Pseudomonas syringae pv. phaseolicola: from ‘has bean’ to supermodel

Pseudomonas syringae pv. phaseolicola causes halo blight of the common bean, Phaseolus vulgaris, worldwide and remains difficult to control. Races of the pathogen cause either disease symptoms or a resistant hypersensitive response on a series of differentially reacting bean cultivars. The molecular genetics of the interaction between P. syringae pv. phaseolicola and bean, and the evolution of bacterial virulence, have been investigated in depth and this research has led to important discoveries in the field of plant-microbe interactions. In this review, we discuss several of the areas of study that chart the rise of P. syringae pv. phaseolicola from a common pathogen of bean plants to a molecular plant-pathogen supermodel bacterium. Taxonomy: Bacteria; Proteobacteria, gamma subdivision; order Pseudomonadales; family Pseudomonadaceae; genus Pseudomonas; species Pseudomonas syringae; Genomospecies 2; pathogenic variety phaseolicola. Microbiological properties: Gram-negative, aerobic, motile, rod-shaped, 1.5 µm long, 0.7-1.2 µm in diameter, at least one polar flagellum, optimal temperatures for growth of 25-30 °C, oxidase negative, arginine dihydrolase negative, levan positive and elicits the hypersensitive response on tobacco. Host range: Major bacterial disease of common bean (Phaseolus vulgaris) in temperate regions and above medium altitudes in the tropics. Natural infections have been recorded on several other legume species, including all members of the tribe Phaseoleae with the exception of Desmodium spp. and Pisum sativum. Disease symptoms: Water-soaked lesions on leaves, pods, stems or petioles, that quickly develop greenish-yellow haloes on leaves at temperatures of less than 23 °C. Infected seeds may be symptomless, or have wrinkled or buttery-yellow patches on the seed coat. Seedling infection is recognized by general chlorosis, stunting and distortion of growth. Epidemiology: Seed borne and disseminated from exudation by water-splash and wind occurring during rainfall. Bacteria invade through wounds and natural openings (notably stomata). Weedy and cultivated alternative hosts may also harbour the bacterium. Disease control: Some measure of control is achieved with copper formulations and streptomycin. Pathogen-free seed and resistant cultivars are recommended. Useful websites: Pseudomonas-plant interaction http://www.pseudomonas-syringae.org/; PseudoDB http://xbase.bham.ac.uk/pseudodb/; Plant Associated and Environmental Microbes Database (PAMDB) http://genome.ppws.vt.edu/cgi-bin/MLST/home.pl; PseudoMLSA Database http://www.uib.es/microbiologiaBD/Welcome.html.

Chess endgame news

Reports the availability on the web of the entire run of Beasley's 'British Endgame Study News', and reviews a recent report by Bourzutschky and Konoval on their discoveries with 7-man endgame tables.

Biomimetic soft matter

Biomaterials are often soft materials. There is now growing interest in designing, synthesizing and characterising soft materials that mimic the properties of biological materials such as tissue, proteins, DNA or cells. Research on biomimetic soft matter is therefore a developing theme with important emerging applications in biomedicine including tissue engineering, diagnostics, gene therapy, drug delivery and many others. There are also important basic science questions concerning the use of concepts from colloid and polymer science to understand the self-assembly of biomimetic soft materials. This issue of Soft Matter presents a selection of extremely topical articles on a diversity of biomimetic soft matter systems. I thank the contributors for this quite remarkable collection of papers, which report many fascinating discoveries and insights.

Grid computing solutions for distributed repositories of protein folding and unfolding simulations

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data and a data warehouse. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular we look at two aspects, first how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories --- this is an important and challenging aspect of P-found because the data volumes involved are too large to be centralised. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling new scientific discoveries.

The world at one's fingertips: interactive interpretation of environmental data

This chapter introduces the latest practices and technologies in the interactive interpretation of environmental data. With environmental data becoming ever larger, more diverse and more complex, there is a need for a new generation of tools that provides new capabilities over and above those of the standard workhorses of science. These new tools aid the scientist in discovering interesting new features (and also problems) in large datasets by allowing the data to be explored interactively using simple, intuitive graphical tools. In this way, new discoveries are made that are commonly missed by automated batch data processing. This chapter discusses the characteristics of environmental science data, common current practice in data analysis and the supporting tools and infrastructure. New approaches are introduced and illustrated from the points of view of both the end user and the underlying technology. We conclude by speculating as to future developments in the field and what must be achieved to fulfil this vision.

Progress in the genetics of common obesity and type 2 diabetes

The prevalence of obesity and diabetes, which are heritable traits that arise from the interactions of multiple genes and lifestyle factors, continues to rise worldwide, causing serious health problems and imposing a substantial economic burden on societies. For the past 15 years, candidate gene and genome-wide linkage studies have been the main genetic epidemiological approaches to identify genetic loci for obesity and diabetes, yet progress has been slow and success limited. The genome-wide association approach, which has become available in recent years, has dramatically changed the pace of gene discoveries. Genome-wide association is a hypothesis-generating approach that aims to identify new loci associated with the disease or trait of interest. So far, three waves of large-scale genome-wide association studies have identified 19 loci for common obesity and 18 for common type 2 diabetes. Although the combined contribution of these loci to the variation in obesity and diabetes risk is small and their predictive value is typically low, these recently identified loci are set to substantially improve our insights into the pathophysiology of obesity and diabetes. This will require integration of genetic epidemiological methods with functional genomics and proteomics. However, the use of these novel insights for genetic screening and personalised treatment lies some way off in the future.

