Differentiation of Rice Tungro Spherical Virus Variants by RTPCR and RFLP

Differentiation of rice tungro spherical virus variants by RTPCR and RFLP tungro bacilliform virus (RTBV), the other causal agent, which causes the symptoms. RTSV is a single-stranded RNA virus of 12,180 nucleotides (Hull 1996).

Complete Nucleotide Sequence of Rice Tungro Spherical Virus Genome of a Highly Virulent Strain Vt6

The complete nucleotide sequence of rice tungro spherical virus (RTSV) strain Vt6, originally from Mindanao, the Philippines, with higher virulence to resistant rice cultivars, was determined and compared with the published sequence for the Philippine-type strain A (RTSV-A-Shen). It was reported that RTSV-A was not able to infect a rice resistant cultivar TKM 6 (10). RTSV-Vt6 and RTSV-A-Shen share 90% and 95% homology at nucleotide and amino-acid levels, respectively. The N-terminal leader sequence of RTSV-Vt6 contained a 39-amino acids-region (positions 65 to 103) which was totally different from that of RTSV-A-Shen; the difference resulted from frame shifting by nucleotide insertions and deletions. To confirm the amino-acid sequence differences of the leader polypeptide, the same region was cloned and sequenced using a newly obtained variant of RTSV-type 6, which had been collected in the field of IRRI, and seven field isolates from Mindanao, the Philippines. Since all the sequences of the target region are identical to that of the Vt6 leader polypeptide, the sequence difference in the leader region seems not to correlate with the virulence of Vt6.

Genetic Diversity of Rice Tungro Spherical Virus in Tungro-Endemic Provinces of the Philippines and Indonesia

The two adjacent genes of coat protein 1 and 2 of rice tungro spherical virus (RTSV) were amplified from total RNA extracts of serologically indistinguishable field isolates from the Philippines and Indonesia, using reverse transcriptase polymerase chain reaction (RT-PCR). Digestion with HindIII and BstYI restriction endonucleases differentiated the amplified DNA products into eight distinct coat protein genotypes. These genotypes were then used as indicators of virus diversity in the field. Inter- and intra-site diversities were determined over three cropping seasons. At each of the sites surveyed, one or two main genotypes prevailed together with other related minor or mixed genotypes that did not replace the main genotype over the sampling time. The cluster of genotypes found at the Philippines sites was significantly different from the one at the Indonesia sites, suggesting geographic isolation for virus populations. Phylogenetic studies based on the nucleotide sequences of 38 selected isolates confirm the spatial distribution of RTSV virus populations but show that gene flow may occur between populations. Under the present conditions, rice varieties do not seem to exert selective pressure on the virus populations. Based on the selective constraints in the coat protein amino acid sequences and the virus genetic composition per site, a negative selection model followed by random-sampling events due to vector transmissions is proposed to explain the inter-site diversity observed

Inheritance of Resistance to Rice Tungro Spherical Virus in a Near-Isogenic Line Derived from Utri Merah and in Rice Cultivar TKM6

Resistance to rice virus diseases is an important requirement in many Southeast Asian rice breeding programs. Inheritance of resistance to rice tungro spherical virus (RTSV) in TW5, a near-isogenic line derived from Indonesian rice cultivar Utri Merah, was compared to that in TKM6, an Indian rice cultivar. Both TKM6 and Utri Merah are cultivars resistant to RTSV infections. Crosses were made between TKM6 and TN1, a susceptible cultivar, and between TW5 and TN1, and F3 lines were evaluated for their resistance to RTSV using two RTSV inoculum sources and a serological assay (ELISA). In TKM6, the resistance to the mixture of RTSV-V + RTBV inoculum source was controlled by a single recessive gene, whereas in TW5, the resistance was controlled by two recessive genes. A single recessive gene, however, controlled the resistance in TW5 when another RTSV variant, RTSV-VI, was used, suggesting that the resistance in TW5 depends on the nature of the RTSV inoculum used. RT-PCR, sequence, and phylogenetic analyses confirmed that RTSV-VI inoculum differs from RTSV-V inoculum and accurate phenotyping of the resistance to RTSV requires the use of a genetic marker.

