Comparative analysis of panicum streak virus and maize streak virus diversity, recombination patterns and phylogeography

Background: Panicum streak virus (PanSV; Family Geminiviridae; Genus Mastrevirus) is a close relative of Maize streak virus (MSV), the most serious viral threat to maize production in Africa. PanSV and MSV have the same leafhopper vector species, largely overlapping natural host ranges and similar geographical distributions across Africa and its associated Indian Ocean Islands. Unlike MSV, however, PanSV has no known economic relevance. Results: Here we report on 16 new PanSV full genome sequences sampled throughout Africa and use these together with others in public databases to reveal that PanSV and MSV populations in general share very similar patterns of genetic exchange and geographically structured diversity. A potentially important difference between the species, however, is that the movement of MSV strains throughout Africa is apparently less constrained than that of PanSV strains. Interestingly the MSV-A strain which causes maize streak disease is apparently the most mobile of all the PanSV and MSV strains investigated. Conclusion: We therefore hypothesize that the generally increased mobility of MSV relative to other closely related species such as PanSV, may have been an important evolutionary step in the eventual emergence of MSV-A as a serious agricultural pathogen. The GenBank accession numbers for the sequences reported in this paper are GQ415386-GQ415401. © 2009 Varsani et al; licensee BioMed Central Ltd.

Prediction of transcriptional regulatory interactions in bacteria : a comparative genomics approach

Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become more sophisticated, and move toward comparisons across large datasets, computational approaches have become essential. One of the most important biological questions is to understand the mechanisms underlying gene regulation. Genetic regulation is commonly investigated and modelled through the use of transcriptional regulatory network (TRN) structures. These model the regulatory interactions between two key components: transcription factors (TFs) and the target genes (TGs) they regulate. Transcriptional regulatory networks have proven to be invaluable scientific tools in Bioinformatics. When used in conjunction with comparative genomics, they have provided substantial insights into the evolution of regulatory interactions. Current approaches to regulatory network inference, however, omit two additional key entities: promoters and transcription factor binding sites (TFBSs). In this study, we attempted to explore the relationships among these regulatory components in bacteria. Our primary goal was to identify relationships that can assist in reducing the high false positive rates associated with transcription factor binding site predictions and thereupon enhance the reliability of the inferred transcription regulatory networks. In our preliminary exploration of relationships between the key regulatory components in Escherichia coli transcription, we discovered a number of potentially useful features. The combination of location score and sequence dissimilarity scores increased de novo binding site prediction accuracy by 13.6%. Another important observation made was with regards to the relationship between transcription factors grouped by their regulatory role and corresponding promoter strength. Our study of E.coli ��70 promoters, found support at the 0.1 significance level for our hypothesis | that weak promoters are preferentially associated with activator binding sites to enhance gene expression, whilst strong promoters have more repressor binding sites to repress or inhibit gene transcription. Although the observations were specific to �70, they nevertheless strongly encourage additional investigations when more experimentally confirmed data are available. In our preliminary exploration of relationships between the key regulatory components in E.coli transcription, we discovered a number of potentially useful features { some of which proved successful in reducing the number of false positives when applied to re-evaluate binding site predictions. Of chief interest was the relationship observed between promoter strength and TFs with respect to their regulatory role. Based on the common assumption, where promoter homology positively correlates with transcription rate, we hypothesised that weak promoters would have more transcription factors that enhance gene expression, whilst strong promoters would have more repressor binding sites. The t-tests assessed for E.coli �70 promoters returned a p-value of 0.072, which at 0.1 significance level suggested support for our (alternative) hypothesis; albeit this trend may only be present for promoters where corresponding TFBSs are either all repressors or all activators. Nevertheless, such suggestive results strongly encourage additional investigations when more experimentally confirmed data will become available. Much of the remainder of the thesis concerns a machine learning study of binding site prediction, using the SVM and kernel methods, principally the spectrum kernel. Spectrum kernels have been successfully applied in previous studies of protein classification [91, 92], as well as the related problem of promoter predictions [59], and we have here successfully applied the technique to refining TFBS predictions. The advantages provided by the SVM classifier were best seen in `moderately'-conserved transcription factor binding sites as represented by our E.coli CRP case study. Inclusion of additional position feature attributes further increased accuracy by 9.1% but more notable was the considerable decrease in false positive rate from 0.8 to 0.5 while retaining 0.9 sensitivity. Improved prediction of transcription factor binding sites is in turn extremely valuable in improving inference of regulatory relationships, a problem notoriously prone to false positive predictions. Here, the number of false regulatory interactions inferred using the conventional two-component model was substantially reduced when we integrated de novo transcription factor binding site predictions as an additional criterion for acceptance in a case study of inference in the Fur regulon. This initial work was extended to a comparative study of the iron regulatory system across 20 Yersinia strains. This work revealed interesting, strain-specific difierences, especially between pathogenic and non-pathogenic strains. Such difierences were made clear through interactive visualisations using the TRNDifi software developed as part of this work, and would have remained undetected using conventional methods. This approach led to the nomination of the Yfe iron-uptake system as a candidate for further wet-lab experimentation due to its potential active functionality in non-pathogens and its known participation in full virulence of the bubonic plague strain. Building on this work, we introduced novel structures we have labelled as `regulatory trees', inspired by the phylogenetic tree concept. Instead of using gene or protein sequence similarity, the regulatory trees were constructed based on the number of similar regulatory interactions. While the common phylogentic trees convey information regarding changes in gene repertoire, which we might regard being analogous to `hardware', the regulatory tree informs us of the changes in regulatory circuitry, in some respects analogous to `software'. In this context, we explored the `pan-regulatory network' for the Fur system, the entire set of regulatory interactions found for the Fur transcription factor across a group of genomes. In the pan-regulatory network, emphasis is placed on how the regulatory network for each target genome is inferred from multiple sources instead of a single source, as is the common approach. The benefit of using multiple reference networks, is a more comprehensive survey of the relationships, and increased confidence in the regulatory interactions predicted. In the present study, we distinguish between relationships found across the full set of genomes as the `core-regulatory-set', and interactions found only in a subset of genomes explored as the `sub-regulatory-set'. We found nine Fur target gene clusters present across the four genomes studied, this core set potentially identifying basic regulatory processes essential for survival. Species level difierences are seen at the sub-regulatory-set level; for example the known virulence factors, YbtA and PchR were found in Y.pestis and P.aerguinosa respectively, but were not present in both E.coli and B.subtilis. Such factors and the iron-uptake systems they regulate, are ideal candidates for wet-lab investigation to determine whether or not they are pathogenic specific. In this study, we employed a broad range of approaches to address our goals and assessed these methods using the Fur regulon as our initial case study. We identified a set of promising feature attributes; demonstrated their success in increasing transcription factor binding site prediction specificity while retaining sensitivity, and showed the importance of binding site predictions in enhancing the reliability of regulatory interaction inferences. Most importantly, these outcomes led to the introduction of a range of visualisations and techniques, which are applicable across the entire bacterial spectrum and can be utilised in studies beyond the understanding of transcriptional regulatory networks.

