Land plants and DNA barcodes: short-term and long-term goals

Land plants have had the reputation of being problematic for DNA barcoding for two general reasons: (i) the standard DNA regions used in algae, animals and fungi have exceedingly low levels of variability and (ii) the typically used land plant plastid phylogenetic markers (e.g. rbcL, trnL-F, etc.) appear to have too little variation. However, no one has assessed how well current phylogenetic resources might work in the context of identification (versus phylogeny reconstruction). In this paper, we make such an assessment, particularly with two of the markers commonly sequenced in land plant phylogenetic studies, plastid rbcL and internal transcribed spacers of the large subunits of nuclear ribosomal DNA (ITS), and find that both of these DNA regions perform well even though the data currently available in GenBank/EBI were not produced to be used as barcodes and BLAST searches are not an ideal tool for this purpose. These results bode well for the use of even more variable regions of plastid DNA (such as, for example, psbA-trnH) as barcodes, once they have been widely sequenced. In the short term, efforts to bring land plant barcoding up to the standards being used now in other organisms should make swift progress. There are two categories of DNA barcode users, scientists in fields other than taxonomy and taxonomists. For the former, the use of mitochondrial and plastid DNA, the two most easily assessed genomes, is at least in the short term a useful tool that permits them to get on with their studies, which depend on knowing roughly which species or species groups they are dealing with, but these same DNA regions have important drawbacks for use in taxonomic studies (i.e. studies designed to elucidate species limits). For these purposes, DNA markers from uniparentally (usually maternally) inherited genomes can only provide half of the story required to improve taxonomic standards being used in DNA barcoding. In the long term, we will need to develop more sophisticated barcoding tools, which would be multiple, low-copy nuclear markers with sufficient genetic variability and PCR-reliability; these would permit the detection of hybrids and permit researchers to identify the 'genetic gaps' that are useful in assessing species limits.

Monitoring growth of hard corals as performance indicators for coral reefs

Digital videophotography, computer image analysis and physical measurements have been used to monitor sedimentation rates, coral cover, genera richness, rugosity and estimated recruitment dates of massive corals at three different sites in the Wakatobi Marine National Park, Indonesia, and on the reefs around Discovery Bay, Jamaica. Semi-structured interviews with key stakeholders in the Wakatobi Marine National Park indicated that coral mining was extensively practised, and is responsible for the absence of large non-branching corals on the Sampela reef Blast fishing is also practised in the Wakatobi Marine Park, and the authors, together with students, showed that blast fishing resulted in coral bleaching and not mortality of two Porites lutea colonies. In addition, we showed that monitoring of bleaching in Porites colonies induced by blast fishing could be a useful way of monitoring blast fishing practices in susceptible areas in the Indo-Pacific. The techniques used in this study are appropriate for use by volunteers with sufficient training, and provide excellent projects for dissertation students reading undergraduate degrees.

Electrospinning atactic polystyrene: a neutron scattering study

Electrospinning is a method used to produce nanoscale to microscale sized polymer fibres. In this study we electrospin 1:1 blends of deuterated and hydrogenated atactic- Polystyrene from N,N-Dimethylformamide for small angle neutron scattering experiments in order to analyse the chain conformation in the electrospun fibres. Small angle neutron scattering was carried out on randomly orientated fibre mats obtained using applied voltages of 10kV-15kV and needle tip to collector distances of 20cm and 30cm. Fibre diameters varied from 3μm – 20μm. Neutron scattering data from fibre samples were compared with bulk samples of the same polymer blend. The scattering data indicates that there are pores and nanovoiding present in the fibres; this was confirmed by scanning electron microscopy. A model that combines the scattering from the pores and the labelled polymer chains was used to extract values for the radius of gyration. The radius of gyration in the fibres is found to vary little with the applied voltage, but varies with the initial solution concentration and fibre diameter. The values for the radius of gyration in the fibres are broadly equivalent to that of the bulk state.

An efficient numerical scheme for the Euler equations

A finite difference scheme based on flux difference splitting is presented for the solution of the Euler equations for the compressible flow of an ideal gas. A linearised Riemann problem is defined, and a scheme based on numerical characteristic decomposition is presented for obtaining approximate solutions to the linearised problem. An average of the flow variables across the interface between cells is required, and this average is chosen to be the arithmetic mean for computational efficiency, leading to arithmetic averaging. This is in contrast to the usual ‘square root’ averages found in this type of Riemann solver, where the computational expense can be prohibitive. The method of upwind differencing is used for the resulting scalar problems, together with a flux limiter for obtaining a second order scheme which avoids nonphysical, spurious oscillations. The scheme is applied to a shock tube problem and a blast wave problem. Each approximate solution compares well with those given by other schemes, and for the shock tube problem is in agreement with the exact solution.

