Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East

Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.

An improved real-time PCR assay for the detection of Old World screwworm flies

The Old World screwworm (OWS) fly, Chrysomya bezziana, is a serious pest of livestock, wildlife and humans in tropical Africa, parts of the Middle East, the Indian subcontinent, south-east Asia and Papua New Guinea. Although to date Australia remains free of OWS flies, an incursion would have serious economic and animal welfare implications. For these reasons Australia has an OWS fly preparedness plan including OWS fly surveillance with fly traps. The recent development of an improved OWS fly trap and synthetic attractant and a specific and sensitive real-time PCR molecular assay for the detection of OWS flies in trap catches has improved Australia's OWS fly surveillance capabilities. Because all Australian trap samples gave negative results in the PCR assay, it was deemed necessary to include a positive control mechanism to ensure that fly DNA was being successfully extracted and amplified and to guard against false negative results. A new non-competitive internal amplification control (IAC) has been developed that can be used in conjunction with the OWS fly PCR assay in a multiplexed single-tube reaction. The multiplexed assay provides an indicator of the performance of DNA extraction and amplification without greatly increasing labour or reagent costs. The fly IAC targets a region of the ribosomal 16S mitochondrial DNA which is conserved across at least six genera of commonly trapped flies. Compared to the OWS fly assay alone, the multiplexed OWS fly and fly IAC assay displayed no loss in sensitivity or specificity for OWS fly detection. The multiplexed OWS fly and fly IAC assay provides greater confidence for trap catch samples returning negative OWS fly results. © 2014 International Atomic Energy Agency.

Panel of real-time PCRs for the multiplexed detection of two tomato-infecting begomoviruses and their cognate whitefly vector species

A new approach for the simultaneous identification of the viruses and vectors responsible for tomato yellow leaf curl disease (TYLCD) epidemics is presented. A panel of quantitative multiplexed real-time PCR assays was developed for the sensitive and reliable detection of Tomato yellow leaf curl virus-Israel (TYLCV-IL), Tomato leaf curl virus (ToLCV), Bemisia tabaci Middle East Asia Minor 1 species (MEAM1, B biotype) and B.tabaci Mediterranean species (MED, Q biotype) from either plant or whitefly samples. For quality-assurance purposes, two internal control assays were included in the assay panel for the co-amplification of solanaceous plant DNA or B.tabaci DNA. All assays were shown to be specific and reproducible. The multiplexed assays were able to reliably detect as few as 10 plasmid copies of TYLCV-IL, 100 plasmid copies of ToLCV, 500fg B.tabaci MEAM1 and 300fg B.tabaci MED DNA. Evaluated methods for routine testing of field-collected whiteflies are presented, including protocols for processing B.tabaci captured on yellow sticky traps and for bulking of multiple B.tabaci individuals prior to DNA extraction. This work assembles all of the essential features of a validated and quality-assured diagnostic method for the identification and discrimination of tomato-infecting begomovirus and B.tabaci vector species in Australia. This flexible panel of assays will facilitate improved quarantine, biosecurity and disease-management programmes both in Australia and worldwide.

An Investigation of Environmental Conditions Experienced During the Life of High Value Wood Components and Products

Australian forest industries have a long history of export trade of a wide range of products from woodchips(for paper manufacturing), sandalwood (essential oils, carving and incense) to high value musical instruments, flooring and outdoor furniture. For the high value group, fluctuating environmental conditions brought on by changes in mperature and relative humidity, can lead to performance problems due to consequential swelling, shrinkage and/or distortion of the wood elements. A survey determined the types of value-added products exported, including species and dimensions packaging used and export markets. Data loggers were installed with shipments to monitor temperature and relative humidity conditions. These data were converted to timber equilibrium moisture content values to provide an indication of the environment that the wood elements would be acclimatising to. The results of the initial survey indicated that primary high value wood export products included guitars, flooring, decking and outdoor furniture. The destination markets were mainly located in the northern hemisphere, particularly the United States of America, China, Hong Kong, Europe including the United Kingdom), Japan, Korea and the Middle East. Other regions importing Australian-made wooden articles were south-east Asia, New Zealand and South Africa. Different timber species have differing rates of swelling and shrinkage, so the types of timber were also recorded during the survey. Results from this work determined that the major species were ash-type eucalypts from south-eastern Australia (commonly referred to in the market as Tasmanian oak), jarrah from Western Australia, spotted gum, hoop pine, white cypress, black butt, brush box and Sydney blue gum from Queensland and New South Wales. The environmental conditions data indicated that microclimates in shipping containers can fluctuate extensively during shipping. Conditions at the time of manufacturing were usually between 10 and 12% equilibrium moisture content, however conditions during shipping could range from 5 (very dry) to 20% (very humid). The packaging systems incorporated were reported to be efficient at protecting the wooden articles from damage during transit. The research highlighted the potential risk for wood components to ‘move’ in response to periods of drier or more humid conditions than those at the time of manufacturing, and the importance of engineering a packaging system that can account for the environmental conditions experienced in shipping containers. Examples of potential dimensional changes in wooden components were calculated based on published unit shrinkage data for key species and the climatic data returned from the logging equipment. The information highlighted the importance of good design to account for possible timber movement during shipping. A timber movement calculator was developed to allow designers to input component species, dimensions, site of manufacture and destination, to see validate their product design. This calculator forms part of the free interactive website www.timbers.com.au.

