Detection and differentiation of bovine herpesvirus 1 and 5 using a multiplex real-time polymerase chain reaction.

A multiplex real-time PCR was developed for the detection and differentiation of two closely related bovine herpesviruses 1 (BoHV-1) and 5 (BoHV-5). The multiplex real-time PCR combines a duplex real-time PCR that targets the DNA polymerase gene of BoHV-1 and BoHV-5 and a real-time PCR targeting mitochondrial DNA, as a house-keeping gene, described previously by Cawthraw et al. (2009). The assay correctly identified 22 BoHV-1 and six BoHV-5 isolates from the Biosecurity Sciences Laboratory virus collection. BoHV-1 and BoHV-5 were also correctly identified when incorporated in spiked semen and brain tissue samples. The detection limits of the duplex assay were 10 copies of BoHV-1 and 45 copies of BoHV-5. The multiplex real-time PCR had reaction efficiencies of 1.04 for BoHV-1 and 1.08 for BoHV-5. Standard curves relating Ct value to template copy number had correlation coefficients of 0.989 for BoHV-1 and 0.978 for BoHV-5. The assay specificity was demonstrated by testing bacterial and viral DNA from pathogens commonly isolated from bovine respiratory and reproductive tracts. The validated multiplex real-time PCR was used to detect and differentiate BoHV-1 and BoHV-5 in bovine clinical samples with known histories.

Albert Einstein's Weekend Home; Caputh, near Berlin Architecture; Residences; Exterior

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Deck; Albert Einstein's Weekend Home; Caputh, near Berlin Architecture; Residences; Exterior

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Study; Albert Einstein's Weekend Home; Caputh, near Berlin Architecture; Residences; Interior

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Staircase; Albert Einstein's Weekend Home; Caputh, near Berlin Architecture; Residences; Interior

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Albert Einstein's Weekend Home; Caputh, near Berlin Architecture; Residences; Exterior

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Deck; Albert Einstein's Weekend Home; Caputh, near Berlin Architecture; Residences; Exterior

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View from Deck; Albert Einstein's Weekend Home; Caputh, near Berlin Architecture; Residences; Exterior

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Elsa Einstein with unidentified woman sitting on the porch of Albert Einstein's Weekend Home; Caputh, near Berlin Architecture; Residences; Exterior

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Simultaneous prediction of acidity parameters (pH and titratable acidity) in Kefir using near infrared reflectance spectroscopy.

Acidity in terms of pH and titratable acids influences the texture and flavour of fermented dairy products, such as Kefir. However, the methods for determining pH and titratable acidity (TA) are time consuming. Near infrared (NIR) spectroscopy is a non-destructive method, which simultaneously predicts multiple traits from a single scan and can be used to predict pH and TA. The best pH NIR calibration model was obtained with no spectral pre-treatment applied, whereas smoothing was found to be the best pre-treatment to develop the TA calibration model. Using cross-validation, the prediction results were found acceptable for both pH and TA. With external validation, similar results were found for pH and TA, and both models were found to be acceptable for screening purposes.

Hierarchical Bayesian modelling of early detection surveillance for plant pest invasions

Early detection surveillance programs aim to find invasions of exotic plant pests and diseases before they are too widespread to eradicate. However, the value of these programs can be difficult to justify when no positive detections are made. To demonstrate the value of pest absence information provided by these programs, we use a hierarchical Bayesian framework to model estimates of incursion extent with and without surveillance. A model for the latent invasion process provides the baseline against which surveillance data are assessed. Ecological knowledge and pest management criteria are introduced into the model using informative priors for invasion parameters. Observation models assimilate information from spatio-temporal presence/absence data to accommodate imperfect detection and generate posterior estimates of pest extent. When applied to an early detection program operating in Queensland, Australia, the framework demonstrates that this typical surveillance regime provides a modest reduction in the estimate that a surveyed district is infested. More importantly, the model suggests that early detection surveillance programs can provide a dramatic reduction in the putative area of incursion and therefore offer a substantial benefit to incursion management. By mapping spatial estimates of the point probability of infestation, the model identifies where future surveillance resources can be most effectively deployed.

