The Rpf/DSF system and the regulation of virulence in the plant pathogen Xanthomonas campestris

The full virulence of Xanthomonas campestris pv. campestris (Xcc) to plants depends upon cell-to-cell signalling mediated by the signal molecule DSF (for diffusible signal factor), that has been characterised as cis-11-methyl-2-dodecenoic acid. DSF-mediated signalling regulates motility, biofilm dynamics and the synthesis of particular virulence determinants. The synthesis and perception of the DSF signal molecule involves products of the rpf (regulation of pathogenicity factors) gene cluster. DSF synthesis is fully dependent on RpfF, which encodes a putative enoyl-CoA hydratase. A two-component system, comprising the complex sensor histidine kinase RpfC and the HD-GYP domain regulator RpfG, is implicated in DSF perception. The HD-GYP domain of RpfG is a phosphodiesterase working on cyclic di-GMP; DSF perception is thereby linked to the turnover of this intracellular second messenger. The full range of regulatory influences of the Rpf/DSF system and of cyclic di-GMP in Xcc has yet to be established. In order to further characterise the Rpf/DSF regulatory network in Xcc, a proteomic approach was used to compare protein expression in the wildtype and defined rpf mutants. This work shows that the Rpf/DSF system regulates a range of biological functions that are associated with virulence and biofilm formation but also reveals new functions mediated by DSF regulation. These functions include antibiotic resistance, detoxification and stress tolerance. Mutational analysis showed that several of these regulated protein functions contribute to virulence in Chinese radish. Interestingly, it was demonstrated that different patterns of protein expression are associated with mutations of rpfF, rpfC and rpfG. This suggests that RpfG and RpfC have broader roles in regulation other than perception and transduction of DSF. Taken together, this analysis indicates the broad and complex regulatory role of Rpf/DSF system and identifies a number of new functions under Rpf/DSF control, which were shown to play a role in virulence.

Characterisation and application of fruit by-products as novel ingredients in gluten-free products

The physicochemical and nutritional properties of two fruit by-products were initially studied. Apple pomace (AP) contained a high level of fibre and pectin. The isolated AP pectin had a high level of methylation which developed viscous pastes. Orange pomace also had high levels of fibre and pectin, and it was an abundant source of minerals such as potassium and magnesium. Due to the fibrous properties of orange pomace flour, proofing and water addition were studied in a bread formulation. When added at levels greater than 6%, the loaf volume decreased. An optimised formulation and proofing time was derived using the optimisation tool; these consisted of 5.5% orange pomace, 94.6% water inclusion and with 49 minutes proofing. These optimised parameters doubled the total dietary fibre content of the bread compared to the original control. Pasting results showed how orange pomace inclusions reduced the final viscosity of the batter, reducing the occurrence of starch gelatinisation. Rheological properties i.e. the storage modulus (G') and complex modulus (G*) increased in the orange pomace batter compared to the control batter. This demonstrates how the orange pomace as an ingredient improved the robustness of the formulation. Sensory panellists scored the orange pomace bread comparably to the control bread. Milled apple pomace was studied as a potential novel ingredient in an extruded snack. Parameters studied included apple pomace addition, die head temperature and screw speed. As screw speed increased the favourable extrudate characteristics such as radical expansion ratio, porosity and specific volume decreased. The inclusion of apple pomace had a negative effect on extrudate characteristics at levels greater than 8% addition. Including apple pomace reduced the hardness and increased the crispiness of the snack. The optimised and validated formulation and extrusion process contained the following parameters: 7.7% apple pomace, 150°C die head temperature and a screw speed of 69 rpm.

Practice-based personas: integrated user and practice models

Practices are routinised behaviours with social and material components and complex relationships over space and time. Practice-based design goes beyond interaction design to consider how these components and their relationships impact on the formation and enactment of a practice, where technology is just one part of the practice. Though situated user-centred design methods such as participatory design are employed for the design of practice, demand exists for additional methods and tools in this area. This paper introduces practice-based personas as an extension of the persona approach popular in interaction design, and demonstrates how a set of practice-based personas was developed for a given domain – academic practice. The three practice-based personas developed here are linked to a catalogue of forty practices, offering designers both a user perspective and a practice perspective when designing for the domain.

