Assessment of genetic diversity and population structure in cultured Australian Pacific oysters.

The recent development of Pacific oyster (Crassostrea gigas) SNP genotyping arrays has allowed detailed characterisation of genetic diversity and population structure within and between oyster populations. It also raises the potential of harnessing genomic selection for genetic improvement in oyster breeding programmes. The aim of this study was to characterise a breeding population of Australian oysters through genotyping and analysis of 18 027 SNPs, followed by comparison with genotypes of oyster sampled from Europe and Asia. This revealed that the Australian populations had similar population diversity (HE ) to oysters from New Zealand, the British Isles, France and Japan. Population divergence was assessed using PCA of genetic distance and revealed that Australian oysters were distinct from all other populations tested. Australian Pacific oysters originate from planned introductions sourced from three Japanese populations. Approximately 95% of these introductions were from geographically, and potentially genetically, distinct populations from the Nagasaki oysters assessed in this study. Finally, in preparation for the application of genomic selection in oyster breeding programmes, the strength of LD was evaluated and subsets of loci were tested for their ability to accurately infer relationships. Weak LD was observed on average; however, SNP subsets were shown to accurately reconstitute a genomic relationship matrix constructed using all loci. This suggests that low-density SNP panels may have utility in the Australian population tested, and the findings represent an important first step towards the design and implementation of genomic approaches for applied breeding in Pacific oysters.

Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon.

Farmed Atlantic salmon (Salmo salar) is a globally important production species, including in Australia where breeding and selection has been in progress since the 1960s. The recent development of SNP genotyping platforms means genome-wide association and genomic prediction can now be implemented to speed genetic gain. As a precursor, this study collected genotypes at 218 132 SNPs in 777 fish from a Tasmanian breeding population to assess levels of genetic diversity, the strength of linkage disequilibrium (LD) and imputation accuracy. Genetic diversity in Tasmanian Atlantic salmon was lower than observed within European populations when compared using four diversity metrics. The distribution of allele frequencies also showed a clear difference, with the Tasmanian animals carrying an excess of low minor allele frequency variants. The strength of observed LD was high at short distances (<25 kb) and remained above background for marker pairs separated by large chromosomal distances (hundreds of kb), in sharp contrast to the European Atlantic salmon tested. Genotypes were used to evaluate the accuracy of imputation from low density (0.5 to 5 K) up to increased density SNP sets (78 K). This revealed high imputation accuracies (0.89-0.97), suggesting that the use of low density SNP sets will be a successful approach for genomic prediction in this population. The long-range LD, comparatively low genetic diversity and high imputation accuracy in Tasmanian salmon is consistent with known aspects of their population history, which involved a small founding population and an absence of subsequent introgression. The findings of this study represent an important first step towards the design of methods to apply genomics in this economically important population.

Atmospheric pressure X-ray photoelectron spectroscopy apparatus: Bridging the pressure gap.

One of the main goals in catalysis is the characterization of solid/gas interfaces in a reaction environment. The electronic structure and chemical composition of surfaces become heavily influenced by the surrounding environment. However, the lack of surface sensitive techniques that are able to monitor these modifications under high pressure conditions hinders the understanding of such processes. This limitation is known throughout the community as the "pressure gap." We have developed a novel experimental setup that provides chemical information on a molecular level under atmospheric pressure and in presence of reactive gases and at elevated temperatures. This approach is based on separating the vacuum environment from the high-pressure environment by a silicon nitride grid-that contains an array of micrometer-sized holes-coated with a bilayer of graphene. Using this configuration, we have investigated the local electronic structure of catalysts by means of photoelectron spectroscopy and in presence of gases at 1 atm. The reaction products were monitored online by mass spectrometry and gas chromatography. The successful operation of this setup was demonstrated with three different examples: the oxidation/reduction reaction of iridium (noble metal) and copper (transition metal) nanoparticles and with the hydrogenation of propyne on Pd black catalyst (powder).

Evidence for multiple sex-determining loci in Tasmanian Atlantic salmon (Salmo salar).

Phenotypic sex in salmonids is determined primarily by a genetic male heterogametic system; yet, sex reversal can be accomplished via hormonal treatment. In Tasmanian Atlantic salmon aquaculture, to overcome problems associated with early sexual maturation in males, sex-reversed females are crossed with normal females to produce all female stock. However, phenotypic distinction of sex-reversed females (neo-males) from true males is problematic. We set out to identify genetic markers that could make this distinction. Microsatellite markers from chromosome 2 (Ssa02), to which the sex-determining locus (SEX) has been mapped in two Scottish Atlantic salmon families, did not predict sex in a pilot study of seven families. A TaqMan 64 SNP genome-wide scan suggested SEX was on Ssa06 in these families, and this was confirmed by microsatellite markers. A survey of 58 families in total representing 38 male lineages in the SALTAS breeding program found that 34 of the families had SEX on Ssa02, in 22 of the families SEX was on Ssa06, and two of the families had a third SEX locus, on Ssa03. A PCR test using primers designed from the recently published sdY gene is consistent with Tasmanian Atlantic salmon having a single sex-determining gene that may be located on at least three linkage groups.

Analysis and assessment of heavy metal pollution in suspended solids and sediments of the river Danube.

