Genetic Composition and Complexity of Virus Populations at Tungro-Endemic and Outbreak Rice Sites

We have recently demonstrated the geographic isolation of rice tungro bacilliform virus (RTBV) populations in the tungro-endemic provinces of Isabela and North Cotabato, Philippines. In this study, we examined the genetic structure of the virus populations at the tungro-outbreak sites of Lanao del Norte, a province adjacent to North Cotabato. We also analyzed the virus populations at the tungro-endemic sites of Subang, Indonesia, and Dien Khanh, Vietnam. Total DNA extracts from 274 isolates were digested with EcoRV restriction enzyme and hybridized with a full-length probe of RTBV. In the total population, 22 EcoRV-restricted genome profiles (genotypes) were identified. Although overlapping genotypes could be observed, the outbreak sites of Lanao del Norte had a genotype combination distinct from that of Subang or Dien Khanh but a genotype combination similar to that identified earlier from North Cotabato, the adjacent endemic province. Sequence analysis of the intergenic region and part of the ORF1 RTBV genome from randomly selected genotypes confirms the geographic clustering of RTBV genotypes and, combined with restriction analysis, the results suggest a fragmented spatial distribution of RTBV local populations in the three countries. Because RTBV depends on rice tungro spherical virus (RTSV) for transmission, the population dynamics of both tungro viruses were then examined at the endemic and outbreak sites within the Philippines. The RTBV genotypes and the coat protein RTSV genotypes were used as indicators for virus diversity. A shift in population structure of both viruses was observed at the outbreak sites with a reduced RTBV but increased RTSV gene diversity

The Spartan-3E Tutorial 1 : Introduction to FPGA Programming, Version 1.0

This tutorial is designed to help new users become familiar with using the Spartan-3E board. The tutorial steps through the following: writing a small program in VHDL which carries out simple combinational logic; connecting the program inputs and outputs to the switches, buttons and LEDs on the Spartan-3E board; and downloading the program to the Spartan-3E board using the Project Navigator software.

QoS-oriented resource allocation and scheduling of multiple composite Web services in a hybrid cloud using a random-key genetic algorithm

In cloud computing resource allocation and scheduling of multiple composite web services is an important challenge. This is especially so in a hybrid cloud where there may be some free resources available from private clouds but some fee-paying resources from public clouds. Meeting this challenge involves two classical computational problems. One is assigning resources to each of the tasks in the composite web service. The other is scheduling the allocated resources when each resource may be used by more than one task and may be needed at different points of time. In addition, we must consider Quality-of-Service issues, such as execution time and running costs. Existing approaches to resource allocation and scheduling in public clouds and grid computing are not applicable to this new problem. This paper presents a random-key genetic algorithm that solves new resource allocation and scheduling problem. Experimental results demonstrate the effectiveness and scalability of the algorithm.

Genetic analysis reveals two stocks of skipjack tuna (Katsuwonus pelamis) in the north western Indian Ocean

Skipjack (SJT) (Katsuwonus pelamis) is a medium sized, pelagic, highly dispersive tuna species that occurs widely across tropical and subtropical waters. SJT constitute the largest tuna fishery in the Indian Ocean, and are currently managed as a single stock. Patterns of genetic variation in a mtDNA gene and 6 microsatellite loci were examined to test for stock structure in the northwestern Indian Ocean. 324 individuals were sampled from five major fishing grounds around Sri Lanka, and single sites in the Maldive Islands and the Laccadive Islands. Phylogenetic reconstruction of mtDNA revealed two coexisting divergent clades in the region. AMOVA (Analysis of Molecular Variance) of mtDNA data revealed significant genetic differentiation among sites (ΦST = 0.2029, P < 0.0001), also supported by SAMOVA results. AMOVA of microsatellite data also showed significant differentiation among most sampled sites (FST = 0.0256, P<0.001) consistent with the mtDNA pattern. STRUCTURE analysis of the microsatellite data revealed two differentiated stocks. While the both two marker types examined identified two genetic groups, microsatellite analysis indicates that the sampled SJT are likely to represent individuals sourced from discrete breeding grounds that are mixed in feeding grounds in Sri Lankan waters.