Dear living person

This chapter is written from the perspective of a recently deceased corpse. It examines the claims art makes to moving beyond boundaries and testing limits (of medium, discipline, and category) as a cliché of transcendence. This is described in relation to the operation of the false ‘master’ limit between the living and the dead, with reference to Reza Negarestani’s vivid reenactment of Etruscan torture, and contemporary performances of institutional critique: Fraser, Krebber and Carpenter.

Improvement of the GenTHREADER method for genomic fold recognition

Motivation: In order to enhance genome annotation, the fully automatic fold recognition method GenTHREADER has been improved and benchmarked. The previous version of GenTHREADER consisted of a simple neural network which was trained to combine sequence alignment score, length information and energy potentials derived from threading into a single score representing the relationship between two proteins, as designated by CATH. The improved version incorporates PSI-BLAST searches, which have been jumpstarted with structural alignment profiles from FSSP, and now also makes use of PSIPRED predicted secondary structure and bi-directional scoring in order to calculate the final alignment score. Pairwise potentials and solvation potentials are calculated from the given sequence alignment which are then used as inputs to a multi-layer, feed-forward neural network, along with the alignment score, alignment length and sequence length. The neural network has also been expanded to accommodate the secondary structure element alignment (SSEA) score as an extra input and it is now trained to learn the FSSP Z-score as a measurement of similarity between two proteins. Results: The improvements made to GenTHREADER increase the number of remote homologues that can be detected with a low error rate, implying higher reliability of score, whilst also increasing the quality of the models produced. We find that up to five times as many true positives can be detected with low error rate per query. Total MaxSub score is doubled at low false positive rates using the improved method.

Political economy of state-building: power after peace

The purpose of this volume is to examine and evaluate the impact of international state-building interventions on the political economy of post-conflict countries over the last 20 years. It analyses how international interventions have shaped political and economic dynamics and structures – both formal and informal – and what kind of state, and what kind of state-society relations have been created as a result, through three different lenses: first, through the approaches taken by different international actors like the UN, the International Financial Institutions, or the European Union, to state-building; second, through detailed analysis of key state-building policies; and third, through a wide range of country case studies. Amongst the recurring themes that are highlighted by the book’s focus on the political economy of state-building, and that help to explain why international state-building interventions have tended to fall short of the visions of interveners and local populations alike are evidence of important continuities between war-time and “post-conflict” economies and authority structures, which are often consolidated as a consequence of international involvement; tensions arising from what are often the competing interests and values held by different interveners and local actors; and, finally, the continuing salience of economic and political violence in state-building processes and war-to-peace transitions. The book aims to offer a more nuanced understanding of the complex impact of state-building practices on post-conflict societies, and of the political economy of post-conflict state-building.

Introduction: power after peace

The chapter provides a substantive conceptual introduction to the volume, examining what is meant by the concept of "political economy of statebuilding", and what the implications for the study of statebuilding are

The political economy of state-building in Kosovo

The chapter examines the impact of international statbuilding efforts on political and economic dynamics in Kosovo from 1999 to 2011

Natural ventilation assessment in typical open an semi-open urban environments under various wind directions

Semi-open street roofs protect pedestrians from intense sunshine and rains. Their effects on natural ventilation of urban canopy layers (UCL) are less understood. This paper investigates two idealized urban models consisting of 4(2×2) or 16(4×4) buildings under a neutral atmospheric condition with parallel (0°) or non-parallel (15°,30°,45°) approaching wind. The aspect ratio (building height (H) / street width (W)) is 1 and building width is B=3H. Computational fluid dynamic (CFD) simulations were first validated by experimental data, confirming that standard k-ε model predicted airflow velocity better than RNG k-ε model, realizable k–ε model and Reynolds stress model. Three ventilation indices were numerically analyzed for ventilation assessment, including flow rates across street roofs and openings to show the mechanisms of air exchange, age of air to display how long external air reaches a place after entering UCL, and purging flow rate to quantify the net UCL ventilation capacity induced by mean flows and turbulence. Five semi-open roof types are studied: Walls being hung above street roofs (coverage ratio λa=100%) at z=1.5H, 1.2H, 1.1H ('Hung1.5H', 'Hung1.2H', 'Hung1.1H' types); Walls partly covering street roofs (λa=80%) at z=H ('Partly-covered' type); Walls fully covering street roofs (λa=100%) at z=H ('Fully-covered' type).They basically obtain worse UCL ventilation than open street roof type due to the decreased roof ventilation. 'Hung1.1H', 'Hung1.2H', 'Hung1.5H' types are better designs than 'Fully-covered' and 'Partly-covered' types. Greater urban size contains larger UCL volume and requires longer time to ventilate. The methodologies and ventilation indices are confirmed effective to quantify UCL ventilation.