The Joint Danube Survey (JDS)--a comprehensive monitoring survey to assess the environmental pollution status of the river Danube--was carried out in 2001. Samples were taken at 74 positions along the river from Neu-Ulm (River-km 2589) down to the Danube Delta at the Black Sea (River-km 0) and in 24 main tributaries and anabranches. Besides other biological and chemical parameters, concentrations of Al, As, Cd, Cr, Cu, Fe, Pb, Mn, Hg, Ni, and Zn were determined in sediments and suspended solids. Lowest heavy metal concentrations were measured around River-km 1800. After an increase down to River-km 1000 (the Irongate Reservoir), a constant level or a slight decrease could be found down to and in the Danube Delta. Very high element concentrations were determined at only a few stations of the river Danube and in some tributaries. An evaluation of the pollution status of the river was carried out by enrichment factors (EFs) calculated using adapted background concentrations of heavy metals. Except single sampling sites and some tributaries, the pollution of the river Danube by As, Cr, Cu, Pb, Hg, Ni, and Zn can be regarded as rather low. However, elevated concentrations of Cd were found in both investigated matrices, particularly in the lower stretch of the river Danube beginning at the Irongate.

Measurement and classification of retinal vascular tortuosity.

Automatic measurement of blood vessel tortuosity is a useful capability for automatic ophthalmological diagnostic tools. We describe a suite of automated tortuosity measures for blood vessel segments extracted from RGB retinal images. The tortuosity measures were evaluated in two classification tasks: (1) classifying the tortuosity of blood vessel segments and (2) classifying the tortuosity of blood vessel networks. These tortuosity measures were able to achieve a classification rate of 91% for the first problem and 95% on the second problem, which confirms that they capture much of the ophthalmologists' notion of tortuosity. Finally, we discuss how the accuracy of these measures can be influence by the method used to extract the blood vessel segments.

Distribution, density and heterogeneity of canine mast cells and influence of fixation techniques.

The present study was carried out to determine the physiological distribution of mast cell numbers and types in the dog according to tissue location, staining and fixation methods. Tissue samples from stomach, duodenum, lung, lymph node, skin and uterus were evaluated. Samples were fixed in formalin as well as in Carnoy's fluid. The average number of mast cells was determined using a metachromatic staining method. Protease content of mast cells was examined with a double enzyme-immunohistochemical staining technique, using a histochemical reaction for chloroacetate esterase to detect chymase activity and an immunohistochemical staining method for the detection of tryptase. Canine mast cells can be subdivided into formalin-sensitive and -resistant mast cells. Three subtypes were identified according to their content of the mast cell-specific proteases tryptase (T) and chymase (C): T-, TC- and C-mast cells. Significant differences regarding the distribution of mast cell subtypes as well as the influence of the fixation method can be observed. This underlines the fact that data regarding mast cell heterogeneity from other species, obtained by different fixation methods, are not comparable. This fact has to be taken into consideration when evaluating mast cell subtypes under pathological conditions.

Bovine mast cells: distribution, density, heterogeneity, and influence of fixation techniques.

Mast cells can be distinguished according to various characteristics: rodent mast cells have been subtyped by histochemical criteria, whereas canine and human mast cells have been classified according to their proteases. Comparisons of mast cells from different species have therefore resulted in contradictory and confusing opinions on mast cell heterogeneity. Thus, it is essential to obtain species-specific data on mast cell density and heterogeneity. The present study was carried out to determine the physiological distribution of mast cell numbers and types in bovines according to tissue location, staining, and fixation methods. Samples were fixed in formalin or Carnoy's fluid. The average number of mast cells was determined by using a metachromatic staining method. Protease content of mast cells was examined with a double-enzyme-immunohistochemical staining technique. Three mast cell subtypes were distinguished: T-, TC-, and C-mast cells. The T-mast cell was the predominant subtype in nearly all investigated organs and tissue locations. Only tryptase-positive mast cells could be demonstrated in bovine skin and uterus. No chymase activity was found in these organs, regardless of the fixation type. A larger number of mast cells was observed after fixation in Carnoy's fluid. The three different mast cell subtypes were only demonstrated in formalin-fixed tissue; chymase-positive mast cells were not found after fixation in Carnoy's fluid. Increasing experimental data suggest that mast cell subtypes have different functions in promoting and modulating inflammation and in remodeling the extracellular matrix. Since mast cell tryptase and chymase have different functional properties, these results may clarify the different reaction patterns observed in various organs and species.

Automated measurement of retinal vascular tortuosity.

Automatic measurement of blood vessel tortuosity is a useful capability for automatic ophthalmological diagnostic tools. We describe a suite of automated tortuosity measures for blood vessel segments extracted from RGB retinal images. The tortuosity measures were evaluated in two classification tasks: (1) classifying the tortuosity of blood vessel segments and (2) classifying the tortuosity of blood vessel networks. These tortuosity measures were able to achieve a classification rate of 91% for the first problem and 95% on the second problem, which confirms that they capture much of the ophthalmologists' notion of tortuosity.

Reference frame effects on shape perception in two versus three dimensions.

Three experiments are reported in which it is tested whether the Gestalt effect of configural orientation on shape perception operates on two-dimensional (2-D) or three-dimensional (3-D) representations of space. It is known that gravitationally defined squares and diamonds take longer to discriminate in diagonal arrays than in horizontal or vertical arrays. In the first experiment it is shown that this interference effect decreases dramatically in magnitude when pictorial depth information is added so that subjects perceive the target shapes in different depth planes. In the second experiment this difference is shown not to be due to relative size of the target shapes or to occlusion of a background plane. It is also shown, in the final experiment, that this difference is not due to linear perspective information or merely to perception of the target figures in a 3-D scene. The overall pattern of results supports the position that this configural reference frame effect arises primarily when the elements of the configuration are coplanar, and that the principal organization underlying it is the structure of the perceived 3-D environment rather than that of the 2-D image. In all three experiments, however, there is also a small interference effect in the noncoplanar 3-D conditions. This might be due either to some aspect of reference frame selection operating on the 2-D image representation or to the failure of subjects to see depth in the 3-D stimuli on some proportion of the trials.