Decentralised particle filtering for multiple target tracking in wireless sensor networks

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The impact of sulphur content of diesel fuel on ultrafine particle formation

Early this year the Australian Department of Environment and Heritage commissioned a desktop literature review with a focus on ultrafine particles including analysis of health impacts of the particles as well as the impact of sulphur content of diesel fuel on ultrafine particle emission. This paper summarizes the findings of the report on the link between the sulphur content of diesel fuels and the number of ultrafine particles in diesel emissions. The literature search on this topic resulted in over 150 publications. The majority of these publications, although investigating different aspects of the influence of fuel sulphur level on diesel vehicle emissions, were not directly concerned with ultrafine particle emissions. A specific focus of the paper is on: ----- ----- summary of state of knowledge established by the review, and ----- ----- summary of recommendations on the research priorities for Australia to address the information gaps for this issue, and on the appropriate management responses.

Electrospraying a reproducible method for production of polymeric microspheres for biomedical applications

The ability to reproducibly load bioactive molecules into polymeric microspheres is a challenge. Traditional microsphere fabrication methods typically provide inhomogeneous release profiles and suffer from lack of batch to batch reproducibility, hindering their potential to up-scale and their translation to the clinic. This deficit in homogeneity is in part attributed to broad size distributions and variability in the morphology of particles. It is thus desirable to control morphology and size of non-loaded particles in the first instance, in preparation for obtaining desired release profiles of loaded particles in the later stage. This is achieved by identifying the key parameters involved in particle production and understanding how adapting these parameters affects the final characteristics of particles. In this study, electrospraying was presented as a promising technique for generating reproducible particles made of polycaprolactone, a biodegradable, FDA-approved polymer. Narrow size distributions were obtained by the control of electrospraying flow rate and polymer concentration, with average particle sizes ranging from 10 to 20 um. Particles were shown to be spherical with a homogenous embossed texture, determined by the polymer entanglement regime taking place during electrospraying. No toxic residue was detected by this process based on preliminary cell work using DNA quantification assays, validating this method as suitable for further loading of bioactive components.

Depth of focus and visual acuity with primary and secondary spherical aberration

It is known that the depth of focus (DOF) of the human eye can be affected by the higher order aberrations. We estimated the optimal combinations of primary and secondary Zernike spherical aberration to expand the DOF and evaluated their efficiency in real eyes using an adaptive optics system. The ratio between increased DOF and loss of visual acuity was used as the performance indicator. The results indicate that primary or secondary spherical aberration alone shows similar effectiveness in extending the DOF. However, combinations of primary and secondary spherical aberration with different signs provide better efficiency for expanding the DOF. This finding suggests that the optimal combinations of primary and secondary spherical aberration may be useful in the design of optical presbyopic corrections. © 2011 Elsevier Ltd. All rights reserved.

Relationships between rainfall intensity, duration and suspended particle washoff from an urban road surface

A basic understanding of the relationships between rainfall intensity, duration of rainfall and the amount of suspended particles in stormwater runoff generated from road surfaces has been gained mainly from past washoff experiments using rainfall simulators. Simulated rainfall was generally applied at constant intensities, whereas rainfall temporal patterns during actual storms are typically highly variable. This paper discusses a rationale for the application of the constant-intensity washoff concepts to actual storm event runoff. The rationale is tested using suspended particle load data collected at a road site located in Toowoomba, Australia. Agreement between the washoff concepts and measured data is most consistent for intermediate-duration storms (duration <5 h and >1 h). Particle loads resulting from these storm events increase linearly with average rainfall intensity. Above a threshold intensity, there is evidence to suggest a constant or plateau particle load is reached. The inclusion of a peak discharge factor (maximum 6 min rainfall intensity) enhances the ability to predict particle loads.

SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Train service timetabling in railway open markets by particle swarm optimisation

Railway timetabling is an important process in train service provision as it matches the transportation demand with the infrastructure capacity while customer satisfaction is also considered. It is a multi-objective optimisation problem, in which a feasible solution, rather than the optimal one, is usually taken in practice because of the time constraint. The quality of services may suffer as a result. In a railway open market, timetabling usually involves rounds of negotiations among a number of self-interested and independent stakeholders and hence additional objectives and constraints are imposed on the timetabling problem. While the requirements of all stakeholders are taken into consideration simultaneously, the computation demand is inevitably immense. Intelligent solution-searching techniques provide a possible solution. This paper attempts to employ a particle swarm optimisation (PSO) approach to devise a railway timetable in an open market. The suitability and performance of PSO are studied on a multi-agent-based railway open-market negotiation simulation platform.