Correlation of plasma IGF-I concentrations and growth rate in aquacultured finfish: a tool for assessing the potential of new diets

A recently developed radioimmunoassay (RIA) for measuring insulin-like growth factor (IGF-I) in a variety of fish species was used to investigate the correlation between growth rate and circulating IGF-I concentrations of barramundi (Lates calcarifer), Atlantic salmon (Salmo salar) and Southern Bluefin tuna (Thunnus maccoyii). Plasma IGF-I concentration significantly increased with increasing ration size in barramundi and IGF-I concentration was positively correlated to growth rates obtained in Atlantic salmon (r2=0.67) and barramundi (r2=0.65) when fed a variety of diet formulations. IGF-I was also positively correlated to protein concentration (r2=0.59). This evidence suggested that measuring IGF-I concentration may provide a useful tool for monitoring fish growth rate and also as a method to rapidly assess different aquaculture diets. However, no such correlation was demonstrated in the tuna study probably due to seasonal cooling of sea surface temperature shortly before blood was sampled. Thus, some recommendations for the design and sampling strategy of nutritional trials where IGF-I concentrations are measured are discussed

Pasteurella multocida detection by 5' Taq nuclease assay: a new tool for use in diagnosing fowl cholera

A 5′ Taq nuclease assay utilising minor groove binder technology and targeting the 16S rRNA gene was designed to detect Pasteurella multocida (the causative agent of fowl cholera) in swabs collected from poultry. The assay was first evaluated using pure cultures. The assay correctly identified four P. multocida taxonomic type strains, 18 P. multocida serovar reference strains and 40 Australian field isolates (17 from poultry, 11 from pigs and 12 from cattle). Representatives of nine other Pasteurella species, 26 other bacterial species (18 being members of the family Pasteurellaceae) and four poultry virus isolates did not react in the assay. The assay detected a minimum of approximately 10 cfu of P. multocida per reaction. Of 79 poultry swabs submitted to the laboratory for routine bacteriological culture, 17 were positive in the 5′ Taq nuclease assay, but only 10 were positive by culture. The other 62 swabs were negative for P. multocida by both 5′ Taq nuclease assay and culture. The assay is suitable for use in diagnosing fowl cholera, is more rapid than bacteriological culture, and may also have application in diagnosing P. multocida infections in cattle and pigs.

Incorporating dugong habitats into the marine protected area design for the Great Barrier Reef Marine Park, Queensland, Australia.

Dugong habitats were considered in the design for the new zoning network for the Great Barrier Reef Marine Park as part of the Representative Areas Program. One of the specific design guidelines developed as part of the biophysical operational principles recommended that 50% of all high priority dugong habitats should be incorporated in the network of no-take areas. The high priority dugong habitat incorporated in no-take protection increased from 1396 to 3476 km2 (or 16.9-42.0% of all identified sites). Although this increase in protection fell short of the recommended 50%, overall the level of protection afforded by the Great Barrier Reef Marine Park Zoning Plan 2003 increased for all the locations identified.

Near infrared spectroscopy as a rapid tool to measure volatile aroma compounds in Riesling wine: Possibilities and limits

Volatile chemical compounds responsible for the aroma of wine are derived from a number of different biochemical and chemical pathways. These chemical compounds are formed during grape berry metabolism, crushing of the berries, fermentation processes (i.e. yeast and malolactic bacteria) and also from the ageing and storage of wine. Not surprisingly, there are a large number of chemical classes of compounds found in wine which are present at varying concentrations (ng L-1 to mg L-1), exhibit differing potencies, and have a broad range of volatilities and boiling points. The aim of this work was to investigate the potential use of near infrared (NIR) spectroscopy combined with chemometrics as a rapid and low-cost technique to measure volatile compounds in Riesling wines. Samples of commercial Riesling wine were analyzed using an NIR instrument and volatile compounds by gas chromatography (GC) coupled with selected ion monitoring mass spectrometry. Correlation between the NIR and GC data were developed using partial least-squares (PLS) regression with full cross validation (leave one out). Coefficients of determination in cross validation (R 2) and the standard error in cross validation (SECV) were 0.74 (SECV: 313.6 μg L−1) for esters, 0.90 (SECV: 20.9 μg L−1) for monoterpenes and 0.80 (SECV: 1658 ?g L-1) for short-chain fatty acids. This study has shown that volatile chemical compounds present in wine can be measured by NIR spectroscopy. Further development with larger data sets will be required to test the predictive ability of the NIR calibration models developed.

