Experimental observations of rapid maize streak virus evolution reveal a strand-specific nucleotide substitution bias

Background. Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ∼10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered. Results. We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year. Conclusion. These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules. © 2008 Walt et al; licensee BioMed Central Ltd.

Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution

Background Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA. Results Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots - of the breakpoints required to re-create MSV-MatA. Although the MSV-sensitive maize genotype gave rise to the greatest variety of recombinants, the measured fitness of each of these recombinants correlated with their similarity to MSV-MatA. Conclusions The mechanistic predispositions of different MSV genomic regions to recombination can strongly influence the accessibility of high-fitness MSV recombinants. The frequency with which the fittest recombinant MSV genomes arise also correlates directly with the escalating selection pressures imposed by increasingly MSV-resistant maize hosts.

The clay-size fraction of CI chondrites Alais and Orgueil : an AEM study

CI chondrites are used pervasively in the meteorite literature as a cosmochemical reference point for bulk compositions[1], isotope analyses[2] and, within certain models of meteorite evolution, as an important component of an alteration sequence within the carbonaceous chondrite subset[3]. More recently, the chemical variablity of CI chondrite matrices (which comprise >80% of the meteorite), has been cited in discussions about the "chondritic" nature of spectroscopic data from P/comet Halley missions[4] and of chemical data from related materials such as interplanetary dust particles[5]. Most CI chondrites have been studied as bulk samples(e.g. major and trace element abundances)and considerable effort has also been focussed on accessory phases such as magnetites, olivine, sulphates and carbonates [6-8]. A number of early studies showed that the primary constituents of CI matrices are layer silicates and the most definitive structural study on powdered samples identified two minerals: montmorillonite and serpentine[9]. In many cases, as with the study by Bass[9],the relative scarcity of most CI chondrites restricts such bulk analyses to the Orgueil meteorite. The electron microprobe/SEM has been used on petrographic sections to more precisely define the "bulk" composition of at least four CI matrices[3], and as recently summarised by McSween[3], these data define a compositional trend quite different to that obtained for CM chondrite matrices. These "defocussed-beam" microprobe analyses average major element compositions over matrix regions ~lOOµm in diameter and provide only an approximation to silicate mineral composition(s) because their grain sizes are much less than the diameter of the beam. In order to (a) more precisely define the major element compositions of individual mineral grains within CI matrices, and (b)complement previous TEM studies [11,12], we have undertaken an analytical electron microscopy (AEM) study of Alais and Orgueil matrices.

Front interactions in a three-component system

The three-component reaction-diffusion system introduced in [C. P. Schenk et al., Phys. Rev. Lett., 78 (1997), pp. 3781–3784] has become a paradigm model in pattern formation. It exhibits a rich variety of dynamics of fronts, pulses, and spots. The front and pulse interactions range in type from weak, in which the localized structures interact only through their exponentially small tails, to strong interactions, in which they annihilate or collide and in which all components are far from equilibrium in the domains between the localized structures. Intermediate to these two extremes sits the semistrong interaction regime, in which the activator component of the front is near equilibrium in the intervals between adjacent fronts but both inhibitor components are far from equilibrium there, and hence their concentration profiles drive the front evolution. In this paper, we focus on dynamically evolving N-front solutions in the semistrong regime. The primary result is use of a renormalization group method to rigorously derive the system of N coupled ODEs that governs the positions of the fronts. The operators associated with the linearization about the N-front solutions have N small eigenvalues, and the N-front solutions may be decomposed into a component in the space spanned by the associated eigenfunctions and a component projected onto the complement of this space. This decomposition is carried out iteratively at a sequence of times. The former projections yield the ODEs for the front positions, while the latter projections are associated with remainders that we show stay small in a suitable norm during each iteration of the renormalization group method. Our results also help extend the application of the renormalization group method from the weak interaction regime for which it was initially developed to the semistrong interaction regime. The second set of results that we present is a detailed analysis of this system of ODEs, providing a classification of the possible front interactions in the cases of $N=1,2,3,4$, as well as how front solutions interact with the stationary pulse solutions studied earlier in [A. Doelman, P. van Heijster, and T. J. Kaper, J. Dynam. Differential Equations, 21 (2009), pp. 73–115; P. van Heijster, A. Doelman, and T. J. Kaper, Phys. D, 237 (2008), pp. 3335–3368]. Moreover, we present some results on the general case of N-front interactions.

