Rapid host adaptation by extensive recombination

Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses from which they are constructed. In mixed infections of defective reciprocal chimaeras, selection strongly favours recombinant progeny genomes that recover a portion of wild-type fitness. Characterizing these evolved progeny viruses can highlight both important genetic fitness determinants and the contribution that recombination makes to the evolution of their natural relatives. Moreover, these experiments supply precise information about the frequency and distribution of recombination breakpoints, which can shed light on the mechanistic processes underlying recombination. We demonstrate the value of this approach using the small single-stranded DNA geminivirus, maize streak virus (MSV). Our results show that adaptive recombination in this virus is extremely efficient and can yield complex progeny genomes comprising up to 18 recombination breakpoints. The patterns of recombination that we observe strongly imply that the mechanistic processes underlying rolling circle replication are the prime determinants of recombination breakpoint distributions found in MSV genomes sampled from nature. © 2009 SGM.

Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates

Psittacine beak and feather disease (PBFD) has a broad host range and is widespread in wild and captive psittacine populations in Asia, Africa, the Americas, Europe and Australasia. Beak and feather disease circovirus (BFDV) is the causative agent. BFDV has an ~2 kb single stranded circular DNA genome encoding just two proteins (Rep and CP). In this study we provide support for demarcation of BFDV strains by phylogenetic analysis of 65 complete genomes from databases and 22 new BFDV sequences isolated from infected psittacines in South Africa. We propose 94% genome-wide sequence identity as a strain demarcation threshold, with isolates sharing > 94% identity belonging to the same strain, and strain subtypes sharing> 98% identity. Currently, BFDV diversity falls within 14 strains, with five highly divergent isolates from budgerigars probably representing a new species of circovirus with three strains (budgerigar circovirus; BCV-A, -B and -C). The geographical distribution of BFDV and BCV strains is strongly linked to the international trade in exotic birds; strains with more than one host are generally located in the same geographical area. Lastly, we examined BFDV and BCV sequences for evidence of recombination, and determined that recombination had occurred in most BFDV and BCV strains. We established that there were two globally significant recombination hotspots in the viral genome: the first is along the entire intergenic region and the second is in the C-terminal portion of the CP ORF. The implications of our results for the taxonomy and classification of circoviruses are discussed. © 2011 SGM.

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.

Signal transduction mechanisms underlying growth hormone receptor action

Our understanding of the mechanisms of action of GH and its receptor, the GHR, has advanced significantly in the last decade and has provided some important surprises. It is now clear that the GH-GHR axis activates a number of inter-related signalling pathways, not all of which are dependent on the intracellular tyrosine kinase, JAK2 as originally postulated. JAK2-independent pathways, mediated via the Src family kinases, together with a number of negative regulators of GH signalling and emerging cross-talk mechanisms with other growth factor receptors, provide a complex array of mechanisms that are capable of fine-tuning responses to GH in a cell context dependent manner. Additionally, it is also now clear that GH and the GHR can translocate to the nucleus of target cells and initiate, as yet not well defined, nuclear responses. Continued emphasis on elucidation of these complex mechanisms is critical to provide further insights into the diverse physiological and pathophysiological effects of GH.

Affecting interference

This collaborative project by Daniel Mafe and Andrew Brown, one of a number in they have been involved in together, conjoins painting and digital sound into a single, large scale, immersive exhibition/installation. The work as a whole acts as an interstitial point between contrasting approaches to abstraction: the visual and aural, the digital and analogue are pushed into an alliance and each works to alter perceptions of the other. For example, the paintings no longer mutely sit on the wall to be stared into. The sound seemingly emanating from each work shifts the viewer’s typical visual perception and engages their aural sensibilities. This seems to make one more aware of the objects as objects – the surface of each piece is brought into scrutiny – and immerses the viewer more viscerally within the exhibition. Similarly, the sonic experience is focused and concentrated spatially by each painted piece even as the exhibition is dispersed throughout the space. The sounds and images are similar in each local but not identical, even though they may seem to be the same from casual interaction, closer attention will quickly show this is not the case. In preparing this exhibition each artist has had to shift their mode of making to accommodate the other’s contribution. This was mainly done by a process of emptying whereby each was called upon to do less to the works they were making and to iterate the works toward a shared conception, blurring notions of individual imagination while maintaining material authorship. Empting was necessary to enable sufficient porosity where each medium allowed the other entry to its previously gated domain. The paintings are simple and subtle to allow the odd sonic textures a chance to work on the viewer’s engagement with them. The sound remains both abstract, using noise-like textures, and at a low volume to allow the audience’s attention to wander back and forth between aspects of the works.

