Nature and extent of genetic diversity of dengue viruses determined by 454 pyrosequencing

Dengue virus (DENV) populations are characteristically highly diverse. Regular lineage extinction and replacement is an important dynamic DENV feature, and most DENV lineage turnover events are associated with increased incidence of disease. The role of genetic diversity in DENV lineage extinctions is not understood. We investigated the nature and extent of genetic diversity in the envelope (E) gene of DENV serotype 1 representing different lineages histories. A region of the DENV genome spanning the E gene was amplified and sequenced by Roche/454 pyrosequencing. The pyrosequencing results identified distinct sub-populations (haplotypes) for each DENV-1 E gene. A phylogenetic tree was constructed with the consensus DENV-1 E gene nucleotide sequences, and the sequences of each constructed haplotype showed that the haplotypes segregated with the Sanger consensus sequence of the population from which they were drawn. Haplotypes determined through pyrosequencing identified a recombinant DENV genome that could not be identified through Sanger sequencing. Nucleotide level sequence diversities of DENV-1 populations determined from SNP analysis were very low, estimated from 0.009-0.01. There were also no stop codon, frameshift or non-frameshift mutations observed in the E genes of any lineage. No significant correlations between the accumulation of deleterious mutations or increasing genetic diversity and lineage extinction were observed (p>0.5). Although our hypothesis that accumulation of deleterious mutations over time led to the extinction and replacement of DENV lineages was ultimately not supported by the data, our data does highlight the significant technical issues that must be resolved in the way in which population diversity is measured for DENV and other viruses. The results provide an insight into the within-population genetic structure and diversity of DENV-1 populations.

Analysis of genome survey sequences and SSR marker development for Siamese Mud Carp, Henicorhynchus siamensis, using 454 Pyrosequencing

Siamese mud carp (Henichorynchus siamensis) is a freshwater teleost of high economic importance in the Mekong River Basin. However, genetic data relevant for delineating wild stocks for management purposes currently are limited for this species. Here, we used 454 pyrosequencing to generate a partial genome survey sequence (GSS) dataset to develop simple sequence repeat (SSR) markers from H. siamensis genomic DNA. Data generated included a total of 65,954 sequence reads with average length of 264 nucleotides, of which 2.79% contain SSR motifs. Based on GSS-BLASTx results, 10.5% of contigs and 8.1% singletons possessed significant similarity (E value < 10–5) with the majority matching well to reported fish sequences. KEGG analysis identified several metabolic pathways that provide insights into specific potential roles and functions of sequences involved in molecular processes in H. siamensis. Top protein domains detected included reverse transcriptase and the top putative functional transcript identified was an ORF2-encoded protein. One thousand eight hundred and thirty seven sequences containing SSR motifs were identified, of which 422 qualified for primer design and eight polymorphic loci have been tested with average observed and expected heterozygosity estimated at 0.75 and 0.83, respectively. Regardless of their relative levels of polymorphism and heterozygosity, microsatellite loci developed here are suitable for further population genetic studies in H. siamensis and may also be applicable to other related taxa.

Transcriptomics approaches to identify genes and markers for production traits in giant freshwater prawn Macrobrachium rosenbergii

This study used next generation sequencing technologies to investigate growth in a cultured crustacean. The objective was to identify and characterise specific gene loci that contribute important phenotypic variation to growth as well as to develop a large set of SNP markers in candidate genes for assessing correlations between specific mutations and individual growth performance. The genomic dataset generated provides a fundamental resource for application in future crustacean stock improvement programs. Ultimately, the data can be applied to development of culture lines with improved growth performance.

IgE-Associated IGHV Genes from Venom and Peanut Allergic Individuals Lack Mutational Evidence of Antigen Selection

Antigen selection of B cells within the germinal center reaction generally leads to the accumulation of replacement mutations in the complementarity-determining regions (CDRs) of immunoglobulin genes. Studies of mutations in IgE-associated VDJ gene sequences have cast doubt on the role of antigen selection in the evolution of the human IgE response, and it may be that selection for high affinity antibodies is a feature of some but not all allergic diseases. The severity of IgE-mediated anaphylaxis is such that it could result from higher affinity IgE antibodies. We therefore investigated IGHV mutations in IgE-associated sequences derived from ten individuals with a history of anaphylactic reactions to bee or wasp venom or peanut allergens. IgG sequences, which more certainly experience antigen selection, served as a control dataset. A total of 6025 unique IgE and 5396 unique IgG sequences were generated using high throughput 454 pyrosequencing. The proportion of replacement mutations seen in the CDRs of the IgG dataset was significantly higher than that of the IgE dataset, and the IgE sequences showed little evidence of antigen selection. To exclude the possibility that 454 errors had compromised analysis, rigorous filtering of the datasets led to datasets of 90 core IgE sequences and 411 IgG sequences. These sequences were present as both forward and reverse reads, and so were most unlikely to include sequencing errors. The filtered datasets confirmed that antigen selection plays a greater role in the evolution of IgG sequences than of IgE sequences derived from the study participants.