Optimal power system stabilizer tuning in multi-machine system via an improved differential evolution

Power system stabilizer (PSS) is one of the most important controllers in modern power systems for damping low frequency oscillations. Many efforts have been dedicated to design the tuning methodologies and allocation techniques to obtain optimal damping behaviors of the system. Traditionally, it is tuned mostly for local damping performance, however, in order to obtain a globally optimal performance, the tuning of PSS needs to be done considering more variables. Furthermore, with the enhancement of system interconnection and the increase of system complexity, new tools are required to achieve global tuning and coordination of PSS to achieve optimal solution in a global meaning. Differential evolution (DE) is a recognized as a simple and powerful global optimum technique, which can gain fast convergence speed as well as high computational efficiency. However, as many other evolutionary algorithms (EA), the premature of population restricts optimization capacity of DE. In this paper, a modified DE is proposed and applied for optimal PSS tuning of 39-Bus New-England system. New operators are introduced to reduce the probability of getting premature. To investigate the impact of system conditions on PSS tuning, multiple operating points will be studied. Simulation result is compared with standard DE and particle swarm optimization (PSO).

Cometary evolution : Clues from chondritic interplanetary dust particles

Cometary and interplanetary dust particles (IDP) are compared, and the mineralogical evolution of comet nuclei is discussed. Chondritic IDP have properties consistent with properties expected for cometary dust. The complex and varied mineralogy of these particles may indicate mineral alteration processes that occur in comet nuclei. Depending on the thermal budget of a comet, the upper few meters of nucleus material may maintain temperatures within regimes of hydrocryogenic (200 to 237K) and low-temperature aqueous (274 to 400K) alteration. Thus, layer silicates, carbonates, and sulfates may be important components of cometary dust and, correspondingly are common constituents of chondritic IDPs. Alteration of comet starting materials may be a common occurrence, and depends on the specific physical and chemical properties of each individual comet.

Visualizing the evolution of knowledge management capability in construction firms

A firm, as a dynamic, evolving, and quasi-autonomous system of knowledge production and application, develops knowledge management capability (KMC) through strategic learning in order to sustain competitive advantages in a dynamic environment. Knowledge governance mechanisms and knowledge processes connect and interact with each other forming learning mechanisms, which carry out double loop learning that drives genesis and evolution of KMC to modify operating routines that effect desired performance. This paper reports a study that was carried out within a context of construction contractors, a type of project-based firms, operating within the dynamic Hong Kong construction market. A multiple-case design was used to incorporate evidence from the literature and interviews, with the help of system dynamics modeling, to visualize the evolution of KMC. The study demonstrates the feasibility to visualize how a firm's KMC matches its operating environment over time. The findings imply that knowledge management (KM) applications can be better planned and controlled through evaluation of KM performance over time from a capability perspective.

Smartphone malware evolution revisited : Android next target?

Smartphones started being targets for malware in June 2004 while malware count increased steadily until the introduction of a mandatory application signing mechanism for Symbian OS in 2006. From this point on, only few news could be read on this topic. Even despite of new emerging smartphone platforms, e.g. android and iPhone, malware writers seemed to lose interest in writing malware for smartphones giving users an unappropriate feeling of safety. In this paper, we revisit smartphone malware evolution for completing the appearance list until end of 2008. For contributing to smartphone malware research, we continue this list by adding descriptions on possible techniques for creating the first malware(s) for Android platform. Our approach involves usage of undocumented Android functions enabling us to execute native Linux application even on retail Android devices. This can be exploited to create malicious Linux applications and daemons using various methods to attack a device. In this manner, we also show that it is possible to bypass the Android permission system by using native Linux applications.