The Application of Near Infrared Spectroscopy for the Assessment of Avocado Quality Attributes, Infrared Spectroscopy. Chapter 14

Quality and safety evaluation of agricultural products has become an increasingly important consideration in market/commercial viability and systems for such evaluations are now demanded by customers, including distributors and retailers. Unfortunately, most horticultural products struggle with delivering adequate and consistent quality to the consumer. Removing inconsistencies and providing what the consumer expects is a key factor for retaining and expanding both domestic and international markets. Most commercial quality classification systems for fruit and vegetables are based on external features of the product, for example: shape, colour, size, weight and blemishes. However, the external appearance of most fruit is generally not an accurate guide to the internal or eating quality of the fruit. Internal quality of fruit is currently subjectively judged on attributes such as volatiles, firmness, and appearance. Destructive subjective measures such as internal flesh colour, or objective measures such as extraction of juice to measure sweetness (oBrix) or assessment of dry matter (DM) content are also used, although obviously not for every fruit – just a sample to represent the whole consignment. For avocado fruit, external colour is not a maturity characteristic, and its smell is too weak and appears later in its maturity stage (Gaete-Garreton et al., 2005). Since maturity is a major component of avocado quality and palatability, it is important to harvest mature fruit, so as to ensure that fruit will ripen properly and have acceptable eating quality. Currently, commercial avocado maturity estimation is based on destructive assessment of the %DM, and sometimes percent oil, both of which are highly correlated with maturity (Clark et al., 2003; Mizrach & Flitsanov, 1999). Avocados Australia Limited (AAL (2008)) recommend a minimum maturity standard for its growers of 23 %DM (greater than 10% oil content) for the ‘Hass’ cultivar, although consumer studies indicate a preference for at least 25 %DM (Harker et al., 2007).

Significant evidence of one or more susceptibility loci for endometriosis with near-Mendelian inheritance on chromosome 7p13-15

BACKGROUND: Endometriosis is a common disease with a heritable component. The collaborative International Endogene Study consists of two data sets (Oxford and Australia) comprising 1176 families with multiple affected. The aim was to investigate whether the apparent concentration of cases in a proportion of families could be explained by one or more rare variants with (near-)Mendelian autosomal inheritance. METHODS AND RESULTS: Linkage analyses (aimed at finding chromosomal regions harbouring disease-predisposing genes) were conducted in families with three or more affected (Oxford: n = 52; Australia: n = 196). In the Oxford data set, a non-parametric linkage score (Kong & Cox (K&C) Log of ODds (LOD)) of 3.52 was observed on chromosome 7p (genome-wide significance P = 0.011). A parametric MOD score (equal to maximum LOD maximized over 357 possible inheritance models) of 3.89 was found at 65.72 cM (D7S510) for a dominant model with reduced penetrance. After including the Australian data set, the non-parametric K&C LOD of the combined data set was 1.46 at 57.3 cM; the parametric analysis found an MOD score of 3.30 at D7S484 (empirical significance: P = 0.035) for a recessive model with high penetrance. Critical recombinant analysis narrowed the probable region of linkage down to overlapping 6.4 Mb and 11 Mb intervals containing 48 and 96 genes, respectively. CONCLUSIONS: This is the first report to suggest that there may be one or more high-penetrance susceptibility loci for endometriosis with (near-)Mendelian inheritance.

Burnt area mapping in insular Southeast Asia using medium resolution satellite imagery

Burnt area mapping in humid tropical insular Southeast Asia using medium resolution (250-500m) satellite imagery is characterized by persisting cloud cover, wide range of land cover types, vast amount of wetland areas and highly varying fire regimes. The objective of this study was to deepen understanding of three major aspects affecting the implementation and limits of medium resolution burnt area mapping in insular Southeast Asia: 1) fire-induced spectral changes, 2) most suitable multitemporal compositing methods and 3) burn scars patterns and size distribution. The results revealed a high variation in fire-induced spectral changes depending on the pre-fire greenness of burnt area. It was concluded that this variation needs to be taken into account in change detection based burnt area mapping algorithms in order to maximize the potential of medium resolution satellite data. Minimum near infrared (MODIS band 2, 0.86μm) compositing method was found to be the most suitable for burnt area mapping purposes using Moderate Resolution Imaging Spectroradiometer (MODIS) data. In general, medium resolution burnt area mapping was found to be usable in the wetlands of insular Southeast Asia, whereas in other areas the usability was seriously jeopardized by the small size of burn scars. The suitability of medium resolution data for burnt area mapping in wetlands is important since recently Southeast Asian wetlands have become a major point of interest in many fields of science due to yearly occurring wild fires that not only degrade these unique ecosystems but also create regional haze problem and release globally significant amounts of carbon into the atmosphere due to burning peat. Finally, super-resolution MODIS images were tested but the test failed to improve the detection of small scars. Therefore, super-resolution technique was not considered to be applicable to regional level burnt area mapping in insular Southeast Asia.

Alice Burlin nee Molling, Therese Gottschalk nee Molling, and Line Stern nee Wallerstein at Alice Burlins's home; Linton near Cambridge, England.

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