Predicting survival of western rock lobsters Panulirus cygnus using discriminant analysis of hemolymph parameters taken immediately following simulated handling treatments

Instances of morbidity amongst rock lobsters (Panulirus cygnus) arriving at factories in Western Australia (WA) have been attributed to stress during post-harvest handling. This study used discriminant analysis to determine whether physiological correlates of stress following a period of simulated post-harvest handling had any validity as predictors of future rejection or morbidity of western rock lobsters. Groups of 230 western rock lobsters were stored for 6 h in five environments (submerged/flowing sea water, submerged/re-circulating sea water, humid air, flowing sea water spray, and re-circulated sea water spray). The experiment was conducted in late spring (ambient sea water 22°C), and repeated again in early autumn (ambient sea water 26°C). After 6 h treatment, each lobster was graded for acceptability for live export, numbered, and its hemolymph was sampled. The samples were analysed for a number of physiological and health status parameters. The lobsters were then stored for a week in tanks in the live lobster factory to record mortality. The mortality of lobsters in the factory was associated with earlier deviations in hemolymph parameters as they emerged from the storage treatments. Discriminant analysis (DA) of the hemolymph assays enabled the fate of 80-90% of the lobsters to be correctly categorised within each experiment. However, functions derived from one experiment were less accurate at predicting mortality when applied to the other experiments. One of the reasons for this was the higher mortality and the more severe patho-physiological changes observed in lobsters stored in humid air or sprays at the higher temperature. The analysis identified lactate accumulation during emersion and associated physiological and hemocyte-related effects as a major correlate of mortality. Reducing these deviations, for example by submerged transport, is expected to ensure high levels of survival. None of the indicators tested predicted mortality with total accuracy. The simplest and most accurate means of comparing emersed treatments was to count the mortality afterwards.

SSR analysis of cultivated groundnut (Arachis hypogaea L.) germplasm resistant to rust and late leaf spot diseases

Cultivated groundnut (Arachis hypogaea L.) is an agronomically and economically important oilseed crop grown extensively throughout the semi-arid tropics of Asia, Africa and Latin America. Rust (Puccinia arachidis) and late leaf spot (LLS, Phaseoisariopsis personata) are among the major diseases causing significant yield loss in groundnut. The development of varieties with high levels of resistance has been constrained by adaptation of disease isolates to resistance sources and incomplete resistance in resistant sources. Despite the wide range of morphological diversity observed in the cultivated groundnut gene pool, molecular marker analyses have thus far been unable to detect a parallel level of genetic diversity. However, the recent development of simple sequence repeat (SSR) markers presents new opportunities for molecular diversity analysis of cultivate groundnut. The current study was conducted to identify diverse disease resistant germplasm for the development of mapping populations and for their introduction into breeding programs. Twenty-three SSRs were screened across 22 groundnut genotypes with differing levels of resistance to rust and LLS. Overall, 135 alleles across 23 loci were observed in the 22 genotypes screened. Twelve of the 23 SSRs (52%) showed a high level of polymorphism, with PIC values ≥0.5. This is the first report detecting such high levels of genetic polymorphism in cultivated groundnut. Multi-dimensional scaling and cluster analyses revealed three well-separated groups of genotypes. Locus by locus AMOVA and Kruskal-Wallis one-way ANOVA identified candidate SSR loci that may be valuable for mapping rust and LLS resistance. The molecular diversity analysis presented here provides valuable information for groundnut breeders designing strategies for incorporating and pyramiding rust and late leaf spot resistances and for molecular biologists wishing to create recombinant inbred line populations to map these traits.

Maize kernel hardness classification by near infrared (NIR) hyperspectral imaging and multivariate data analysis.

The use of near infrared (NIR) hyperspectral imaging and hyperspectral image analysis for distinguishing between hard, intermediate and soft maize kernels from inbred lines was evaluated. NIR hyperspectral images of two sets (12 and 24 kernels) of whole maize kernels were acquired using a Spectral Dimensions MatrixNIR camera with a spectral range of 960-1662 nm and a sisuChema SWIR (short wave infrared) hyperspectral pushbroom imaging system with a spectral range of 1000-2498 nm. Exploratory principal component analysis (PCA) was used on absorbance images to remove background, bad pixels and shading. On the cleaned images. PCA could be used effectively to find histological classes including glassy (hard) and floury (soft) endosperm. PCA illustrated a distinct difference between glassy and floury endosperm along principal component (PC) three on the MatrixNIR and PC two on the sisuChema with two distinguishable clusters. Subsequently partial least squares discriminant analysis (PLS-DA) was applied to build a classification model. The PLS-DA model from the MatrixNIR image (12 kernels) resulted in root mean square error of prediction (RMSEP) value of 0.18. This was repeated on the MatrixNIR image of the 24 kernels which resulted in RMSEP of 0.18. The sisuChema image yielded RMSEP value of 0.29. The reproducible results obtained with the different data sets indicate that the method proposed in this paper has a real potential for future classification uses.

