canola, Ravjit Khangura and Martin J. Barbetti, Agriculture Western Australia 13. Impact-IFÒ: Intergral in the control of Blackleg, Peter Carlton, Trials Coordinator, Elders Limited 14. Forecasting aphid and virus risk in canola, Debbie Thackray, Jenny Hawkes and Roger Jones, Agriculture Western Australia and Centre for Legumes in Mediterranean Agriculture 15. Beet western yellow virus in canola: 1999 survey results, wild radish weed reservoir and suppression by insecticide, Roger Jones and Brenda Coutts, Agriculture Western Australia 16. Are canola crops resilient to damage by aphids and diamond back moths? Françoise Berlandier, Agriculture Western Australia ECONOMIC OUTLOOK 17. Outlook for prices and implications for rotations, Ross Kingwell1,2, Michael O’Connell1 and Simone Blennerhasset11Agriculture Western Australia 2University of Western Australi

Waves of endemic foot-and-mouth disease in eastern Africa suggest feasibility of proactive vaccination approaches

Livestock production in Africa is key to national economies, food security and rural livelihoods, and > 85% of livestock keepers live in extreme poverty. With poverty elimination central to the Sustainable Development Goals, livestock keepers are therefore critically important. Foot-and-mouth disease is a highly contagious livestock disease widespread in Africa that contributes to this poverty. Despite its US$2.3 billion impact, control of the disease is not prioritized: standard vaccination regimens are too costly, its impact on the poorest is underestimated, and its epidemiology is too weakly understood. Our integrated analysis in Tanzania shows that the disease is of high concern, reduces household budgets for human health, and has major impacts on milk production and draft power for crop production. Critically, foot-and-mouth disease outbreaks in cattle are driven by livestock-related factors with a pattern of changing serotype dominance over time. Contrary to findings in southern Africa, we find no evidence of frequent infection from wildlife, with outbreaks in cattle sweeping slowly across the region through a sequence of dominant serotypes. This regularity suggests that timely identification of the epidemic serotype could allow proactive vaccination ahead of the wave of infection, mitigating impacts, and our preliminary matching work has identified potential vaccine candidates. This strategy is more realistic than wildlife-livestock separation or conventional foot-and-mouth disease vaccination approaches. Overall, we provide strong evidence for the feasibility of coordinated foot-and-mouth disease control as part of livestock development policies in eastern Africa, and our integrated socioeconomic, epidemiological, laboratory and modelling approach provides a framework for the study of other disease systems

Genetic Characterization of Foot-and-Mouth Disease Viruses, Ethiopia, 1981–2007

Virus diversity indicates a virus reservoir in this country

A calcite reference material for LA-ICP-MS U-Pb geochronology

U-Pb dating of calcite is an emerging but rapidly growing field of application in geochronology with great potential to inform problems in landscape, basin and mountain belt evolution, through age determination of diagenetic cements, vein mineralisation and geological formations difficult to date otherwise. In this brief, we present isotope dilution U-Pb isotope measurements on a sample of calcite (WC-1) that has been and will continue to be used as a reference material for in-situ U-Pb Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) dating, and which is suitable to be distributed to the geochronological community. We present in-situ measurements using LA-ICP-MS to demonstrate the suitability of WC-1 for use as a U-Pb dating reference material, in spite of it not being isotopically homogeneous. The WC-1 calcite sample is 254.4 ± 6.4 Ma old, and comprised of 85 to 98% radiogenic lead. It presents a suitable reference material that can facilitate dating of calcite ranging in age from Precambrian to late Neogene age

The Warnie volcanic province : Jurassic intraplate volcanism in Central Australia

We wish to thank Santos Ltd. for providing us with the Snowball 3D seismic survey. In particular we wish to thank Jenni Clifford and Lance Holmes who provided helpful feedback and 2D seismic lines covering the Lambda 1, Orientos 2 and Warnie East 1 wells. We also wish to thank Beach Energy, in particular Rob Menpes, for the helpful discussions and feedback on the manuscript in addition to helping us with the analysis of the magnetic data. The work contained in this paper contains work conducted during a PhD study undertaken as part of the Natural Environment Research Council (NERC) Centre for Doctoral Training (CDT) in Oil & Gas [grant number NEM00578X/1] and is fully funded by NERC whose support is gratefully acknowledged. Lastly, the two anonymous reviews of the manuscript are thanked for their insightful and constructive comments that significantly improved the work presented.Peer reviewedPostprin