Timing and emplacement dynamics of newly recognised mass flow deposits at ~ 8–12 ka offshore Soufrière Hills volcano, Montserrat : how submarine stratigraphy can complement subaerial eruption histories

This contribution describes two mass movement deposits (total volume ~0.5 km3) identified in seven marine cores located 8 to 15 km offshore southern Montserrat, West Indies. The deposits were emplaced in the last 35 ka and have not previously been recognised in either the subaerial or distal submarine records. Age constraints, provided by radiocarbon dating, show that an explosive volcanic eruption occurred at ca 8–12 ka, emplacing a primary eruption-related deposit that overlies a large (~0.3 km3) reworked bioclastic and volcaniclastic flow deposit, formed from a shelf collapse between 8 and 35 ka. The origin of these deposits has been deduced through the correlation of marine sediment cores, component analysis and geochemical analysis. The 8–12 ka primary volcanic deposit was likely derived from a highly-erosive pyroclastic flow from the Soufrière Hills volcano that entered the ocean and mixed with the water column forming a water-supported density current. Previous investigations of the eruption record suggested that there was a hiatus in activity at the Soufrière Hills volcano between 16 and 6 ka. The ca 8–12 ka eruptive episode identified here shows that this hiatus was shorter than previously hypothesised, and thus highlights the importance of obtaining an accurate and completemarine record of events offshore from volcanic islands and incorporating such data into eruption history reconstructions. Comparisons with the submarine deposit characteristics of the 2003 dome collapse also suggests that the ~8–12 ka eruptive episode was more explosive than eruptions from the current eruptive episode.

Early-mid Cretaceous tectonic evolution of eastern Gondwana : from silicic LIP magmatism to continental rupture

The Early–mid Cretaceous marks the confluence of three major continental-scale events in eastern Gondwana: (1) the emplacement of a Silicic Large Igneous Province (LIP) near the continental margin; (2) the volcaniclastic fill, transgression and regression of a major epicontinental seaway developed over at least a quarter of the Australian continent; and (3) epeirogenic uplift, exhumation and continental rupturing culminating in the opening of the Tasman Basin c. 84 Ma. The Whitsunday Silicic LIP event had widespread impact, producing both substantial extrusive volumes of dominantly silicic pyroclastic material and coeval first-cycle volcanogenic sediment that accumulated within many eastern Australian sedimentary basins, and principally in the Great Australian Basin system (>2 Mkm3 combined volume). The final pulse of volcanism and volcanogenic sedimentation at c. 105–95 Ma coincided with epicontinental seaway regression, which shows a lack of correspondence with the global sea-level curve, and alternatively records a wider, continental-scale effect of volcanism and rift tectonism. Widespread igneous underplating related to this LIP event is evident from high paleogeothermal gradients and regional hydrothermal fluid flow detectable in the shallow crust and over a broad region. Enhanced CO2 fluxing through sedimentary basins also records indirectly, large-scale, LIP-related mafic underplating. A discrete episode of rapid crustal cooling and exhumation began c. 100–90 Ma along the length of the eastern Australian margin, related to an enhanced phase of continental rifting that was largely amagmatic, and probably a switch from wide–more narrow rift modes. Along-margin variations in detachment fault architecture produced narrow (SE Australia) and wide continental margins with marginal, submerged continental plateaux (NE Australia). Long-lived NE-trending cross-orogen lineaments controlled the switch from narrow to wide continental margin geometries.

New insights into magmatism and changing rift styles in the evolution of the Gulf of California

The Gulf of California (GoC) has been an important focus site for understanding the spatial and temporal evolution of rifts, with recent studies concluding: 1) rapid crustal rupturing within 10 Myrs; 2) surprisingly abrupt variations in rifting style and magmatism with apparently wide magma-poor and narrow, magmatic rift segments; and 3) that high sedimentation rates may promote switching from wide to narrow rift modes or thermally blanket the crust to enhance rift magmatism. Critical to these conclusions is the onset of rifting at~12 Ma following the cessation of subduction. New field-based volcanostratigraphic and geochronologic studies along the southeastern GoC margin reveal Early Miocene (~25-18 Ma) bimodal volcanism in wide rifting mode (~400 km width), followed by a mid-Miocene (~18-12 Ma) phase of dominantly intermediate composition magmatism in and around the nascent GoC with lavas/domes often emplaced into actively subsiding basins, but contemporaneous with bimodal volcanism regionally. Flat-lying intraplate basaltic lava fields emplaced ~12-10 Ma along the GoC east coast abut tilted blocks of ~20 Ma ignimbrites onshore, and also occur offshore. The reduction in crustal thickness from ~55 to 20 km along the eastern GoC edge must have been largely achieved by 12 Ma. Extension has demonstrably began earlier than previously thought, downplaying rapid rifting and any thermal effects from <6 Ma sedimentation. New age data from onshore indicate significant structurally controlled corridors of magmatism during 18-12 Ma extension in apparently magma-poor rift segments, and this magmatism temporally coincides with the switch from wide to narrow rifting.