Rolling in the aisles : a comparative study of male and female grocery shopper typologies

The purpose of this paper is to segment male and female grocery shoppers based on store and product attribute evaluations. A rich profile for each segment is developed. Gender comparisons are operationalised and these developed contemporary shopper typologies are further contrasted against earlier works. Data of 560 grocery shoppers was attained by a survey questionnaire. Factor analysis, cluster analysis and ANOVA were employed to develop specific segments of shoppers. Four distinct cohorts of male shoppers and three cohorts of female shoppers emerge from the data of eight constructs, measured by 46 items. One new shopper type, not found in earlier typology literature, emerged from this research. This shopper presented as a young, well educated, at the commencement of their career and family lifecycle, attracted by a strong value offer and willingness to share the family food shopping responsibilities. This research makes a contribution to segmentation literature and grocery retail practice in several ways. It presents the first retail typology of male supermarket shoppers, employing a cluster analysis technique. Comparisons between male and female grocery shopping typologies are accordingly facilitated. The research provides insights into the modern family food shopping behaviour of men; a channel in which men are now recognised as equal contributors. Research outcomes encourage supermarket retailers to implement targeted marketing and rationalized operational strategies that deliver on attributes of importance. Finally, this research provides the basis for further cross-cultural, cross-contextual comparative studies.

