Showing papers by "Queen's University Belfast published in 2006"

The distillation and volatility of ionic liquids

Abstract: It is widely believed that a defining characteristic of ionic liquids (or low-temperature molten salts) is that they exert no measurable vapour pressure, and hence cannot be distilled. Here we demonstrate that this is unfounded, and that many ionic liquids can be distilled at low pressure without decomposition. Ionic liquids represent matter solely composed of ions, and so are perceived as non-volatile substances. During the last decade, interest in the field of ionic liquids has burgeoned, producing a wealth of intellectual and technological challenges and opportunities for the production of new chemical and extractive processes, fuel cells and batteries, and new composite materials. Much of this potential is underpinned by their presumed involatility. This characteristic, however, can severely restrict the attainability of high purity levels for ionic liquids (when they contain poorly volatile components) in recycling schemes, as well as excluding their use in gas-phase processes. We anticipate that our demonstration that some selected families of commonly used aprotic ionic liquids can be distilled at 200-300 degrees C and low pressure, with concomitant recovery of significant amounts of pure substance, will permit these currently excluded applications to be realized.

The WASP project and the superWASP cameras

Abstract: The SuperWASP cameras are wide‐field imaging systems at the Observatorio del Roque de los Muchachos on the island of La Palma in the Canary Islands, and at the Sutherland Station of the South African Astronomical Observatory. Each instrument has a field of view of some 482 deg2 with an angular scale of 13 \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} ewcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} ormalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $\farcs$\end{document} 7 pixel−1, and is capable of delivering photometry with accuracy better than 1% for objects having \documentclass{aastex} \usepackage{amsbsy} \usepa...

Self-cooling of a micromirror by radiation pressure

Abstract: Cooling of mechanical resonators is currently a popular topic in many fields of physics including ultra-high precision measurements1, detection of gravitational waves, and the study of the transition between classical and quantum behaviour of a mechanical system. Here we report the observation of self-cooling of a micromirror by radiation pressure inside a high-finesse optical cavity. In essence, changes in intensity in a detuned cavity, as caused by the thermal vibration of the mirror, provide the mechanism for entropy flow from the mirror's oscillatory motion to the low-entropy cavity field. The crucial coupling between radiation and mechanical motion was made possible by producing free-standing micromirrors of low mass (m ≈ 400 ng), high reflectance (more than 99.6%) and high mechanical quality (Q ≈ 10,000). We observe cooling of the mechanical oscillator by a factor of more than 30; that is, from room temperature to below 10 K. In addition to purely photothermal effects we identify radiation pressure as a relevant mechanism responsible for the cooling. In contrast with earlier experiments, our technique does not need any active feedback. We expect that improvements of our method will permit cooling ratios beyond 1,000 and will thus possibly enable cooling all the way down to the quantum mechanical ground state of the micromirror.

Direct active and reactive power control of DFIG for wind energy generation

Abstract: This paper presents a new direct power control (DPC) strategy for a doubly fed induction generator (DFIG)-based wind energy generation system. The strategy is based on the direct control of stator active and reactive power by selecting appropriate voltage vectors on the rotor side. It is found that the initial rotor flux has no impact on the changes of the stator active and reactive power. The proposed method only utilizes the estimated stator flux so as to remove the difficulties associated with rotor flux estimation. The principles of this method are described in detail in this paper. The only machine parameter required by the proposed DPC method is the stator resistance whose impact on the system performance is found to be negligible. Simulation results on a 2 MW DFIG system are provided to demonstrate the effectiveness and robustness of the proposed control strategy during variations of active and reactive power, rotor speed, machine parameters, and converter dc link voltage

A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region.

Abstract: In this study we report convincing statistical support for a sixth type 1 diabetes (T1D) locus in the innate immunity viral RNA receptor gene region IFIH1 (also known as mda-5 or Helicard) on chromosome 2q24.3. We found the association in an interim analysis of a genome-wide nonsynonymous SNP (nsSNP) scan, and we validated it in a case-control collection and replicated it in an independent family collection. In 4,253 cases, 5,842 controls and 2,134 parent-child trio genotypes, the risk ratio for the minor allele of the nsSNP rs1990760 A → G (A946T) was 0.86 (95% confidence interval = 0.82–0.90) at P = 1.42 × 10−10.

