A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts

The computational approach for identifying promoters on increasingly large genomic sequences has led to many false positives. The biological significance of promoter identification lies in the ability to locate true promoters with and without prior sequence contextual knowledge. Prior approaches to promoter modelling have involved artificial neural networks (ANNs) or hidden Markov models (HMMs), each producing adequate results on small scale identification tasks, i.e. narrow upstream regions. In this work, we present an architecture to support prokaryote promoter identification on large scale genomic sequences, i.e. not limited to narrow upstream regions. The significant contribution involved the hybrid formed via aggregation of the profile HMM with the ANN, via Viterbi scoring optimizations. The benefit obtained using this architecture includes the modelling ability of the profile HMM with the ability of the ANN to associate elements composing the promoter. We present the high effectiveness of the hybrid approach in comparison to profile HMMs and ANNs when used separately. The contribution of Viterbi optimizations is also highlighted for supporting the hybrid architecture in which gains in sensitivity (+0.3), specificity (+0.65) and precision (+0.54) are achieved over existing approaches.

Genomic analyses and cloning of novel chicken natriuretic peptide genes reveal new insights into natriuretic peptide evolution

The natriuretic peptide (NP) family consists of multiple subtypes in teleosts, including atrial, B-type, ventricular, and C-type NPs (ANP, BNP, VNP, CNP-1–4, respectively), but only ANP, BNP, CNP-3, and CNP-4 have been identified in tetrapods. As part of understanding the molecular evolution of NPs in the tetrapod lineage, we identified NP genes in the chicken genome. Previously, only BNP and CNP-3 have been identified in birds, but we characterized two new chicken NP genes by cDNA cloning, synteny and phylogenetic analyses. One gene is an orthologue of CNP-1, which has only ever been reported in teleostei and bichir. The second gene could not be assigned to a particular NP subtype because of high sequence divergence and was named renal NP (RNP) due to its predominant expression in the kidney. CNP-1 mRNA was only detected in brain, while CNP-3 mRNA was expressed in kidney, heart, and brain. In the developing embryo, BNP and RNP transcripts were most abundant 24 h post-fertilization, while CNP mRNA increased in a stage-dependant manner. Synthetic chicken RNP stimulated an increase in cGMP production above basal level in chicken kidney membrane preparations and caused a potent dose-dependant vasodilation of pre-constricted dorsal aortic rings. From conserved chromosomal synteny, we propose that the CNP-4 and ANP genes have been lost in chicken, and that RNP may have evolved from a VNP-like gene. Furthermore, we have demonstrated for the first time that CNP-1 is retained in the tetrapod lineage.

Dispersion statistics and a sampling plan for Helicoverpa (Lepidoptera : Noctuidae) on fresh-market tomatoes (Lycopersicon esculentum)

Helicoverpa spp. is the primary pest in the Australian fresh-market tomato industry. We describe the spatial distribution of Helicoverpa spp. eggs on fresh-market tomato crops in the Goulburn Valley region of Victoria, and present a sequential sampling plan for monitoring population densities. The distribution of Helicoverpa spp. eggs was highly contagious, as indicated by a Taylor's b-value of 1.59. This high level of contagion meant that relatively large sample sizes would need to be collected to obtain an estimate of population density. High-precision sampling plans generally necessitated impractical sample sizes, and thus the plan we present is a relatively low-precision level plan (SE/mean = 0.3). Nonetheless, this level of precision is considered adequate for most agronomic scenarios. The plan was validated using a statistical re-sampling approach. The level of precision achieved was generally close to the nominal level. Likewise, the number of samples collected generally showed little departure from the theoretically calculated minimum sample size.

A genomic approach to understanding the cause and effect of annual ryegrass toxicity

Annual Ryegrass Toxicity (ARGT) is a potentially lethal disease affecting livestock grazing on pastures or consuming fodder that include annual ryegrass (Lolium rigidum) contaminated with corynetoxins. The corynetoxins (CTs), among the most lethal toxins produced in nature, are produced by the bacterium Rathayibacter toxicus that uses a nematode vector to attach to and infect the seedheads of L.rigidum. There is little known of the factors that control toxin production. Several studies have speculated that a bacteriophage specific to R.toxicus may be implicated in CT production. We have developed a PCR-based assay to test for both bacterium and phage in ryegrass material and results indicate that there is a correlation between phage and bacterial presence in all toxic ryegrass samples tested so far. This PCR-based technique may ultimately allow for a rapid, high-throughput screening assay to identify potentially toxic pastures and feed in the field. Currently, ~80% of the 45 Kb genome has been sequenced an investigation to further elucidate its potential role in toxin production.Furthermore, specific alterations in gene expression as a result of exposure to CTs or the closely related tunicamycins (TMs), which are commercially available and considered biologically indistinguishable from CTs, will be evaluated for use as biomarkers of exposure. The effects of both toxins will be analysed in vitro using a rat hepatocyte cell line and screened on a low-density DNA micro array “CT-Chip” that contains <100 selected rat hepatic genes. The results are expected to further define the bioequivalence of CTs and TMs and to identify levels of exposure that are related to specific toxic effects or have no adverse effect on livestock.

