Genetic variability of Tomato spotted wilt virus in Australia and validation of real time RT-PCR for its detection in single and bulked leaf samples

The potential for large-scale use of a sensitive real time reverse transcription polymerase chain reaction (RT-PCR) assay was evaluated for the detection of Tomato spotted wilt virus (TSWV) in single and bulked leaf samples by comparing its sensitivity with that of DAS-ELISA. Using total RNA extracted with RNeasy® or leaf soak methods, real time RT-PCR detected TSWV in all infected samples collected from 16 horticultural crop species (including flowers, herbs and vegetables), two arable crop species, and four weed species by both assays. In samples in which DAS-ELISA had previously detected TSWV, real time RT-PCR was effective at detecting it in leaf tissues of all 22 plant species tested at a wide range of concentrations. Bulk samples required more robust and extensive extraction methods with real time RT-PCR, but it generally detected one infected sample in 1000 uninfected ones. By contrast, ELISA was less sensitive when used to test bulked samples, once detecting up to 1 infected in 800 samples with pepper but never detecting more than 1 infected in 200 samples in tomato and lettuce. It was also less reliable than real time RT-PCR when used to test samples from parts of the leaf where the virus concentration was low. The genetic variability among Australian isolates of TSWV was small. Direct sequencing of a 587 bp region of the nucleoprotein gene (S RNA) of 29 isolates from diverse crops and geographical locations yielded a maximum of only 4.3% nucleotide sequence difference. Phylogenetic analysis revealed no obvious groupings of isolates according to geographic origin or host species. TSWV isolates, that break TSWV resistance genes in tomato or pepper did not differ significantly in the N gene region studied, indicating that a different region of the virus genome is responsible for this trait.

Assessing the relationship between shire winter crop yield and seasonal variability of the MODIS NDVI and EVI images

Australian researchers have been developing robust yield estimation models, based mainly on the crop growth response to water availability during the crop season. However, knowledge of spatial distribution of yields within and across the production regions can be improved by the use of remote sensing techniques. Images of Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation indices, available since 1999, have the potential to contribute to crop yield estimation. The objective of this study was to analyse the relationship between winter crop yields and the spectral information available in MODIS vegetation index images at the shire level. The study was carried out in the Jondaryan and Pittsworth shires, Queensland , Australia . Five years (2000 to 2004) of 250m resolution, 16-day composite of MODIS Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI) images were used during the winter crop season (April to November). Seasonal variability of the profiles of the vegetation index images for each crop season using different regions of interest (cropping mask) were displayed and analysed. Correlation analysis between wheat and barley yield data and MODIS image values were also conducted. The results showed high seasonal variability in the NDVI and EVI profiles, and the EVI values were consistently lower than those of the NDVI. The highest image values were observed in 2003 (in contrast to 2004), and were associated with rainfall amount and distribution. The seasonal variability of the profiles was similar in both shires, with minimum values in June and maximum values at the end of August. NDVI and EVI images showed sensitivity to seasonal variability of the vegetation and exhibited good association (e.g. r = 0.84, r = 0.77) with winter crop yields.

Effect of surface-applied treatments on the above-ground performance of simulated timber joinery

We examined the effect of surface-applied treatments on the above-ground decay resistance of the tenon of mortice-and-tenon timber joints designed to simulate joinery that is exposed to the weather. Joints made from untreated radiata pine, Douglas-fir, brush box, spotted gum and copper-chrome-arsenic (CCA) treated radiata pine were exposed to the weather for 9 y on above-ground racks at five sites throughout eastern Australia. Results indicate (1) a poorly maintained external paint film generally accelerated decay, (2) a brush coat of water-repellent preservative inside the joints often extended serviceability (in some cases by a factor of up to seven times that of untreated joints) and (3) the level of protection provided by a coat of primer applied inside the joint varied and in most cases was not as effective as the water-repellent preservative treatment.

An absolute method for the determination of surface tension of liquids using pendent drop profiles

Drop formation at conical tips which is of relevance to metallurgists is investigated based on the principle of minimization of free energy using the variational approach. The dimensionless governing equations for drop profiles are computer solved using the fourth order Runge-Kutta method. For different cone angles, the theoretical plots of XT and ZT vs their ratio, are statistically analyzed, where XT and ZT are the dimensionless x and z coordinates of the drop profile at a plane at the conical tip, perpendicular to the axis of symmetry. Based on the mathematical description of these curves, an absolute method has been proposed for the determination of surface tension of liquids, which is shown to be preferable in comparison with the earlier pendent-drop profile methods.

