Molecular discrimination of Perna (Mollusca: Bivalvia) species using the polymerase chain reaction and species-specific mitochondrial primers

This work was prompted by the need to be able to identify the invasive mussel species, Perna viridis, in tropical Australian seas using techniques that do not rely solely on morphology. DNA-based molecular methods utilizing a polymerase chain reaction (PCR) approach were developed to distinguish unambiguously between the three species in the genus Perna. Target regions were portions of two mitochondrial genes, cox1 and nad4, and the intergenic spacer between these that occurs in at least two Perna species. Based on interspecific sequence comparisons of the nad4 gene, a conserved primer has been designed that can act as a forward primer in PCRs for any Perna species. Four reverse primers have also been designed, based on nad4 and intergenic spacer sequences, which yield species-specific products of different lengths when paired with the conserved forward primer. A further pair of primers has been designed that will amplify part of the cox1 gene of any Perna species, and possibly other molluscs, as a positive control to demonstrate that the PCR is working.

Salmonella and on-farm risk factors in healthy slaughter-age cattle and sheep in eastern Australia

To examine healthy slaughter-age cattle and sheep on-farm for the excretion of Salmonella serovars in faeces and to identify possible risk factors using a questionnaire. The study involved 215 herds and flocks in the four eastern states of Australia, 56 with prior history of salmonellosis. Production systems examined included pasture beef cattle, feedlot beef cattle, dairy cattle, prime lambs and mutton sheep and animals were all at slaughter age. From each herd or flock, 25 animals were sampled and the samples pooled for Salmonella culture. All Salmonella isolated were serotyped and any Salmonella Typhimurium isolates were phage typed. Questionnaires on each production system, prepared in Epi Info 6.04, were designed to identify risk factors associated with Salmonella spp excretion, with separate questionnaires designed for each production system. Salmonellae were identified in all production systems and were more commonly isolated from dairies and beef feedlots than other systems. Statistical analysis revealed that dairy cattle were significantly more likely to shed Salmonella in faeces than pasture beef cattle, mutton sheep and prime lambs (P < 0.05). A wide diversity of Salmonella serovars, all of which have been isolated from humans in Australia, was identified in both cattle and sheep. Analysis of the questionnaires showed access to new arrivals was a significant risk factor for Salmonella excretion on dairy properties. For beef feedlots, the presence of large numbers of flies in the feedlot pens or around stored manure were significant risk factors for Salmonella excretion. Dairy cattle pose the highest risk of all the slaughter-age animals tested. Some of the identified risk factors can be overcome by improved management practices, especially in relation to hygiene.

Growth and carcass characteristics of cast-for-age Merino ewes fed sorghum-based feedlot diets

Grain feeding low bodyweight, cast-for-age (CFA) sheep from pastoral areas of eastern Australia at the end of the growing season can enable critical carcass weight grades to be achieved and thus yield better economic returns. The aim of this work was to compare growth and carcass characteristics for CFA Merino ewes consuming either simple diets based on whole sorghum grain or commercial feed pellets. The experiment also compared various sources of additional nitrogen (N) for inclusion in sorghum diets and evaluated several introductory regimes. Seventeen ewes were killed initially to provide baseline carcass data and the remaining 301 ewes were gradually introduced to the concentrate diets over 14 days before being fed concentrates and wheaten hay ad libitum for 33 or 68 days. Concentrate treatments were: (i) commercial feed pellets, (ii) sorghum mix (SM; whole sorghum grain, limestone, salt and molasses) + urea and ammonium sulfate (SMU), (iii) SMU + whole cottonseed at 286 g/kg of concentrate dry matter (DM), (iv) SM + cottonseed meal at 139 g/kg of concentrate DM, (v) SMU + virginiamycin (20 mg/kg of concentrate) for the first 21 days of feeding, and (vi) whole cottonseed gradually replaced by SMU over the first 14 days of feeding. The target carcass weight of 18 kg was achieved after only 33 days on feed for the pellets and the SM + cottonseed meal diet. All other whole grain sorghum diets required between 33 and 68 days on feed to achieve the target carcass weight. Concentrates based on whole sorghum grain generally produced significantly (P < 0.05) lower carcass weight and fat score than pellets and this may have been linked to the significantly (P < 0.05) higher faecal starch concentrations for ewes consuming sorghum-based diets (270 v. 72 g/kg DM on day 51 of feeding for sorghum-based diets and pellets, respectively). Source of N in whole grain sorghum rations and special introductory regimes had no significant (P > 0.05) effects on carcass weight or fat score of ewes with the exception of carcass weight for SMU + whole cottonseed being significantly lower than SM + cottonseed meal at day 33. Ewes finished on all diets produced acceptable carcasses although muscle pH was high in all ewe carcasses (average 5.8 and 5.7 at 33 and 68 days, respectively). There were no significant (P > 0.05) differences between diets in concentrate DM intake, rumen fluid pH, meat colour score, fat colour score, eye muscle area, meat pH or meat temperature.