Global and regional dispersion of publishing in the field of international marketing

This paper empirically examines the research productivity of academic institutions in the leading international marketing journals, leading generalist marketing journals, and leading international business journals between the years 1999 and 2003 from a regional and country-specific perspective. The research found that across the three groups of journals, the majority of works were authored by academics at institutions located in North America, although North Americans contribute significantly less in the international marketing and international business journals than leading generalist marketing journals. The findings suggest that there is a broadening of non-U.S. influence within the international marketing and international business journals, which should lead to a broadening of international marketing theory.

Immunostimulatory polysaccharides from Chlorella pyrenoidosa. A new galactofuranan. Measurement of molecular weight and molecular weight dispersion by DOSY NMR.

Fractionation of the hot water extract of Chlorella pyrenoidosa was performed using a combination of ethanol precipitation, size exclusion chromatography, and anion exchange chromatography. One fraction contained a new polysaccharide, and this compound was shown to be a 1→2-linked β-d-galactofuranan from its 1D and 2D 1H and 13C NMR spectra, with a molecular weight of 15 kDa from DOSY NMR measurements. A number of other fractions were shown to have the same repeating unit as the previously identified arabinogalactan. However, arabinogalactans from different fractions were shown by DOSY NMR to have different molecular weights, which ranged from 27 to 1020 kDa. Agreement with molecular weights measured for some of these fractions by SEC-MALS was very good, further confirming the relationship established by Viel et al. between molecular weights of neutral polysaccharides and self-diffusion coefficients. The smaller molecular weight polysaccharides, the galactofuranan and the 27 and 50 kDa arabinogalactans, were shown to be close to monodisperse by analysis of the distributions of the self-diffusion coefficients for the polymers. The larger arabinogalactans had considerable variation in their molecular weights (188 ± 109 kDa and 1020 ± 370 kDa). Only the two larger arabinogalactans showed immunostimulatory activity.

Dispersion of information or market behaviour : general public trading in S & P 500 index futures

This paper considers 15 minute records of trading volume and traded prices coinciding with the reporting intervals required by the Commodity Futures Trading Commission. Records are extracted from trade records for two way trade between market makers (CTI1) and the general public (CTI4) from January 1994 to June 2004. Futures price records are matched with S&P500 cash index price records. Simultaneous volatility models are specified and estimated to test trading volume to futures volatility lead/lag effects and also futures volatility to cash index volatility lead/lag effects. There is evidence that existing theoretical models of the general public trading behaviour do not explain such behaviour in these very actively traded markets. These effects can depend more on market conditions than what is suggested in theoretical models.

Familial and genomic analyses of postural changes in systolic and diastolic blood pressure

The physiological adaptation to the erect posture involves integrated neural and cardiovascular responses that might be determined by genetic factors. We examined the familial- and individual-specific components of variance for postural changes in systolic and diastolic blood pressure in 767 volunteer nuclear adult families from the Victorian Family Heart Study. In 274 adult sibling pairs, we made a genome-wide scan using 400 markers for quantitative trait loci linked with the postural changes in systolic and diastolic pressures. Overall, systolic pressure did not change on standing, but there was considerable variation in this phenotype (SD=8.1 mm Hg). Familial analyses revealed that 25% of the variance of change in systolic pressure was attributable to genetic factors. In contrast, diastolic pressure increased by 6.3 mm Hg (SD=7.0 mm Hg) on standing and there was no evidence of contributory genetic factors. Multipoint quantitative genome linkage mapping suggested evidence (Z=3.2) of linkage of the postural change in systolic pressure to chromosome 12 but found no genome-wide evidence of linkage for the change in diastolic pressure. These findings suggest that genetic factors determine whether systolic pressure decreases or increases when one stands, possibly as the result of unidentified alleles on chromosome 12. The genetics of postural changes in systolic blood pressure might reflect the general buffering function of the baroreflex; thereby, the predisposition to sudden decreases or increases in systolic pressure might cause postural hypotension or vessel wall disruption, respectively.