Rule-based transit signal priority control method using a real-time transit travel time prediction model

An advanced rule-based Transit Signal Priority (TSP) control method is presented in this paper. An on-line transit travel time prediction model is the key component of the proposed method, which enables the selection of the most appropriate TSP plans for the prevailing traffic and transit condition. The new method also adopts a priority plan re-development feature that enables modifying or even switching the already implemented priority plan to accommodate changes in the traffic conditions. The proposed method utilizes conventional green extension and red truncation strategies and also two new strategies including green truncation and queue clearance. The new method is evaluated against a typical active TSP strategy and also the base case scenario assuming no TSP control in microsimulation. The evaluation results indicate that the proposed method can produce significant benefits in reducing the bus delay time and improving the service regularity with negligible adverse impacts on the non-transit street traffic.

RcppArmadillo : accelerating R with high-performance C++ linear algebra

The R statistical environment and language has demonstrated particular strengths for interactive development of statistical algorithms, as well as data modelling and visualisation. Its current implementation has an interpreter at its core which may result in a performance penalty in comparison to directly executing user algorithms in the native machine code of the host CPU. In contrast, the C++ language has no built-in visualisation capabilities, handling of linear algebra or even basic statistical algorithms; however, user programs are converted to high-performance machine code, ahead of execution. A new method avoids possible speed penalties in R by using the Rcpp extension package in conjunction with the Armadillo C++ matrix library. In addition to the inherent performance advantages of compiled code, Armadillo provides an easy-to-use template-based meta-programming framework, allowing the automatic pooling of several linear algebra operations into one, which in turn can lead to further speedups. With the aid of Rcpp and Armadillo, conversion of linear algebra centered algorithms from R to C++ becomes straightforward. The algorithms retains the overall structure as well as readability, all while maintaining a bidirectional link with the host R environment. Empirical timing comparisons of R and C++ implementations of a Kalman filtering algorithm indicate a speedup of several orders of magnitude.

Cutting on action : interference strategies in contemporary art practice

The domestication of creative software and hardware has been a significant factor in the recent proliferation of still and moving image creation. Booming numbers of amateur image-makers have the resources, skills and ambitions to create and distribute their work on a mass scale. At the same time, contemporary art seems increasingly dominated by ‘post-medium’ practices that adopt and adapt the representational techniques of mass culture, rather than overtly reject or oppose them. As a consequence of this network of forces, the field of image and video production is no longer the exclusive specialty of art and the mass media, and art may no longer be the most prominent watchdog of mass image culture. Intuitively and intentionally, contemporary artists are responding to these shifting conditions. From the position of a creative practitioner and researcher, this paper examines the strategies that contemporary artists use to engage with the changing relationships between image culture, lived experience and artistic practice. By examining the intersections between W.J.T. Mitchell’s detailed understanding of visual literacy and Jacques Derrida’s philosophical models of reading and writing, I identify ‘editing’ as a broad methodology that describes how practitioners creatively and critically engage with the field of still and moving images. My contention is that by emphasising the intersections of looking and making, ‘reading’ and ‘writing’, artists provide crucial jump cuts, pauses and distortions in the medley of our mediated experiences.

Small signal stability analysis of a DFIG based wind power system with tuned damping controller under super/sub-synchronous mode of operation

This paper focuses on the super/sub-synchronous operation of the doubly fed induction generator (DFIG) system. The impact of a damping controller on the different modes of operation for the DFIG based wind generation system is investigated. The co-ordinated tuning of the damping controller to enhance the damping of the oscillatory modes using bacteria foraging (BF) technique is presented. The results from eigenvalue analysis are presented to elucidate the effectiveness of the tuned damping controller in the DFIG system. The robustness issue of the damping controller is also investigated

Social signal processing for pain monitoring using a hidden conditional random field

utomatic pain monitoring has the potential to greatly improve patient diagnosis and outcomes by providing a continuous objective measure. One of the most promising methods is to do this via automatically detecting facial expressions. However, current approaches have failed due to their inability to: 1) integrate the rigid and non-rigid head motion into a single feature representation, and 2) incorporate the salient temporal patterns into the classification stage. In this paper, we tackle the first problem by developing a “histogram of facial action units” representation using Active Appearance Model (AAM) face features, and then utilize a Hidden Conditional Random Field (HCRF) to overcome the second issue. We show that both of these methods improve the performance on the task of pain detection in sequence level compared to current state-of-the-art-methods on the UNBC-McMaster Shoulder Pain Archive.

Optimized strategy for integrated traffic and transit signal control

This paper proposes a unique and innovative approach to integrate transit signal priority control into a traffic adaptive signal control strategy. The proposed strategy was named OSTRAC (Optimized Strategy for integrated TRAffic and TRAnsit signal Control). The cornerstones of OSTRAC include an online microscopic traffic f low prediction model and a Genetic Algorithm (GA) based traffic signal timing module. A sensitivity analysis was conducted to determine the critical GA parameters. The developed traffic f low model demonstrated reliable prediction results through a test. OSTRAC was evaluated by comparing its performance to three other signal control strategies. The evaluation results revealed that OSTRAC efficiently and effectively reduced delay time of general traffic and also transit vehicles.

