Evaluation of the environmental specificity of fluorescence in situ hybridization (FISH) using fluorescence-activated cell sorting (FACS) of probe (PSE1284)-positive cells extracted from rhizosphere soil

We explicitly tested for the first time the ‘environmental specificity’ of traditional 16S rRNAtargeted fluorescence in situ hybridization (FISH) through comparison of the bacterial diversity actually targeted in the environment with the diversity that should be exactly targeted (i.e. without mismatches) according to in silico analysis. To do this, we exploited advances in modern Flow Cytometry that enabled improved detection and therefore sorting of sub-micron-sized particles and used probe PSE1284 (designed to target Pseudomonads) applied to Lolium perenne rhizosphere soil as our test system. The 6-carboxyfluorescein (6-FAM)-PSE1284-hybridised population, defined as displaying enhanced green fluorescence in Flow Cytometry, represented 3.51±1.28% of the total detected population when corrected using a nonsense (NON-EUB338) probe control. Analysis of 16S rRNA gene libraries constructed from Fluorescence Activated Cell Sorted (FACS) -recovered fluorescent populations (n=3), revealed that 98.5% (Pseudomonas spp. comprised 68.7% and Burkholderia spp. 29.8%) of the total sorted population was specifically targeted as evidenced by the homology of the 16S rRNA sequences to the probe sequence. In silico evaluation of probe PSE1284 with the use of RDP-10 probeMatch justified the existence of Burkholderia spp. among the sorted cells. The lack of novelty in Pseudomonas spp. sequences uncovered was notable, probably reflecting the well-studied nature of this functionally important genus. To judge the diversity recorded within the FACS-sorted population, rarefaction and DGGE analysis were used to evaluate, respectively, the proportion of Pseudomonas diversity uncovered by the sequencing effort and the representativeness of the Nycodenz® method for the extraction of bacterial cells from soil.

A metabolic system-wide characterisation of the pig: a model for human physiology

The pig is a single-stomached omnivorous mammal and is an important model of human disease and nutrition. As such, it is necessary to establish a metabolic framework from which pathology-based variation can be compared. Here, a combination of one and two-dimensional (1)H and (13)C nuclear magnetic resonance spectroscopy (NMR) and high-resolution magic angle spinning (HR-MAS) NMR was used to provide a systems overview of porcine metabolism via characterisation of the urine, serum, liver and kidney metabolomes. The metabolites observed in each of these biological compartments were found to be qualitatively comparable to the metabolic signature of the same biological matrices in humans and rodents. The data were modelled using a combination of principal components analysis and Venn diagram mapping. Urine represented the most metabolically distinct biological compartment studied, with a relatively greater number of NMR detectable metabolites present, many of which are implicated in gut-microbial co-metabolic processes. The major inter-species differences observed were in the phase II conjugation of extra-genomic metabolites; the pig was observed to conjugate p-cresol, a gut microbial metabolite of tyrosine, with glucuronide rather than sulfate as seen in man. These observations are important to note when considering the translatability of experimental data derived from porcine models.

Wide-angle X-ray scattering study of structural parameters in non-crystalline polymers

The paper presents an analysis of WAXS (wide-angle X-ray scattering) data which aids an understanding of the structure of non-crystalline polymers. Experimental results are compared with calculations of scattering from possible models. Evidence is presented which supports the view that the chains in molten PE do not lie parallel but have a conformation in accord with the predictions of energy calculations. However, the evidence indicates that in “molten” PTFE the chains lie parallel over distances well in excess of their diameters. WAXS-based proposals are made for the conformations of a-PMMA and a-PS.

A wide-angle X-ray study of the development of molecular orientation in crosslinked natural rubber

Molecular orientation parameters have been measured for the non-crystalline component of crosslinked natural rubber samples deformed in uniaxial tension as a function of the extension ratio and of temperature. The orientation parapeters 〈P2(cosα)〉 and 〈P4(cosα)〉 were obtained by an analysis of the anisotropy of the wide-angle X-ray scattering functions. For the measurements made at high temperatures the level of crystallinity detected was negligible and the orientation-strain behaviour could be compared directly with the predictions of molecular models of rubber elasticity. The molecular orientation behaviour with strain was found to be at variance with the estimates of the affine model particularly at low and moderate strains. Extension of the crosslinked rubber at room temperature led to strain-crystallization and measurements of both the molecular orientation of the non-crystalline chains and the degree of crystallinity during extension and relaxation enabled the role of the crystallites in the deformation process to be considered in detail. The intrinsic birefringence of the non-crystalline component was estimated, through the use of the 〈P2(cosα)〉 values obtained from X-ray scattering measurements, to be 0.20±0.02.