Dispersion characterization of Mechanochemically Synthesized nanoparticles using UV/Vis Spectroscopy

Dispersion characterization of nanoparticles was carried out using UV/Vis spectroscopy. ZnO and CeO2 nanoparticles of sizes ranging 10 - 250 nm were investigated for slurries having various concentrations. The particles were synthesized by mechanochemical processing, which allows the formation of agglomeration-free nanoparticles. It was found that the UV/Vis spectra were highly sensitive to mean particle sizes and agglomeration states. The results showed that UV/Vis spectroscopy is a highly promising technique for studying nanoparticle dispersions having a wide range of concentrations in various media.

Dispersion of boron nitride nanotubes in aqueous solution with the help of ionic surfactants

We report that ammonium oleate surfactants can help the dispersion of multiwalled boron nitride nanotubes (BNNTs) in water to form a BNNT solution stable for several months, which was due to the non-covalent functionalization of nanotube surfaces. Fourier Transform Infrared Spectroscopy (FTIR) and Photoluminescence (PL) analysis with synchrotron radiation source revealed that this BNNT aqueous solution preserves the intrinsic optical properties of BNNTs. © 2009 Elsevier Ltd. All rights reserved.

Extensible motif and aberrant nucleotide extraction in genomic sequences

The project focusses on the discovery of conserved DNA sequences in bacterial genomes and comparative analysis of bacterial genomes to elicit evolutionary trends. The outcomes have produced novel techniques for modelling motifs in DNA and the characterisation of evolutionary processes in medically significant bacterial pathogens.

A genomic approach for improved detection of annual ryegrass toxicity

Annual Ryegrass Toxicity is a severe and constant threat to the Australian agricultural industry. Current diagnostic and detection strategies to predict and monitor ARGT are limited. This thesis utilised genomic-based technologies to develop improved strategies for detection of molecular indicators of toxicity in field and livestock to facilitate pre-clinical detection.

Bacterial genomic G + C composition-eliciting environmental adaptation

Bacterial genomes reflect their adaptation strategies through nucleotide usage trends found in their chromosome composition. Bacteria, unlike eukaryotes contain a wide range of genomic G + C. This wide variability may be viewed as a response to environmental adaptation. Two overarching trends are observed across bacterial genomes, the first, correlates genomic G + C to environmental niches and lifestyle, while the other utilizees intra-genomic G + C incongruence to delineate horizontally transferred material. In this review, we focus on the influence of several properties including biochemical, genetic flows, selection biases, and the biochemical-energetic properties shaping genome composition. Outcomes indicate a trend toward high G + C and larger genomes in free-living organisms, as a result of more complex and varied environments (higher chance for horizontal gene transfer). Conversely, nutrient limiting and nutrient poor environments dictate smaller genomes of low GC in attempts to conserve replication expense. Varied processes including translesion repair mechanisms, phage insertion and cytosine degradation has been shown to introduce higher AT in genomic sequences. We conclude the review with an analysis of current bioinformatics tools seeking to elicit compositional variances and highlight the practical implications when using such techniques.

Improving the dispersion and mechanical properties of epoxy/carbon nanotube composites

The incorporation and uniform dispersion of carbon nanotubes (CNTs) in polymer matrix could facilitate engineers to create high performance nanocomposites that potentially compete with most advanced materials in nature. The unique combination of outstanding mechanical, thermal, and electrical properties of CNTs makes them excellent nanofillers for the fabrication of advanced materials. Successful enhancement in mechanical properties via reinforcement is expected only when the nanofillers are well dispersed in the polymer matrix. Moreover, the orientation as well as the CNT/matrix interfacial strength also determines the effective physical properties of the nanocomposites. However, CNTs typically assemble to give bundles, which are heavily entangled to each other with a high aspect ratio and a large π-electronic surface. In this work, we outline some preliminary results in preparing high performance epoxy composites. Composites with fine dispersion and superior mechanical properties were prepared using epoxy and multiwalled carbon nanotubes (MWCNTs). The fine dispersion of the nanocomposites can be identified in the high resolution SEM image shown in Figure 1. This method can provide an alternative route for the preparation of new structural and functional nanocomposites.

On the welfare gains of price dispersion

Can price dispersion be associated with higher levels of welfare? To answer we compare two economies that differ only in the way prices are formed. In the first, sellers post a unique price–quantity pair, with no price dispersion. In the second, sellers post a quantity only and let prices be determined ex post by realized demand, resulting in price dispersion. We show that while agents trade lower quantities when prices are dispersed (an intensive margin effect), they also trade more often (an extensive margin effect). At low inflation, the extensive margin dominates making agents better off with price dispersion.