Discovery of a cool planet of 5.5 Earth masses through gravitational microlensing

Abstract: Over 170 extrasolar planets have so far been discovered, with a wide range of masses and orbital periods, but until last July no planet of Neptune's mass or less had been detected any more than 0.15 astronomical units (AU) from a normal star. (That's close — Earth is one AU from the Sun). On 11 July 2005 the OGLE Early Warning System recorded a notable event: gravitational lensing of light from a distant object by a foreground star revealed a small planet of about 5.5 Earth masses, orbiting at about 2.6 AU from the foreground star. This is the lowest known mass for an extrasolar planet orbiting a main sequence star, and its detection suggests that cool, sub-Neptune mass planets are more common than gas giants, as predicted by the favoured core accretion theory of planet formation. In the favoured core-accretion model of formation of planetary systems, solid planetesimals accumulate to build up planetary cores, which then accrete nebular gas if they are sufficiently massive. Around M-dwarf stars (the most common stars in our Galaxy), this model favours the formation of Earth-mass (M⊕) to Neptune-mass planets with orbital radii of 1 to 10 astronomical units (au), which is consistent with the small number of gas giant planets known to orbit M-dwarf host stars1,2,3,4. More than 170 extrasolar planets have been discovered with a wide range of masses and orbital periods, but planets of Neptune's mass or less have not hitherto been detected at separations of more than 0.15 au from normal stars. Here we report the discovery of a M⊕ planetary companion at a separation of au from a M⊙ M-dwarf star, where M⊙ refers to a solar mass. (We propose to name it OGLE-2005-BLG-390Lb, indicating a planetary mass companion to the lens star of the microlensing event.) The mass is lower than that of GJ876d (ref. 5), although the error bars overlap. Our detection suggests that such cool, sub-Neptune-mass planets may be more common than gas giant planets, as predicted by the core accretion theory.

A common CFH haplotype, with deletion of CFHR1 and CFHR3, is associated with lower risk of age-related macular degeneration.

Abstract: Age-related macular degeneration (AMD; OMIM #603075) is the most frequent cause of visual impairment in the elderly population, with severe disease affecting nearly 10% of individuals of European descent over the age of 75 years. It is a complex disease in which genetic and environmental factors contribute to susceptibility. Complement factor H (CFH) has recently been identified as a major AMD susceptibility gene, and the Y402H polymorphism has been proposed as the likely causative factor. We genotyped polymorphisms spanning the cluster of CFH and five CFH-related genes on chromosome 1q23 in 173 individuals with severe neovascular AMD and 170 elderly controls with no signs of AMD. Detailed analysis showed a common haplotype associated with decreased risk of AMD that was present on 20% of chromosomes of controls and 8% of chromosomes of individuals with AMD. We found that this haplotype carried a deletion of CFHR1 and CFHR3, and the proteins encoded by these genes were absent in serum of homozygotes. The protective effect of the deletion haplotype cannot be attributed to linkage disequilibrium with Y402H and was replicated in an independent sample.

Solvent-free synthesis of a microporous metal–organic framework

Abstract: We describe the first solvent-free mechanochemical synthesis of a microporous metal–organic framework [Cu(INA)2] (INA = isonicotinic acid); the product has robust 3-dimensional connectivity and is obtained quantitatively by grinding together copper acetate and isonicotinic acid for 10 minutes without any applied heating—the high efficiency of the synthesis suggests that mechanochemical synthesis should be further investigated as a convenient method for the preparation of microporous metal–organic frameworks (MOFs).