Cometary evolution : clues on physical properties from chondritic interplanetary dust particles

The degree of diversity or similarity detected in comets depends primarily on the lifetimes of the individual cometary nuclei at the time of analysis. It is inherent in our understanding of cometary orbital dynamics and the seminal model of comet origins that cometary evolution is the natural order of events in our Solar System. Thus, predictions of cometary behaviour in terms of bulk physical, mineralogical or chemical parameters should contain an appreciation of temporal variation(s). Previously, Rietmeijer and Mackinnon [1987] developed mineralogical bases for the chemical evolution of cometary nuclei primarily with regard to the predominantly silicate fraction of comet nuclei. We suggested that alteration of solids in cometary nuclei should be expected and that indications of likely reactants and products can be derived from judicious comparison with terrestrial diagenetic environments which include hydrocryogenic and low-temperature aqueous alterations. In a further development of this concept, Rietmeijer [1988] provides indirect evidence for the formation of sulfides and oxides in comet nuclei. Furthermore, Rietmeijer [1988] noted that timescales for hydrocryogenic and low-temperature reactions involving liquid water are probably adequate for relatively mature comets, e.g. P/comet Halley. In this paper, we will address the evolution of comet nuclei physical parameters such as solid particle grain size, porosity and density. In natural environments, chemical evolution (e.g. mineral reactions) is often accompanied by changes in physical properties. These concurrent changes are well-documented in the terrestrial geological literature, especially in studies of sediment diagenesis and we suggest that similar basic principles apply within the upper few meters of active comet nuclei. The database for prediction of comet nuclei physical parameters is, in principle, the same as used for the proposition of chemical evolution. We use detailed mineralogical studies of chondritic interplanetary dust particles (IDPS) as a guide to the likely constitution of mature comets traversing the inner Solar System. While there is, as yet, no direct proof that a specific sub-group or type of chondritic IDP is derived from a specific comet, it is clear that these particles are extraterrestrial in origin and that a certain portion of the interplanetary flux received by the Earth is cometary in origin. Two chondritic porous (CP) IDPS, sample numbers W701OA2 and W7029CI, from the Johnson Space Center Cosmic Dust Collection have been selected for this study of putative cometary physical parameters. This particular type of particle is considered a likely candidate for a cometary origin on the basis of mineralogy, bulk composition and morphology. While many IDPs have been subjected to intensive study over the past decade, we can develop a physical parameter model on only these two CP IDPs because few others have been studied in sufficient detail.

Evolution and innovation in guardianship laws: Assisted decision-making

Guardianship laws in most Western societies provide decision-making mechanisms for adults with impaired capacity. Since the inception of these laws, the principle of autonomy and recognition of human rights for those coming within guardianship regimes has gained prominence. A new legal model has emerged, which seeks to incorporate ‘assisted decision-making’ models into guardianship laws. Such models legally recognise that an adult’s capacity may be maintained through assistance or support provided by another person, and provide formal recognition of the person in that ‘assisting’ role. This article situates this latest legal innovation within a historical context, examining the social and legal evolution of guardianship laws and determining whether modern assisted decision-making models remain consistent with guardianship reform thus far. It identifies and critically analyses the different assisted decision-making models which exist internationally. Finally, it discusses a number of conceptual, legal and practical concerns that remain unresolved. These issues require serious consideration before assisted decisionmaking models are adopted in guardianship regimes in Australia.