Sequence Changes in Six Variants of Rice Tungro Bacilliform Virus and Their Phylogenetic Relationships

The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.

Comparison of Nucleotide Sequences between Northern and Southern Philippine Isolates of Rice Grassy Stunt Virus Indicates Occurrence of Natural Genetic Reassortment

Rice grassy stunt virus is a member of the genus Tenuivirus, is persistently transmitted by a brown planthopper, and has occurred in rice plants in South, Southeast, and East Asia (similar to North and South America). We determined the complete nucleotide (nt) sequences of RNAs 1 (9760 nt), 2 (4069 nt), 3 (3127 nt), 4 (2909 nt), 5 (2704 nt), and 6 (2590 nt) of a southern Philippine isolate from South Cotabato and compared them with those of a northern Philippine isolate from Laguna (Toriyama et al., 1997, 1998). The numbers of nucleotides in the terminal untranslated regions and open reading frames were identical between the two isolates except for the 5′ untranslated region of the complementary strand of RNA 4. Overall nucleotide differences between the two isolates were only 0.08% in RNA 1, 0.58% in RNA 4, and 0.26% in RNA 5, whereas they were 2.19% in RNA 2, 8.38% in RNA 3, and 3.63% in RNA 6. In the intergenic regions, the two isolates differed by 9.12% in RNA 2, 11.6% in RNA 3, and 6.86% in RNA 6 with multiple consecutive nucleotide deletion/insertions, whereas they differed by only 0.78% in RNA 4 and 0.34% in RNA 5. The nucleotide variation in the intergenic region of RNA 6 within the South Cotabato isolate was only 0.33%. These differences in accumulation of mutations among individual RNA segments indicate that there was genetic reassortment in the two geographical isolates; RNAs 1, 4, and 5 of the two isolates came from a common ancestor, whereas RNAs 2, 3, and 6 were from two different ancestors.

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.

Inter-and Intra-Site Genetic Diversity of Natural Field Populations of Rice Tungro Bacilliform Virus in the Philippines

The genetic structure of rice tungro bacilliform virus (RTBV) populations within and between growing sites was analyzed in a collection of natural field isolates from different rice varieties grown in eight tungro-endemic sites of the Philippines. Total DNA extracts from 345 isolates were digested with EcoRV restriction enzyme and hybridized with a full-length probe of RTBV, a procedure shown in preliminary experiments capable of revealing high levels of polymorphism in RTBV field isolates. In the total population, 17 distinct EcoRV-based genome profiles (genotypes) were identified and used as indicators for virus diversity. Distinct sets of genotypes occurred in Isabela and North Cotabato provinces suggesting a geographic isolation of virus populations. However, among the sites in each province, there were few significant differences in the genotype compositions of virus populations. The number of genotypes detected at a site varied from two to nine with a few genotypes dominating. In general the isolates at a site persisted from season to season indicating a genetic stability for the local virus population. Over the sampling time, IRRI rice varieties, which have green leafhopper resistance genes, supported similar virus populations to those supported by other varieties, indicating that the variety of the host exerted no apparent selection pressures. Insect transmission experiments on selected RTBV field isolates showed that dramatic shifts in genotype and phenotype distributions can occur in response to host /environmental shifts.

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.

Spatial stimulus : Model making in the architectural design studio

This action research examines the enhancement of visual communication within the architectural design studio through physical model making. „It is through physical model making that designers explore their conceptual ideas and develop the creation and understanding of space,‟ (Salama & Wilkinson 2007:126). This research supplements Crowther‟s findings extending the understanding of visual dialogue to include physical models. „Architecture Design 8‟ is the final core design unit at QUT in the fourth year of the Bachelor of Design Architecture. At this stage it is essential that students have the ability to communicate their ideas in a comprehensive manner, relying on a combination of skill sets including drawing, physical model making, and computer modeling. Observations within this research indicates that students did not integrate the combination of the skill sets in the design process through the first half of the semester by focusing primarily on drawing and computer modeling. The challenge was to promote deeper learning through physical model making. This research addresses one of the primary reasons for the lack of physical model making, which was the limited assessment emphasis on the physical models. The unit was modified midway through the semester to better correlate the lecture theory with studio activities by incorporating a series of model making exercises conducted during the studio time. The outcome of each exercise was assessed. Tutors were surveyed regarding the model making activities and a focus group was conducted to obtain formal feedback from students. Students and tutors recognised the added value in communicating design ideas through physical forms and model making. The studio environment was invigorated by the enhanced learning outcomes of the students who participated in the model making exercises. The conclusions of this research will guide the structure of the upcoming iteration of the fourth year design unit.