Comparative effects of posterior eye cup tissues from Myopic and Hyperopic chick eyes on cultured scleral fibroblasts

The role of individual ocular tissues in mediating changes to the sclera during myopia development is unclear. The aim of this study was to examine the effects of retina, RPE and choroidal tissues from myopic and hyperopic chick eyes on the DNA and glycosaminoglycan (GAG) content in cultures of chick scleral fibroblasts. Primary cultures of fibroblastic cells expressing vimentin and -smooth muscle actin were established in serum-supplemented growth medium from 8-day-old normal chick sclera. The fibroblasts were subsequently co-cultured with posterior eye cup tissue (full thickness containing retina, RPE and choroid) obtained from untreated eyes and eyes wearing translucent diffusers (form-deprivation myopia, FDM) or -15D lenses (lens-induced myopia, LIM) for 3 days (post hatch day 5 to 8) (n=6 per treatment group). The effect of tissues (full thickness and individual retina, RPE, and choroid layers) from -15D (LIM) versus +15D (lens-induced hyperopia, LIH) treated eyes was also determined. Refraction changes in the direction predicted by the visual treatments were confirmed by retinoscopy prior to tissue collection. Glycosaminoglycan (GAG) and DNA content of the scleral fibroblast cultures were measured using GAG and PicoGreen assays. There was no significant difference in the effect of full thickness tissue from either FDM or LIM treated eyes on DNA and GAG content of scleral fibroblasts (DNA 8.9±2.6 µg and 8.4±1.1 µg, p=0.12; GAG 11.2±0.6 µg and 10.1±1.0 µg, p=0.34). Retina from LIM eyes did not alter fibroblast DNA or GAG content compared to retina from LIH eyes (DNA 27.2±1.7 µg versus 23.2±1.5 µg, p=0.21; GAG 28.1±1.7 µg versus. 28.7±1.2 µg, p=0.46). Similarly, the choroid from LIH and LIM eyes did not produce a differential effect on DNA content (DNA, LIM 46.9±6.4 versus LIH 51.5±4.7 µg, p=0.31), whereas GAG content was higher for cells in co-culture with choroid from LIH eyes (GAG 32.5±0.7 µg versus 18.9±1.2 µg, F1,6=9.210, p=0.0002). In contrast, fibroblast DNA was greater in co-culture with RPE from LIM eyes than the empty basket and DNA content less for co-culture with RPE from LIH eyes (LIM: 72.4±6.3 µg versus Empty basket: 46.03±1.0 µg; F1,6=69.99, p=0.0005 and LIH: 27.9±2.3 µg versus empty basket: 46.03±1.0 µg; p=0.0004). GAG content was higher with RPE from LIH eyes (LIH: 33.7±1.9 µg versus empty basket: 29.5±0.8 µg, F1,6=13.99, p=0.010) and lower with RPE from LIM eyes (LIM: 27.7±0.9 µg versus empty basket: 29.5±0.8 µg, p=0.021). GAG content of cells in co-culture with choroid from LIH eyes was higher compared to co-culture with choroid from LIM eyes (32.5±0.7 µg versus 18.9±1.2 µg respectively, F1,6=9.210, p=0.0002). In conclusion, these experiments provide evidence for a directional growth signal that is present (and remains) in the ex-vivo RPE, but that does not remain in the ex-vivo retina. The identity of this factor(s) that can modify scleral cell DNA and GAG content requires further research.

Comparative study of depth-dependent characteristics of equine and human osteochondral tissue from the medial and lateral femoral condyles

Articular cartilage defects are common after joint injuries. When left untreated, the biomechanical protective function of cartilage is gradually lost, making the joint more susceptible to further damage, causing progressive loss of joint function and eventually osteoarthritis (OA). In the process of translating promising tissue-engineering cartilage repair approaches from bench to bedside, pre-clinical animal models including mice, rabbits, goats, and horses, are widely used. The equine species is becoming an increasingly popular model for the in vivo evaluation of regenerative orthopaedic approaches. As there is also an increasing body of evidence suggesting that successful lasting tissue reconstruction requires an implant that mimics natural tissue organization, it is imperative that depth-dependent characteristics of equine osteochondral tissue are known, to assess to what extent they resemble those in humans. Therefore, osteochondral cores (4-8 mm) were obtained from the medial and lateral femoral condyles of equine and human donors. Cores were processed for histology and for biochemical quantification of DNA, glycosaminoglycan (GAG) and collagen content. Equine and human osteochondral tissues possess similar geometrical (thickness) and organizational (GAG, collagen and DNA distribution with depth) features. These comparable trends further underscore the validity of the equine model for the evaluation of regenerative approaches for articular cartilage.

