A maize bacterial artificial chromosome (BAC) library from the European flint inbred line F2

We report here the construction and characterisation of a BAC library from the maize flint inbred line F2, widely used in European maize breeding programs. The library contains 86,858 clones with an average insert size of approximately 90 kb, giving approximately 3.2-times genome coverage. High-efficiency BAC cloning was achieved through the use of a single size selection for the high-molecular-weight genomic DNA, and co-transformation of the ligation with yeast tRNA to optimise transformation efficiency. Characterisation of the library showed that less than 0.5% of the clones contained no inserts, while 5.52% of clones consisted of chloroplast DNA. The library was gridded onto 29 nylon filters in a double-spotted 8 × 8 array, and screened by hybridisation with a number of single-copy and gene-family probes. A 3-dimensional DNA pooling scheme was used to allow rapid PCR screening of the library based on primer pairs from simple sequence repeat (SSR) and expressed sequence tag (EST) markers. Positive clones were obtained in all hybridisation and PCR screens carried out so far. Six BAC clones, which hybridised to a portion of the cloned Rp1-D rust resistance gene, were further characterised and found to form contigs covering most of this complex resistance locus.

City futures: exploring urban retrofit and sustainable transitions

Cities are responsible for up to 70% of global carbon emissions and 75% of global energy consumption. By 2050 it is estimated that 70% of the world's population will live in cities. The critical challenge for contemporary urbanism, therefore, is to understand how to develop the knowledge, capacity and capability for public agencies, the private sector and multiple users in city-regions (i.e. the city and its wider hinterland) to re-engineer systemically their built environment and urban infrastructure in response to climate change and resource constraints. To inform transitions to urban sustainability, key stakeholders' perceptions were sought though a participatory backcasting and scenario foresight process in order to illuminate challenging but realistic socio-technical scenarios for the systemic retrofit of core UK city-regions. The challenge of conceptualizing complex urban transitions is explored across multiple socio-technical ‘regimes’ (housing, non-domestic buildings, urban infrastructure), scales (building, neighbourhood, city-region), and domains (energy, water, use of resources) within a participatory process. The development of three archetypal ‘guiding visions’ of retrofit city-regional futures developed through this process are discussed, along with the contribution that such foresight processes might play in ‘opening up’ the governance and strategic navigation of urban sustainability.

Tandem quadruplication of HMA4 in the zinc (Zn) and cadmium (Cd) hyperaccumulator Noccaea caerulescens

Zinc (Zn) and cadmium (Cd) hyperaccumulation may have evolved twice in the Brassicaceae, in Arabidopsis halleri and in the Noccaea genus. Tandem gene duplication and deregulated expression of the Zn transporter, HMA4, has previously been linked to Zn/Cd hyperaccumulation in A. halleri. Here, we tested the hypothesis that tandem duplication and deregulation of HMA4 expression also occurs in Noccaea. A Noccaea caerulescens genomic library was generated, containing 36,864 fosmid pCC1FOS (TM) clones with insert sizes similar to 20-40 kbp, and screened with a PCR-generated HMA4 genomic probe. Gene copy number within the genome was estimated through DNA fingerprinting and pooled fosmid pyrosequencing. Gene copy numbers within individual clones was determined by PCR analyses with novel locus specific primers. Entire fosmids were then sequenced individually and reads equivalent to 20-fold coverage were assembled to generate complete whole contigs. Four tandem HMA4 repeats were identified in a contiguous sequence of 101,480 bp based on sequence overlap identities. These were flanked by regions syntenous with up and downstream regions of AtHMA4 in Arabidopsis thaliana. Promoter-reporter beta-glucuronidase (GUS) fusion analysis of a NcHMA4 in A. thaliana revealed deregulated expression in roots and shoots, analogous to AhHMA4 promoters, but distinct from AtHMA4 expression which localised to the root vascular tissue. This remarkable consistency in tandem duplication and deregulated expression of metal transport genes between N. caerulescens and A. halleri, which last shared a common ancestor > 40 mya, provides intriguing evidence that parallel evolutionary pathways may underlie Zn/Cd hyperaccumulation in Brassicaceae.

The Brownian traveller on manifolds

We study the inuence of the intrinsic curvature on the large time behaviour of the heat equation in a tubular neighbourhood of an unbounded geodesic in a two-dimensional Riemannian manifold. Since we consider killing boundary conditions, there is always an exponential-type decay for the heat semigroup. We show that this exponential-type decay is slower for positively curved manifolds comparing to the at case. As the main result, we establish a sharp extra polynomial-type decay for the heat semigroup on negatively curved manifolds comparing to the at case. The proof employs the existence of Hardy-type inequalities for the Dirichlet Laplacian in the tubular neighbourhoods on negatively curved manifolds and the method of self-similar variables and weighted Sobolev spaces for the heat equation.