Wide-angle X-ray scattering for swollen and glassy poly(2-hydroxyethyl methacrylate)

The wide angle X-ray scattering from glassy poly(2-hydroxyethyl methacrylate) (1) is presented together with that obtained from oriented and swollen samples. The scattering is compared with that previously reported for poly(methyl methacrylate) (PMMA) and the structure discussed in relation to this polymer. The chain conformation is similar to that of PMMA, although some measure of molecular interlocking appears to reduce the main interchain peak while correlated regions of inaccessible free volume between the substantial side groups are held responsible for the main peak at s = 1,25 Å−1.

Application of cylindrical distribution functions to wide-angle X-ray scattering from oriented polymers

A systematic approach is presented for obtaining cylindrical distribution functions (CDF's) of noncrystalline polymers which have been oriented by extension. The scattering patterns and CDF's are also sharpened by the method proposed by Deas and by Ruland. Data from atactic poly(methyl methacrylate) and polystyrene are analysed by these techniques. The methods could also be usefully applied to liquid crystals.

Conformational analysis of oriented non-crystalline polymers using wide angle X-ray scattering

A procedure is presented for obtaining conformational parameters from oriented but non-crystalline polymers. This is achieved by comparison of the experimental wide angle X-ray scattering with that calculated from models but in such a way that foreknowledge of the orientation distribution function is not required. X-ray scattering intensity values for glassy isotactic poly(methylmethacrylate) are analysed by these techniques. The method could be usefully applied to other oriented molecular systems such as liquid crystalline materials.

The impact of installer business models on the uptake of residential microgeneration in the UK: Evidence from a nation-wide survey

This paper arises from a doctoral thesis comparing the impact of alternative installer business models on the rate at which microgeneration is taken up in homes and installation standards across the UK. The paper presents the results of the first large-scale academic survey of businesses certified to install residential microgeneration. The aim is to systematically capture those characteristics which define the business model of each surveyed company, and relate these to the number, location and type of technologies that they install, and the quality of these installations. The methodology comprised a pilot web survey of 235 certified installer businesses, which was carried out in June last year and achieved a response rate of 30%. Following optimisation of the design, the main web survey was emailed to over 2000 businesses between October and December 2011, with 317 valid responses received. The survey is being complemented during summer 2012 by semi-structured interviews with a representative sample of installers who completed the main survey. The survey results are currently being analysed. The early results indicate an emerging and volatile market where solar PV, solar hot water and air source heat pumps are the dominant technologies. Three quarters of respondents are founders of their installer business, while only 22 businesses are owned by another company. Over half of the 317 businesses have five employees or less, while 166 businesses are no more than four years old. In addition, half of the businesses stated that 100% of their employees work on microgeneration-related activities. 85% of the surveyed companies have only one business location in the UK. A third of the businesses are based either in the South West or South East regions of England. This paper outlines the interim results of the survey combined with the outcomes from additional interviews with installers to date. The research identifies some of the business models underpinning microgeneration installers and some of the ways in which installer business models impact on the rate and standards of microgeneration uptake. A tentative conclusion is that installer business models are profoundly dependent on the levels and timing of support from the UK Feed-in Tariffs and Renewable Heat Incentive.

Specific detection and localization of microsporidian parasites in invertebrate hosts using in situ hybridization

We designed FISH-probes for two distinct microsporidian clades and demonstrated their application in detecting respectively Nosema/Vairimorpha and Dictyoceola species. We applied them to study the vertical transmission of two microsporidia infecting the amphipod Gammarus duebeni

Robust abandoned object detection integrating wide area visual surveillance and social context

This paper presents a video surveillance framework that robustly and efficiently detects abandoned objects in surveillance scenes. The framework is based on a novel threat assessment algorithm which combines the concept of ownership with automatic understanding of social relations in order to infer abandonment of objects. Implementation is achieved through development of a logic-based inference engine based on Prolog. Threat detection performance is conducted by testing against a range of datasets describing realistic situations and demonstrates a reduction in the number of false alarms generated. The proposed system represents the approach employed in the EU SUBITO project (Surveillance of Unattended Baggage and the Identification and Tracking of the Owner).

Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome

Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ∼500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene HvbHLH1 identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.

Area-wide development viability appraisals: the concept of threshold land value within a UK planning context

Area-wide development viability appraisals are undertaken to determine the economic feasibility of policy targets in relation to planning obligations. Essentially, development viability appraisals consist of a series of residual valuations of hypothetical development sites across a local authority area at a particular point in time. The valuations incorporate the estimated financial implications of the proposed level of planning obligations. To determine viability the output land values are benchmarked against threshold land value and therefore the basis on which this threshold is established and the level at which it is set is critical to development viability appraisal at the policy-setting (area-wide) level. Essentially it is an estimate of the value at which a landowner would be prepared to sell. If the estimated site values are higher than the threshold land value the policy target is considered viable. This paper investigates the effectiveness of existing methods of determining threshold land value. They will be tested against the relationship between development value and costs. Modelling reveals that threshold land value that is not related to shifts in development value renders marginal sites unviable and fails to collect proportionate planning obligations from high value/low cost sites. Testing the model against national average house prices and build costs reveals the high degree of volatility in residual land values over time and underlines the importance of making threshold land value relative to the main driver of this volatility, namely development value.

A metabolic system-wide characterisation of the pig: a model for human physiology

The pig is a single-stomached omnivorous mammal and is an important model of human disease and nutrition. As such, it is necessary to establish a metabolic framework from which pathology-based variation can be compared. Here, a combination of one and two-dimensional 1H and 13C nuclear magnetic resonance spectroscopy (NMR) and high-resolution magic angle spinning (HR-MAS) NMR was used to provide a systems overview of porcine metabolism via characterisation of the urine, serum, liver and kidney metabolomes. The metabolites observed in each of these biological compartments were found to be qualitatively comparable to the metabolic signature of the same biological matrices in humans and rodents. The data were modelled using a combination of principal components analysis and Venn diagram mapping. Urine represented the most metabolically distinct biological compartment studied, with a relatively greater number of NMR detectable metabolites present, many of which are implicated in gut-microbial co-metabolic processes. The major interspecies differences observed were in the phase II conjugation of extra-genomic metabolites; the pig was observed to conjugate p-cresol, a gut microbial metabolite of tyrosine, with glucuronide rather than sulfate as seen in man. These observations are important to note when considering the translatability of experimental data derived from porcine models.

Candidate genes for obesity-susceptibility show enriched association within a large genome-wide association study for BMI

Before the advent of genome-wide association studies (GWASs), hundreds of candidate genes for obesity-susceptibility had been identified through a variety of approaches. We examined whether those obesity candidate genes are enriched for associations with body mass index (BMI) compared with non-candidate genes by using data from a large-scale GWAS. A thorough literature search identified 547 candidate genes for obesity-susceptibility based on evidence from animal studies, Mendelian syndromes, linkage studies, genetic association studies and expression studies. Genomic regions were defined to include the genes ±10 kb of flanking sequence around candidate and non-candidate genes. We used summary statistics publicly available from the discovery stage of the genome-wide meta-analysis for BMI performed by the genetic investigation of anthropometric traits consortium in 123 564 individuals. Hypergeometric, rank tail-strength and gene-set enrichment analysis tests were used to test for the enrichment of association in candidate compared with non-candidate genes. The hypergeometric test of enrichment was not significant at the 5% P-value quantile (P = 0.35), but was nominally significant at the 25% quantile (P = 0.015). The rank tail-strength and gene-set enrichment tests were nominally significant for the full set of genes and borderline significant for the subset without SNPs at P < 10(-7). Taken together, the observed evidence for enrichment suggests that the candidate gene approach retains some value. However, the degree of enrichment is small despite the extensive number of candidate genes and the large sample size. Studies that focus on candidate genes have only slightly increased chances of detecting associations, and are likely to miss many true effects in non-candidate genes, at least for obesity-related traits.