Parasites as indicators of movement and population connectivity of a non-diadromous, tropical estuarine teleost: king threadfin Polydactylus macrochir

Temporal and spatial patterns in parasite assemblages were examined to evaluate the degree of movement and connectivity of post-recruitment life-history stages of a large, non-diadromous tropical estuarine teleost, king threadfin Polydactylus macrochir, collected from 18 locations across northern Australia. Ten parasites types (juvenile stages of two nematodes and seven cestodes, and adults of an acanthocephalan) were deemed to be suitable for use as biological tags, in that they were considered to have a long residence time in the fish, were relatively easy to find and were morphologically very different to each other which aided discrimination. Univariate and discriminant function analysis of these parasites revealed little difference in temporal replicates collected from five locations, suggesting that the parasite communities were stable over the timeframes explored. Univariate, discriminant function, and BrayCurtis similarity analyses indicated significant spatial heterogeneity, with BrayCurtis classification accuracies ranging from 55 to 100% for locations in north-western and northern Australia, 24 to 88% in the Gulf of Carpentaria, and 39 to 88% on the east coast of Queensland. Few differences were observed among locations separated by <200 km. The observed patterns of parasite infection are in agreement with concurrent studies of movement and connectivity of P. macrochir in that they indicate a complex population structure across northern Australia. These results should be considered when reviewing the management arrangements for this species.

Identification of diverse full-length endogenous betaretroviruses in megabats and microbats

Background: Betaretroviruses infect a wide range of species including primates, rodents, ruminants, and marsupials. They exist in both endogenous and exogenous forms and are implicated in animal diseases such as lung cancer in sheep, and in human disease, with members of the human endogenous retrovirus-K (HERV-K) group of endogenous betaretroviruses (βERVs) associated with human cancers and autoimmune diseases. To improve our understanding of betaretroviruses in an evolutionarily distinct host species, we characterized βERVs present in the genomes and transcriptomes of mega- and microbats, which are an important reservoir of emerging viruses.Results: A diverse range of full-length βERVs were discovered in mega- and microbat genomes and transcriptomes including the first identified intact endogenous retrovirus in a bat. Our analysis revealed that the genus Betaretrovirus can be divided into eight distinct sub-groups with evidence of cross-species transmission. Betaretroviruses are revealed to be a complex retrovirus group, within which one sub-group has evolved from complex to simple genomic organization through the acquisition of an env gene from the genus Gammaretrovirus. Molecular dating suggests that bats have contended with betaretroviral infections for over 30 million years.Conclusions: Our study reveals that a diverse range of betaretroviruses have circulated in bats for most of their evolutionary history, and cluster with extant betaretroviruses of divergent mammalian lineages suggesting that their distribution may be largely unrestricted by host species barriers. The presence of βERVs with the ability to transcribe active viral elements in a major animal reservoir for viral pathogens has potential implications for public health. © 2013 Hayward et al.; licensee BioMed Central Ltd.

Characterisation of grain quality in diverse sorghum germplasm using a Rapid Visco-Analyzer and near infrared reflectance spectroscopy

BACKGROUND: Twenty-two diverse sorghum landraces, classified as normal and opaque types obtained from Ethiopia, were characterised for grain quality parameters using near infra-red spectroscopy (NIRS), chemical and Rapid Visco-Analyzer (RVA) characteristics. RESULTS: Protein content ranged from 77 to 182 g kg-1, and starch content from 514 to 745 g kg(-1). The NIRS analysis indicated the pig faecal digestible energy range from 14.6 to 15.7MJ kg(-1) as fed, and the ileal digestible energy range from 11.3 to 13.9MJ kg(-1) as fed. The normal sorghums had higher digestible energy than the opaque sorghums, which exhibited lower RVA viscosities, and higher pasting temperatures and setback ratios. The RVA parameterswere positively correlated with the starch content and negatively correlated with the protein content. The normal and opaque types formed two distinct groups based on principal component and cluster analyses. CONCLUSION: The landraces were different for the various grain quality parameters with some landraces displaying unique RVA and NIRS profiles. This study will guide utilisation of the sorghum landraces in plant improvement programs, and provides a basis for further studies into how starch and other constituents behave in and affect the properties of these landraces. (C) 2011 Society of Chemical Industry

Otolith morphology of four mackerel species (Scomberomorus spp.) in Australia: Species differentiation and prediction for fisheries monitoring and assessment

Four species of large mackerels (Scomberomorus spp.) co-occur in the waters off northern Australia and are important to fisheries in the region. State fisheries agencies monitor these species for fisheries assessment; however, data inaccuracies may exist due to difficulties with identification of these closely related species, particularly when specimens are incomplete from fish processing. This study examined the efficacy of using otolith morphometrics to differentiate and predict among the four mackerel species off northeastern Australia. Seven otolith measurements and five shape indices were recorded from 555 mackerel specimens. Multivariate modelling including linear discriminant analysis (LDA) and support vector machines, successfully differentiated among the four species based on otolith morphometrics. Cross validation determined a predictive accuracy of at least 96% for both models. An optimum predictive model for the four mackerel species was an LDA model that included fork length, feret length, feret width, perimeter, area, roundness, form factor and rectangularity as explanatory variables. This analysis may improve the accuracy of fisheries monitoring, the estimates based on this monitoring (i.e. mortality rate) and the overall management of mackerel species in Australia.