Estimating the potential yield of small wind turbines in urban areas: a case study for Greater London, UK

To optimise the placement of small wind turbines in urban areas a detailed understanding of the spatial variability of the wind resource is required. At present, due to a lack of observations, the NOABL wind speed database is frequently used to estimate the wind resource at a potential site. However, recent work has shown that this tends to overestimate the wind speed in urban areas. This paper suggests a method for adjusting the predictions of the NOABL in urban areas by considering the impact of the underlying surface on a neighbourhood scale. In which, the nature of the surface is characterised on a 1 km2 resolution using an urban morphology database. The model was then used to estimate the variability of the annual mean wind speed across Greater London at a height typical of current small wind turbine installations. Initial validation of the results suggests that the predicted wind speeds are considerably more accurate than the NOABL values. The derived wind map therefore currently provides the best opportunity to identify the neighbourhoods in Greater London at which small wind turbines yield their highest energy production. The model does not consider street scale processes, however previously derived scaling factors can be applied to relate the neighbourhood wind speed to a value at a specific rooftop site. The results showed that the wind speed predicted across London is relatively low, exceeding 4 ms-1 at only 27% of the neighbourhoods in the city. Of these sites less than 10% are within 10 km of the city centre, with the majority over 20 km from the city centre. Consequently, it is predicted that small wind turbines tend to perform better towards the outskirts of the city, therefore for cities which fit the Burgess concentric ring model, such as Greater London, ‘distance from city centre’ is a useful parameter for siting small wind turbines. However, there are a number of neighbourhoods close to the city centre at which the wind speed is relatively high and these sites can only been identified with a detailed representation of the urban surface, such as that developed in this study.

Climate and more sustainable cities: climate information for improved planning and management of cities (producers/capabilities perspective)

In the last two decades substantial advances have been made in the understanding of the scientific basis of urban climates. These are reviewed here with attention to sustainability of cities, applications that use climate information, and scientific understanding in relation to measurements and modelling. Consideration is given from street (micro) scale to neighbourhood (local) to city and region (meso) scale. Those areas where improvements are needed in the next decade to ensure more sustainable cities are identified. High-priority recommendations are made in the following six strategic areas: observations, data, understanding, modelling, tools and education. These include the need for more operational urban measurement stations and networks; for an international data archive to aid translation of research findings into design tools, along with guidelines for different climate zones and land uses; to develop methods to analyse atmospheric data measured above complex urban surfaces; to improve short-range, high-resolution numerical prediction of weather, air quality and chemical dispersion through improved modelling of the biogeophysical features of the urban land surface; to improve education about urban meteorology; and to encourage communication across scientific disciplines at a range of spatial and temporal scales.

Parallel editing, multi-positionality and maximalism: cosmopolitan effects as explored in some art works by Melanie Jackson and Vivienne Dick

Garfield produces a critique of neo-minimalist art practice by demonstrating how the artist Melanie Jackson’s Some things you are not allowed to send around the world (2003 and 2006) and the experimental film-maker Vivienne Dick’s Liberty’s booty (1980) – neither of which can be said to be about feeling ‘at home’ in the world, be it as a resident or as a nomad – examine global humanity through multi-positionality, excess and contingency, and thereby begin to articulate a new cosmopolitan relationship with the local – or, rather, with many different localities – in one and the same maximalist sweep of the work. ‘Maximalism’ in Garfield’s coinage signifies an excessive overloading (through editing, collage, and the sheer density of the range of the material) that enables the viewer to insert themselves into the narrative of the work. In the art of both Jackson and Dick Garfield detects a refusal to know or to judge the world; instead, there is an attempt to incorporate the complexities of its full range into the singular vision of the work, challenging the viewer to identify what is at stake.

Approximation by harmonic polynomials in star-shaped domains and exponential convergence of Trefftz hp-dGFEM

We study the approximation of harmonic functions by means of harmonic polynomials in two-dimensional, bounded, star-shaped domains. Assuming that the functions possess analytic extensions to a delta-neighbourhood of the domain, we prove exponential convergence of the approximation error with respect to the degree of the approximating harmonic polynomial. All the constants appearing in the bounds are explicit and depend only on the shape-regularity of the domain and on delta. We apply the obtained estimates to show exponential convergence with rate O(exp(−b square root N)), N being the number of degrees of freedom and b>0, of a hp-dGFEM discretisation of the Laplace equation based on piecewise harmonic polynomials. This result is an improvement over the classical rate O(exp(−b cubic root N )), and is due to the use of harmonic polynomial spaces, as opposed to complete polynomial spaces.