Melaleuca densispicata in Currawinya National Park, South-West Queensland: Ecology and preliminary implications for management of a rare plant species

Melaleuca densispicata Byrnes is an uncommon species with a limited distribution, comprising disjunct populations in inland southern Queensland and northern New South Wales, Australia. It is a dense, woody shrub, 2–4 m in height, which exhibits a marked 'clumping' growth habit. It has thick, papery bark and displays many white flowers during spring or early summer. Although it has long been known to exist, M. densispicata was only formally described in 1984, and very little is currently known about its ecology or specific management requirements. There are only seven known subpopulations of the species across its range. A major population at the western limit of its distribution occurs on Currawinya National Park (28°52'S, 144°30'E). Here, it is locally abundant and listed as a noteworthy plant species under the Management Plan (Queensland Parks & Wildlife Service 2001). This study aimed to identify patterns in the distribution of M. densispicata in Currawinya National Park, describe its ecological niche and role, and provide management recommendations for the species within the study area. Recent anecdotal observations of recruitment failure in south-western Queensland (Peter McRae, QPWS, October 2004, pers. comm.; Dick O'Connell, local grazier, July 2005 pers. comm.) caused additional emphasis to be placed on the examination of recruitment and recruitment factors.

Rapid and sensitive detection of Avibacterium paragallinarum in the presence of other bacteria using a 5' Taq nuclease assay: A new tool for diagnosing infectious coryza

A 5' Taq nuclease assay specific for Avibacterium paragallinarum was designed and optimized for use in diagnosing infectious coryza. The region chosen for assay design was one of known specificity for Av. paragallinarum. The assay detected Av. paragallinarum reference strains representing the three Page and the eight Kume serovars, and field isolates from diverse geographical locations. No cross-reactions were observed with other Avibacterium species, with other bacteria taxonomically related to Av. paragallinarum nor with bacteria and viruses likely to be present in swabs collected from suspected infectious coryza cases. The detection limit for the assay was 6 to 60 colony-forming units per reaction. Twenty-two out of 53 swabs collected from sick birds reacted in the 5' Taq nuclease assay, whereas Av. paragallinarum was not isolated from any of the swabs. All of the 22 swabs yielded other bacteria in culture. The presence of Av. paragallinarum in the swabs was also demonstrated by sequencing, thereby confirming the ability of the assay to detect Av. paragallinarum in the presence of other bacteria. The ability to quantify bacterial load in the swabs using the 5' Taq nuclease assay was demonstrated.

An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles

Based on morphological features alone, there is considerable difficulty in identifying the 5 most economically damaging weed species of Sporobolus [viz. S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur and Schinz, S. fertilis (Steud.) Clayton, S. africanus (Poir.) Robyns and Tourney, and S. jacquemontii Kunth.] found in Australia. A polymerase chain reaction (PCR)-based random amplified polymorphic DNA (RAPD) technique was used to create a series of genetic markers that could positively identify the 5 major weeds from the other less damaging weedy and native Sporobolus species. In the initial RAPD profiling experiment, using arbitrarily selected primers and involving 12 species of Sporobolus, 12 genetic markers were found that, when used in combination, could consistently identify the 5 weedy species from all others. Of these 12 markers, the most diagnostic were UBC51490 for S. pyramidalis and S. natalensis; UBC43310.2000.2100 for S. fertilis and S. africanus; and ORA20850 and UBC43470 for S. jacquemontii. Species-specific markers could be found only for S. jacquemontii. In an effort to understand why there was difficulty in obtaining species-specific markers for some of the weedy species, a RAPD data matrix was created using 40 RAPD products. These 40 products amplified by 6 random primers from 45 individuals belonging to 12 species, were then subjected to numerical taxonomy and multivariate system (NTSYS pc version 1.70) analysis. The RAPD similarity matrix generated from the analysis indicated that S. pyramidalis was genetically more similar to S. natalensis than to other species of the 'S. indicus complex'. Similarly, S. jacquemontii was more similar to S. pyramidalis, and S. fertilis was more similar to S. africanus than to other species of the complex. Sporobolus pyramidalis, S. jacquemontii, S. africanus, and S. creber exhibited a low within-species genetic diversity, whereas high genetic diversity was observed within S. natalensis, S. fertilis, S. sessilis, S. elongates, and S. laxus. Cluster analysis placed all of the introduced species (major and minor weedy species) into one major cluster, with S. pyramidalis and S. natalensis in one distinct subcluster and S. fertilis and S. africanus in another. The native species formed separate clusters in the phenograms. The close genetic similarity of S. pyramidalis to S. natalensis, and S. fertilis to S. africanus may explain the difficulty in obtaining RAPD species-specific markers. The importance of these results will be within the Australian dairy and beef industries and will aid in the development of integrated management strategy for these weeds.