An investigation of environmental conditions experienced during the life of high-value wood components and products

Australian forest industries have a long history of export trade of a wide range of products from woodchips (for paper manufacturing), sandalwood (essential oils, carving and incense) to high value musical instruments, flooring and outdoor furniture. For the high value group, fluctuating environmental conditions brought on by changes in temperature and relative humidity, can lead to performance problems due to consequential swelling, shrinkage and/or distortion of the wood elements. A survey determined the types of value-added products exported, including species and dimensions packaging used and export markets. Data loggers were installed with shipments to monitor temperature and relative humidity conditions. These data were converted to timber equilibrium moisture content values to provide an indication of the environment that the wood elements would be acclimatising to. The results of the initial survey indicated that primary high value wood export products included guitars, flooring, decking and outdoor furniture. The destination markets were mainly located in the northern hemisphere, particularly the United States of America, China, Hong Kong, Europe (including the United Kingdom), Japan, Korea and the Middle East. Other regions importing Australian-made wooden articles were south-east Asia, New Zealand and South Africa. Different timber species have differing rates of swelling and shrinkage, so the types of timber were also recorded during the survey. Results from this work determined that the major species were ash-type eucalypts from south-eastern Australia (commonly referred to in the market as Tasmanian oak), jarrah from Western Australia, spotted gum, hoop pine, white cypress, black butt, brush box and Sydney blue gum from Queensland and New South Wales. The environmental conditions data indicated that microclimates in shipping containers can fluctuate extensively during shipping. Conditions at the time of manufacturing were usually between 10 and 12% equilibrium moisture content, however conditions during shipping could range from 5 (very dry) to 20% (very humid). The packaging systems incorporated were reported to be efficient at protecting the wooden articles from damage during transit. The research highlighted the potential risk for wood components to ‘move’ in response to periods of drier or more humid conditions than those at the time of manufacturing, and the importance of engineering a packaging system that can account for the environmental conditions experienced in shipping containers. Examples of potential dimensional changes in wooden components were calculated based on published unit shrinkage data for key species and the climatic data returned from the logging equipment. The information highlighted the importance of good design to account for possible timber movement during shipping. A timber movement calculator was developed to allow designers to input component species, dimensions, site of manufacture and destination, to see validate their product design.

The physiological and behavioral responses of steers to gaseous ammonia in simulated long distance transport by ship.

Ammonia (NH3) can accumulate in high density cattle accommodation during live export shipments and could potentially threaten the animals' health and welfare. The effects of 4 NH3 concentrations, control (<8), 15, 30, and 45 ppm, on the physiology and behavior of steers were recorded. The animals were held for 12 d under a micro-climate and stocking density similar to shipboard conditions experienced on voyages from Australia to the Middle East during the northern hemispheric summer. In bronchoalveolar lavage samples, ammonia increased (P < 0.05) macrophage activity in proportion to NH3 concentration and it increased (P < 0.05) neutrophil percentage at 30 and 45 ppm, indicating active pulmonary inflammation. It also increased (P < 0.05) lacrimation, nasal secretions and coughing, particularly at 45 ppm, indicating that the NH3 was irritating the mucous membranes of the eyes, nasal cavity and respiratory tract. Ammonia had no effect (P > 0.05) on hematological parameters or body weight. Twenty-eight days after exposure to NH3, the steers' pulmonary macrophage activity and neutrophil levels had returned to normal. It was concluded that ammonia concentrations of 30 and 45 ppm induced temporary inflammatory responses which indicate an adverse effect on the welfare of steers.