The power of perceptions: exploring the role of urban design in cycling behaviours and healthy ageing

Good urban design has the power to aid in the provision of inclusive journey environments, yet traditionally neglects the perspective of the cyclist. This paper starts from the premise that more can be done to understand and articulate cyclists’ experiences and perceptions of the urban environment in which they cycle, as part of a closer linking of urban design qualities with transport planning and infrastructure interventions. This approach is particularly applicable in relation to older cyclists, a group whose needs are often poorly understood and for whom perceptions can significantly influence mobile behaviours. Currently, knowledge regarding the relationship between the built environment and physical activity, including cycling, in older adults is limited. As European countries face up to the challenges associated with ageing populations, some metropolitan regions, such as Munich, Germany, are making inroads into widening cycling’s appeal across generations through a combination of urban design, policy and infrastructure initiatives. The paper provides a systematic understanding of the urban design qualities and built environment features that affect cycling participation and have the potential to contribute towards healthy ageing. Urban design features such as legibility, aesthetics, scale and open space have been shown to influence and affect other mobile behaviours (e.g. walking), but their role as a mediator in cycle behaviour remains under-explored. Many of these design ‘qualities’ are related to individual perceptions; capturing these can help build a picture of quality in the built environment that includes an individual’s relationship with their local neighbourhood and its influences on their mobility choices. Issues of accessibility, facilities, and safety in cycling remain crucial, and, when allied to these design ‘qualities‘, provides a more rounded reflection of everyday journeys and trips taken or desired. The paper sets out the role that urban design might play in mediating these critical mobility issues, and in particular, in better understanding the ‘quality of the journey’. It concludes by highlighting the need for designers, policy makers, planners and academics to consider the role that design can play in encouraging cycle participation, especially as part of a healthy ageing agenda.

(Re)shaping the South Bank: the (post)politics of sustainable place-making

While the private sector has long been in the vanguard of shaping and managing urban environs, under the New Labour government business actors were also heralded as key agents in the delivery of sustainable places. Policy interventions, such as Business Improvement Districts (BIDs), saw business-led local partnerships positioned as key drivers in the production of economically, socially and environmentally sustainable urban communities. This research considers how one business-led body, South Bank Employer’s Group (SBEG), has inserted itself into, and influenced, local (re)development trajectories. Interview, observational and archival data are used to explore how, in a neighbourhood noted for its turbulent and conflictual development past, SBEG has led on a series of regeneration programmes that it asserts will create a “better South Bank for all”. A belief in consensual solutions underscored New Labour’s urban agenda and cast regeneration as a politically neutral process in which different stakeholders can reach mutually beneficial solutions (Southern, 2001). For authors such as Mouffe (2005), the search for consensus represents a move towards a ‘post-political’ approach to governing in which the (necessarily) antagonistic nature of the political is denied. The research utilises writings on the ‘post-political’ condition to frame an empirical exploration of regeneration at the neighbourhood level. It shows how SBEG has brokered a consensual vision of regeneration with the aim of overriding past disagreements about local development. While this may be seen as an attempt to enact what Honig (1993: 3) calls the ‘erasure of resistance from political orderings’ by assuming control of regeneration agendas (see also Baeten, 2009), the research shows that ‘resistances’ to SBEG’s activities continue to be expressed in a series of ways. These resistances suggest that, while increasingly ‘post-political’ in character, local place shaping continues to evidence what Massey (2005: 10) calls the ‘space of loose ends and missing links’ from which political activity can, at least potentially, emerge.

Progress in observing and modelling the urban boundary layer

The urban boundary layer (UBL) is the part of the atmosphere in which most of the planet’s population now lives, and is one of the most complex and least understood microclimates. Given potential climate change impacts and the requirement to develop cities sustainably, the need for sound modelling and observational tools becomes pressing. This review paper considers progress made in studies of the UBL in terms of a conceptual framework spanning microscale to mesoscale determinants of UBL structure and evolution. Considerable progress in observing and modelling the urban surface energy balance has been made. The urban roughness sub-layer is an important region requiring attention as assumptions about atmospheric turbulence break down in this layer and it may dominate coupling of the surface to the UBL due to its considerable depth. The upper 90% of the UBL (mixed and residual layers) remains under-researched but new remote sensing methods and high resolution modelling tools now permit rapid progress. Surface heterogeneity dominates from neighbourhood to regional scales and should be more strongly considered in future studies. Specific research priorities include humidity within the UBL, high-rise urban canopies and the development of long-term, spatially extensive measurement networks coupled strongly to model development.