Seabed discrimination data from SeaScan™

Raw data from SeaScan™ transects off Wide Bay (south Queensland) taken in August 2007 as part of a study of ecological factors influencing the distribution of spanner crabs (Ranina ranina). The dataset (comma-delimited ascii file) comprises the following fields: 1. record number 2. date-time (GMT) 3. date-time (AEST) 4. latitude (signed decimal degrees) 5. longitude (decimal degrees) 6. speed over ground (knots) 7. depth (m) 8. seabed roughness (v) 9. hardness (v) Indices of roughness and hardness (from the first and second echoes respectively) were obtained using a SeaScan™ 100 system (un-referenced) on board the Research Vessel Tom Marshall, with the ship’s Furuno FCV 1100 echo sounder and 1 kW, 50 kHz transducer. Generally vessel speed was kept below about 14 kt (typically ~12 kt), and the echo-sounder range set to 80 m. The data were filtered to remove errors due to data drop-out, straying beyond system depth limits (min. 10 m), or transducer interference.

Telomere dynamics in the Sydney rock oyster (Saccostrea glomerata): an investigation into the effects of age, tissue type, location and time of sampling.

Telomere length has been purported as a biomarker for age and could offer a non-lethal method for determining the age of wild-caught individuals. Molluscs, including oysters and abalone, are the basis of important fisheries globally and have been problematic to accurately age. To determine whether telomere length could provide an alternative means of ageing molluscs, we evaluated the relationship between telomere length and age using the commercially important Sydney rock oyster (Saccostrea glomerata). Telomere lengths were estimated from tissues of known age individuals from different age classes, locations and at different sampling times. Telomere length tended to decrease with age only in young oysters less than 18 months old, but no decrease was observed in older oysters aged 2-4 years. Regional and temporal differences in telomere attrition rates were also observed. The relationship between telomere length and age was weak, however, with individuals of identical age varying significantly in their telomere length making it an imprecise age biomarker in oysters.

Liveweight prediction from hip height, condition score, fetal age and breed in tropical female cattle

Hip height, body condition, subcutaneous fat, eye muscle area, percentage Bos taurus, fetal age and diet digestibility data were collected at 17 372 assessments on 2181 Brahman and tropical composite (average 28% Brahman) female cattle aged between 0.5 and 7.5 years of age at five sites across Queensland. The study validated the subtraction of previously published estimates of gravid uterine weight to correct liveweight to the non-pregnant status. Hip height and liveweight were linearly related (Brahman: P<0.001, R-2 = 58%; tropical composite P<0.001, R-2 = 67%). Liveweight varied by 12-14% per body condition score (5-point scale) as cows differed from moderate condition (P<0.01). Parallel effects were also found due to subcutaneous rump fat depth and eye muscle area, which were highly correlated with each other and body condition score (r = 0.7-0.8). Liveweight differed from average by 1.65-1.66% per mm of rump fat depth and 0.71-0.76% per cm(2) of eye muscle area (P<0.01). Estimated dry matter digestibility of pasture consumed had no consistent effect in predicting liveweight and was therefore excluded from final models. A method developed to estimate full liveweight of post-weaning age female beef cattle from the other measures taken predicted liveweight to within 10 and 23% of that recorded for 65 and 95% of cases, respectively. For a 95% chance of predicted group average liveweight (body condition score used) being within 5, 4, 3, 2 and 1% of actual group average liveweight required 23, 36, 62, 137 and 521 females, respectively, if precision and accuracy of measurements matches that used in the research. Non-pregnant Bos taurus female cattle were calculated to be 10-40% heavier than Brahmans at the same hip height and body condition, indicating a substantial conformational difference. The liveweight prediction method was applied to a validation population of 83 unrelated groups of cattle weighed in extensive commercial situations on 119 days over 18 months (20 917 assessments). Liveweight prediction in the validation population exceeded average recorded liveweight for weigh groups by an average of 19 kg (similar to 6%) demonstrating the difficulty of achieving accurate and precise animal measurements under extensive commercial grazing conditions.

