Evidence of ancient papillomavirus recombination

An open question amongst papillomavirus taxonomists is whether recombination has featured in the evolutionary history of these viruses. Since the onset of the global AIDS epidemic, the question is somewhat less academic, because immune-compromised human immunodeficiency virus patients are often co-infected with extraordinarily diverse mixtures of human papillomavirus (HPV) types. It is expected that these conditions may facilitate the emergence of HPV recombinants, some of which might have novel pathogenic properties. Here, a range of rigorous analyses is applied to full-genome sequences of papillomaviruses to provide convincing statistical and phylogenetic evidence that evolutionarily relevant papillomavirus recombination can occur. © 2006 SGM.

A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family

Background. We have characterised a new highly divergent geminivirus species, Eragrostis curvula streak virus (ECSV), found infecting a hardy perennial South African wild grass. ECSV represents a new genus-level geminivirus lineage, and has a mixture of features normally associated with other specific geminivirus genera. Results. Whereas the ECSV genome is predicted to express a replication associated protein (Rep) from an unspliced complementary strand transcript that is most similar to those of begomoviruses, curtoviruses and topocuviruses, its Rep also contains what is apparently a canonical retinoblastoma related protein interaction motif such as that found in mastreviruses. Similarly, while ECSV has the same unusual TAAGATTCC virion strand replication origin nonanucleotide found in another recently described divergent geminivirus, Beet curly top Iran virus (BCTIV), the rest of the transcription and replication origin is structurally more similar to those found in begomoviruses and curtoviruses than it is to those found in BCTIV and mastreviruses. ECSV also has what might be a homologue of the begomovirus transcription activator protein gene found in begomoviruses, a mastrevirus-like coat protein gene and two intergenic regions. Conclusion. Although it superficially resembles a chimaera of geminiviruses from different genera, the ECSV genome is not obviously recombinant, implying that the features it shares with other geminiviruses are those that were probably present within the last common ancestor of these viruses. In addition to inferring how the ancestral geminivirus genome may have looked, we use the discovery of ECSV to refine various hypotheses regarding the recombinant origins of the major geminivirus lineages. © 2009 Varsani et al; licensee BioMed Central Ltd.

Frame-rate stereopsis using non-parametric transforms and programmable logic

A frame-rate stereo vision system, based on non-parametric matching metrics, is described. Traditional metrics, such as normalized cross-correlation, are expensive in terms of logic. Non-parametric measures require only simple, parallelizable, functions such as comparators, counters and exclusive-or, and are thus very well suited to implementation in reprogrammable logic.

Chlamydia pneumoniae : modern insights into an ancient pathogen

Chlamydia pneumoniae is an enigmatic human and animal pathogen. Originally discovered in association with acute human respiratory disease, it is now associated with a remarkably wide range of chronic diseases as well as having a cosmopolitan distribution within the animal kingdom. Molecular typing studies suggest that animal strains are ancestral to human strains and that C. pneumoniae crossed from animals to humans as the result of at least one relatively recent zoonotic event. Whole genome analyses appear to support this concept – the human strains are highly conserved whereas the single animal strain that has been fully sequenced has a larger genome with several notable differences. When compared to the other, better known chlamydial species that is implicated in human infection, Chlamydia trachomatis, C. pneumoniae demonstrates pertinent differences in its cell biology, development, and genome structure. Here, we examine the characteristic facets of C. pneumoniae biology, offering insights into the diversity and evolution of this silent and ancient pathogen.

The ancient gene C12orf29 : an exploration of its role in the chordate body plan

The sheep (Ovis aries) is commonly used as a large animal model in skeletal research. Although the sheep genome has been sequenced there are still only a limited number of annotated mRNA sequences in public databases. A complementary DNA (cDNA) library was constructed to provide a generic resource for further exploration of genes that are actively expressed in bone cells in sheep. It was anticipated that the cDNA library would provide molecular tools for further research into the process of fracture repair and bone homeostasis, and add to the existing body of knowledge. One of the hallmarks of cDNA libraries has been the identification of novel genes and in this library the full open reading frame of the gene C12orf29 was cloned and characterised. This gene codes for a protein of unknown function with a molecular weight of 37 kDa. A literature search showed that no previous studies had been conducted into the biological role of C12orf29, except for some bioinformatics studies that suggested a possible link with cancer. Phylogenetic analyses revealed that C12orf29 had an ancient pedigree with a homologous gene found in some bacterial taxa. This implied that the gene was present in the last common eukaryotic ancestor, thought to have existed more than 2 billion years ago. This notion was further supported by the fact that the gene is found in taxa belonging to the two major eukaryotic branches, bikonts and unikonts. In the bikont supergroup a C12orf29-like gene was found in the single celled protist Naegleria gruberi, whereas in the unikont supergroup, encompassing the metazoa, the gene is universal to all chordate and, therefore, vertebrate species. It appears to have been lost to the majority of cnidaria and protostomes taxa; however, C12orf29-like genes have been found in the cnidarian freshwater hydra and the protostome Pacific oyster. The experimental data indicate that C12orf29 has a structural role in skeletal development and tissue homeostasis, whereas in silico analysis of the human C12orf29 promoter region suggests that its expression is potentially under the control of the NOTCH, WNT and TGF- developmental pathways, as well SOX9 and BAPX1; pathways that are all heavily involved in skeletogenesis. Taken together, this investigation provides strong evidence that C12orf29 has a very important role in the chordate body plan, in early skeletal development, cartilage homeostasis, and also a possible link with spina bifida in humans.