High harmonic generation in the relativistic limit

Abstract: The generation of extremely bright coherent X-ray pulses in the femtosecond and attosecond regime is currently one of the most exciting frontiers of physics–allowing, for the first time, measurements with unprecedented temporal resolution1,2,3,4,5,6. Harmonics from laser–solid target interactions have been identified as a means of achieving fields as high as the Schwinger limit2,7 (E=1.3×1016 V m−1) and as a highly promising route to high-efficiency attosecond (10−18 s) pulses8 owing to their intrinsically phase-locked nature. The key steps to attain these goals are achieving high conversion efficiencies and a slow decay of harmonic efficiency to high orders by driving harmonic production to the relativistic limit1. Here we present the first experimental demonstration of high harmonic generation in the relativistic limit, obtained on the Vulcan Petawatt laser9. High conversion efficiencies (η>10−6 per harmonic) and bright emission (>1022 photons s−1 mm−2 mrad−2 (0.1% bandwidth)) are observed at wavelengths <4 nm (the `water-window' region of particular interest for bio-microscopy).

The folk psychology of souls

Abstract: The present article examines how people's belief in an afterlife, as well as closely related supernatural beliefs, may open an empirical backdoor to our understanding of the evolution of human social cognition. Recent findings and logic from the cognitive sciences contribute to a novel theory of existential psychology, one that is grounded in the tenets of Darwinian natural selection. Many of the predominant questions of existential psychology strike at the heart of cognitive science. They involve: causal attribution (why is mortal behavior represented as being causally related to one's afterlife? how are dead agents envisaged as communicating messages to the living?), moral judgment (why are certain social behaviors, i.e., transgressions, believed to have ultimate repercussions after death or to reap the punishment of disgruntled ancestors?), theory of mind (how can we know what it is "like" to be dead? what social-cognitive strategies do people use to reason about the minds of the dead?), concept acquisition (how does a common-sense dualism interact with a formalized socio-religious indoctrination in childhood? how are supernatural properties of the dead conceptualized by young minds?), and teleological reasoning (why do people so often see their lives as being designed for a purpose that must be accomplished before they perish? how do various life events affect people's interpretation of this purpose?), among others. The central thesis of the present article is that an organized cognitive "system" dedicated to forming illusory representations of (1) psychological immortality, (2) the intelligent design of the self, and (3) the symbolic meaning of natural events evolved in response to the unique selective pressures of the human social environment.

Resource and Capability Constraints to Innovation in Small and Large Plants

Abstract: In an attempt to enhance firm’s competitiveness, policy initiatives have sought to encourage more firms to innovate, with a particular focus on small firms. The success of such initiatives, however, depends on a clear understanding of the factors that are constraining innovation activity, and whether these differ for firms of different sizes. This paper examines those resources and capabilities that firms identify as constraining their innovation activity, the difference in these for small and larger plants and the actual impact of these perceived constraints on the probability of innovating and the degree of innovation success. Drawing on longitudinal data the paper demonstrates that innovation is an evolutionary process with the constraints to innovation being different for small and larger plants. From a policy perspective, initiatives to overcome constraints to innovation in small plants should extend beyond those of finance to include greater networking opportunities, cost reduction programmes and marketing strategies to increase the profit margin on new products, human resource management practices on implementing change and easier access to information about new technologies. In contrast policies to promote innovation in larger plants should focus on minimising the risk of development and enhancing access to specialist expertise.

Gold catalysts for pure hydrogen production in the water–gas shift reaction: activity, structure and reaction mechanism