Tipping the balance : sclerotinia sclerotiorum secreted oxalic acid suppresses host defenses by manipulating the host redox environment

Sclerotinia sclerotiorum is a necrotrophic ascomycete fungus with an extremely broad host range. This pathogen produces the non-specific phytotoxin and key pathogenicity factor, oxalic acid (OA). Our recent work indicated that this fungus and more specifically OA, can induce apoptotic-like programmed cell death (PCD) in plant hosts, this induction of PCD and disease requires generation of reactive oxygen species (ROS) in the host, a process triggered by fungal secreted OA. Conversely, during the initial stages of infection, OA also dampens the plant oxidative burst, an early host response generally associated with plant defense. This scenario presents a challenge regarding the mechanistic details of OA function; as OA both suppresses and induces host ROS during the compatible interaction. In the present study we generated transgenic plants expressing a redox-regulated GFP reporter. Results show that initially, Sclerotinia (via OA) generates a reducing environment in host cells that suppress host defense responses including the oxidative burst and callose deposition, akin to compatible biotrophic pathogens. Once infection is established however, this necrotroph induces the generation of plant ROS leading to PCD of host tissue, the result of which is of direct benefit to the pathogen. In contrast, a non-pathogenic OA-deficient mutant failed to alter host redox status. The mutant produced hypersensitive response-like features following host inoculation, including ROS induction, callose formation, restricted growth and cell death. These results indicate active recognition of the mutant and further point to suppression of defenses by the wild type necrotrophic fungus. Chemical reduction of host cells with dithiothreitol (DTT) or potassium oxalate (KOA) restored the ability of this mutant to cause disease. Thus, Sclerotinia uses a novel strategy involving regulation of host redox status to establish infection. These results address a long-standing issue involving the ability of OA to both inhibit and promote ROS to achieve pathogenic success.

Speech interference and transmission on residential balconies with road traffic noise

Balcony acoustic treatments can mitigate the effects of community road traffic noise. To further investigate, a theoretical study into the effects of balcony acoustic treatment combinations on speech interference and transmission is conducted for various street geometries. Nine different balcony types are investigated using a combined specular and diffuse reflection computer model. Diffusion in the model is calculated using the radiosity technique. The balcony types include a standard balcony with or without a ceiling and with various combinations of parapet, ceiling absorption and ceiling shield. A total of 70 balcony and street geometrical configurations are analyzed with each balcony type, resulting in 630 scenarios. In each scenario the reverberation time, speech interference level (SIL) and speech transmission index (STI) are calculated. These indicators are compared to determine trends based on the effects of propagation path, inclusion of opposite buildings and difference with a reference position outside the balcony. The results demonstrate trends in SIL and STI with different balcony types. It is found that an acoustically treated balcony reduces speech interference. A parapet provides the largest improvement, followed by absorption on the ceiling. The largest reductions in speech interference arise when a combination of balcony acoustic treatments are applied.

Learning in host selection in Helicoverpa armigera (Hubner) (Lepidoptera : Noctuidae)

The effect of experience on pre- and post-alighting host selection in adult female Helicoverpa armigera was tested in an indoor flight cage, and in a large greenhouse. The moths had experienced either tobacco or tomato plants (both are hosts of H. armigera) for 3 days, or were given no experience. Individuals were then released and their host selection assessed. All individuals caught in the greenhouse were identified and tested for post-alighting acceptance on each host. Experience significantly influenced both pre- and post-alighting host selection in ovipositing moths. This modification in behaviour is attributed to 'learning', and presents the first detailed evidence for learning in moths. Possible behavioural mechanisms involved are discussed, and a hypothesis is presented regarding learning in post-alighting host acceptance. The existence of learning in H. armigera, a highly polyphagous agricultural pest, is discussed in the light of current theories on environmental predictability and the advantages of learning. Copyright 1998 The Association for the Study of Animal Behaviour.

Host selection in phytophagous insects: a new explanation for learning in adults

Insect learning can change the preferences an egg laying female displays towards different host plant species. Current hypotheses propose that learning may be advantageous in adult host selection behaviour through improved recognition, accuracy or selectivity in foraging. In this paper, we present a hypothesis for when learning can be advantageous without such improvements in adult host foraging. Specifically, that learning can be an advantageous strategy for egg laying females when larvae must feed on more than one plant in order to complete development, if the fitness of larvae is reduced when they switch to a different host species. Here, larvae benefit from developing on the most abundant host species, which is the most likely choice of host for an adult insect which increases its preference for a host species through learning. The hypothesis is formalised with a mathematical model and we provide evidence from studies on the behavioural ecology of a number of insect species which demonstrate that the assumptions of this hypothesis may frequently be fulfilled in nature. We discuss how multiple mechanisms may convey advantages in insect learning and that benefits to larval development, which have so far been overlooked, should be considered in explanations for the widespread occurrence of learning.