Spatial analysis of notified dengue fever infections

This study aimed to investigate the spatial clustering and dynamic dispersion of dengue incidence in Queensland, Australia. We used Moran’s I statistic to assess the spatial autocorrelation of reported dengue cases. Spatial empirical Bayes smoothing estimates were used to display the spatial distribution of dengue in postal areas throughout Queensland. Local indicators of spatial association (LISA) maps and logistic regression models were used to identify spatial clusters and examine the spatio-temporal patterns of the spread of dengue. The results indicate that the spatial distribution of dengue was clustered during each of the three periods of 1993–1996, 1997–2000 and 2001–2004. The high-incidence clusters of dengue were primarily concentrated in the north of Queensland and low-incidence clusters occurred in the south-east of Queensland. The study concludes that the geographical range of notified dengue cases has significantly expanded in Queensland over recent years.

Design and implementation of sensor networks for the observation and research of harmful algal blooms in southern California coastal waters

Harmful Algal Blooms (HABs) have become an important environmental concern along the western coast of the United States. Toxic and noxious blooms adversely impact the economies of coastal communities in the region, pose risks to human health, and cause mortality events that have resulted in the deaths of thousands of fish, marine mammals and seabirds. One goal of field-based research efforts on this topic is the development of predictive models of HABs that would enable rapid response, mitigation and ultimately prevention of these events. In turn, these objectives are predicated on understanding the environmental conditions that stimulate these transient phenomena. An embedded sensor network (Fig. 1), under development in the San Pedro Shelf region off the Southern California coast, is providing tools for acquiring chemical, physical and biological data at high temporal and spatial resolution to help document the emergence and persistence of HAB events, supporting the design and testing of predictive models, and providing contextual information for experimental studies designed to reveal the environmental conditions promoting HABs. The sensor platforms contained within this network include pier-based sensor arrays, ocean moorings, HF radar stations, along with mobile sensor nodes in the form of surface and subsurface autonomous vehicles. FreewaveTM radio modems facilitate network communication and form a minimally-intrusive, wireless communication infrastructure throughout the Southern California coastal region, allowing rapid and cost-effective data transfer. An emerging focus of this project is the incorporation of a predictive ocean model that assimilates near-real time, in situ data from deployed Autonomous Underwater Vehicles (AUVs). The model then assimilates the data to increase the skill of both nowcasts and forecasts, thus providing insight into bloom initiation as well as the movement of blooms or other oceanic features of interest (e.g., thermoclines, fronts, river discharge, etc.). From these predictions, deployed mobile sensors can be tasked to track a designated feature. This focus has led to the creation of a technology chain in which algorithms are being implemented for the innovative trajectory design for AUVs. Such intelligent mission planning is required to maneuver a vehicle to precise depths and locations that are the sites of active blooms, or physical/chemical features that might be sources of bloom initiation or persistence. The embedded network yields high-resolution, temporal and spatial measurements of pertinent environmental parameters and resulting biology (see Fig. 1). Supplementing this with ocean current information and remotely sensed imagery and meteorological data, we obtain a comprehensive foundation for developing a fundamental understanding of HAB events. This then directs labor- intensive and costly sampling efforts and analyses. Additionally, we provide coastal municipalities, managers and state agencies with detailed information to aid their efforts in providing responsible environmental stewardship of their coastal waters.

Modification and validation of a microwave-assisted digestion method for subsequent ICP-MS determination of selected heavy metals in sediment and fish samples in Agusan River, Philippines

This study investigated, validated, and applied the optimum conditions for a modified microwave assisted digestion method for subsequent ICP-MS determination of mercury, cadmium, and lead in two matrices relevant to water quality, that is, sediment and fish. Three different combinations of power, pressure, and time conditions for microwave-assisted digestion were tested, using two certified reference materials representing the two matrices, to determine the optimum set of conditions. Validation of the optimized method indicated better recovery of the studied metals compared to standard methods. The validated method was applied to sediment and fish samples collected from Agusan River and one of its tributaries, located in Eastern Mindanao, Philippines. The metal concentrations in sediment ranged from 2.85 to 341.06 mg/kg for Hg, 0.05 to 44.46 mg/kg for Cd and 2.20 to 1256.16 mg/kg for Pb. The results indicate that the concentrations of these metals in the sediments rapidly decrease with distance downstream from sites of contamination. In the selected fish species, the metals were detected but at levels that are considered safe for human consumption, with concentrations of 2.14 to 6.82 μg/kg for Hg, 0.035 to 0.068 μg/kg for Cd, and 0.019 to 0.529 μg/kg for Pb.