Comparative eye tracking of experts and novices in web single sign-on

Security indicators in web browsers alert users to the presence of a secure connection between their computer and a web server; many studies have shown that such indicators are largely ignored by users in general. In other areas of computer security, research has shown that technical expertise can decrease user susceptibility to attacks. In this work, we examine whether computer or security expertise affects use of web browser security indicators. Our study takes place in the context of web-based single sign-on, in which a user can use credentials from a single identity provider to login to many relying websites; single sign-on is a more complex, and hence more difficult, security task for users. In our study, we used eye trackers and surveyed participants to examine the cues individuals use and those they report using, respectively. Our results show that users with security expertise are more likely to self-report looking at security indicators, and eye-tracking data shows they have longer gaze duration at security indicators than those without security expertise. However, computer expertise alone is not correlated with recorded use of security indicators. In survey questions, neither experts nor novices demonstrate a good understanding of the security consequences of web-based single sign-on.

Impact fees and new housing cost: A comparative analysis of the empirical models

Developers and policy makers are consistently at odds over the debate as to whether impact fees increase house prices. This debate continues despite the extensive body of theoretical and empirical international literature that discusses the passing on to home buyers of impact fees, and the corresponding increase to housing prices. In attempting to quantify this impact, over a dozen empirical studies have been carried out in the US and Canada since the 1980’s. However the methodologies used vary greatly, as do the results. Despite similar infrastructure funding policies in numerous developed countries, no such empirical works exist outside of the US/Canada. The purpose of this research is to analyse the existing econometric models in order to identify, compare and contrast the theoretical bases, methodologies, key assumptions and findings of each. This research will assist in identifying if further model development is required and/or whether any of these models have external validity and are readily transferable outside of the US. The findings conclude that there is very little explicit rationale behind the various model selections and that significant model deficiencies appear still to exist.

The ‘Russian doll’ approach : developing nested case-studies to support international comparative research in education

International comparison is complicated by the use of different terms, classification methods, policy frameworks and system structures, not to mention different languages and terminology. Multi-case studies can assist in the understanding of the influence wielded by cultural, social, economic, historical and political forces upon educational decisions, policy construction and changes over time. But case studies alone are not enough. In this paper, we argue for an ecological or scaled approach that travels through macro, meso and micro levels to build nested case-studies to allow for more comprehensive analysis of the external and internal factors that shape policy-making and education systems. Such an approach allows for deeper understanding of the relationship between globalizing trends and policy developments.

Anatomical MR imaging of long bones : comparative performance of MRI at 1.5 T and 3 T

The current gold standard for the design of orthopaedic implants is 3D models of long bones obtained using computed tomography (CT). However, high-resolution CT imaging involves high radiation exposure, which limits its use in healthy human volunteers. Magnetic resonance imaging (MRI) is an attractive alternative for the scanning of healthy human volunteers for research purposes. Current limitations of MRI include difficulties of tissue segmentation within joints and long scanning times. In this work, we explore the possibility of overcoming these limitations through the use of MRI scanners operating at a higher field strength. We quantitatively compare the quality of anatomical MR images of long bones obtained at 1.5 T and 3 T and optimise the scanning protocol of 3 T MRI. FLASH images of the right leg of five human volunteers acquired at 1.5 T and 3 T were compared in terms of signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR). The comparison showed a relatively high CNR and SNR at 3 T for most regions of the femur and tibia, with the exception of the distal diaphyseal region of the femur and the mid diaphyseal region of the tibia. This was accompanied by an ~65% increase in the longitudinal spin relaxation time (T1) of the muscle at 3 T compared to 1.5 T. The results suggest that MRI at 3 T may be able to enhance the segmentability and potentially improve the accuracy of 3D anatomical models of long bones, compared to 1.5 T. We discuss how the total imaging times at 3 T can be kept short while maximising the CNR and SNR of the images obtained.

Public service versus private interest : a comparative analysis of the Australian and British debates