Genetic Options for nematode control

Root-lesion nematodes (Pratylenchus thornei and P. neglectus) cause severe economic loss in wheat in Australia. This project aims to develop adaptaed wheat lines with resistance and tolerance to both species. These lines will be made available to Australian wheat breeding companies for further crossing and development of resistant and tolerant wheat varieties. Sources of resistance will be synthetic hexaploid and landrace wheats from the Middle East. Suitable double haploid populations will be phenotyped for the development of molecular markers to resistance and tolerance genes. The value of resistance and tolerance will be extended to growers through collaboration in demonstration trials with NGA and ORANA and presentations at GRDC Updates.

Physiological and behavioral responses of sheep to gaseous ammonia

Ammonia can accumulate in highly stocked sheep accommodation, for example during live export shipments, and could affect sheep health and welfare. Thus, the objective of this experiment was to test the effects of 4 NH3 concentrations, 4 (control), 12, 21, and 34 mg/m(3), on the physiology and behavior of wether sheep. Sheep were held for 12 d under a micro-climate and stocking density similar to shipboard conditions recorded on voyages from Australia to the Middle East during the northern hemispheric summer. Ammonia increased macrophage activity in transtracheal aspirations, indicating active pulmonary infl ammation; however, it had no effect (P > 0.05) on hematological variables. Feed intake decreased (P = 0.002) in proportion to ammonia concentration, and BW gain decreased (P < 0.001) at the 2 greatest concentrations. Exposure to ammonia increased (P = 0.03) the frequency of sneezing, and at the greatest ammonia concentration, sheep were less active, with less locomotion, pawing, and panting. Twenty-eight days after exposure to NH3, the pulmonary macrophage activity and BW of the sheep returned to that of sheep exposed to only 4 mg/m(3). It was concluded that NH3 induced a temporary inflammatory response of the respiratory system and reduced BW gain, which together indicated a transitory adverse effect on the welfare of sheep.

Prospects for the classical biological control of Calotropis procera (Apocynaceae) using co-evolved insects

Calotropis procera (Apocynaceae), a native of tropical Africa, the Middle East and the Indian subcontinent, is a serious environmental and rangeland weed of Australia and Brazil. It is also a weed in Hawaii in USA, the Caribbean Islands, the Seychelles, Mexico, Thailand, Vietnam and many Pacific Islands. In the native range C. procera has many natural enemies, thus classical biological control could be the most cost-effective option for its long-term management. Based on field surveys in India and a literature search, some 65 species of insects and five species of mites have been documented on C. procera and another congeneric-invador C. gigantea in the native range. All the leaf-feeding and stem-boring agents recorded on Calotropis spp. have wide host range. Three pre-dispersal seed predators,the Aak weevil Paramecops farinosus and the Aak fruit fly Dacuspersicus in the Indian subcontinent, and the Sodom apple fruit fly Dacus longistylus in the Middle East have been identified as prospective biological control agents based on their field host range. In Australia and Brazil, where C. procera has the potential to spread across vast areas, pre-dispersal seed predators would help to limit the spread of the weed. While the fruits of C. procera vary in size and shape across its range, those from India are similar to the ones in Australia and Brazil. Hence, seed-feeding insects from India are more likely to be suitable due to adaptation to fruit size and morphology. Future survey efforts for potential biological control agents should focus on North Africa.

Assessing the sustainability of wheat-based cropping systems using simulation modelling: sustainability

Concepts of agricultural sustainability and possible roles of simulation modelling for characterising sustainability were explored by conducting, and reflecting on, a sustainability assessment of rain-fed wheat-based systems in the Middle East and North Africa region. We designed a goal-oriented, model-based framework using the cropping systems model Agricultural Production Systems sIMulator (APSIM). For the assessment, valid (rather than true or false) sustainability goals and indicators were identified for the target system. System-specific vagueness was depicted in sustainability polygons-a system property derived from highly quantitative data-and denoted using descriptive quantifiers. Diagnostic evaluations of alternative tillage practices demonstrated the utility of the framework to quantify key bio-physical and chemical constraints to sustainability. Here, we argue that sustainability is a vague, emergent system property of often wicked complexity that arises out of more fundamental elements and processes. A 'wicked concept of sustainability' acknowledges the breadth of the human experience of sustainability, which cannot be internalised in a model. To achieve socially desirable sustainability goals, our model-based approach can inform reflective evaluation processes that connect with the needs and values of agricultural decision-makers. Hence, it can help to frame meaningful discussions, from which actions might emerge.

Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination – a driving force in the emergence of new strains

In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.