Plasmodiophora brassicae in its Environment

Plasmodiophora brassicae Wor. is viewed in this article from the standpoint of a highly evolved and successful organism, well fitted for the ecological niche that it occupies. Physical, chemical, and biological components of the soil environment are discussed in relation to their effects on the survival, growth, and reproduction of this microbe. It is evident that P. brassicae is well equipped by virtue of its robust resting spores for survival through many seasonal cycles. Germination is probably triggered as a result of signals initiated by root exudates. The resultant motile zoospore moves rapidly to the root hair surface and penetration and colonization follow. The short period between germination and penetration is one of greatest vulnerability for P. brassicae. In this phase survival is affected at the very least by soil texture and structure; its moisture; pH; calcium, boron, and nitrogen content; and the presence of active microbial antagonists. These factors influence the inoculum potential (sensu Garrett, 1956) and its viability and invasive capacity. There is evidence that these effects may also influence differentially the survival of some physiologic races of P. brassicae. Considering the interaction of P. brassicae with the soil environment from the perspective of its biological fitness is an unusual approach; most authors consider only the opportunities to destroy this organism. The approach adopted here is borne of several decades spent studying P. brassicae and the respect that has been engendered for it as a biological entity. This review stops at the point of penetration, although some of the implications of the environment for successful colonization are included because they form a continuum. Interactions with the molecular and biochemical cellular environment are considered in other sections in this special edition.

Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment

The genome of the plant-colonizing bacterium Pseudomonas fluorescens SBW25 harbors a subset of genes that are expressed specifically on plant surfaces. The function of these genes is central to the ecological success of SBW25, but their study poses significant challenges because no phenotype is discernable in vitro. Here, we describe a genetic strategy with general utility that combines suppressor analysis with IVET (SPyVET) and provides a means of identifying regulators of niche-specific genes. Central to this strategy are strains carrying operon fusions between plant environment-induced loci (EIL) and promoterless 'dapB. These strains are prototrophic in the plant environment but auxotrophic on laboratory minimal medium. Regulatory elements were identified by transposon mutagenesis and selection for prototrophs on minimal medium. Approximately 106 mutants were screened for each of 27 strains carrying 'dapB fusions to plant EIL and the insertion point for the transposon determined in approximately 2,000 putative regulator mutants. Regulators were functionally characterized and used to provide insight into EIL phenotypes. For one strain carrying a fusion to the cellulose-encoding wss operon, five different regulators were identified including a diguanylate cyclase, the flagella activator, FleQ, and alginate activator, AmrZ (AlgZ). Further rounds of suppressor analysis, possible by virtue of the SPyVET strategy, revealed an additional two regulators including the activator AlgR, and allowed the regulatory connections to be determined.

Origin of avian genome size and structure in non-avian dinosaurs

Avian genomes are small and streamlined compared with those of other amniotes by virtue of having fewer repetitive elements and less non-coding DNA(1,2). This condition has been suggested to represent a key adaptation for flight in birds, by reducing the metabolic costs associated with having large genome and cell sizes(3,4). However, the evolution of genome architecture in birds, or any other lineage, is difficult to study because genomic information is often absent for long-extinct relatives. Here we use a novel bayesian comparative method to show that bone-cell size correlates well with genome size in extant vertebrates, and hence use this relationship to estimate the genome sizes of 31 species of extinct dinosaur, including several species of extinct birds. Our results indicate that the small genomes typically associated with avian flight evolved in the saurischian dinosaur lineage between 230 and 250 million years ago, long before this lineage gave rise to the first birds. By comparison, ornithischian dinosaurs are inferred to have had much larger genomes, which were probably typical for ancestral Dinosauria. Using comparative genomic data, we estimate that genome-wide interspersed mobile elements, a class of repetitive DNA, comprised 5 - 12% of the total genome size in the saurischian dinosaur lineage, but was 7 - 19% of total genome size in ornithischian dinosaurs, suggesting that repetitive elements became less active in the saurischian lineage. These genomic characteristics should be added to the list of attributes previously considered avian but now thought to have arisen in non-avian dinosaurs, such as feathers(5), pulmonary innovations 6, and parental care and nesting

Sigmatropic rearrangements of 'onium' ylids

Rearrangement reactions occupy a special place within the canon of organic synthesis, by virtue of the inherently high efficiency of chemical processes which form and breyak bonds by redistribution of electrons around a retained atomic framework. Within the broader class, sigmatropic rearrangements are chemical processes defined by mechanisms involving unimolecular migration of sigma-bonds with concomitant redistribution of one or more pi-bonds. Sigmatropic processes may involve uncharged or charged species, with the charges located on carbon or heteroatoms; the latter reaction type is the subject of this tutorial review.