Site classification and estimation of surface level seismic hazard using geophysical data and probabilistic approach

This paper presents the site classification of Bangalore Mahanagar Palike (BMP) area using geophysical data and the evaluation of spectral acceleration at ground level using probabilistic approach. Site classification has been carried out using experimental data from the shallow geophysical method of Multichannel Analysis of Surface wave (MASW). One-dimensional (1-D) MASW survey has been carried out at 58 locations and respective velocity profiles are obtained. The average shear wave velocity for 30 m depth (Vs(30)) has been calculated and is used for the site classification of the BMP area as per NEHRP (National Earthquake Hazards Reduction Program). Based on the Vs(30) values major part of the BMP area can be classified as ``site class D'', and ``site class C'. A smaller portion of the study area, in and around Lalbagh Park, is classified as ``site class B''. Further, probabilistic seismic hazard analysis has been carried out to map the seismic hazard in terms spectral acceleration (S-a) at rock and the ground level considering the site classes and six seismogenic sources identified. The mean annual rate of exceedance and cumulative probability hazard curve for S. have been generated. The quantified hazard values in terms of spectral acceleration for short period and long period are mapped for rock, site class C and D with 10% probability of exceedance in 50 years on a grid size of 0.5 km. In addition to this, the Uniform Hazard Response Spectrum (UHRS) at surface level has been developed for the 5% damping and 10% probability of exceedance in 50 years for rock, site class C and D These spectral acceleration and uniform hazard spectrums can be used to assess the design force for important structures and also to develop the design spectrum.

Perception of surface brightness

The human visual system has adapted to function in different lighting environments and responds to contrast instead of the amount of light as such. On the one hand, this ensures constancy of perception, for example, white paper looks white both in bright sunlight and in dim moonlight, because contrast is invariant to changes in overall light level. On the other hand, the brightness of the surfaces has to be reconstructed from the contrast signal because no signal from surfaces as such is conveyed to the visual cortex. In the visual cortex, the visual image is decomposed to local features by spatial filters that are selective for spatial frequency, orientation, and phase. Currently it is not known, however, how these features are subsequently integrated to form objects and object surfaces. In this thesis the integration mechanisms of achromatic surfaces were studied by psychophysically measuring the spatial frequency and orientation tuning of brightness perception. In addition, the effect of textures on the spread of brightness and the effect of phase of the inducing stimulus on brightness were measured. The novel findings of the thesis are that (1) a narrow spatial frequency band, independent of stimulus size and complexity, mediates brightness information (2) figure-ground brightness illusions are narrowly tuned for orientation (3) texture borders, without any luminance difference, are able to block the spread of brightness, and (4) edges and even- and odd-symmetric Gabors have a similar antagonistic effect on brightness. The narrow spatial frequency tuning suggests that only a subpopulation of neurons in V1 is involved in brightness perception. The independence of stimulus size and complexity indicates that the narrow tuning reflects hard-wired processing in the visual system. Further, it seems that figure-ground segregation and mechanisms integrating contrast polarities are closely related to the low level mechanisms of brightness perception. In conclusion, the results of the thesis suggest that a subpopulation of neurons in visual cortex selectively integrates information from different contrast polarities to reconstruct surface brightness.

X-ray photoelectron spectroscopic studies of surface oxidation of metallic glasses

Surface oxidation of the metallic glass Fe40Ni38Mo4B18 has been studied by X-ray photoelectron spectroscopy. The oxidation behaviour of the metallic glass has been compared with a crystallized sample of the same composition. A similar study has been carried out on the metallic glass Ni76Si12B12,which shows the importance of chemical composition in determining the surface oxidation behaviour of these alloys.

Study of surface acidity of oxide catalysts by photoacoustic spectroscopy

Photoacoustic spectroscopy has been employed to estimate quantitatively the acid sites on oxide catalysts. The technique involves the measurement of the ratio of intensities of absorption bands due to conjugate bases and acids of indicators adsorbed on the catalyst surface as a function of the amount of added n-butylamine. Basic sites in sodium-impregnated alumina samples have been examined by adsorbing phenolphthalein on these surfaces.

Influence of the electric field on the low-temperature thermal decomposition of ammonium perchlorate/polystyrene propellant

An electric field (100 V/cm at 230°C and 150°C) has been applied to ammonium perchlorate (AP)/polystyrene (PS) propellant mixtures in order to understand the low temperature decomposition behavior of the propellant. The charge-carrying species is anionic in nature at 230°C, which could be ClO4−, but is cationic at 150°C, which could be either NH4+ or H+. These results are parallel to that observed for pure ammonium perchlorate (AP) pellets [1]. The burning rate (r' ) of the propellant was found to follow the same trend as that for the thermal decomposition of the propellant on application of an electric field. At 150°C Image was higher at the −ve electrode than at the +ve electrode, but at 230°C just the opposite was observed. Kinetic studies have confirmed that the decomposition of the orthorhombic AP follows two mechanism corresponding to E = 30 kcal mol−1 (180–230°C) and E = 15 kcal mol−1 (150–180°C).

XPS and XAES studies of surface segregation and oxidation of Cu-Ge alloy

Surface segregation of Ge is seen in the Cu-5at%Ge alloy with an activation enthalpy equal to 17 kJ/mol. Oxidation of the alloy in the temperature range 400 to 600 K shows the formation of Cu2O and GeO which on further heating in vacuum at 650 K converts to GeO2 with the reduction of Cu2O to Cu.