Long term individual load forecast under different electrical vehicles uptake scenarios

More and more households are purchasing electric vehicles (EVs), and this will continue as we move towards a low carbon future. There are various projections as to the rate of EV uptake, but all predict an increase over the next ten years. Charging these EVs will produce one of the biggest loads on the low voltage network. To manage the network, we must not only take into account the number of EVs taken up, but where on the network they are charging, and at what time. To simulate the impact on the network from high, medium and low EV uptake (as outlined by the UK government), we present an agent-based model. We initialise the model to assign an EV to a household based on either random distribution or social influences - that is, a neighbour of an EV owner is more likely to also purchase an EV. Additionally, we examine the effect of peak behaviour on the network when charging is at day-time, night-time, or a mix of both. The model is implemented on a neighbourhood in south-east England using smart meter data (half hourly electricity readings) and real life charging patterns from an EV trial. Our results indicate that social influence can increase the peak demand on a local level (street or feeder), meaning that medium EV uptake can create higher peak demand than currently expected.

Evidence for interplay between genes and maternal stress in utero: monoamine oxidase A polymorphism moderates effects of life events during pregnancy on infant negative emotionality at 5 weeks

The low activity variant of the monoamine oxidase A (MAOA) functional promoter polymorphism, MAOA-LPR, in interaction with adverse environments (G × E) is associated with child and adult antisocial behaviour disorders. MAOA is expressed during foetal development so in utero G × E may influence early neurodevelopment. We tested the hypothesis that MAOA G × E during pregnancy predicts infant negative emotionality soon after birth. In an epidemiological longitudinal study starting in pregnancy, using a two stage stratified design, we ascertained MAOA-LPR status (low vs. high activity variants) from the saliva of 209 infants (104 boys and 105 girls), and examined predictions to observed infant negative emotionality at 5 weeks post-partum from life events during pregnancy. In analyses weighted to provide estimates for the general population, and including possible confounders for life events, there was an MAOA status by life events interaction (P = 0.017). There was also an interaction between MAOA status and neighbourhood deprivation (P = 0.028). Both interactions arose from a greater effect of increasing life events on negative emotionality in the MAOA-LPR low activity, compared with MAOA-LPR high activity infants. The study provides the first evidence of moderation by MAOA-LPR of the effect of the social environment in pregnancy on negative emotionality in infancy, an early risk for the development of child and adult antisocial behaviour disorders.

Spatial evaluation of volcanic ash forecasts using satellite observations

The decision to close airspace in the event of a volcanic eruption is based on hazard maps of predicted ash extent. These are produced using output from volcanic ash transport and dispersion (VATD)models. In this paper an objectivemetric to evaluate the spatial accuracy of VATD simulations relative to satellite retrievals of volcanic ash is presented. The 5 metric is based on the fractions skill score (FSS). Thismeasure of skill provides more information than traditional point-bypoint metrics, such as success index and Pearson correlation coefficient, as it takes into the account spatial scale overwhich skill is being assessed. The FSS determines the scale overwhich a simulation has skill and can differentiate between a "near miss" and a forecast that is badly misplaced. The 10 idealised scenarios presented show that even simulations with considerable displacement errors have useful skill when evaluated over neighbourhood scales of 200–700km2. This method could be used to compare forecasts produced by different VATDs or using different model parameters, assess the impact of assimilating satellite retrieved ash data and evaluate VATD forecasts over a long time period.

A new method for the characterisation and verification of local spatial predictability for convective scale ensembles

The use of kilometre-scale ensembles in operational forecasting provides new challenges for forecast interpretation and evaluation to account for uncertainty on the convective scale. A new neighbourhood based method is presented for evaluating and characterising the local predictability variations from convective scale ensembles. Spatial scales over which ensemble forecasts agree (agreement scales, S^A) are calculated at each grid point ij, providing a map of the spatial agreement between forecasts. By comparing the average agreement scale obtained from ensemble member pairs (S^A(mm)_ij), with that between members and radar observations (S^A(mo)_ij), this approach allows the location-dependent spatial spread-skill relationship of the ensemble to be assessed. The properties of the agreement scales are demonstrated using an idealised experiment. To demonstrate the methods in an operational context the S^A(mm)_ij and S^A(mo)_ij are calculated for six convective cases run with the Met Office UK Ensemble Prediction System. The S^A(mm)_ij highlight predictability differences between cases, which can be linked to physical processes. Maps of S^A(mm)_ij are found to summarise the spatial predictability in a compact and physically meaningful manner that is useful for forecasting and for model interpretation. Comparison of S^A(mm)_ij and S^A(mo)_ij demonstrates the case-by-case and temporal variability of the spatial spread-skill, which can again be linked to physical processes.