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.

Ask : a health advocacy program for adolescents with an intellectual disability : a cluster randomised controlled trial

Background Adolescents with intellectual disability often have poor health and healthcare. This is partly as a consequence of poor communication and recall difficulties, and the possible loss of specialised paediatric services. Methods/Design A cluster randomised trial was conducted with adolescents with intellectual disability to investigate a health intervention package to enhance interactions among adolescents with intellectual disability, their parents/carers, and general practitioners (GPs). The trial took place in Queensland, Australia, between February 2007 and September 2010. The intervention package was designed to improve communication with health professionals and families’ organisation of health information, and to increase clinical activities beneficial to improved health outcomes. It consisted of the Comprehensive Health Assessment Program (CHAP), a one-off health check, and the Ask Health Diary, designed for on-going use. Participants were drawn from Special Education Schools and Special Education Units. The education component of the intervention was delivered as part of the school curriculum. Educators were surveyed at baseline and followed-up four months later. Carers were surveyed at baseline and after 26 months. Evidence of health promotion, disease prevention and case-finding activities were extracted from GPs clinical records. Qualitative interviews of educators occurred after completion of the educational component of the intervention and with adolescents and carers after the CHAP. Discussion Adolescents with intellectual disability have difficulty obtaining many health services and often find it difficult to become empowered to improve and protect their health. The health intervention package proposed may aid them by augmenting communication, improving documentation of health encounters, and improving access to, and quality of, GP care. Recruitment strategies to consider for future studies in this population include ensuring potential participants can identify themselves with the individuals used in promotional study material, making direct contact with their families at the start of the study, and closely monitoring the implementation of the educational intervention.

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.

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.

Methane activation on Fe4 cluster : a density functional theory study

We report a comprehensive theoretical study on reaction of methane by Fe4 cluster. This Letter gains insight into the mechanism of the reaction and indicate the Fe4 cluster has strong catalytic effect on the activation reaction of methane. In detail, the results show the cleavage of the first C–H bond is both an energetically and kinetically favourable process and the breaking of the second C–H is the rate-determining step. Moreover, our Letter demonstrates that the different cluster size of iron can not only determine the catalytic activity of methane but also control the product selectivity.

ClusterEval 1.0 : Cluster quality Evaluation software

This report describes the available functionality and use of the ClusterEval evaluation software. It implements novel and standard measures for the evaluation of cluster quality. This software has been used at the INEX XML Mining track and in the MediaEval Social Event Detection task.

Structure character in small-carbon-cluster deposition on diamond surface

Experimentally, hydrogen-free diamond-like carbon (DLC) films were assembled by means of pulsed laser deposition (PLD), where energetic small-carbon-clusters were deposited on the substrate. In this paper, the chemisorption of energetic C2 and C10 clusters on diamond (001)-( 2×1) surface was investigated by molecular dynamics simulation. The influence of cluster size and the impact energy on the structure character of the deposited clusters is mainly addressed. The impact energy was varied from a few tens eV to 100 eV. The chemisorption of C10 was found to occur only when its incident energy is above a threshold value ( E th). While, the C2 cluster was easily to adsorb on the surface even at much lower incident energy. With increasing the impact energy, the structures of the deposited C2 and C10 are different from the free clusters. Finally, the growth of films synthesized by energetic C2 and C10 clusters were simulated. The statistics indicate the C2 cluster has high probability of adsorption and films assembled of C2 present slightly higher SP3 fraction than that of C10-films, especially at higher impact energy and lower substrate temperature. Our result supports the experimental findings. Moreover, the simulation underlines the deposition mechanism at atomic scale.

Molecular dynamics simulation of structural characteristics in metal cluster deposition on surfaces

The deposition of small metal clusters (Cu, Au and Al) on f.c.c. metals (Cu, Au and Ni) has been studied by molecular dynamics simulation using Finnis–Sinclair (FS) potential. The impact energy varied from 0.01 to 10 eV/atom. First, the deposition of single cluster was simulated. We observed that, even at much lower energy, a small cluster with (Ih) icosahedral symmetry was reconstructed to match the substrate structure (f.c.c.) after deposition. Next, clusters were modeled to drop, one after the other, on the surface. The nanostructure was found by soft landing of Au clusters on Cu with increasing coverage, where interfacial energy dominates. While at relatively higher deposition energy (a few eV), the ordered f.c.c.-like structure was observed in the first adlayer of the film formed by Al clusters depositing on Ni substrate. This characteristic is mainly attributive to the ballistic collision. Our results indicate that the surface morphology synthesized by cluster deposition could be controlled by experimental parameters, which will be helpful for controlled design of nanostructure.