Developing executive capability — banking and beyond

The transition to becoming a leader is perhaps the least understood and most difficult in business. This Portfolio of Exploration examines the development of conscious awareness and meaning complexity as key transformational requirements to operate competently at leadership level and to succeed in a work environment characterised by change and complexity. It recognises that developing executive leadership capability is not just an issue of personality increasing what we know or expertise. It requires development of complexity in terms of how we know ourselves, relate to others, construe leadership and organisation, problem solve in business and understand the world as a whole. The exploration is grounded in the theory of adult mental development as outlined by Robert Kegan (1982, 1994) and in his collaborations with Lisa Laskow Lahey (2001, 2009). The theory points to levels of consciousness which impact on how we make meaning of and experience the world around us and respond to it. Critically it also points to transformational processes which enable us to evolve how we make meaning of our world as a means to close the mismatch between the demands of this world and our ability to cope. The exploration is laid out in three stages. Using Kegan’s (1982, 1994) theory as a framework it begins with a reflection of my career to surface how I made meaning of banking, management and subsequently leadership. In stage two I engage with a range of source thinkers in the areas of leadership, decision making, business, organisation, growth and complexity in a transformational process of developing greater conscious and complex understanding of organisational leadership (also recognising ever increasing complexity in the world). Finally, in stage three, I explore how qualitative changes as a result of this transformational effort have benefitted my professional, leadership and organisational capabilities.

The past, present, and future of human centromere genomics.

The centromere is the chromosomal locus essential for chromosome inheritance and genome stability. Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome. Contiguous alpha satellite DNA sequence is absent from the assembled reference genome, limiting current understanding of centromere organization and function. Here, we review the progress in centromere genomics spanning the discovery of the sequence to its molecular characterization and the work done during the Human Genome Project era to elucidate alpha satellite structure and sequence variation. We discuss exciting recent advances in alpha satellite sequence assembly that have provided important insight into the abundance and complex organization of this sequence on human chromosomes. In light of these new findings, we offer perspectives for future studies of human centromere assembly and function.

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

Associating genetic variation with quantitative measures of gene regulation offers a way to bridge the gap between genotype and complex phenotypes. In order to identify quantitative trait loci (QTLs) that influence the binding of a transcription factor in humans, we measured binding of the multifunctional transcription and chromatin factor CTCF in 51 HapMap cell lines. We identified thousands of QTLs in which genotype differences were associated with differences in CTCF binding strength, hundreds of them confirmed by directly observable allele-specific binding bias. The majority of QTLs were either within 1 kb of the CTCF binding motif, or in linkage disequilibrium with a variant within 1 kb of the motif. On the X chromosome we observed three classes of binding sites: a minority class bound only to the active copy of the X chromosome, the majority class bound to both the active and inactive X, and a small set of female-specific CTCF sites associated with two non-coding RNA genes. In sum, our data reveal extensive genetic effects on CTCF binding, both direct and indirect, and identify a diversity of patterns of CTCF binding on the X chromosome.

Wave transformation and wave-driven flow across a steep coral reef

Observations of waves, setup, and wave-driven mean flows were made on a steep coral forereef and its associated lagoonal system on the north shore of Moorea, French Polynesia. Despite the steep and complex geometry of the forereef, and wave amplitudes that are nearly equal to the mean water depth, linear wave theory showed very good agreement with data. Measurements across the reef illustrate the importance of including both wave transport (owing to Stokes drift), as well as the Eulerian mean transport when computing the fluxes over the reef. Finally, the observed setup closely follows the theoretical relationship derived from classic radiation stress theory, although the two parameters that appear in the model-one reflecting wave breaking, the other the effective depth over the reef crest-must be chosen to match theory to data. © 2013 American Meteorological Society.

The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.

Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.

Assessing the suitability of ship design for human factors issues associated with evacuation and normal operations

Evaluating ship layout for human factors (HF) issues using simulation software such as maritimeEXODUS can be a long and complex process. The analysis requires the identification of relevant evaluation scenarios; encompassing evacuation and normal operations; the development of appropriate measures which can be used to gauge the performance of crew and vessel and finally; the interpretation of considerable simulation data. In this paper we present a systematic and transparent methodology for assessing the HF performance of ship design which is both discriminating and diagnostic. The methodology is demonstrated using two variants of a hypothetical naval ship.