Abstract: The production of hydrogen containing very low levels of carbon monoxide for use in polymer electrolyte fuel cells requires the development of catalysts that show very high activity at low temperatures where the equilibrium for the removal of carbon monoxide using the water–gas shift reaction is favourable. It has been claimed that oxide-supported gold catalysts have the required high activity but there is considerable uncertainty in the literature about the feasibility of using these catalysts under real conditions. By comparing the activity of gold catalysts with that of platinum catalysts it is shown that well-prepared gold catalysts are significantly more active than the corresponding platinum catalysts. However, the method of preparation and pre-treatment of the gold catalysts is critical and activity variations of several orders of magnitude can be observed depending on the methods chosen. It is shown that an intimate contact between gold and the oxide support is important and any preparative procedure that does not generate such an interaction, or any subsequent treatment that can destroy such an interaction, may result in catalysts with low activity. The oxidation state and structure of active gold catalysts for the water–gas shift reaction is shown to comprise gold primarily in a zerovalent metallic state but in intimate contact with the support. This close contact between small metallic gold particles and the support may result in the “atoms” at the point of contact having a net charge (most probably cationic) but the high activity is associated with the presence of metallic gold. Both in situ XPS and XANES appear unequivocal on this point and this conclusion is consistent with similar measurements on gold catalysts even when used for CO oxidation. In situ EXAFS measurements under water gas shift conditions show that the active form of gold is a small gold cluster in intimate contact with the oxide support. The importance of the gold/oxide interface is indicated but the possible role of special sites (e.g., edge sites) on the gold clusters cannot be excluded. These may be important for CO oxidation but the fact that water has to be activated in the water gas shift reaction may point towards a more dominant role for the interfacial sites. The mechanism of the water gas shift reaction on gold and other low temperature catalysts has been widely investigated but little agreement exists. However, it is shown that a single “universal” model is consistent with much of the experimental literature. In this, it is proposed that the dominant surface intermediate is a function of reaction conditions. For example, as the temperature is increased the dominant species changes from a carbonate or carboxylate species, to a formate species and eventually at high temperatures to a mechanism that is characteristic of a redox process. Similar changes in the dominant intermediate are observed with changes in the gas composition. Overall, it is shown that reported variations in the kinetics, structure and reaction mechanism for the water gas shift reaction on gold catalysts can now be understood and rationalised.

Surface-enhanced Raman spectroscopy (SERS) for sub-micromolar detection of DNA/RNA mononucleotides.

Abstract: Surface-enhanced Raman (SER) spectra of all the DNA/RNA mononucleotides have been obtained with high sensitivity using citrate-reduced silver colloids aggregated with MgSO4, rather than the more usual halide ions, which were found to prevent enhancement of these compounds. The SERS spectra of adenine, guanine, thymine, cytosine, and uracil were recorded along with their corresponding nucleosides and 5'-deoxynucleotides. For the cytosine series, all three spectra had similar relative band intensities but the spectra of adenine were different from those of adenosine and dAMP, probably due to differences in orientation on the surface. No enhanced bands from the phosphate or sugar groups were observed. There were general similarities between the SERS spectra of the purine mononucleotides and the pyrimidine mononucleotides, but the spectra were sufficiently different to allow each of them to be distinguished. This method can therefore be used for high sensitivity, label-free identification of mononucleotides.

A fundamental attribution error? Rethinking cognitive distortions †

Abstract: The notion of ‘cognitive distortion’ has become enshrined in the offender treatment literature over the last 20 years, yet the concept still suffers from a lack of definitional clarity. In particular, the umbrella term is often used to refer to offence-supportive attitudes, cognitive processing during an offence sequence, as well as post-hoc neutralisations or excuses for offending. Of these very different processes, the last one might be the most popular and problematic. Treatment programmes for offenders often aim to eliminate excuse-making as a primary aim, and decision-makers place great weight on the degree to which an offender “takes responsibility” for his or her offending. Yet, the relationship between these after-the-fact explanations and future crime is not at all clear. Indeed, the designation of post hoc excuses as criminogenic may itself be an example of fallacious thinking. After all, outside of the criminal context, post hoc excuse-making is widely viewed as normal, healthy, and socially rewarded behaviour. We argue that the open exploration of contextual risk factors leading to offending can help in the identification of criminogenic factors as well as strengthen the therapeutic experience. Rather than insist that offenders take “responsibility” for the past, we suggest that efforts should focus on helping them take responsibility for the future, shifting the therapeutic focus from post hoc excuses to offence-supportive attitudes and underlying cognitive schemas that are empirically linked to re-offending.

