Influence of environmental and instrumental variables on the non-invasive prediction of Brix in pineapple using near infrared spectroscopy

The Brix content of pineapple fruit can be non-invasively predicted from the second derivative of near infrared reflectance spectra. Correlations obtained using a NIRSystems 6500 spectrophotometer through multiple linear regression and modified partial least squares analyses using a post-dispersive configuration were comparable with that from a pre-dispersive configuration in terms of accuracy (e.g. coefficient of determination, R2, 0.73; standard error of cross validation, SECV, 1.01°Brix). The effective depth of sample assessed was slightly greater using the post-dispersive technique (about 20 mm for pineapple fruit), as expected in relation to the higher incident light intensity, relative to the pre-dispersive configuration. The effect of such environmental variables as temperature, humidity and external light, and instrumental variables such as the number of scans averaged to form a spectrum, were considered with respect to the accuracy and precision of the measurement of absorbance at 876 nm, as a key term in the calibration for Brix, and predicted Brix. The application of post-dispersive near infrared technology to in-line assessment of intact fruit in a packing shed environment is discussed.

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.

Buffel grass in Queensland's semi-arid woodlands: response to local and landscape scale variables, and relationship with grass, forb and reptile species.

Buffel grass [Pennisetum ciliare (L.) Link] has been widely introduced in the Australian rangelands as a consequence of its value for productive grazing, but tends to competitively establish in non-target areas such as remnant vegetation. In this study, we examined the influence landscape-scale and local-scale variables had upon the distribution of buffel grass in remnant poplar box (Eucalyptus populnea F. Muell.) dominant woodland fragments in the Brigalow Bioregion, Queensland. Buffel grass and variables thought to influence its distribution in the region were measured at 60 sites, which were selected based on the amount of native woodland retained in the landscape and patch size. An information-theoretic modelling approach and hierarchical partitioning revealed that the most influential variable was the percent of retained vegetation within a 1-km spatial extent. From this, we identified a critical threshold of similar to 30% retained vegetation in the landscape, above which the model predicted buffel grass was not likely to occur in a woodland fragment. Other explanatory variables in the model were site based, and included litter cover and long-term rainfall. Given the paucity of information on the effect of buffel grass upon biodiversity values, we undertook exploratory analyses to determine whether buffel grass cover influenced the distribution of grass, forb and reptile species. We detected some trends; hierarchical partitioning revealed that buffel grass cover was the most important explanatory variable describing habitat preferences of four reptile species. However, establishing causal links - particularly between native grass and forb species and buffel grass - was problematic owing to possible confounding with grazing pressure. We conclude with a set of management recommendations aimed at reducing the spread of buffel grass into remnant woodlands.

High-resolution melt-curve analysis of random-amplified-polymorphic-DNA markers, for the characterisation of pathogenic Leptospira.

A new test for pathogenic Leptospira isolates, based on RAPD-PCR and high-resolution melt (HRM) analysis (which measures the melting temperature of amplicons in real time, using a fluorescent DNA-binding dye), has recently been developed. A characteristic profile of the amplicons can be used to define serovars or detect genotypes. Ten serovars, of leptospires from the species Leptospira interrogans (serovars Australis, Robinsoni, Hardjo, Pomona, Zanoni, Copenhageni and Szwajizak), L. borgpetersenii (serovar Arborea), L. kirschneri (serovar Cynopteri) and L. weilii (serovar Celledoni), were typed against 13 previously published RAPD primers, using a real-time cycler (the Corbett Life Science RotorGene 6000) and the optimised reagents from a commercial kit (Quantace SensiMix). RAPD-HRM at specific temperatures generated defining amplicon melt profiles for each of the tested serovars. These profiles were evaluated as difference-curve graphs generated using the RotorGene software package, with a cut-off of at least 8 'U' (plus or minus). The results demonstrated that RAPD-HRM can be used to measure serovar diversity and establish identity, with a high degree of stability. The characterisation of Leptospira serotypes using a DNA-based methodology is now possible. As an objective and relatively inexpensive and rapid method of serovar identification, at least for cultured isolates, RAPD-HRM assays show convincing potentia.