Weed age affects chemical control of Conyza bonariensis in fallows

In the last decade, Conyza bonariensis has become a widespread and difficult-to-control weed in Australian broad-acre cropping, particularly in glyphosate-based zero-tilled fallows of the subtropical grain region. The first Australian populations of C. bonariensis, where it is known as flaxleaf fleabane, were confirmed resistant to glyphosate in 2010. Control with alternative herbicides in fallows has been inconsistent, with earlier research indicating that weed age could be a potential contributing factor. In two field experiments, the impact of weed age (one, two and three months) was measured on the efficacy of six non-selective herbicide mixtures and sequential applications for control in fallows. In another two experiments we evaluated 11 non-selective herbicides, mixtures and sequential applications applied to one and three month old weeds using higher rates on older weeds. When herbicide rates were consistent for different weed ages, efficacy was reduced only by an average of 1% when two month old weeds were treated compared to one month old weeds. However when applied to three month old weeds, efficacy of treatments was significantly (P < 0.001) reduced by 3-30%. When herbicide rates were increased, weed age had no adverse effect on efficacy, which ranged from 90 to 100%, for amitrole, glyphosate mixed with 2,4-D amine plus picloram, and three sequential application treatments of glyphosate mixtures followed with bipyridyl products. Thus, this problem weed can be controlled effectively and consistently at the rosette stage of one to two months old, or three month old weeds with several different treatments at robust rates. These effective glyphosate alternatives and sequential-application tactics will minimise replenishment of the soil seed-bank and further reduce the risk for further evolution of glyphosate resistance. (C) 2012 Elsevier Ltd. All rights reserved.

Age-based demographics of the pearl perch Glaucosoma scapulare (Ramsay, 1881)

Summary: This research represents the first age-based demographic assessment of pearl perch, Glaucosoma scapulare (Ramsay, 1881), a highly valued species endemic to coastal waters off central eastern Australia. The study was conducted across the species' distribution that encompasses two state jurisdictions (Queensland in the north and New South Wales in the south) using data collected approximately 10 years apart in each state. Estimates of age were made by counting annuli (validated using marginal increment ratios) in sectioned sagittal otoliths. The maximum estimated age was 19 years. Pearl perch attained approx. 12 cm fork length (FL) after one year, 21 cm FL after 2 years and 29 cm FL after 3 years. Fish from the southern end of the species' distribution grew significantly more slowly than those from the northern part of its range. Commercial landings in the north were characterized by greater proportions of larger (>40 cm FL) and older (>6 years) fish than those in the south, with landings mainly of fish between 3 and 6 years of age. The observed variations in age-based demographics of pearl perch highlight the need for a better understanding of patterns of movement and reproduction in developing a model of population dynamics and life-history for this important species. There is a clear need for further, concurrent, age-based studies on pearl perch in the northern and southern parts of its distribution to support the conclusions of the present study based on data collected a decade apart. © 2013 Blackwell Verlag GmbH.

Development of a Multiplexed Bead-Based Suspension Array for the Detection and Discrimination of Pospiviroid Plant Pathogens

Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies.