A systematic review of the effect of dietary exposure that could be achieved through normal dietary intake on learning and performance of school-aged children of relevance to UK schools

The aim of the present review was to perform a systematic in-depth review of the best evidence from controlled trial studies that have investigated the effects of nutrition, diet and dietary change on learning, education and performance in school-aged children (4-18 years) from the UK and other developed countries. The twenty-nine studies identified for the review examined the effects of breakfast consumption, sugar intake, fish oil and vitamin supplementation and 'good diets'. In summary, the studies included in the present review suggest there is insufficient evidence to identify any effect of nutrition, diet and dietary change on learning, education or performance of school-aged children from the developed world. However, there is emerging evidence for the effects of certain fatty acids which appear to be a function of dose and time. Further research is required in settings of relevance to the UK and must be of high quality, representative of all populations, undertaken for longer durations and use universal validated measures of educational attainment. However, challenges in terms of interpreting the results of such studies within the context of factors such as family and community context, poverty, disease and the rate of individual maturation and neurodevelopment will remain. Whilst the importance of diet in educational attainment remains under investigation, the evidence for promotion of lower-fat, -salt and -sugar diets, high in fruits, vegetables and complex carbohydrates, as well as promotion of physical activity remains unequivocal in terms of health outcomes for all schoolchildren.

Preparation of o/w emulsions stabilized by solid particles and their characterization by oscillatory rheology

The purpose of this investigation was to examine the preparation and characterisation of hexane-in-water emulsions stabilised by clay particles. These emulsions, called Pickering emulsions, are characterised by the adsorption of solid particles at the oil/water (o/w) interface. The development of an elastic film at the o/w interface following the adsorption of colloidal particles helps to promote emulsion stability. Three different solid materials were used: silica sand, kaolin, and bentonite. Particles were added to the liquid mixtures in the range of 0.5–10 g dm−3. Emulsions were prepared using o/w ratios of 0.1, 0.2, 0.3, and 0.4. The effect of sodium chloride, on the stability of the prepared emulsions, was assessed in the range of 0–0.5 mol dm−3. In addition the use of a cationic surfactant hexadecyl-trimethylammonium bromide (CTAB) as an aid to improving emulsion stability was assessed in the concentration range of 0–0.05% (w/v). Characterisation of emulsion stability was realised through measurements of rheological properties including non-Newtonian viscosity, the elastic modulus, G', the loss modulus, G", and complex modulus, G*. The stability of the emulsions was evaluated immediately after preparation and 4 weeks later. Using the stability criteria, that for highly stable emulsions: G' > G" and both G' and G" are independent of frequency (varpi) it was concluded that highly stable emulsions could be prepared using a bentonite concentration of 2% (or more); an o/w ratio greater than 0.2; a CTAB concentration of 0.01%; and a salt concentration of 0.05 M or less—though salt was required.

Plastic and marine turtles: a review and call for research

Plastic debris is now ubiquitous in the marine environment affecting a wide range of taxa, from microscopic zooplankton to large vertebrates. Its persistence and dispersal throughout marine ecosystems has meant that sensitivity toward the scale of threat is growing, particularly for species of conservation concern, such as marine turtles. Their use of a variety of habitats, migratory behaviour, and complex life histories leave them subject to a host of anthropogenic stressors, including exposure to marine plastic pollution. Here, we review the evidence for the effects of plastic debris on turtles and their habitats, highlight knowledge gaps, and make recommendations for future research. We found that, of the seven species, all are known to ingest or become entangled in marine debris. Ingestion can cause intestinal blockage and internal injury, dietary dilution, malnutrition, and increased buoyancy which in turn can result in poor health, reduced growth rates and reproductive output, or death. Entanglement in plastic debris (including ghost fishing gear) is known to cause lacerations, increased drag—which reduces the ability to forage effectively or escape threats—and may lead to drowning or death by starvation. In addition, plastic pollution may impact key turtle habitats. In particular, its presence on nesting beaches may alter nest properties by affecting temperature and sediment permeability. This could influence hatchling sex ratios and reproductive success, resulting in population level implications. Additionally, beach litter may entangle nesting females or emerging hatchlings. Lastly, as an omnipresent and widespread pollutant, plastic debris may cause wider ecosystem effects which result in loss of productivity and implications for trophic interactions. By compiling and presenting this evidence, we demonstrate that urgent action is required to better understand this issue and its effects on marine turtles, so that appropriate and effective mitigation policies can be developed.