High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) for the characterisation of pathogenic leptospires: intra-serovar divergence, interserovar convergence, and evidence of attenuation in Leptospira reference collections.

High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) is a novel technology that has emerged as a possible method to characterise leptospires to serovar level. RAPD-HRM has recently been used to measure intra-serovar convergence between strains of the same serovar as well as inter-serovar divergence between strains of different serovars. The results indicate that intra-serovar heterogeneity and inter-serovar homogeneity may limit the application of RAPD-HRM in routine diagnostics. They also indicate that genetic attenuation of aged, high-passage-number isolates could undermine the use of RAPD-HRM or any other molecular technology. Such genetic attenuation may account for a general decrease seen in titres of rabbit hyperimmune antibodies over time. Before RAPD-HRM can be further advanced as a routine diagnostic tool, strains more representative of the wild-type serovars of a given region need to be identified. Further, RAPD-HRM analysis of reference strains indicates that the routine renewal of reference collections, with new isolates, may be needed to maintain the genetic integrity of the collections.

Salmonella Virchow and Salmonella Weltevreden in a Random Survey of the Asian House Gecko, Hemidactylus frenatus, in Houses in Northern Australia.

Background: Salmonella enterica serotype Virchow is the most common cause of invasive nontyphoid salmonellosis in North Queensland, particularly in infants, but the zoonotic source is unknown. This study aimed at determining (i) the prevalence of the introduced Asian house gecko, Hemidactylus frenatus, in houses in North Queensland and (ii) whether they were a potential source of Salmonella Virchow. Methods: Asian house geckos were collected in a random survey of houses in Townsville, North Queensland. Gut contents underwent microbiological analysis within 2 h of removal using both direct plating and enrichment broth methods. Any organism found to be a presumptive Salmonella spp. was then sent to a reference lab for confirmation of genus/species, serotyping, and phage typing if indicated. Results: One hundred Asian house geckos were collected from 57 houses. Geckos were present in 100% of houses surveyed, and prevalence of Salmonella in large intestinal contents was 7% (95% confidence interval 2, 12%). Three serotypes were found: Virchow (phage type 8), Weltevreden, and an untypable subspecies 1 serotype 11:-:1,7. Conclusion: Since Salmonella Virchow (phage type 8) is associated with invasive disease, the introduced Asian house gecko may play a significant role in the epidemiology of sporadic salmonellosis in places invaded by these peridomestic reptiles. These results justify more detailed epidemiological studies on the role of the Asian house gecko in sporadic salmonellosis and development of evidence-based strategies to decrease this potential zoonotic hazard.

Bactrocera frauenfeldi (Diptera: Tephritidae), an invasive fruit fly in Australia that may have reached the extent of its spread due to environmental variables

Bactrocera frauenfeldi (Schiner), the ‘mango fruit fly’, is a horticultural pest originating from the Papua New Guinea region. It was first detected in Australia on Cape York Peninsula in north Queensland in 1974 and had spread to Cairns by 1994 and Townsville by 1997. Bactrocera frauenfeldi has not been recorded further south since then despite its invasive potential, an absence of any controls and an abundance of hosts in southern areas. Analysis of cue-lure trapping data from 1997 to 2012 in relation to environmental variables shows that the distribution of B. frauenfeldi in Queensland correlates to locations with a minimum temperature for the coldest month >13.2°C, annual temperature range <19.3°C, mean temperature of the driest quarter >20.2°C, precipitation of the wettest month >268 mm, precipitation of the wettest quarter >697 mm, temperature seasonality <30.9°C (i.e. lower temperature variability) and areas with higher human population per square kilometre. Annual temperature range was the most important variable in predicting this species' distribution. Predictive distribution maps based on an uncorrelated subset of these variables reasonably reflected the current distribution of this species in northern Australia and predicted other areas in the world potentially at risk from invasion by this species. This analysis shows that the distribution of B. frauenfeldi in Australia is correlated to certain environmental variables that have most likely limited this species' spread southward in Queensland. This is of importance to Australian horticulture in demonstrating that B. frauenfeldi is unlikely to establish in horticultural production areas further south than Townsville.