Four generations of sequencing: Is it ready for the clinic yet?

Next-generation sequencing techniques have revolutionized over the last decade providing researchers with low cost, high-throughput alternatives compared to the traditional Sanger sequencing methods. These sequencing techniques have rapidly evolved from first-generation to fourth-generation with very broad applications such as unravelling the complexity of the genome, in terms of genetic variations, and having a high impact on the biological field. In this review, we discuss the transition of sequencing from the second-generation to the third- and fourth-generations, and describe some of their novel biological applications. With the advancement in technology, the earlier challenges of minimal size of the instrument, flexibility of throughput, ease of data analysis and short run times are being addressed. However, the need for prospective analysis and effectiveness to test whether the knowledge of any given new variants identified has an effect on clinical outcome may need improvement.

Next generation sequencing identifies novel CACNA1A gene mutations in Episodic Ataxia type 2

Episodic Ataxia type 2 (EA2) is a rare autosomal dominantly inherited neurological disorder characterized by recurrent disabling imbalance, vertigo and episodes of ataxia lasting minutes to hours. EA2 is caused most often by loss of function mutations of the calcium channel gene CACNA1A. In addition to EA2, mutations in CACNA1A are responsible for two other allelic disorders: familial hemiplegic migraine type1 (FHM1) and spinocerebellar ataxia type 6 (SCA6). Herein, we have utilised Next Generation Sequencing (NGS) to screen the coding sequence, exon-intron boundaries and UTRs of five genes where mutation is known to produce symptoms related to EA2, including CACNA1A. We performed this screening in a group of 31 unrelated patients with EA2 symptoms. Both novel and known mutations were detected through NGS technology, and confirmed through Sanger sequencing. Genetic testing showed in total 15 mutation bearing patients (48%), of which 9 were novel mutations (6 missense and 3 small frameshift deletion mutations) and six known mutations (4 missense and 2 nonsense).These results demonstrate the efficiency of our NGS-panel for detecting known and novel mutations for EA2 in the CACNA1A gene, also identifying a novel missense mutation in ATP1A2 which is not a normal target for EA2 screening.

The Behavior of Hydroxyl Units of Synthetic Goethite and its Dehydroxylated Product Hematite

The behavior of the hydroxyl units of synthetic goethite and its dehydroxylated product hematite was characterized using a combination of Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) during the thermal transformation over a temperature range of 180-270 degrees C. Hematite was detected at temperatures above 200 degrees C by XRD while goethite was not observed above 230 degrees C. Five intense OH vibrations at 3212-3194, 1687-1674, 1643-1640, 888-884 and 800-798 cm(-1), and a H2O vibration at 3450-3445 cm(-1) were observed for goethite. The intensity of hydroxyl stretching and bending vibrations decreased with the extent of dehydroxylation of goethite. Infrared absorption bands clearly show the phase transformation between goethite and hematite: in particular. the migration of excess hydroxyl units from goethite to hematite. Two bands at 536-533 and 454-452 cm(-1) are the low wavenumber vibrations of Fe-O in the hematite structure. Band component analysis data of FTIR spectra support the fact that the hydroxyl units mainly affect the a plane in goethite and the equivalent c plane in hematite.

Feasibility studies on using microwave-heating techniques for recycling lead waste

Lead is present everywhere in the environment and has been defined as one of the greatest threats to the human health. In this paper, attempts have been made to study a way of recycling the lead produced from waste usage and disposed of in such a way as to avoid degrading the surrounding environment. In order to contain the waste, recycled asphalt material is mixed with the lead and then heated with microwave energy. This is an attempt to solidify and reduce the lead contaminants and use the final product as sub-base material in road pavement construction. The microwave heating of the specimens is carried out with 30%, 50%, 80% and 100% of power at 800W. The optimum power mode is used to compare with the conventional heating of asphalt with sulfur additive. The results are characterized by compact density, permeability, and subjected to toxicity test with regards to lead concentration. A mechanical test to evaluate the stability is also performed on the three methods of solidification and to prove that microwave zapping method allow to convert into an environmentally stable material for recycling without having to be deposited in a landfill site.