Cluster's last stand?

On 4 June last year the first attempt to make three-dimensional measurements in space was lost when the Ariane 5 rocket veered off course and self-destructed, 39 s into its maiden flight. On board were four identical spacecraft which made up Cluster,a mission that the European Space Agency called a “cornerstone” of its Horizon 2000 scientific programme. A full description of the Cluster satellites is given in a special issue of Space Science Reviews (Escoubet et al. 1997). Their loss dealt a devastating blow to the Cluster scientists and to those working on other missions and projects planned to interact with Cluster. Many discoveries have been made during the 15 years in which Cluster progressed from an idea to the state-of-the-art satellites that were on top of Ariane 501 on 4 June. However, these discoveries invariably underline rather than undermine the importance of Cluster. Now plans to recover the unique and exciting research that was to be done using Cluster are well advanced.

A comparative review of skill assessment: performance, prediction and profiling

The assessment of chess players is an increasingly attractive opportunity and an unfortunate necessity. The chess community needs to limit potential reputational damage by inhibiting cheating and unjustified accusations of cheating: there has been a recent rise in both. A number of counter-intuitive discoveries have been made by benchmarking the intrinsic merit of players’ moves: these call for further investigation. Is Capablanca actually, objectively the most accurate World Champion? Has ELO rating inflation not taken place? Stimulated by FIDE/ACP, we revisit the fundamentals of the subject to advance a framework suitable for improved standards of computational experiment and more precise results. Other domains look to chess as the demonstrator of good practice, including the rating of professionals making high-value decisions under pressure, personnel evaluation by Multichoice Assessment and the organization of crowd-sourcing in citizen science projects. The ‘3P’ themes of performance, prediction and profiling pervade all these domains.

Commentary: not just genes - reclaiming a role for environmental influences on aetiology and outcome in autism. A commentary on Mandy and Lai (2016)

Mandy and Lai (2015) do the field a service in 'reclaiming' the role of pre- and postnatal environmental influences on the aetiology and course of autism spectrum conditions (ASC). This follows several decades where now discredited theories about putative psychogenic and biological disease models held sway, not least in the public mind. We discuss issues that arise from their review; including the need to identify how large the environmental influences on ASC are likely to be; the specificity of these environmental influences to ASC as opposed to a broader range of neurodevelopmental conditions and outcomes; how best to study complex interactions between genetic and environmental influences; and the promise of novel insights into their mechanisms of action. The review highlights current research that aims to better our understanding of the role of environmental factors in the aetiology and course of ASC and, in the near future, may offer the potential for personalised medicine approaches to intervention based on these discoveries.

Science drives horticulture's progress and profit

Horticultural science linked with basic studies in biology, chemistry, physics and engineering has laid the foundation for advances in applied knowledge which are at the heart of commercial, environmental and social horticulture. In few disciplines is science more rapidly translated into applicable technologies than in the huge range of man’s activities embraced within horticulture which are discussed in this Trilogy. This chapter surveys the origins of horticultural science developing as an integral part of the 16th century “Scientific Revolution”. It identifies early discoveries during the latter part of the 19th and early 20th centuries which rationalized the control of plant growth, flowering and fruiting and the media in which crops could be cultivated. The products of these discoveries formed the basis on which huge current industries of worldwide significance are founded in fruit, vegetable and ornamental production. More recent examples of the application of horticultural science are used in an explanation of how the integration of plant breeding, crop selection and astute marketing highlighted by the New Zealand industry have retained and expanded the viability of production which supplies huge volumes of fruit into the world’s markets. This is followed by an examination of science applied to tissue and cell culture as an example of technologies which have already produced massive industrial applications but hold the prospect for generating even greater advances in the future. Finally, examples are given of nascent scientific discoveries which hold the prospect for generating horticultural industries with considerable future impact. These include systems modeling and biology, nanotechnology, robotics, automation and electronics, genetics and plant breeding, and more efficient and effective use of resources and the employment of benign microbes. In conclusion there is an estimation of the value of horticultural science to society.

The circulation of romances from England in late-medieval Ireland

The fifteenth century saw a striking upturn in the number of texts from foreign vernaculars that were translated into Irish. Indeed, one might go so far as to speak in terms of a ‘translation trend’ in Ireland during the mid to late fifteenth century. A notable feature of this trend is that a particularly high number of these Irish translations are of romances; contextual and textual evidence suggests that the original exemplars for many of these translated texts appear to have come from England, though not all of them were necessarily in English. Irish translations of eight romances have survived to the present day: Guy of Warwick; Bevis of Hampton; La Queste de Saint Graal; Fierabras; Caxton’s Recuyell of the Histories of Troie; William of Palerne; the Seven Sages of Rome; and Octavian. This paper addresses two aspects of these texts of particular relevance to romance scholars who do not work within the sphere of Celtic studies. Firstly, it argues that certain aspects of the dissemination and reception of romance in Ireland are quite distinctive. Manuscript and textual evidence suggests that the religious orders, particularly the Franciscans, seem to have played a role in the importation and translation of these narratives. Secondly, examination of the Irish versions of romance tends to bear out an observation made by Flower many years ago, but not pursued by subsequent scholars: ‘texts of an unusual kind were current in Ireland, and it may be that interesting discoveries are to be made here’. Certain narrative features of several of these Irish translations diverge from all the surviving versions of the relevant romance in other languages and may witness to a variant exemplar that has since been lost from its own linguistic corpus.