Detecting the attributes of a wheat crop using digital imagery acquired from a low-altitude platform

A low-altitude platform utilising a 1.8-m diameter tethered helium balloon was used to position a multispectral sensor, consisting of two digital cameras, above a fertiliser trial plot where wheat (Triticum spp.) was being grown. Located in Cecil Plains, Queensland, Australia, the plot was a long-term fertiliser trial being conducted by a fertiliser company to monitor the response of crops to various levels of nutrition. The different levels of nutrition were achieved by varying nitrogen application rates between 0 and 120 units of N at 40 unit increments. Each plot had received the same application rate for 10 years. Colour and near-infrared images were acquired that captured the whole 2 ha plot. These images were examined and relationships sought between the captured digital information and the crop parameters imaged at anthesis and the at-harvest quality and quantity parameters. The statistical analysis techniques used were correlation analysis, discriminant analysis and partial least squares regression. A high correlation was found between the image and yield (R2 = 0.91) and a moderate correlation between the image and grain protein content (R2 = 0.66). The utility of the system could be extended by choosing a more mobile platform. This would increase the potential for the system to be used to diagnose the causes of the variability and allow remediation, and/or to segregate the crop at harvest to meet certain quality parameters.

Identifying major contributing sources to odour annoyance using a non-specific gas sensor array

Identification of major contributors to odour annoyance in areas with multiple emission sources is necessary to address and resolve odour disputes. In an effort to develop an appropriate tool for this task, odour samples were collected on-site at a piggery and an abattoir (the major odour sources in the area) and at surrounding off-site areas, then analysed using a commercial non-specific chemical sensor array to develop an odour fingerprint database. The developed odour fingerprint database was analysed using two pattern recognition algorithms including a partial least squares-discriminant analysis (PLS-DA) and a Kohonen self-organising map (KSOM). The KSOM model could identify odour samples sourced from the piggery shed 15, piggery pond 8, piggery pond 9, abattoir, motel and others with mean percentage values of 77.5, 65.0, 90.2, 75.7, 44.8 and 64.6%, respectively.

Deviant near-infrared spectra identifies Corymbia hybrids

The study examined the potential of Near Infrared Reflectance (NIR) spectroscopy for field diagnosis of hybrids between Corymbia (formerly Eucalyptus) species. NIR profiles were generated by scanning foliage from a total of 383 hybrid and 533 parental seedlings grown in a common garden and partial least squares discriminant analysis was used to test three-way model power to assign individuals to their appropriate taxon; either a parental or F1 hybrid class. Using the optimised conditions, fresh foliage from eight-month-old seedlings and a handheld NIR instrument (950–1800 nm), the mean assignment rates for the three hybrid groups ranged from 76% to 90%. Hybrid-parent contrast of NIR spectra deviated more so than parent–parent contrast. The F1 taxon assignment rates were usually higher than those for parents at 100% and 72%, respectively. Hybrid resolution was even greater for 2nd generation backcross hybrids. Similar to studies of morphology, taxon assignments tended to be more accurate for hybrid groups in which the parental taxa were more divergent. The practical application of this technique for hybrid diagnosis of seedlings in the nursery will require careful attention to control environmental factors because seedling age and storage effects influenced the ability of NIR to identify hybrids. The technique may also necessitate the generation of comparable reference populations, although exclusions approaches to analysis may circumvent the need for reference populations. The application of NIR in field diagnosis will be further complicated by the need to generate global models across environments but such models have been obtained for reliable prediction of chemistries in other situations.

Sensory Systems in Sawfishes. 1. The Ampullae of Lorenzini

The distribution and density of the ampullary electroreceptors in the skin of elasmobranchs are influenced by the phylogeny and ecology of a species. Sensory maps were created for 4 species of pristid sawfish. Their ampullary pores were separated into pore fields based on their innervation and cluster formation. Ventrally, ampullary pores are located in 6 areas (5 in Pristis microdon), covering the rostrum and head to the gills. Dorsally, pores are located in 4 areas (3 in P. microdon), which cover the rostrum, head and may extend slightly onto the pectoral fins. In all species, the highest number of pores is found on the dorsal and ventral sides of the rostrum. The high densities of pores along the rostrum combined with the low densities around the mouth could indicate that sawfish use their rostrum to stun their prey before ingesting it, but this hypothesis remains to be tested. The directions of ampullary canals on the ventral side of the rostrum are species specific. P. microdon possesses the highest number of ampullary pores, which indicates that amongst the study species this species is an electroreception specialist. As such, juvenile P. microdon inhabit low-visibility freshwater habitats.

Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus

Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.