How parasites affect interactions between competitors and predators

Abstract: We present a synthesis of empirical and theoretical work investigating how parasites influence competitive and predatory interactions between other species. We examine the direct and indirect effects of parasitism and discuss examples of density and parasite-induced trait-mediated effects. Recent work reveals previously unrecognized complexity in parasite-mediated interactions. In addition to parasite-modified and apparent competition leading to species exclusion or enabling coexistence, parasites and predators interact in different ways to regulate or destablize the population dynamics of their joint prey. An emerging area is the impact of parasites on intraguild predation (IGP). Parasites can increase vulnerability of infected individuals to cannibalism or predation resulting in reversed species dominance in IGP hierarchies. We discuss the potential significance of parasites for community structure and biodiversity, in particular their role in promoting species exclusion or coexistence and the impact of emerging diseases. Ongoing invasions provide examples where parasites mediate native/invader interactions and play a key role in determining the outcome of invasions. We highlight the need for more quantitative data to assess the impact of parasites on communities, and the combination of theoretical and empirical studies to examine how the effects of parasitism scale up to community-level processes.

Local Models for Spatial Analysis

Abstract: Introduction Remit of This Book Local Models and Methods What Is Local? Spatial Dependence Spatial Scale Stationarity Spatial Data Models Data Sets Used for Illustrative Purposes A Note on Notation Overview Local Modeling Approaches to Local Adaptation Stratification or Segmentation of Spatial Data Moving Window/Kernel Methods Locally Varying Model Parameters Transforming and Detrending Spatial Data Overview Grid Data Exploring Spatial Variation in Single Variables Global Univariate Statistics Local Univariate Statistics Analysis of Grid Data Moving Windows for Grid Analysis Wavelets Segmentation Analysis of Digital Elevation Models Overview Spatial Relations Spatial Autocorrelation: Global Measures Spatial Autocorrelation: Local Measures Global Regression Local Regression Regression and Spatial Data Spatial Autoregressive Models Multilevel Modeling Allowing for Local Variation in Model Parameters Moving Window Regression (MWR) Geographically Weighted Regression (GWR) Spatially Weighted Classification Overview Spatial Prediction 1: Deterministic Methods Point Interpolation Global Methods Local Methods Areal Interpolation General Approaches: Overlay Local Models and Local Data Limitations: Point and Areal Interpolation Overview Spatial Prediction 2: Geostatistics Random Function Models Stationarity Global Models Exploring Spatial Variation Kriging Equivalence of Splines and Kriging Conditional Simulation The Change of Support Problem Other Approaches Local Approaches: Nonstationary Models Nonstationary Mean Nonstationary Models for Prediction Nonstationary Variogram Variograms in Texture Analysis Summary Point Patterns Point Patterns Visual Examination of Point Patterns Density and Distance Methods Statistical Tests of Point Patterns Global Methods Distance Methods Other Issues Local Methods Density Methods Accounting for the Population at Risk The Local K Function Point Patterns and Detection of Clusters Overview Summary: Local Models for Spatial Analysis Review Key Issues Software Future Developments Summary References Index

Electronic structure calculations for solids and molecules : theory and computational methods

Abstract: Electronic structure problems are studied in condensed matter physics and theoretical chemistry to provide important insights into the properties of matter. This 2006 graduate textbook describes the main theoretical approaches and computational techniques, from the simplest approximations to the most sophisticated methods. It starts with a detailed description of the various theoretical approaches to calculating the electronic structure of solids and molecules, including density-functional theory and chemical methods based on Hartree-Fock theory. The basic approximations are thoroughly discussed, and an in-depth overview of recent advances and alternative approaches in DFT is given. The second part discusses the different practical methods used to solve the electronic structure problem computationally, for both DFT and Hartree-Fock approaches. Adopting a unique and open approach, this textbook is aimed at graduate students in physics and chemistry, and is intended to improve communication between these communities. It also serves as a reference for researchers entering the field.