This paper will compare and evaluate the effectiveness of commercial media lobbying and advocacy against public service media in two countries, the United Kingdom and Australia. The paper will focus empirically on the commercial media coverage of public service media issues in these countries (relating to the BBC and ABC respectively) over the period since the election of the Conservative-led Coalition in Britain in June 2010, and the election of the Gillard government in Australia in August 2010. Reference will be made to preceding periods as relevant to an understanding of the current environment. In both countries the main commercial media rival to public service media is News Corp and its associated organisations – News Ltd and Sky News in Australia, and News International and BSkyB in the UK. The paper will examine with analysis of print and online news and commentary content how News Corp outlets have reported and commented on the activities and plans of public service media as the latter have developed and extended their presence on digital TV and online platforms. It will also consider the responses of the ABC and BBC to these interventions. It will consider, thirdly, the responses of Australian and British governments to these debates, and the policy outcomes. This section of the paper will seek to evaluate the trajectory of the policy-public-private dynamic in recent years, and to draw conclusions as to the future direction of policy. Particular attention will be devoted to recent key moments in this unfolding dialogue. In Britain, debates around the efforts of News Corp to take over 100% of BSkyB, both before and after the breaking of the phone-hacking scandal in July 2011; in Australia, the debate around the National Broadband Network and the competitive tender process for ABC World, that country’s public service transnational broadcaster; and other key moments where rivalry between News Corp companies and public service media became mainstream news stories provoking wider public debate. The paper will conclude with recommendations as to how public service media organisations might engage constructively with commercial organisations in the future, including News Corp, and taking into account emerging technological and financial challenges to traditional rationales for public service provision.

Comparative study of analytical rental model and statistical models for predicting house rental levels

The need for a house rental model in Townsville, Australia is addressed. Models developed for predicting house rental levels are described. An analytical model is built upon a priori selected variables and parameters of rental levels. Regression models are generated to provide a comparison to the analytical model. Issues in model development and performance evaluation are discussed. A comparison of the models indicates that the analytical model performs better than the regression models.

A comparative study on the mineralogy, chemistry and chronology of the Apollo 16 crystalline impact melt breccias. Part II: Chronology.

The controversy on how to interpret the ages of lunar highland breccias has recently been discussed by James [1]. Are the measured ages testimony of true events in lunar history; do they represent the age of the ancient crustal rocks, mixed ages of unequilibrated matrix-phenocryst relationships, or merely thermal events subsequent to the formational event ? It is certain from analyses of terrestrial impact melt breccias that the melt matrix of whole impact melt sheets is isotopically equilibrated due to the extensive mixing process of the early cratering stage [2,3]. It has been shown that isotopic equilibration takes place between impact melt matrix and target rock clasts therein, with the intensity of isotopic exchange depending on the degree of shock metamorphism, thermal metamorphism and the size of the clasts [4]. Therefore, impact melt breccias - if they are relatively clast-poor and mineralogically well studied - can be considered to be the most reliable source for information on the impact history of the lunar highland.

A comparative analysis of the integration of SOA elements in widely-used enterprise architecture frameworks

In recent years, enterprise architecture (EA) has captured increasing interest as a means to systematically consolidate and manage various enterprise artefacts in order to provide holistic decision support for business/IT alignment and business/IT landscapes management. To provide a holistic perspective on the enterprise over time, EA frameworks need to co-evolve with the changes in the enterprise and its IT over time. In this paper we focus on the emergence of Service-Oriented Architecture (SOA). There is a need to integrate SOA with EA to keep EA relevant and to use EA products to help drive successful SOA. This paper investigates and compares the integration of SOA elements in five widely used EA frameworks: Archimate, The Open Group Architecture Framework (TOGAF), Federal Enterprise Architecture Framework (FEAF), Department of Defence Architecture Framework (DoDAF) and the Ministry of Defence Architecture Framework (MODAF). It identifies what SOA elements are considered and their relative position in the overall structure. The results show that services and related elements are far from being well-integrated constructs in current EA frameworks and that the different EA frameworks integrated SOA elements in substantially different ways. Our results can support the academic EA and SOA communities with a closer and more consistent integration of EA and SOA and support practitioners in identifying an EA framework that provides the SOA support that matches their requirements.

A comparative study of governmental one-stop portals for public service delivery

The continuing need for governments to radically improve the delivery of public services has led to a new, holistic government reform strategy labeled “Transformational Government” that strongly emphasizes customer-centricity. Attention has turned to online portals as a cost effective front-end to deliver services and engage customers as well as to the corresponding organizational approaches for the back-end to decouple the service interface from the departmental structures. The research presented in this paper makes three contributions: Firstly, a systematic literature review of approaches to the evaluation of online portal models in the public sector is presented. Secondly, the findings of a usability study comparing the online presences of the Queensland Government, the UK Government and the South Australian Government are reported and the relative strengths and weaknesses of the different approaches are discussed. And thirdly, the limitations of the usability study in the context of a broader “Transformational Government” approach are identified and service bundling is suggested as an innovative solution to further improve online service delivery.