Tangible programming elements for young children

Tangible programming elements offer the dynamic and programmable properties of a computer without the complexity introduced by the keyboard, mouse and screen. This paper explores the extent to which programming skills are used by children during interactions with a set of tangible programming elements: the Electronic Blocks. An evaluation of the Electronic Blocks indicates that children become heavily engaged with the blocks, and learn simple programming with a minimum of adult support.

Assessing genetic diversity in cultured aquatic species : the Sydney Rock Oyster (Saccostrea glomerata) stock improvement program as a model

Genetic variation is the resource animal breeders exploit in stock improvement programs. Both the process of selection and husbandry practices employed in aquaculture will erode genetic variation levels overtime, hence the critical resource can be lost and this may compromise future genetic gains in breeding programs. The amount of genetic variation in five lines of Sydney Rock Oyster (SRO) that had been selected for QX (Queensland unknown) disease resistance were examined and compared with that in a wild reference population using seven specific SRO microsatellite loci. The five selected lines had significantly lower levels of genetic diversity than did the wild reference population with allelic diversity declining approximately 80%, but impacts on heterozygosity per locus were less severe. Significant deficiencies in heterozygotes were detected at six of the seven loci in both mass selected lines and the wild reference population. Against this trend however, a significant excess of heterozygotes was recorded at three loci Sgo9, Sgo14 and Sgo21 in three QX disease resistant lines (#2, #5 and #13). All populations were significantly genetic differentiated from each other based on pairwise FST values. A neighbour joining tree based on DA genetic distances showed a clear separation between all culture and wild populations. Results of this study show clearly, that the impacts of the stock improvement program for SRO has significantly eroded natural levels of genetic variation in the culture lines. This could compromise long-term genetic gains and affect sustainability of the SRO breeding program over the long-term.

Spatial population genetic structure reveals strong natal site fidelity in Echinocladius martini (Diptera: Chironomidae) in northeast Queensland, Australia

1. A diverse array of patterns has been reported regarding the spatial extent of population genetic structure and effective dispersal in freshwater macroinvertebrates. In river systems, the movements of many taxa can be restricted to varying degrees by the natural stream channel hierarchy. 2. In this study, we sampled populations of the non-biting freshwater midge Echinocladius martini in the Paluma bioregion of tropical northeast Queensland to investigate fine scale patterns of within- and among-stream dispersal and gene flow within a purported historical refuge. We amplified a 639 bp fragment of mitochondrial COI and analysed genetic structure using pairwise ΦST, hierarchical AMOVA, Mantel tests and a parsimony network. Genetic variation was partitioned among stream sections using Streamtree to investigate the effect of potential instream dispersal barriers. 3. The data revealed strong natal site fidelity and significant differentiation among neighbouring, geographically proximate streams. We found evidence for only episodic adult flight among sites on separate stream reaches. Overall, however, our data suggested that both larval and adult dispersal was largely limited to within a stream channel. 4. This may arise from a combination of the high density of riparian vegetation physically restricting dispersal and from the joint effects of habitat stability and large population sizes. Together these may mitigate the requirement for movement among streams to avoid inbreeding and local extinction due to habitat change and may thus enable persistence of upstream populations in the absence of regular compensatory upstream flight. Taken together, these data suggest that dispersal of E. martini is highly restricted, to the scale of only a few kilometres, and hence occurs predominantly within the natal stream.

Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species

Background Chlamydia pneumoniae is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on four essentially clonal (> 99% identity) C. pneumoniae human genomes (AR39, CWL029, J138 and TW183), providing relatively little insight into strain diversity and evolution of this species. Results We performed individual gene-by-gene comparisons of the recently sequenced C. pneumoniae koala genome and four C. pneumoniae human genomes to identify species-specific genes, and more importantly, to gain an insight into the genetic diversity and evolution of the species. We selected genes dispersed throughout the chromosome, representing genes that were specific to C. pneumoniae, genes with a demonstrated role in chlamydial biology and/or pathogenicity (n = 49), genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6), and extrachromosomal elements (9 plasmid and 2 bacteriophage genes). Conclusions We have identified strain-specific differences and targets for detection of C. pneumoniae isolates from both human and animal origin. Such characterisation is necessary for an improved understanding of disease transmission and intervention.