The primary school as a logic machine

This paper makes a case for thinking about the primary school as a logic machine (apparatus) as a way of thinking about processes of in-school stratification. Firstly we discuss related literature on in-school stratification in primary schools, particularly as it relates to literacy learning. Secondly we explain how school reform can be thought about in terms of the idea of the machine or apparatus. In which case the processes of in-school stratification can be mapped as more than simply concerns about school organisation (such as students grouping) but also involve a politics of truth, played out in each school, that constitutes school culture and what counts as ‘good’ pedagogy. Thirdly, the chapter will focus specifically on research conducted into primary schools in the Northern Suburbs of Adelaide, one of the most educationally disadvantaged regions in Australia, as a case study of the relationship between in-school stratification and the reproduction of inequality. We will draw from more than 20 years of ethnographic work in primary school in the northern suburbs of Adelaide and provide a snapshot of a recent attempt to improve literacy achievement in a few Northern Suburbs public primary schools (SILA project). The SILA project, through diagnostic reviews, has provided a significant analysis of the challenges facing policy and practice in such challenging school contexts that also maps onto existing (inter)national research. These diagnostic reviews said ‘hard things’ that required attention by SILA schools and these included: · an over reliance on whole class, low level, routine tasks and hence a lack of challenge and rigour in the learning tasks offered to students ; · a focus on the 'code breaking' function of language at the expense of richer conceptualisations of literacy that might guide teachers’ understanding of challenging pedagogies ; · the need for substantial shifts in the culture of schools, especially unsettling deficit views of students and their communities ; · a need to provide a more ‘consistent’ approach to teaching literacy across the school; · a need to focus School Improvement Plans in order to implement a clear focus on literacy learning; and, · a need to sustain professional learning to produce new knowledge and practice . The paper will conclude with suggestions for further research and possible reform projects into the primary school as a logic machine.

An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotyp

Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus × domestica), an R2R3 MYB transcription factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10) and fruit skin color (MYB1). However, the pattern of expression and allelic variation at these loci does not explain all anthocyanin-related apple phenotypes. One such example is an open-pollinated seedling of cv Sangrado that has green foliage and develops red flesh in the fruit cortex late in maturity. We used methods that combine plant breeding, molecular biology, and genomics to identify duplicated MYB transcription factors that could control this phenotype. We then demonstrated that the red-flesh cortex phenotype is associated with enhanced expression of MYB110a, a paralog of MYB10. Functional characterization of MYB110a showed that it was able to up-regulate anthocyanin biosynthesis in tobacco (Nicotiana tabacum). The chromosomal location of MYB110a is consistent with a whole-genome duplication event that occurred during the evolution of apple within the Maloideae family. Both MYB10 and MYB110a have conserved function in some cultivars, but they differ in their expression pattern and response to fruit maturity.

Logic-gate devices based on printed polymer semiconducting nanostripes

The applications of organic semiconductors in complex circuitry such as printed CMOS-like logic circuits demand miniaturization of the active structures to the submicrometric and nanoscale level while enhancing or at least preserving the charge transport properties upon processing. Here, we addressed this issue by using a wet lithographic technique, which exploits and enhances the molecular order in polymers by spatial confinement, to fabricate ambipolar organic field effect transistors and inverter circuits based on nanostructured single component ambipolar polymeric semiconductor. In our devices, the current flows through a precisely defined array of nanostripes made of a highly ordered diketopyrrolopyrrole-benzothiadiazole copolymer with high charge carrier mobility (1.45 cm2 V-1 s-1 for electrons and 0.70 cm2 V-1 s-1 for holes). Finally, we demonstrated the functionality of the ambipolar nanostripe transistors by assembling them into an inverter circuit that exhibits a gain (105) comparable to inverters based on single crystal semiconductors.

Purposeful program theory: Effective use of theories of change and logic models [Book Review]

The purpose of this book by two Australian authors is to: introduce the audience to the full complement of contextual elements found within program theory; offer practical suggestions to engage with theories of change, theories of action and logic models; and provide substantial evidence for this approach through scholarly literature, practice case studies together with the authors' combined experience of 60 years.

Analysis of ancient pottery and ceramic objects using X-ray fluorescence spectrometry

Archaeology has been called 'the science of the artefact' and nothing demonstrates this point better than the current interest displayed in provenance studies of archaeological objects. In theory, every vessel carries a chemical compositional pattern or 'fingerprint' identical with the clay from which it was made and this relationship is basic to provenance studies. The reasoning behind provenance or sourcing studies is to probe into this past and attempt to re-create prehistory by obtaining information on exchange and social interaction. This paper discusses the use of XRF spectrometry for the analysis of ancient pottery and ceramics to examine whether it is possible to predict prehictoric cultural exchanges.