A Preliminary Assessment of Aqueous Ethanol Pulping of Bagasse: the Ecopulp Process

SRI has examined the organosolv (organic solvation) pulping of Australian bagasse using technology supplied by Ecopulp. In the process, bagasse is reacted with aqueous ethanol in a digester at elevated temperatures (between 150ºC and 200ºC). The products from the digester are separated using proprietary technology before further processing into a range of saleable products. Test trials were undertaken using two batch digesters; the first capable of pulping about 25 g of wet depithed bagasse and the second, larger samples of about 1.5 kg of wet depithed bagasse. From this study, the unbleached pulp produced from fresh bagasse did not have very good strength properties for the production of corrugated medium for cartons and bleached pulp. In particular, the lignin contents as indicated by the Kappa number for the unbleached pulps are high for making bleached pulp. However, in spite of the high lignin content, it is possible to bleach the pulp to acceptable levels of brightness up to 86.6% ISO. The economics were assessed for three tier pricing (namely low, medium and high price). The economic return for a plant that produces 100 air dry t/d of brownstock pulp is satisfactory for both high and medium pricing levels of pricing. The outcomes from the project justify that work should continue through to either pilot plant or upgraded laboratory facility.

Minimising speaker verification utterance length through confidence based early verification decisions

This paper presents a novel approach of estimating the confidence interval of speaker verification scores. This approach is utilised to minimise the utterance lengths required in order to produce a confident verification decision. The confidence estimation method is also extended to address both the problem of high correlation in consecutive frame scores, and robustness with very limited training samples. The proposed technique achieves a drastic reduction in the typical data requirements for producing confident decisions in an automatic speaker verification system. When evaluated on the NIST 2005 SRE, the early verification decision method demonstrates that an average of 5–10 seconds of speech is sufficient to produce verification rates approaching those achieved previously using an average in excess of 100 seconds of speech.

Wireless sensor devices for animal tracking and control

This paper describes some new wireless sensor hardware developed for pastoral and environmental applications. From our early experiments with Mote hardware we were inspired to develop our devices with improved radio range, solar power capability, mechanical and electrical robustness, and with unique combinations of sensors. Here we describe the design and evolution of a small family of devices: radio/processor board, a soil moisture sensor interface, and a single board multi-sensor unit for animal tracking experiments.

Distributing sensitive information in the MPEG-21 multimedia framework

The MPEG-21 Multimedia Framework provides for controlled distribution of multimedia works through its Intellectual Property Management and Protection ("IPMP") Components and Rights Expression Language ("MPEG REL"). The IPMP Components provide a framework by which the components of an MPEG-21 digital item can be protected from undesired access, while MPEG REL provides a mechanism for describing the conditions under which a component of a digital item may be used and distributed. This chapter describes how the IPMP Components and MPEG REL were used to implement a series of digital rights management applications at the Cooperative Research Centre for Smart Internet Technology in Australia. While the IPMP Components and MPEG REL were initially designed to facilitate the protection of copyright, the applications also show how the technology can be adapted to the protection of private personal information and sensitive corporate information.

The hedgehog pathway inhibitor GDC-0449 shows potential in skin and other cancers

Background: The hedgehog signaling pathway is vital in early development, but then becomes dormant, except in some cancer tumours. Hedgehog inhibitors are being developed for potential use in cancer. Objectives/Methods: The objective of this evaluation is to review the initial clinical studies of the hedgehog inhibitor, GDC-0449, in subjects with cancer. Results: Phase I trials have shown that GDC-0449 has benefits in subjects with metastatic or locally advanced basal-cell carcinoma and in one subjects with medulloblastoma. GDC-0449 was well tolerated. Conclusions: Long term efficacy and safety studies of GDC-0449 in these conditions and other solid cancers are now underway. These clinical trials with GDC-0449, and trials with other hedgehog inhibitors, will reveal whether it is beneficial and safe to inhibit the hedgehog pathway, in a wide range of solid tumours or not.

Noise robust voice activity detection using normal probability testing and time-domain histogram analysis

This paper presents a method of voice activity detection (VAD) suitable for high noise scenarios, based on the fusion of two complementary systems. The first system uses a proposed non-Gaussianity score (NGS) feature based on normal probability testing. The second system employs a histogram distance score (HDS) feature that detects changes in the signal through conducting a template-based similarity measure between adjacent frames. The decision outputs by the two systems are then merged using an open-by-reconstruction fusion stage. Accuracy of the proposed method was compared to several baseline VAD methods on a database created using real recordings of a variety of high-noise environments.

Consumer satisfaction and redress with a government third-party complaints agency

As governments around the world adopt a marketing orientation, the importance of consumer satisfaction to the effectiveness of the organization is being recognized. While some investigation of satisfaction with a government agencies' service has occurred, there is little examination of satisfaction with a government agency that acts as a third-party on the behalf of consumers to gain marketplace redress. Given the number of third-party complaints is increasing as a result of internet access to complaint channels, this research is a timely investigation. This study reports the findings of a survey of 454 complainants to an Australian Government agency: the Office of Fair Trading (OFT). The findings show that satisfaction with the service was subjectively experienced, based around individual expectations of the redress and satisfaction levels were higher when the redress sought was financial compared with non-financial forms of redress such as apology.