Microlens OGLE-2005-BLG-169 Implies That Cool Neptune-like Planets Are Common

Abstract: We detect a Neptune mass ratio (q 8 ? 10-5) planetary companion to the lens star in the extremely high magnification (A ~ 800) microlensing event OGLE-2005-BLG-169. If the parent is a main-sequence star, it has mass M ~ 0.5 M?, implying a planet mass of ~13 M? and projected separation of ~2.7 AU. When intensely monitored over their peak, high-magnification events similar to OGLE-2005-BLG-169 have nearly complete sensitivity to Neptune mass ratio planets with projected separations of 0.6-1.6 Einstein radii, corresponding to 1.6-4.3 AU in the present case. Only two other such events were monitored well enough to detect Neptunes, and so this detection by itself suggests that Neptune mass ratio planets are common. Moreover, another Neptune was recently discovered at a similar distance from its parent star in a low-magnification event, which are more common but are individually much less sensitive to planets. Combining the two detections yields 90% upper and lower frequency limits f = 0.38 over just 0.4 decades of planet-star separation. In particular, f > 16% at 90% confidence. The parent star hosts no Jupiter-mass companions with projected separations within a factor 5 of that of the detected planet. The lens-source relative proper motion is ? ~ 7-10 mas yr-1, implying that if the lens is sufficiently bright, I 23.8, it will be detectable by the Hubble Space Telescope by 3 years after peak. This would permit a more precise estimate of the lens mass and distance and, so, the mass and projected separation of the planet. Analogs of OGLE-2005-BLG-169Lb orbiting nearby stars would be difficult to detect by other methods of planet detection, including radial velocities, transits, and astrometry.

Ultrafast laser-driven microlens to focus and energy-select mega-electron volt protons

Abstract: We present a technique for simultaneous focusing and energy selection of high-current, mega–electron volt proton beams with the use of radial, transient electric fields (10 7 to 10 10 volts per meter) triggered on the inner walls of a hollow microcylinder by an intense subpicosecond laser pulse. Because of the transient nature of the focusing fields, the proposed method allows selection of a desired range out of the spectrum of the polyenergetic proton beam. This technique addresses current drawbacks of laser-accelerated proton beams, such as their broad spectrum and divergence at the source.

The Internalization of Externalities in the Production of Electricity: Willingness to Pay for the Attributes of a Policy for Renewable Energy

Abstract: This paper investigates the willingness to pay of a sample of residents of Bath, England, for a hypothetical program that promotes the production of renewable energy. Using choice experiments, we assess the preferences of respondents for a policy for the promotion of renewable energy that (i) contributes to the internalization of the external costs caused by fossil fuel technologies; (ii) affects the security of energy supply; (iii) has an impact on the employment in the energy sector; (iv) and leads to an increase in the electricity bill. Responses to the choice questions show that our respondents are in favour of a policy for renewable energy and that they attach a high value to a policy that brings private and public benefits in terms of climate change and energy security benefits. Our results therefore suggest that consumers are willing to pay a higher price for electricity in order to internalize the external costs in terms of energy security, climate change and air pollution caused by the production of electricity.

Horses for Courses: Explaining the Gap Between the Theory and Practice of Green Supply

Abstract: Researchers and policy-makers have become increasingly enthusiastic about greening purchasing and supply management activities. In theory, greening supply should both limit environmental damage from industrial activities, and deliver bottom line benefits to implementing firms. However, compared with other environmental initiatives, few firms have implemented extensive green supply programmes.

Optical bistability in nonlinear surface-plasmon polaritonic crystals.

Abstract: Nonlinear optical transmission through periodically nanostructured metal films (surface-plasmon polaritonic crystals) has been studied. The surface polaritonic crystals have been coated with a nonlinear polymer. The optical transmission of such nanostructures has been shown to depend on the control-light illumination conditions. The resonant transmission exhibits bistable behavior with the control-light intensity. The bistability is different at different resonant signal wavelengths and for different wavelengths of the control light. The effect is explained by the strong sensitivity of the surface-plasmon mode resonances at the signal wavelength to the surrounding dielectric environment and the electromagnetic field enhancement due to plasmonic excitations at the controlled light wavelengths.