Anomaly detection in online social networks : using data-mining techniques and fuzzy logic

This research is a step forward in improving the accuracy of detecting anomaly in a data graph representing connectivity between people in an online social network. The proposed hybrid methods are based on fuzzy machine learning techniques utilising different types of structural input features. The methods are presented within a multi-layered framework which provides the full requirements needed for finding anomalies in data graphs generated from online social networks, including data modelling and analysis, labelling, and evaluation.

Fuzzy logic to evaluate driving maneuvers: An integrated approach to improve training

Driver training is one of the interventions aimed at mitigating the number of crashes that involve novice drivers. Our failure to understand what is really important for learners, in terms of risky driving, is one of the many drawbacks restraining us to build better training programs. Currently, there is a need to develop and evaluate Advanced Driving Assistance Systems that could comprehensively assess driving competencies. The aim of this paper is to present a novel Intelligent Driver Training System (IDTS) that analyses crash risks for a given driving situation, providing avenues for improvement and personalisation of driver training programs. The analysis takes into account numerous variables acquired synchronously from the Driver, the Vehicle and the Environment (DVE). The system then segments out the manoeuvres within a drive. This paper further presents the usage of fuzzy set theory to develop the safety inference rules for each manoeuvre executed during the drive. This paper presents a framework and its associated prototype that can be used to comprehensively view and assess complex driving manoeuvres and then provide a comprehensive analysis of the drive used to give feedback to novice drivers.

Reflections from damaged modernity

The cliché about modern architecture being the fairy-tale fulfillment of every fantasy ceases to be a cliché only when it is accompanied by the fairy tale’s moral: that the fulfillment of the wishes rarely engenders goodness in the one doing the wishing (Adorno). Wishing for the right things in architecture and the city is the most difficult art of all: since the grim childhood-tales of the twentieth century we have been weaned from dreams and utopias, the stuff of modernism’s bad conscience. For Adorno writing in 1953, Hollywood cinema was a medium of “regression” based on infantile wish fulfillment manufactured by the industrial repetition (mimesis) of the filmic image that he called a modern “hieroglyphics,” like the archaic language of pictures in Ancient Egypt which guaranteed immortality after death in Egyptian burial rites. Arguably, today the iconic architecture industry is the executor of archaic images of modernity linked to rituals of death, promises of omnipotence and immortality. As I will argue in this symposium, such buildings are not a reflection of external ‘reality,’ but regression to an internal architectural polemic that secretly carries out the rituals of modernism’s death and seeks to make good on the liabilities of architectural history.

Fuzzy-logic based frequency controller for wind farms augmented with energy storage systems

Displacement of conventional synchronous generators by non-inertial units such as wind or solar generators will result in reduced-system inertia affecting under-frequency response. Frequency control is important to avoid equipment damage, load shedding, and possible blackouts. Wind generators along with energy storage systems can be used to improve the frequency response of low-inertia power system. This paper proposes a fuzzy-logic based frequency controller (FFC) for wind farms augmented with energy storage systems (wind-storage system) to improve the primary frequency response in future low-inertia hybrid power system. The proposed controller provides bidirectional real power injection using system frequency deviations and rate of change of frequency (RoCoF). Moreover, FFC ensures optimal use of energy from wind farms and storage units by eliminating the inflexible de-loading of wind energy and minimizing the required storage capacity. The efficacy of the proposed FFC is verified on the low-inertia hybrid power system.

The function of the RNA-binding protein TEL1 in moss reveals ancient regulatory mechanisms of shoot development

The shoot represents the basic body plan in land plants. It consists of a repeated structure composed of stems and leaves. Whereas vascular plants generate a shoot in their diploid phase, non-vascular plants such as mosses form a shoot (called the gametophore) in their haploid generation. The evolution of regulatory mechanisms or genetic networks used in the development of these two kinds of shoots is unclear. TERMINAL EAR1-like genes have been involved in diploid shoot development in vascular plants. Here, we show that disruption of PpTEL1 from the moss Physcomitrella patens, causes reduced protonema growth and gametophore initiation, as well as defects in gametophore development. Leafy shoots formed on ΔTEL1 mutants exhibit shorter stems with more leaves per shoot, suggesting an accelerated leaf initiation (shortened plastochron), a phenotype shared with the Poaceae vascular plants TE1 and PLA2/LHD2 mutants. Moreover, the positive correlation between plastochron length and leaf size observed in ΔTEL1 mutants suggests a conserved compensatory mechanism correlating leaf growth and leaf initiation rate that would minimize overall changes in plant biomass. The RNA-binding protein encoded by PpTEL1 contains two N-terminus RNA-recognition motifs, and a third C-terminus non-canonical RRM, specific to TEL proteins. Removal of the PpTEL1 C-terminus (including this third RRM) or only 16–18 amino acids within it seriously impairs PpTEL1 function, suggesting a critical role for this third RRM. These results show a conserved function of the RNA-binding PpTEL1 protein in the regulation of shoot development, from early ancestors to vascular plants, that depends on the third TEL-specific RRM.