Controlled exposure as a management tool for Glasser's disease.

In this study, nasal swabs taken from multiparous sows at weaning time or from sick pigs displaying symptoms of Glasser's disease from farms in Australia [date not given] were cultured and analysed by polymerase chain reaction (PCR). Within each genotype detected on a farm, representative isolates were serotyped by gel diffusion (GD) testing or indirect haemagglutination (IHA) test. Isolates which did not react in any of the tests were regarded as non-typable and were termed serovar NT. Serovars 1, 5, 12, 13 and 14 were classified as highly pathogenic; serovars 2, 4 and 15 being moderately pathogenic; serovar 8 being slightly pathogenic and serovars 3, 6, 7, 9 and 11 being non-pathogenic. Sows were inoculated with the strain of Haemophilus parasuis (serovars 4, 6 and 9 from Farms 1, 2 and 4, respectively) used for controlled challenge 3 and 5 weeks before farrowing. Before farrowing the sows were divided into control and treatment groups. Five to seven days after birth, the piglets of the treatment group were challenged with a strain from the farm which had were used to vaccinate the sows. The effectiveness of the controlled exposure was evaluated by number of piglets displaying clinical signs possibly related to infection, number of antibiotic treatments and pig mortality. Nasal swabs of sick pigs were taken twice a week to find a correlation to infection. A subsample of pigs was weighed after leaving the weaning sheds. The specificity of a realtime PCR amplifying the infB gene was evaluated with 68 H. parasuis isolates and 36 strains of closely related species. 239 samples of DNA from tissues and fluids of 16 experimentally challenged animals were also tested with the realtime PCR, and the results compared with culture and a conventional PCR. The farm experiments showed that none of the controlled challenge pigs showed any signs of illness due to Glasser's disease, although the treatment groups required more antibiotics than the controls. A total of 556 H. parasuis isolates were genotyped, while 150 isolates were serotyped. H. parasuis was detected on 19 of 20 farms, including 2 farms with an extensive history of freedom from Glasser's disease. Isolates belonging to serovars regarded as potentially pathogenic were obtained from healthy pigs at weaning on 8 of the 10 farms with a history of Glasser's disease outbreaks. Sampling 213 sick pigs yielded 115 isolates, 99 of which belonged to serovars that were either potentially pathogenic or of unknown pathogenicity. Only 16 isolates from these sick pigs were of a serovar known to be non-pathogenic. Healthy pigs also had H. parasuis, even on farms free of Glasser's disease. The realtime PCR gave positive results for all 68 H. parasuis isolates and negative results for all 36 non-target bacteria. When used on the clinical material from experimental infections, the realtime PCR produced significantly more positive results than the conventional PCR (165 compared to 86).

WHIPPET: a novel tool for prioritizing invasive plant populations for regional eradication

Large geographic areas can have numerous incipient invasive plant populations that necessitate eradication. However, resources are often deficient to address every infestation. Within the United States, weed lists (either state-level or smaller unit) generally guide the prioritization of eradication of each listed species uniformly across the focus region. This strategy has several limitations that can compromise overall effectiveness, which include spending limited resources on 1) low impact populations, 2) difficult to access populations, or 3) missing high impact populations of low priority species. Therefore, we developed a novel science-based, transparent, analytical ranking tool to prioritize weed populations, instead of species, for eradication and tested it on a group of noxious weeds in California. For outreach purposes, we named the tool WHIPPET (Weed Heuristics: Invasive Population Prioritization for Eradication Tool). Using the Analytic Hierarchy Process that included expert opinion, we developed three major criteria, four sub-criteria, and four sub-sub-criteria, taking into account both species and population characteristics. Subject matter experts weighted and scored these criteria to assess the relative impact, potential spread, and feasibility of eradication (major criteria) for 100 total populations of 19 species. Species-wide population scores indicated that conspecific populations do not necessarily group together in the final ranked output. Thus, priority lists based solely on species-level characteristics are less effective compared to a blended prioritization based on both species attributes and individual population and site parameters. WHIPPET should facilitate a more efficacious decision-making process allocating limited resources to target invasive plant infestations with the greatest predicted impacts to the region under consideration.