Truth in complex adaptive systems models should be based on truth by constructive verification

It is argued that the truth status of emergent properties of complex adaptive systems models should be based on an epistemology of proof by constructive verification and therefore on the ontological axioms of a non-realist logical system such as constructivism or intuitionism. ‘Emergent’ properties of complex adaptive systems (CAS) models create particular epistemological and ontological challenges. These challenges bear directly on current debates in the philosophy of mathematics and in theoretical computer science. CAS research, with its emphasis on computer simulation, is heavily reliant on models which explore the entailments of Formal Axiomatic Systems (FAS). The incompleteness results of Gödel, the incomputability results of Turing, and the Algorithmic Information Theory results of Chaitin, undermine a realist (platonic) truth model of emergent properties. These same findings support the hegemony of epistemology over ontology and point to alternative truth models such as intuitionism, constructivism and quasi-empiricism.

Preminger and Peckinpah: seeing and shaping widescreen worlds

This chapter develops a comparative analysis of sequences from the films of two directors who made eloquent use of widescreen formats but who seem to be in all other respects wholly contrasting figures. The article includes a historiographical element in grounding the argument in the critical history of widescreen aesthetics and the directors’ work. It moves from a close analysis of three sequences, and an exploration of strategies in the use of the widescreen frame, to broader questions of style and its interpretation, narration, point of view and epistemology. The article connects with other work on Preminger, and on the critical history of mise-en-scène, while extending this through the comparative analysis of two figures from different Hollywood contexts and characterised by very different approaches.

Here come the Salafis: the framing of Al-Qaeda's ideology within terrorism research

The purpose of the paper is to analyse different narratives about al Qaeda (AQ) in Terrorism Studies, and to demonstrate the methodological and empirical problems associated with them. It demonstrates that AQ as it emerges within Terrorism Studies is more of an artefact of preconceived notions about fundamentalist ideology than the result of rigid empirical research.

Can microgrids make a major contribution to UK energy supply?

Almost all the electricity currently produced in the UK is generated as part of a centralised power system designed around large fossil fuel or nuclear power stations. This power system is robust and reliable but the efficiency of power generation is low, resulting in large quantities of waste heat. The principal aim of this paper is to investigate an alternative concept: the energy production by small scale generators in close proximity to the energy users, integrated into microgrids. Microgrids—de-centralised electricity generation combined with on-site production of heat—bear the promise of substantial environmental benefits, brought about by a higher energy efficiency and by facilitating the integration of renewable sources such as photovoltaic arrays or wind turbines. By virtue of good match between generation and load, microgrids have a low impact on the electricity network, despite a potentially significant level of generation by intermittent energy sources. The paper discusses the technical and economic issues associated with this novel concept, giving an overview of the generator technologies, the current regulatory framework in the UK, and the barriers that have to be overcome if microgrids are to make a major contribution to the UK energy supply. The focus of this study is a microgrid of domestic users powered by small Combined Heat and Power generators and photovoltaics. Focusing on the energy balance between the generation and load, it is found that the optimum combination of the generators in the microgrid- consisting of around 1.4 kWp PV array per household and 45% household ownership of micro-CHP generators- will maintain energy balance on a yearly basis if supplemented by energy storage of 2.7 kWh per household. We find that there is no fundamental technological reason why microgrids cannot contribute an appreciable part of the UK energy demand. Indeed, an estimate of cost indicates that the microgrids considered in this study would supply electricity at a cost comparable with the present electricity supply if the current support mechanisms for photovoltaics were maintained. Combining photovoltaics and micro-CHP and a small battery requirement gives a microgrid that is independent of the national electricity network. In the short term, this has particular benefits for remote communities but more wide-ranging possibilities open up in the medium to long term. Microgrids could meet the need to replace current generation nuclear and coal fired power stations, greatly reducing the demand on the transmission and distribution network.

Standardised ileal digestibility of crude protein and amino acids of UK-grown peas and faba beans by broilers

In view of the increasing interest in home-grown legumes as components of diets for non-ruminant livestock and in an attempt to reduce the reliance on imported soya bean meal (SBM), two experiments were conducted to evaluate samples of peas and faba beans for their standardised ileal digestibility (SID) of amino acids determined with young broiler chicks. Experiment 1 evaluated six faba bean and seven pea cultivars and Experiment 2 evaluated two faba bean and three pea cultivars as well as a sample of soya bean meal provided as a reference material. Peas and beans were added at 750g/kg as the only source of protein/amino acids in a semi-synthetic diet containing the inert marker titanium dioxide; SBM was added, in a control diet, at 500g/kg. Each diet was fed to six replicates of a cage containing two Ross-type broilers for 96h at which point birds were culled allowing removal of ileal digesta. Chemical analyses allowed the calculation of the coefficient of SID of amino acids. There were no differences between samples of the same pulse species (P>0.05) but peas had higher values (P<0.05), similar to SBM, than beans. Trypsin inhibitor content (expressed as g trypsin inhibitor units/mg sample) of all pea samples was low and in the range 0.83–1.77mg/kg. There was relatively little variation in bean tannin content and composition amongst the coloured-flowered varieties; however, the white-flowered cultivar had no tannins. There was no correlation between tannin content and coefficient of SID. The content of SID of amino acids (g/kg legume) was higher in SBM when compared with peas and beans by virtue of having higher total concentrations.