Quantitative ventilation assessments of idealized urban canopy layers with various urban layouts and the same building packing density

This paper investigates urban canopy layers (UCL) ventilation under neutral atmospheric condition with the same building area density (λp=0.25) and frontal area density (λf=0.25) but various urban sizes, building height variations, overall urban forms and wind directions. Turbulent airflows are first predicted by CFD simulations with standard k-ε model evaluated by wind tunnel data. Then air change rates per hour (ACH) and canopy purging flow rate (PFR) are numerically analyzed to quantify the rate of air exchange and the net ventilation capacity induced by mean flows and turbulence. With a parallel approaching wind (θ=0o), the velocity ratio first decreases in the adjustment region, followed by the fully-developed region where the flow reaches a balance. Although the flow quantities macroscopically keep constant, however ACH decreases and overall UCL ventilation becomes worse if urban size rises from 390m to 5km. Theoretically if urban size is infinite, ACH may reach a minimum value depending on local roof ventilation, and it rises from 1.7 to 7.5 if the standard deviation of building height variations increases (0% to 83.3%). Overall UCL ventilation capacity (PFR) with a square overall urban form (Lx=Ly=390m) is better as θ=0o than oblique winds (θ=15o, 30o, 45o), and it exceeds that of a staggered urban form under all wind directions (θ=0o to 45o), but is less than that of a rectangular urban form (Lx=570m, Ly=270m) under most wind directions (θ=30o to 90o). Further investigations are still required to quantify the net ventilation efficiency induced by mean flows and turbulence.

Ventilation performance in a passage between two non-parallel buildings

A great number of studies on wind conditions in passages between slab-type buildings have been conducted in the past. However, wind conditions under different structure and configuration of buildings is still unclear and studies existed still can’t provide guidance on urban planning and design, due to the complexity of buildings and aerodynamics. The aim of this paper is to provide more insight in the mechanism of wind conditions in passages. In this paper, a simplified passage model with non-parallel buildings is developed on the basis of the wind tunnel experiments conducted by Blocken et al. (2008). Numerical simulation based on CFD is employed for a detailed investigation of the wind environment in passages between two long narrow buildings with different directions and model validation is performed by comparing numerical results with corresponding wind tunnel measurements.

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely-related crop species, lentil, and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2 cM interval of Vf chromosome 2 which was highly collinear with Mt3. The obvious candidate gene from 77 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene (Mt3g092830, Mt3g092840) controlling anthocyanin production in Medicago and re-sequencing of the Vf orthologue showed a putative causative deletion of the entire 5’ end of the gene.

Revisiting the ‘Venturi effect’ in passage ventilation between two non-parallel buildings

A recent study conducted by Blocken et al. (Numerical study on the existence of the Venturi effect in passages between perpendicular buildings. Journal of Engineering Mechanics, 2008,134: 1021-1028) challenged the popular view of the existence of the ‘Venturi effect’ in building passages as the wind is exposed to an open boundary. The present research extends the work of Blocken et al. (2008a) into a more general setup with the building orientation varying from 0° to 180° using CFD simulations. Our results reveal that the passage flow is mainly determined by the combination of corner streams. It is also shown that converging passages have a higher wind-blocking effect compared to diverging passages, explained by a lower wind speed and higher drag coefficient. Fluxes on the top plane of the passage volume reverse from outflow to inflow in the cases of α=135°, 150° and 165°. A simple mathematical expression to explain the relationship between the flux ratio and the geometric parameters has been developed to aid wind design in an urban neighborhood. In addition, a converging passage with α=15° is recommended for urban wind design in cold and temperate climates since the passage flow changes smoothly and a relatively lower wind speed is expected compared with that where there are no buildings. While for the high-density urban area in (sub)tropical climates such as Hong Kong where there is a desire for more wind, a diverging passage with α=150° is a better choice to promote ventilation at the pedestrian level.