Communicating chemical congregation: a molecular AND logic gate with three chemical inputs as a "lab-on-a-molecule" prototype.

Abstract: We demonstrate the first three-input molecular AND logic gate based on three chemical inputs as a direct way of detecting congregations of chemical species. The AND gate operates in water and responds to Na+, H+, and Zn2+ inputs with an enhanced fluorescence signal when pre-set concentration thresholds are exceeded. Future “lab-on-a-molecule” devices could have application in medicine for rapid disease screening.

Molecular and Biological Characterization of Deformed Wing Virus of Honeybees (Apis mellifera L.)

Abstract: Deformed wing virus (DWV) of honeybees (Apis mellifera) is closely associated with characteristic wing deformities, abdominal bloating, paralysis, and rapid mortality of emerging adult bees. The virus was purified from diseased insects, and its genome was cloned and sequenced. The genomic RNA of DWV is 10,140 nucleotides in length and contains a single large open reading frame encoding a 328-kDa polyprotein. The coding sequence is flanked by a 1,144-nucleotide 5 nontranslated leader sequence and a 317-nucleotide 3 nontranslated region, followed by a poly(A) tail. The three major structural proteins, VP1 (44 kDa), VP2 (32 kDa), and VP3 (28 kDa), were identified, and their genes were mapped to the N-terminal section of the polyprotein. The C-terminal part of the polyprotein contains sequence motifs typical of well-characterized picornavirus nonstructural proteins: an RNA helicase, a chymotrypsin-like 3C protease, and an RNA-dependent RNA polymerase. The genome organization, capsid morphology, and sequence comparison data indicate that DWV is a member of the recently established genus Iflavirus. Deformed wing virus (DWV) is the one of the main viruses associated with the collapse of honeybee (Apis mellifera L.) colonies due to infestation with the ectoparasitic mite Varroa destructor (4, 8, 12). The virus was first isolated from a sample of symptomatic honeybees from Japan in the early 1980s and is currently distributed worldwide, wherever varroa mites are found (2, 18). A recent survey of adult bee populations detected DWV in over 90% of French apiaries (66) and in 100% of mite samples. The incidence was slightly reduced when pupal samples were analyzed, especially in the spring (66). DWV has also been detected by serology in the dwarf bee A. florae Fabr. (F. R. Hunter-Fujita, M. S. Mossadegh, and B. V. Ball, Abstr. 36th “Apimondia” Int. Apic. Congr., abstr. 230, 1999) and in the Asian honeybee A. cerana Fabr. (2) and by reverse transcriptase (RT) PCR in bumblebees (29). It is serologically related to Egypt bee virus (8, 9, 13), first isolated in 1977 from infected adults from Egypt (10). Typical symptoms of deformed wing disease are vestigial and crumpled wings, bloated abdomens, paralysis, and a severely shortened adult life span for emerging worker and drone bees (44). For a long time it was believed that these symptoms were due to the feeding activity of the mites (23, 42, 72) until it was shown that, in diseased colonies, deformed bees could emerge from cells not parasitized by varroa mites (49, 55) and that the symptoms

Multilocus sequence typing method for identification and genotypic classification of pathogenic Leptospira species

Abstract: Background Leptospira are the parasitic bacterial organisms associated with a broad range of mammalian hosts and are responsible for severe cases of human Leptospirosis. The epidemiology of leptospirosis is complex and dynamic. Multiple serovars have been identified, each adapted to one or more animal hosts. Adaptation is a dynamic process that changes the spatial and temporal distribution of serovars and clinical manifestations in different hosts. Serotyping based on repertoire of surface antigens is an ambiguous and artificial system of classification of leptospiral agents. Molecular typing methods for the identification of pathogenic leptospires up to individual genome species level have been highly sought after since the decipherment of whole genome sequences. Only a few resources exist for microbial genotypic data based on individual techniques such as Multiple Locus Sequence Typing (MLST), but unfortunately no such databases are existent for leptospires.