Spatio-temporal Bayesian network models with latent variables for revealing trophic dynamics and functional networks in fisheries ecology

Ecosystems consist of complex dynamic interactions among species and the environment, the understanding of which has implications for predicting the environmental response to changes in climate and biodiversity. However, with the recent adoption of more explorative tools, like Bayesian networks, in predictive ecology, few assumptions can be made about the data and complex, spatially varying interactions can be recovered from collected field data. In this study, we compare Bayesian network modelling approaches accounting for latent effects to reveal species dynamics for 7 geographically and temporally varied areas within the North Sea. We also apply structure learning techniques to identify functional relationships such as prey–predator between trophic groups of species that vary across space and time. We examine if the use of a general hidden variable can reflect overall changes in the trophic dynamics of each spatial system and whether the inclusion of a specific hidden variable can model unmeasured group of species. The general hidden variable appears to capture changes in the variance of different groups of species biomass. Models that include both general and specific hidden variables resulted in identifying similarity with the underlying food web dynamics and modelling spatial unmeasured effect. We predict the biomass of the trophic groups and find that predictive accuracy varies with the models' features and across the different spatial areas thus proposing a model that allows for spatial autocorrelation and two hidden variables. Our proposed model was able to produce novel insights on this ecosystem's dynamics and ecological interactions mainly because we account for the heterogeneous nature of the driving factors within each area and their changes over time. Our findings demonstrate that accounting for additional sources of variation, by combining structure learning from data and experts' knowledge in the model architecture, has the potential for gaining deeper insights into the structure and stability of ecosystems. Finally, we were able to discover meaningful functional networks that were spatially and temporally differentiated with the particular mechanisms varying from trophic associations through interactions with climate and commercial fisheries.

Arp2p, a potential substrate for NatB acetyltransferase in fission yeast, is important in actin patch nucleation and motility in arp2-1 and arm1 ts mutants

The actin cytoskeleton is a dynamic and complex structure in fission yeast that plays a major function in many cell processes including cellular growth, septa formation, endocytosis and cellular division. Computational studies have shown that Arp2p, which forms part of the Arp2/3 complex, is a potential substrate of NatB acetyltransferase which has specificity for proteins possessing an N-terminal Met-Asp or Met-Glu sequence motif. In arm1- mutants the loss of function of Arm1p, an auxillary subunit required for NatB activity, results in a temperature sensitive phenotype characterized by multiple septa, failure of endocytosis, and the inability to form actin cables. A temperature sensitive mutant of Schizosaccharomyces pombe arp2 gene exhibits a similar phenotype as seen by the formation of improper septa, slow growth, and the delocalization of actin patches. Four expression vectors encoding the open reading frames of arp2 and cdc8 (tropomyosin) were constructed with a modification changing the second residue to a Histidine, believed to mimic the charge distribution of natural acetylation by NatB. Constructs tested in normal yeast strains remained viable and grew normally in the presence of Met-His Arp2p and tropomyosin. Analysis of their ability to suppress the mutant phenotypes of arp2-1 and arm1- mutants is an area of research to be explored in future studies.

Bystander Narratives: The Fiction of J.M. Coetzee and the Holocaust

J.M. Coetzee’s novels are suffused with a pervasive, though often oblique, Holocaust awareness. Direct references to the event and to the historical era to which it belongs, subtle stylistic and thematic echoes of Holocaust writing, and the recurrent mobilization of Holocaust imagery in Coetzee’s novels all contribute to suggest the significance of the event to the author’s work and thought. Providing Coetzee with a lens through which to view the contemporary situation, both local and global, the Holocaust offers Coetzee a means by which difficult and complex questions of ethics and historiographical truth may be approached. Above all, the Holocaust and its representation contribute to Coetzee’s exploration of the dilemmas of translating the traumatic lived experience of atrocity – including, but not limited to, life in apartheid South Africa – into narrative form. Taken as a whole, Coetzee’s oeuvre initially anticipates and later responds to, in characteristically oblique fashion, the narrative project(s) facing post-apartheid South Africa as the newly-democratic nation sought to make sense of its past through a variety of means, the most important of which was the country’s Truth and Reconciliation Commission. Implicitly challenging the TRC’s findings as well as its narrative assumptions, the Coetzean oeuvre accordingly invites being read as offering a continuous and evolving counter-narrative to the TRC and its construction of a narrative of the apartheid past for the post-apartheid nation. In utilizing the Holocaust, its representations, and the reception thereof to frame his response to apartheid, Coetzee implicates both in a critique of the Western model of modernity, suggesting, in the process, the importance of reconfiguring modernity in a more ethical shape.