Detailed landscape plan for the North section of the Bailang River north of Jiqing Highway, Weifang

International practice-led design research in landscape architecture has identified wetland sites as highly significant and potentially fragile environments in many countries. China has considerable wetland acreage that has been drained and transformed into farmland to address local poverty of farmers. An important gap in knowledge exists as to how to design Chinese public open spaces to reduce water contamination, flood severity and loss of farmland for local villagers as urban development expands. This project responded to the opportunity of introducing a new type of wetland design to Stage 3 of the Bailang River Redevelopment, Weifang City, Shandong Province. The work proposed a range of wetland design innovations for Chinese wetland environments to encourage on-site solutions to contamination and flooding problems.

Stage 1 of the Yueyang Urban Water System Project: Landscape planning and design of Wangjia River

Chinese landscape architects are largely focused on objective practical solutions to environmental problems. In the West, theoretical landscape knowledge is largely conceptual and abstract. This research debated how Australian ecological concepts could or should be transposed to Chinese landscapes. This project responded to severe water and soil pollution issues in the estuarine and riparian zones of rivers flowing into Dongting Lake, in Yueyang City, Hunan Province. This work proposed a range of waterfront design innovations that challenged the notion of corridor as habitat, filter, barrier and conduit in a Chinese riparian context.

Shijiazhuang ecological landscape planning and design comprehensive improvement program for the Hutuo River

International practice-led design research in landscape architecture has identified water quality and water availability as two of the most important environmental issues in developing countries. China is particularly focused on improving water supplies for its rural and urban populations. However a significant gap in knowledge exists between urban planning and environmental engineering in China as to how to design Chinese public open spaces to reduce water pollution in urban rivers. This project responded to traditional zoning methods in Shijiazhuang City, Hebei Province, by proposing a range of water sensitive design innovations from lake construction to planting design to modify standardised engineering solutions in a Chinese context.

Cognitive processes and strategies employed by children to learn spatial representations

Children often have difficulties in learning spatial representations. This study investigated the effect of four different instructional formats on learning outcomes and strategies used when dealing with spatial tasks such as assembly procedures. It was hypothesised that instructional material that imposed least extraneous cognitive load would facilitate enhanced learning. Forty secondary students were presented with four types of instruction; orthographic drawing, isometric drawing, physical model and, isometric and physical model together. The findings provide evidence to suggest that working from physical models caused least extraneous cognitive load compared to the isometric and orthographic groups. The model group took less time, had more correctly completed models, required fewer extra looks, spent less time studying the instruction and made fewer errors. Problem decomposition, forward working and attending to information in the foreground of the graphical representation strategies were analysed.

Ocklawaha River restoration : the fate of the Rodman Reservoir

The Rodman Reservoir, an impoundment on the Ocklawaha River in north central Florida, is a last remnant of the Cross-Florida Barge Canal (CFBC). The canal, conceived in the 1820's, was designed by the U.S. Army Corps of Engineers (USACE) to shorten shipping lanes between the Fulf ports and the Atlantic coast. Opposition to CFBC by Florida's young environmental movement led to a half in construction of the CFBC in 1971, but decommissioning of the already-constructed Rodman dam and the reservoir behind it has been mired in controversy every since.

Long term immunity to live attenuated Japanese encephalitis chimeric virus vaccine : randomized, double-blind, 5-year phase II study in healthy adults.

In a randomized, double-blind study, 202 healthy adults were randomized to receive a live, attenuated Japanese encephalitis chimeric virus vaccine (JE-CV) and placebo 28 days apart in a cross-over design. A subgroup of 98 volunteers received a JE-CV booster at month 6. Safety, immunogenicity, and persistence of antibodies to month 60 were evaluated. There were no unexpected adverse events (AEs) and the incidence of AEs between JE-CV and placebo were similar. There were three serious adverse events (SAE) and no deaths. A moderately severe case of acute viral illness commencing 39 days after placebo administration was the only SAE considered possibly related to immunization. 99% of vaccine recipients achieved a seroprotective antibody titer ≥ 10 to JE-CV 28 days following the single dose of JE-CV, and 97% were seroprotected at month 6. Kaplan Meier analysis showed that after a single dose of JE-CV, 87% of the participants who were seroprotected at month 6 were still protected at month 60. This rate was 96% among those who received a booster immunization at month 6. 95% of subjects developed a neutralizing titer ≥ 10 against at least three of the four strains of a panel of wild-type Japanese encephalitis virus (JEV) strains on day 28 after immunization. At month 60, that proportion was 65% for participants who received a single dose of JE-CV and 75% for the booster group. These results suggest that JE-CV is safe, well tolerated and that a single dose provides long-lasting immunity to wild-type strains