FTO genotype is associated with phenotypic variability of body mass index

There is evidence across several species for genetic control of phenotypic variation of complex traits1, 2, 3, 4, such that the variance among phenotypes is genotype dependent. Understanding genetic control of variability is important in evolutionary biology, agricultural selection programmes and human medicine, yet for complex traits, no individual genetic variants associated with variance, as opposed to the mean, have been identified. Here we perform a meta-analysis of genome-wide association studies of phenotypic variation using ~170,000 samples on height and body mass index (BMI) in human populations. We report evidence that the single nucleotide polymorphism (SNP) rs7202116 at the FTO gene locus, which is known to be associated with obesity (as measured by mean BMI for each rs7202116 genotype)5, 6, 7, is also associated with phenotypic variability. We show that the results are not due to scale effects or other artefacts, and find no other experiment-wise significant evidence for effects on variability, either at loci other than FTO for BMI or at any locus for height. The difference in variance for BMI among individuals with opposite homozygous genotypes at the FTO locus is approximately 7%, corresponding to a difference of ~0.5 kilograms in the standard deviation of weight. Our results indicate that genetic variants can be discovered that are associated with variability, and that between-person variability in obesity can partly be explained by the genotype at the FTO locus. The results are consistent with reported FTO by environment interactions for BMI8, possibly mediated by DNA methylation9, 10. Our BMI results for other SNPs and our height results for all SNPs suggest that most genetic variants, including those that influence mean height or mean BMI, are not associated with phenotypic variance, or that their effects on variability are too small to detect even with samples sizes greater than 100,000.

Study of Friction and Transfer Layer Formation in Copper-Steel Tribo-System: Role of Surface Texture and Roughness Parameters

In the present investigation, experiments were conducted on a tribological couple-copper pin against steel plate-using an inclined pin-on-plate sliding tester to understand the role of surface texture and roughness parameters of the plate on the coefficient friction and transfer layer formation. Two surface characteristics of the steel plates-roughness and texture-were varied in the tests. It was observed that the transfer layer formation and the coefficient of friction along with its two components, namely, the adhesion and plowing, are controlled by the surface texture of the plate. The plowing component of friction was highest for the surface texture that promotes plane strain conditions while it was lowest for the texture that favors plane stress conditions at the interface. Dimensionless quantifiable roughness parameters were formulated to describe the degree of plowing and hence the plane strain/stress type deformations taking place at the asperity level.

A Novel Approach to the Study of Surface Oxidation States and Oxidation of Transition Metals by Auger Electron Spectroscopy

L$_{23}$ M$_{45}$ M$_{45}$/L$_{23}$ M$_{23}$ M$_{45}$, L$_{23}$ M$_{45}$ M$_{45}$/L$_{23}$ M$_{23}$ M$_{23}$ and L$_{23}$ M$_{23}$ M$_{45}$/L$_{23}$ M$_{23}$ M$_{23}$ Auger intensity ratios in transition metal oxides and sulphides are shown to be directly related to the number of valence electrons in the metal as well as to its oxidation state. The metal Auger intensity ratios provide a unique probe, independent of O (KLL) intensity, to study surface oxidation states of metals. These intensity ratios have been effectively employed to investigate surface oxidation of nickel, iron and copper. The oxidation studies have unravelled some interesting aspects of surface oxidation.

Modifications of surface materials and their effects on cleanability as studied by radiochemical methods

Modifications of surface materials and their effects on cleanability have important impacts in many fields of activity. In this study the primary aim was to develop radiochemical methods suitable for evaluating cleanability in material research for different environments. Another aim was to investigate the effects of surface modifications on cleanabilitity and surface properties of plastics, ceramics, concrete materials and also their coatings in conditions simulating their typical environments. Several new 51Cr and 14C labelled soils were developed for testing situations. The new radiochemical methods developed were suitable for examining different surface materials and different soil types, providing quantitative information about the amount of soil on surfaces. They also take into account soil soaked into surfaces. The supporting methods colorimetric determination and ATP bioluminescence provided semi-quantitative results. The results from the radiochemical and supporting methods partly correlated with each other. From a material research point of view numerous new materials were evaluated. These included both laboratory-made model materials and commercial products. Increasing the amount of plasticizer decreased the cleanability of poly(vinyl chloride) (PVC) materials. Microstructured surfaces of plastics improved the cleanability of PVC from particle soils, whereas for oil soil microstructuring reduced the cleanability. In the case of glazed ceramic materials, coatings affected the cleanability. The roughness of surfaces correlated with cleanability from particle soils and the cleanability from oil soil correlated with the contact angles. Organic particle soil was removed more efficiently from TiO2-coated ceramic surfaces after UV-radiation than without UV treatment, whereas no effect was observed on the cleanability of oil soil. Coatings improved the cleanability of concrete flooring materials intended for use in animal houses.