Near infrared spectroscopy as a rapid non-invasive tool for agricultural and industrial process management with special reference to avocado and sandalwood industries

Near infrared spectroscopy (NIRS) can play a vital role as a cost effective, rapid, non-invasive, reproducible diagnostic tool for many environmental management, agricultural and industrial waste water monitoring applications. In this paper we highlight the ability of NIRS technology to be used as a diagnostic tool in agricultural and environmental applications through the successful assessment of Fourier Transform NIRS to predict α santalol in sandalwood chip samples, and maturity of ‘Hass’ avocado fruit based on dry matter content. Presented at the Third International Conference on Challenges in Environmental Science & Engineering, CESE-2010. 26 September – 1 October 2010, The Sebel, Cairns, Queensland, Australia.

Stock structure of exploited shark species in north-eastern Australia

The project has provided management and other stakeholders with information necessary to make informed decisions about the management of four of the key exploited shark species caught in the Queensland inshore net fishery and northern New South Wales line fishery. The project has determined that spatial management of milk sharks within Queensland, and scalloped hammerhead, common black tip and Australian black tip sharks within Queensland and New South Wales is appropriate. The project has determined that both black tip shark species are likely to require co-operative management arrangements between Queensland and New South Wales. For scalloped hammerheads separate stocks between the two jurisdictions were identified from the fisheriesdependent samples, however genetic exchange across borders is likely to be facilitated by movement of adult females and perhaps larger males to a lesser extent. This information will greatly assist compliance with the Commonwealth Environment Protection and Biodiversity Conservation Act (1999) for shark fisheries in north-eastern Australia by providing the necessary basis for robust assessment of the status of stocks of the study species, thereby helping to deliver their sustainable harvest. It also helps to achieve objectives of the Australian National Shark Plan. The project provides the appropriate spatial framework for future monitoring and assessment of the study species. This is at a time when shark fisheries are receiving close attention from all sectors and when monitoring programs are being implemented, aimed at better assessment of stock status. This project has provided the crucial information for developing an appropriate monitoring design as well as the necessary basis for making statements about stock status. The project has addressed research priorities identified by the Queensland Fisheries Research Advisory Board, Great Barrier Reef Marine Park Authority and Queensland Fisheries. Previously management has assumed a single stock for each species on the east coast of Queensland, and management of shark fisheries in New South Wales (NSW) and Queensland has been independent of one another. The project has been able to enhance and develop links between research, management and industry. Strong positive relationships with commercial fishers were crucial in the collection of samples throughout the study area and fisheries managers were part of the project team throughout the study period. During the project the study area was extended to include both Queensland and NSW waters, creating mutualistic and positive links between the States’ research and management agencies. Extension of project results included management representatives from NSW and Queensland, as well as the Northern Territory where similar shark fisheries operate and similar species are targeted. The project was able to provide significant human capital development opportunities providing considerable value to the project outcomes. Use of vertebral microchemistry and life history characteristics as stock determination methods provided material for two PhD students based at James Cook University: Ron Schroeder, vertebral chemistry; and Alastair Harry, life history characteristic. The project has developed novel research methods that have great capacity for future application, including: • Development of a simple and rapid genetic diagnostic tool (RT-HRM-PCR assay) for differentiating among the black tip shark species, for which no simple morphological identifier exists; and • Development of laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) methods for analysing and interpreting microchemical composition of shark vertebrae. The study has provided further confirmation of the effectiveness of using a holistic approach in stock structure studies and justifies investment into such studies.

Controlled exposure as a management tool for Glassers disease

Control of bacterial disease of pigs.

Variety quality management in strawberry, using DNA genotyping as a tool

Quality management strawberry, DNA genotyping.

Remote Sensing - based precision agriculture tool for the sugar industry

The project will produce practical and relevant benchmarks, protocols and recommendations for the adoption of remote sensing technologies for improved in season management and therefore production within the Australian sugar cane industry.

Development and adoption of a web-based irrigation management tool for improved water use efficiency

Develop a web-based tool to assist farmers and consultants make strategic and tactical irrigation decisions.