Sweetcorn colour change and consumer perception associated with increasing zeaxanthin for the amelioration of age-related macular degeneration

Age-related macular degeneration (AMD) is the leading cause of blindness in the developed world. Increasing dietary intake of lutein- and zeaxanthin-rich foods is a potential means of preventing, or at least slowing the progression of AMD. Zeaxanthin levels in tropical super-sweetcorn was increased from 1.1 to 11.9 µg/g FW through conventional breeding and selection, associated with both an increase in the proportion of zeaxanthin relative to other carotenoids, and a general increase in carotenoid synthesis. Increasing zeaxanthin was associated with a colour shift from traditional ‘canary-yellow’ kernels to a golden-orange colour. Kernel colour was most closely correlated (r2=69%) with an increase in beta-arm carotenoid concentration. Consumer analysis revealed that prior to any knowledge of zeaxanthin-related health benefit, consumers would readily purchase both yellow and gold cobs. Once the health benefit was explained, this extended to deep-gold cobs. Colour difference between regular yellow sweetcorn and high-zeaxanthin sweetcorn could potentially be used as a visual means of differentiating high-zeaxanthin sweetcorn in the marketplace.

Age and growth of two newly established invasive populations of Tilapiamariae in northern Australia

Sagittal otoliths were used to age the samples of Tilapia mariae collected from a coastal river and an impoundment. Validation of sagittae checks was achieved using both quantitative marginal increment analysis and by tetracycline marking of the otoliths of fish kept in tanks and in a farm dam. The annulus pattern on the otoliths was generally clear and their formation appeared to be temperature related and largely completed in the Austral spring around September and October. Male T. mariae grow faster and larger than females and the maximum ages of fish from the coastal river and impoundment was 9+ and 4+ years, respectively. Past fish surveys and the absence of older age classes in the impoundment population would suggest that this population was only very recently established.

A novel method for the age estimation of Saddletail snapper (Lutjanus malabaricus) using Fourier Transform-near infrared (FT-NIR) spectroscopy

Near infrared (NIR) spectroscopy was investigated as a potential rapid method of estimating fish age from whole otoliths of Saddletail snapper (Lutjanus malabaricus). Whole otoliths from 209 Saddletail snapper were extracted and the NIR spectral characteristics were acquired over a spectral range of 800–2780 nm. Partial least-squares models (PLS) were developed from the diffuse reflectance spectra and reference-validated age estimates (based on traditional sectioned otolith increments) to predict age for independent otolith samples. Predictive models developed for a specific season and geographical location performed poorly against a different season and geographical location. However, overall PLS regression statistics for predicting a combined population incorporating both geographic location and season variables were: coefficient of determination (R2) = 0.94, root mean square error of prediction (RMSEP) = 1.54 for age estimation, indicating that Saddletail age could be predicted within 1.5 increment counts. This level of accuracy suggests the method warrants further development for Saddletail snapper and may have potential for other fish species. A rapid method of fish age estimation could have the potential to reduce greatly both costs of time and materials in the assessment and management of commercial fisheries.

The utility of near infrared spectroscopy for age estimation of deepwater sharks

Reliable age information is vital for effective fisheries management, yet age determinations are absent for many deepwater sharks as they cannot be aged using traditional methods of growth bands counts. An alternative approach to ageing using near infrared spectroscopy (NIRS) was investigated using dorsal fin spines, vertebrae and fin clips of three species of deepwater sharks. Ages were successfully estimated for the two dogfish, Squalus megalops and Squalus montalbani, and NIRS spectra were correlated with body size in the catshark, Asymbolus pallidus. Correlations between estimated-ages of the dogfish dorsal fin spines and their NIRS spectra were good, with S. megalops R2=0.82 and S. montalbani R2=0.73. NIRS spectra from S. megalops vertebrae and fin clips that have no visible growth bands were correlated with estimated-ages, with R2=0.89 and 0.76, respectively. NIRS has the capacity to non-lethally estimate ages from fin spines and fin clips, and thus could significantly reduce the numbers of sharks that need to be lethally sampled for ageing studies. The detection of ageing materials by NIRS in poorly calcified deepwater shark vertebrae could potentially enable ageing of this group of sharks that are vulnerable to exploitation.